From 7c48011458b60a011cccf1ab6ef310b3023b9b3e Mon Sep 17 00:00:00 2001 From: Christine Stawitz Date: Mon, 9 Dec 2024 22:22:59 +0000 Subject: [PATCH] Docs: run Doxygen --- docs/annotated.html | 36 +- docs/classAgeCompDataInterface-members.html | 9 +- docs/classAgeCompDataInterface.html | 12 - ...ertonHoltRecruitmentInterface-members.html | 18 +- ...classBevertonHoltRecruitmentInterface.html | 109 +- docs/classDataInterfaceBase-members.html | 5 +- docs/classDataInterfaceBase.html | 19 +- docs/classDataInterfaceBase.png | Bin 1607 -> 1328 bytes ...assDistributionsInterfaceBase-members.html | 16 +- docs/classDistributionsInterfaceBase.html | 186 +-- ...sDlnormDistributionsInterface-members.html | 27 +- docs/classDlnormDistributionsInterface.html | 183 +-- ...ultinomDistributionsInterface-members.html | 26 +- .../classDmultinomDistributionsInterface.html | 187 +-- ...ssDnormDistributionsInterface-members.html | 27 +- docs/classDnormDistributionsInterface.html | 180 +-- 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...tructfims__data__object_1_1DataObject.html | 13 +- ...__model__object_1_1FIMSObject-members.html | 13 +- ...ructfims__model__object_1_1FIMSObject.html | 72 +- ...tructfims__model__object_1_1FIMSObject.png | Bin 6033 -> 5398 bytes ..._1_1DoubleLogisticSelectivity-members.html | 14 +- ...s__popdy_1_1DoubleLogisticSelectivity.html | 100 +- ...ructfims__popdy_1_1EWAAgrowth-members.html | 22 +- docs/structfims__popdy_1_1EWAAgrowth.html | 29 +- docs/structfims__popdy_1_1Fleet-members.html | 50 +- docs/structfims__popdy_1_1Fleet.html | 350 +---- ...ructfims__popdy_1_1GrowthBase-members.html | 21 +- docs/structfims__popdy_1_1GrowthBase.html | 3 - ...ms__popdy_1_1LogisticMaturity-members.html | 8 +- ...structfims__popdy_1_1LogisticMaturity.html | 80 +- ..._popdy_1_1LogisticSelectivity-members.html | 8 +- ...uctfims__popdy_1_1LogisticSelectivity.html | 82 +- ...ctfims__popdy_1_1MaturityBase-members.html | 4 +- docs/structfims__popdy_1_1MaturityBase.html | 57 +- ...ructfims__popdy_1_1Population-members.html | 81 +- docs/structfims__popdy_1_1Population.html | 3 - ...ims__popdy_1_1RecruitmentBase-members.html | 25 +- .../structfims__popdy_1_1RecruitmentBase.html | 65 +- ...fims__popdy_1_1SRBevertonHolt-members.html | 31 +- docs/structfims__popdy_1_1SRBevertonHolt.html | 22 +- ...ims__popdy_1_1SelectivityBase-members.html | 4 +- .../structfims__popdy_1_1SelectivityBase.html | 57 +- docs/subpopulation_8hpp_source.html | 55 +- 276 files changed, 7701 insertions(+), 11884 deletions(-) diff --git a/docs/annotated.html b/docs/annotated.html index a5752de..cc29382 100644 --- a/docs/annotated.html +++ b/docs/annotated.html @@ -75,18 +75,12 @@
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 12]
- - - - - - - - - - - - + + + + + + @@ -110,9 +104,9 @@ - - - + + + @@ -120,13 +114,13 @@ - - - - + + + + - - + + diff --git a/docs/classAgeCompDataInterface-members.html b/docs/classAgeCompDataInterface-members.html index 4b3f825..7bc4e74 100644 --- a/docs/classAgeCompDataInterface-members.html +++ b/docs/classAgeCompDataInterface-members.html @@ -81,17 +81,14 @@ - - - - - - + + +
 ▼Nfims
 CLogEntry
 CFIMSLog
 CVector
 CJsonValue
 CJsonParser
 ▼Nfims_data_object
 CDataObject
 ▼Nfims_distributions
 CDensityComponentBaseBase class for all module_name functors
 CLogNormalLPDF
 CMultinomialLPMF
 CNormalLPDF
 Cfims_log
 CVector
 ▼Nfims_data_object
 CDataObject
 ▼Nfims_distributions
 CDistributionsBaseBase class for all module_name functors
 ▼Nfims_info
 CInformationStores FIMS model information and creates model. Contains all objects and data pre-model construction
 ▼Nfims_model
 CBevertonHoltRecruitmentInterfaceRcpp interface for Beverton-Holt as an S4 object. To instantiate from R: beverton_holt <- new(beverton_holt)
 CDataInterfaceBaseRcpp interface for Data as an S4 object. To instantiate from R: fleet <- new(Data)
 CDistributionsInterfaceBaseDistributions Rcpp Interface
 CDlnormDistributionsInterfaceRcpp interface for Dlnorm as an S4 object. To instantiate from R: dlnorm_ <- new(DlnormDistribution)
 CDmultinomDistributionsInterfaceRcpp interface for Dmultinom as an S4 object. To instantiate from R: dmultinom_ <- new(DmultinomDistribution)
 CDnormDistributionsInterfaceRcpp interface for Dnorm as an S4 object. To instantiate from R: dnorm_ <- new(DnormDistribution)
 CDlnormDistributionsInterfaceRcpp interface for Dlnorm as an S4 object. To instantiate from R: dlnorm_ <- new(TMBDlnormDistribution)
 CDmultinomDistributionsInterfaceRcpp interface for Dmultinom as an S4 object. To instantiate from R: dmultinom_ <- new(TMBDmultinomDistribution)
 CDnormDistributionsInterfaceRcpp interface for Dnorm as an S4 object. To instantiate from R: dnorm_ <- new(TMBDnormDistribution)
 CDoubleLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(logistic_selectivity)
 CEWAAGrowthInterfaceRcpp interface for EWAAgrowth as an S4 object. To instantiate from R: ewaa <- new(EWAAgrowth)
 CFIMSRcppInterfaceBaseBase class for all interface objects
 CFleetInterfaceBaseRcpp interface that serves as the parent class for Rcpp fleet interfaces. This type should be inherited and not called from R directly
 CGrowthInterfaceBaseRcpp interface that serves as the parent class for Rcpp growth interfaces. This type should be inherited and not called from R directly
 CIndexDataInterfaceRcpp interface for data as an S4 object. To instantiate from R: fleet <- new(Index)
 CLengthCompDataInterfaceRcpp interface for length comp data as an S4 object. To instantiate from R: lcomp <- new(LengthComp)
 CLogisticMaturityInterfaceRcpp interface for logistic maturity as an S4 object. To instantiate from R: logistic_maturity <- new(logistic_maturity)
 CLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(logistic_selectivity)
 CLPDFInterfaceBaseLPDFInterfaceBase class should be inherited to define different Rcpp interfaces for each possible log probability density function
 CJsonParser
 CJsonValue
 CLogisticMaturityInterfaceRcpp interface for logistic maturity as an S4 object. To instantiate from R: logistic_maturity <- new(logistic_maturity)
 CLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(logistic_selectivity)
 CMaturityInterfaceBaseMaturityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible maturity function
 CParameterRcppInterface class that defines the interface between R and C++ for parameter types
 CParameterVectorRcpp representation of a Parameter vector interface between R and cpp
 CNLLInterfaceBaseNLLInterfaceBase class should be inherited to define different Rcpp interfaces for each possible negative log-likelihood function
 CParameterRcppInterface class that defines the interface between R and C++ for parameter types
 CPopulationInterfaceRcpp interface for a new Population. To instantiate from R: population <- new(population)
 CPopulationInterfaceBasePopulationInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Population function
 CRecruitmentInterfaceBaseRecruitmentInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Recruitment function
amaxAgeCompDataInterface
DataInterfaceBase()DataInterfaceBaseinline
fims_interface_objectsFIMSRcppInterfaceBasestatic
finalize()FIMSRcppInterfaceBaseinlinevirtual
finalizedFIMSRcppInterfaceBase
get_id()AgeCompDataInterfaceinlinevirtual
idDataInterfaceBase
id_gDataInterfaceBasestatic
live_objectsDataInterfaceBasestatic
observed_dataDataInterfaceBase
to_json()AgeCompDataInterfaceinlinevirtual
ymaxAgeCompDataInterface
~AgeCompDataInterface()AgeCompDataInterfaceinlinevirtual
~DataInterfaceBase()DataInterfaceBaseinlinevirtual
ymaxAgeCompDataInterface
~AgeCompDataInterface()AgeCompDataInterfaceinlinevirtual
~DataInterfaceBase()DataInterfaceBaseinlinevirtual
diff --git a/docs/classAgeCompDataInterface.html b/docs/classAgeCompDataInterface.html index bb1cbba..ac3d3f4 100644 --- a/docs/classAgeCompDataInterface.html +++ b/docs/classAgeCompDataInterface.html @@ -106,10 +106,6 @@ virtual uint32_t get_id ()  get the ID of the interface base object
  - -virtual std::string to_json () - Convert the data to json representation for the output.
-  - Public Member Functions inherited from DataInterfaceBase  DataInterfaceBase () @@ -123,11 +119,6 @@ virtual bool add_to_fims_tmb ()  add_to_fims_tmb dummy method
  -- Public Member Functions inherited from FIMSRcppInterfaceBase - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
-  @@ -142,9 +133,6 @@ - - -

Public Attributes

 
uint32_t id
 
- Public Attributes inherited from FIMSRcppInterfaceBase
bool finalized = false
 
diff --git a/docs/classBevertonHoltRecruitmentInterface-members.html b/docs/classBevertonHoltRecruitmentInterface-members.html index 8ac55fb..d0c1a4e 100644 --- a/docs/classBevertonHoltRecruitmentInterface-members.html +++ b/docs/classBevertonHoltRecruitmentInterface-members.html @@ -78,22 +78,18 @@ - - - - + + - - - - - - - + + + + +

Additional Inherited Members

add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual
BevertonHoltRecruitmentInterface() (defined in BevertonHoltRecruitmentInterface)BevertonHoltRecruitmentInterfaceinline
estimate_log_devsBevertonHoltRecruitmentInterface
estimated_log_devsBevertonHoltRecruitmentInterface
estimated_log_rzeroBevertonHoltRecruitmentInterface
estimated_logit_steepBevertonHoltRecruitmentInterface
evaluate(double spawners, double ssbzero)BevertonHoltRecruitmentInterfaceinlinevirtual
evaluate(double spawners, double ssbzero)BevertonHoltRecruitmentInterfaceinlinevirtual
evaluate_nll()BevertonHoltRecruitmentInterfaceinlinevirtual
fims_interface_objectsFIMSRcppInterfaceBasestatic
finalize()BevertonHoltRecruitmentInterfaceinlinevirtual
finalizedFIMSRcppInterfaceBase
get_id()BevertonHoltRecruitmentInterfaceinlinevirtual
idRecruitmentInterfaceBase
id_gRecruitmentInterfaceBasestatic
live_objectsRecruitmentInterfaceBasestatic
log_devsBevertonHoltRecruitmentInterface
log_rzeroBevertonHoltRecruitmentInterface
logit_steepBevertonHoltRecruitmentInterface
RecruitmentInterfaceBase() (defined in RecruitmentInterfaceBase)RecruitmentInterfaceBaseinline
to_json()BevertonHoltRecruitmentInterfaceinlinevirtual
log_devsBevertonHoltRecruitmentInterface
log_rzeroBevertonHoltRecruitmentInterface
log_sigma_recruitBevertonHoltRecruitmentInterface
logit_steepBevertonHoltRecruitmentInterface
RecruitmentInterfaceBase() (defined in RecruitmentInterfaceBase)RecruitmentInterfaceBaseinline
~BevertonHoltRecruitmentInterface() (defined in BevertonHoltRecruitmentInterface)BevertonHoltRecruitmentInterfaceinlinevirtual
~RecruitmentInterfaceBase() (defined in RecruitmentInterfaceBase)RecruitmentInterfaceBaseinlinevirtual
diff --git a/docs/classBevertonHoltRecruitmentInterface.html b/docs/classBevertonHoltRecruitmentInterface.html index 296a5cb..69b6a18 100644 --- a/docs/classBevertonHoltRecruitmentInterface.html +++ b/docs/classBevertonHoltRecruitmentInterface.html @@ -102,14 +102,9 @@ virtual double evaluate (double spawners, double ssbzero)  evaluate method for child recruitment interface objects to inherit
  - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
-  - -virtual std::string to_json () - Convert the data to json representation for the output.
-  +virtual double evaluate_nll () + evaluate recruitment nll More...
+  - Public Member Functions inherited from FIMSRcppInterfaceBase virtual bool add_to_fims_tmb () @@ -118,26 +113,19 @@ - - - - - - + + + + + + + + - - - - - - - - -

Public Attributes

ParameterVector logit_steep
 
ParameterVector log_rzero
 
ParameterVector log_devs
 
Parameter logit_steep
 
Parameter log_rzero
 
Parameter log_sigma_recruit
 
Rcpp::NumericVector log_devs
 
bool estimate_log_devs = false
 
double estimated_logit_steep
 
double estimated_log_rzero
 
Rcpp::NumericVector estimated_log_devs
 
- Public Attributes inherited from RecruitmentInterfaceBase
uint32_t id
 
- Public Attributes inherited from FIMSRcppInterfaceBase
bool finalized = false
 
@@ -152,105 +140,106 @@

Additional Inherited Members

Detailed Description

Rcpp interface for Beverton-Holt as an S4 object. To instantiate from R: beverton_holt <- new(beverton_holt)

-

Member Data Documentation

- -

◆ estimate_log_devs

+

Member Function Documentation

+ +

◆ evaluate_nll()

+ + + + + +
- + + + +
bool BevertonHoltRecruitmentInterface::estimate_log_devs = falsevirtual double BevertonHoltRecruitmentInterface::evaluate_nll ()
+ 		+inlinevirtual
-

boolean describing whether to estimate

-
-
- -

◆ estimated_log_devs

+

evaluate recruitment nll

+
Returns
double
-
-
- - - - -
Rcpp::NumericVector BevertonHoltRecruitmentInterface::estimated_log_devs
-
-

estimated log recruitment deviations

+

Implements RecruitmentInterfaceBase.

- -

◆ estimated_log_rzero

+

Member Data Documentation

+ +

◆ estimate_log_devs

- +
double BevertonHoltRecruitmentInterface::estimated_log_rzerobool BevertonHoltRecruitmentInterface::estimate_log_devs = false
-

estimated recruitment at unfished biomass

+

boolean describing whether to estimate

- -

◆ estimated_logit_steep

+ +

◆ log_devs

- +
double BevertonHoltRecruitmentInterface::estimated_logit_steepRcpp::NumericVector BevertonHoltRecruitmentInterface::log_devs
-

estimated steepness or the productivity of the stock

+

log recruitment deviations

- -

◆ log_devs

+ +

◆ log_rzero

- +
ParameterVector BevertonHoltRecruitmentInterface::log_devsParameter BevertonHoltRecruitmentInterface::log_rzero
-

log recruitment deviations

+

recruitment at unfished biomass

- -

◆ log_rzero

+ +

◆ log_sigma_recruit

- +
ParameterVector BevertonHoltRecruitmentInterface::log_rzeroParameter BevertonHoltRecruitmentInterface::log_sigma_recruit
-

recruitment at unfished biomass

+

the log of the stock recruit standard deviation

- -

◆ logit_steep

+ +

◆ logit_steep

- +
ParameterVector BevertonHoltRecruitmentInterface::logit_steepParameter BevertonHoltRecruitmentInterface::logit_steep
diff --git a/docs/classDataInterfaceBase-members.html b/docs/classDataInterfaceBase-members.html index 2b5ffd7..e486e23 100644 --- a/docs/classDataInterfaceBase-members.html +++ b/docs/classDataInterfaceBase-members.html @@ -78,15 +78,12 @@ add_to_fims_tmb()DataInterfaceBaseinlinevirtual DataInterfaceBase()DataInterfaceBaseinline fims_interface_objectsFIMSRcppInterfaceBasestatic - finalize()FIMSRcppInterfaceBaseinlinevirtual - finalizedFIMSRcppInterfaceBase get_id()DataInterfaceBaseinlinevirtual idDataInterfaceBase id_gDataInterfaceBasestatic live_objectsDataInterfaceBasestatic observed_dataDataInterfaceBase - to_json()FIMSRcppInterfaceBaseinlinevirtual - ~DataInterfaceBase()DataInterfaceBaseinlinevirtual + ~DataInterfaceBase()DataInterfaceBaseinlinevirtual
diff --git a/docs/classDataInterfaceBase.html b/docs/classDataInterfaceBase.html index 1bb4b20..393cf2b 100644 --- a/docs/classDataInterfaceBase.html +++ b/docs/classDataInterfaceBase.html @@ -88,10 +88,9 @@
-FIMSRcppInterfaceBase -AgeCompDataInterface -IndexDataInterface -LengthCompDataInterface +FIMSRcppInterfaceBase +AgeCompDataInterface +IndexDataInterface
@@ -113,15 +112,6 @@ virtual bool  - - - - - - -
add_to_fims_tmb ()
 add_to_fims_tmb dummy method
 
- Public Member Functions inherited from FIMSRcppInterfaceBase
-virtual void finalize ()
 finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
 
-virtual std::string to_json ()
 Convert the data to json representation for the output.
 
@@ -129,9 +119,6 @@ - - -

Public Attributes

 
uint32_t id
 
- Public Attributes inherited from FIMSRcppInterfaceBase
bool finalized = false
 
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Static Public Attributes

add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual
DistributionsInterfaceBase() (defined in DistributionsInterfaceBase)DistributionsInterfaceBaseinline
evaluate()=0DistributionsInterfaceBasepure virtual
evaluate(bool do_log)=0DistributionsInterfaceBasepure virtual
fims_interface_objectsFIMSRcppInterfaceBasestatic
finalize()FIMSRcppInterfaceBaseinlinevirtual
finalizedFIMSRcppInterfaceBase
get_id()=0DistributionsInterfaceBasepure virtual
id_gDistributionsInterfaceBasestatic
id_mDistributionsInterfaceBase
input_type_mDistributionsInterfaceBase
interface_observed_data_id_mDistributionsInterfaceBase
key_mDistributionsInterfaceBase
live_objectsDistributionsInterfaceBasestatic
set_distribution_links(std::string input_type, Rcpp::IntegerVector ids)DistributionsInterfaceBaseinlinevirtual
set_observed_data(int observed_data_id)DistributionsInterfaceBaseinlinevirtual
to_json()FIMSRcppInterfaceBaseinlinevirtual
idDistributionsInterfaceBase
id_gDistributionsInterfaceBasestatic
live_objectsDistributionsInterfaceBasestatic
~DistributionsInterfaceBase() (defined in DistributionsInterfaceBase)DistributionsInterfaceBaseinlinevirtual
diff --git a/docs/classDistributionsInterfaceBase.html b/docs/classDistributionsInterfaceBase.html index e914ba5..d0183d9 100644 --- a/docs/classDistributionsInterfaceBase.html +++ b/docs/classDistributionsInterfaceBase.html @@ -81,7 +81,7 @@

Distributions Rcpp Interface. More...

-

#include <rcpp_distribution.hpp>

+

#include <rcpp_tmb_distribution.hpp>

Inheritance diagram for DistributionsInterfaceBase:
@@ -89,9 +89,9 @@ FIMSRcppInterfaceBase -DlnormDistributionsInterface -DmultinomDistributionsInterface -DnormDistributionsInterface +DlnormDistributionsInterface +DmultinomDistributionsInterface +DnormDistributionsInterface
@@ -101,43 +101,20 @@ virtual uint32_t  - - - - - - - - - + + + - - - - - -
get_id ()=0
 get_id method for child distribution interface objects to inherit
 
virtual bool set_distribution_links (std::string input_type, Rcpp::IntegerVector ids)
 set_distribution_links sets pointers for data observations, random effects, or priors More...
 
virtual bool set_observed_data (int observed_data_id)
 Set the unique id for the Observed Data object. More...
 
-virtual double evaluate ()=0
 evaluate method for child distribution interface objects to inherit
 
+virtual double evaluate (bool do_log)=0
 evaluate method for child distribution interface objects to inherit
 
- Public Member Functions inherited from FIMSRcppInterfaceBase
virtual bool add_to_fims_tmb ()
 virtual method to inherit to add objects to the TMB model
 
-virtual void finalize ()
 finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
 
-virtual std::string to_json ()
 Convert the data to json representation for the output.
 
- - - - - - - - - - - + +

Public Attributes

uint32_t id_m
 
std::vector< uint32_t > key_m
 
std::string input_type_m
 
uint32_t interface_observed_data_id_m
 
- Public Attributes inherited from FIMSRcppInterfaceBase
bool finalized = false
 
uint32_t id
 
@@ -151,91 +128,22 @@

Static Public Attributes

Detailed Description

Distributions Rcpp Interface.

-

Member Function Documentation

- -

◆ set_distribution_links()

+

Member Data Documentation

+ +

◆ id

- - - - - -
- - - - - - - - - - - - - - - - - - -
virtual bool DistributionsInterfaceBase::set_distribution_links (std::string input_type,
Rcpp::IntegerVector ids 
)
- 		-inlinevirtual
-
- -

set_distribution_links sets pointers for data observations, random effects, or priors

-
Parameters
- - - -
input_typeString that sets whether the distribution type is: priors, random_effects, or data.
idsVector of unique ids for each linked parameter/s, derived value/s, or observed data vector
-
-
- -

Reimplemented in DmultinomDistributionsInterface, DlnormDistributionsInterface, and DnormDistributionsInterface.

- -
-
- -

◆ set_observed_data()

- -
-
- - - - - -
- - - - - +
virtual bool DistributionsInterfaceBase::set_observed_data (int observed_data_id)uint32_t DistributionsInterfaceBase::id
- 		-inlinevirtual
- -

Set the unique id for the Observed Data object.

-
Parameters
- - -
observed_data_idUnique id for the Observed Age Comp Data object
-
-
- -

Reimplemented in DmultinomDistributionsInterface, DlnormDistributionsInterface, and DnormDistributionsInterface.

+

local id of the DistributionsInterfaceBase object

-

Member Data Documentation

◆ id_g

@@ -259,68 +167,6 @@

1

static id of the DistributionsInterfaceBase object

- - - -

◆ id_m

- -
-
- - - - -
uint32_t DistributionsInterfaceBase::id_m
-
-

local id of the DistributionsInterfaceBase object

- -
-
- -

◆ input_type_m

- -
-
- - - - -
std::string DistributionsInterfaceBase::input_type_m
-
-

type of density input, options are: prior, re, or data

- -
-
- -

◆ interface_observed_data_id_m

- -
-
- - - - -
uint32_t DistributionsInterfaceBase::interface_observed_data_id_m
-
-Initial value:
=
-
-999
-

id of observed data object

- -
-
- -

◆ key_m

- -
-
- - - - -
std::vector<uint32_t> DistributionsInterfaceBase::key_m
-
-

unique id for variable map that points to a fims::Vector

-
@@ -348,7 +194,7 @@

rcpp_distribution.hpp +
  • inst/include/interface/rcpp/rcpp_objects/rcpp_tmb_distribution.hpp
    • diff --git a/docs/classDlnormDistributionsInterface-members.html b/docs/classDlnormDistributionsInterface-members.html index c5808f8..92b9af4 100644 --- a/docs/classDlnormDistributionsInterface-members.html +++ b/docs/classDlnormDistributionsInterface-members.html @@ -78,26 +78,17 @@ add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual DistributionsInterfaceBase() (defined in DistributionsInterfaceBase)DistributionsInterfaceBaseinline DlnormDistributionsInterface() (defined in DlnormDistributionsInterface)DlnormDistributionsInterfaceinline - evaluate()DlnormDistributionsInterfaceinlinevirtual - expected_valuesDlnormDistributionsInterface - fims_interface_objectsFIMSRcppInterfaceBasestatic - finalize()DlnormDistributionsInterfaceinlinevirtual - finalizedFIMSRcppInterfaceBase - get_id()DlnormDistributionsInterfaceinlinevirtual + evaluate(bool do_log)DlnormDistributionsInterfaceinlinevirtual + fims_interface_objectsFIMSRcppInterfaceBasestatic + get_id()DlnormDistributionsInterfaceinlinevirtual + idDistributionsInterfaceBase id_gDistributionsInterfaceBasestatic - id_mDistributionsInterfaceBase - input_type_mDistributionsInterfaceBase - interface_observed_data_id_mDistributionsInterfaceBase - key_mDistributionsInterfaceBase live_objectsDistributionsInterfaceBasestatic - log_sdDlnormDistributionsInterface - lpdf_vecDlnormDistributionsInterface - set_distribution_links(std::string input_type, Rcpp::IntegerVector ids)DlnormDistributionsInterfaceinlinevirtual - set_observed_data(int observed_data_id)DlnormDistributionsInterfaceinlinevirtual - to_json()DlnormDistributionsInterfaceinlinevirtual - xDlnormDistributionsInterface - ~DistributionsInterfaceBase() (defined in DistributionsInterfaceBase)DistributionsInterfaceBaseinlinevirtual - ~DlnormDistributionsInterface() (defined in DlnormDistributionsInterface)DlnormDistributionsInterfaceinlinevirtual + meanlogDlnormDistributionsInterface + sdlogDlnormDistributionsInterface + xDlnormDistributionsInterface + ~DistributionsInterfaceBase() (defined in DistributionsInterfaceBase)DistributionsInterfaceBaseinlinevirtual + ~DlnormDistributionsInterface() (defined in DlnormDistributionsInterface)DlnormDistributionsInterfaceinlinevirtual
    diff --git a/docs/classDlnormDistributionsInterface.html b/docs/classDlnormDistributionsInterface.html index d1b3b2d..f2989f0 100644 --- a/docs/classDlnormDistributionsInterface.html +++ b/docs/classDlnormDistributionsInterface.html @@ -77,10 +77,10 @@
    -

    Rcpp interface for Dlnorm as an S4 object. To instantiate from R: dlnorm_ <- new(DlnormDistribution) +

    Rcpp interface for Dlnorm as an S4 object. To instantiate from R: dlnorm_ <- new(TMBDlnormDistribution) More...

    -

    #include <rcpp_distribution.hpp>

    +

    #include <rcpp_tmb_distribution.hpp>

    Inheritance diagram for DlnormDistributionsInterface:
    @@ -98,23 +98,9 @@ virtual uint32_t get_id ()  get the id of the Dlnorm distributions interface class object
      -virtual bool set_observed_data (int observed_data_id) - Set the unique id for the Observed Data object. More...
    -  -virtual bool set_distribution_links (std::string input_type, Rcpp::IntegerVector ids) - set_distribution_links sets pointers for data observations, random effects, or priors More...
    -  -virtual double evaluate () - Evaluate lognormal probability density function, default returns the log of the pdf. More...
    -  - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  +virtual double evaluate (bool do_log) + Evaluate lognormal probability density function, default returns the log of the pdf. More...
    +  - Public Member Functions inherited from FIMSRcppInterfaceBase virtual bool add_to_fims_tmb () @@ -123,26 +109,15 @@ - - - - - - - - + + + + + + - - - - - - - - - - - + +

    Public Attributes

    ParameterVector x
     
    ParameterVector expected_values
     
    ParameterVector log_sd
     
    Rcpp::NumericVector lpdf_vec
     
    Parameter x
     
    Parameter meanlog
     
    Parameter sdlog
     
    - Public Attributes inherited from DistributionsInterfaceBase
    uint32_t id_m
     
    std::vector< uint32_t > key_m
     
    std::string input_type_m
     
    uint32_t interface_observed_data_id_m
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    uint32_t id
     
    @@ -156,10 +131,10 @@

    Additional Inherited Members

     

    Detailed Description

    -

    Rcpp interface for Dlnorm as an S4 object. To instantiate from R: dlnorm_ <- new(DlnormDistribution)

    +

    Rcpp interface for Dlnorm as an S4 object. To instantiate from R: dlnorm_ <- new(TMBDlnormDistribution)

    Member Function Documentation

    - -

    ◆ evaluate()

    + +

    ◆ evaluate()

    @@ -170,7 +145,8 @@

    virtual double DlnormDistributionsInterface::evaluate ( - ) + bool  + do_log) @@ -190,102 +166,19 @@

    Returns
    log pdf
    -

    Implements DistributionsInterfaceBase.

    - -

    -
    - -

    ◆ set_distribution_links()

    - -
    -
    - - - - - -
    - - - - - - - - - - - - - - - - - - -
    virtual bool DlnormDistributionsInterface::set_distribution_links (std::string input_type,
    Rcpp::IntegerVector ids 
    )
    -     		-inlinevirtual
    -
    - -

    set_distribution_links sets pointers for data observations, random effects, or priors

    -
    Parameters
    - - - -
    input_typeString that sets whether the distribution type is: priors, random_effects, or data.
    idsVector of unique ids for each linked parameter/s, derived value/s, or observed data vector
    -
    -
    - -

    Reimplemented from DistributionsInterfaceBase.

    - -
    -
    - -

    ◆ set_observed_data()

    - -
    -
    - - - - - -
    - - - - - - - - -
    virtual bool DlnormDistributionsInterface::set_observed_data (int observed_data_id)
    -     		-inlinevirtual
    -
    - -

    Set the unique id for the Observed Data object.

    -
    Parameters
    - - -
    observed_data_idUnique id for the Observed Age Comp Data object
    -
    -
    - -

    Reimplemented from DistributionsInterfaceBase.

    +

    Implements DistributionsInterfaceBase.

    Member Data Documentation

    - -

    ◆ expected_values

    + +

    ◆ meanlog

    - +
    ParameterVector DlnormDistributionsInterface::expected_valuesParameter DlnormDistributionsInterface::meanlog
    @@ -293,45 +186,29 @@

    -

    ◆ log_sd

    - -
    -
    - - - - -
    ParameterVector DlnormDistributionsInterface::log_sd
    -
    -

    the natural logarithm of the standard deviation of the distribution of log(x). The natural log of the standard deviation is necessary because the exponential link function is applied to the log transformed sd to insure sd is positive.
    -

    - -
    -
    - -

    ◆ lpdf_vec

    + +

    ◆ sdlog

    - +
    Rcpp::NumericVector DlnormDistributionsInterface::lpdf_vecParameter DlnormDistributionsInterface::sdlog
    -

    The vector

    +

    standard deviation of the distribution of log(x)

    - -

    ◆ x

    + +

    ◆ x

    - +
    ParameterVector DlnormDistributionsInterface::xParameter DlnormDistributionsInterface::x
    @@ -340,7 +217,7 @@

    rcpp_distribution.hpp +
  • inst/include/interface/rcpp/rcpp_objects/rcpp_tmb_distribution.hpp

    • diff --git a/docs/classDmultinomDistributionsInterface-members.html b/docs/classDmultinomDistributionsInterface-members.html index 9706d6e..6b59797 100644 --- a/docs/classDmultinomDistributionsInterface-members.html +++ b/docs/classDmultinomDistributionsInterface-members.html @@ -76,26 +76,16 @@

    This is the complete list of members for DmultinomDistributionsInterface, including all inherited members.

    - - - - - + + + - - - - - - - - - - - - - + + + + +
    add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual
    dimsDmultinomDistributionsInterface
    DistributionsInterfaceBase() (defined in DistributionsInterfaceBase)DistributionsInterfaceBaseinline
    DmultinomDistributionsInterface() (defined in DmultinomDistributionsInterface)DmultinomDistributionsInterfaceinline
    evaluate()DmultinomDistributionsInterfaceinlinevirtual
    expected_valuesDmultinomDistributionsInterface
    DistributionsInterfaceBase() (defined in DistributionsInterfaceBase)DistributionsInterfaceBaseinline
    DmultinomDistributionsInterface() (defined in DmultinomDistributionsInterface)DmultinomDistributionsInterfaceinline
    evaluate(bool do_log)DmultinomDistributionsInterfaceinlinevirtual
    fims_interface_objectsFIMSRcppInterfaceBasestatic
    finalize()FIMSRcppInterfaceBaseinlinevirtual
    finalizedFIMSRcppInterfaceBase
    get_id()DmultinomDistributionsInterfaceinlinevirtual
    id_gDistributionsInterfaceBasestatic
    id_mDistributionsInterfaceBase
    input_type_mDistributionsInterfaceBase
    interface_observed_data_id_mDistributionsInterfaceBase
    key_mDistributionsInterfaceBase
    live_objectsDistributionsInterfaceBasestatic
    lpdf_vecDmultinomDistributionsInterface
    set_distribution_links(std::string input_type, Rcpp::IntegerVector ids)DmultinomDistributionsInterfaceinlinevirtual
    set_observed_data(int observed_data_id)DmultinomDistributionsInterfaceinlinevirtual
    to_json()FIMSRcppInterfaceBaseinlinevirtual
    xDmultinomDistributionsInterface
    idDistributionsInterfaceBase
    id_gDistributionsInterfaceBasestatic
    live_objectsDistributionsInterfaceBasestatic
    pDmultinomDistributionsInterface
    xDmultinomDistributionsInterface
    ~DistributionsInterfaceBase() (defined in DistributionsInterfaceBase)DistributionsInterfaceBaseinlinevirtual
    ~DmultinomDistributionsInterface() (defined in DmultinomDistributionsInterface)DmultinomDistributionsInterfaceinlinevirtual
    diff --git a/docs/classDmultinomDistributionsInterface.html b/docs/classDmultinomDistributionsInterface.html index 1df4a77..8f97465 100644 --- a/docs/classDmultinomDistributionsInterface.html +++ b/docs/classDmultinomDistributionsInterface.html @@ -77,10 +77,10 @@

    -

    Rcpp interface for Dmultinom as an S4 object. To instantiate from R: dmultinom_ <- new(DmultinomDistribution) +

    Rcpp interface for Dmultinom as an S4 object. To instantiate from R: dmultinom_ <- new(TMBDmultinomDistribution) More...

    -

    #include <rcpp_distribution.hpp>

    +

    #include <rcpp_tmb_distribution.hpp>

    Inheritance diagram for DmultinomDistributionsInterface:
    @@ -98,51 +98,24 @@ virtual uint32_t get_id ()  get_id method for child distribution interface objects to inherit
      -virtual bool set_observed_data (int observed_data_id) - Set the unique id for the Observed Data object. More...
    -  -virtual bool set_distribution_links (std::string input_type, Rcpp::IntegerVector ids) - set_distribution_links sets pointers for data observations, random effects, or priors More...
    -  -virtual double evaluate () - Evaluate multinom probability density function, default returns the log of the pdf. More...
    -  +virtual double evaluate (bool do_log) + Evaluate multinom probability density function, default returns the log of the pdf. More...
    +  - Public Member Functions inherited from FIMSRcppInterfaceBase virtual bool add_to_fims_tmb ()  virtual method to inherit to add objects to the TMB model
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - - - - - - - - + + + + - - - - - - - - - - - + +

    Public Attributes

    ParameterVector x
     
    ParameterVector expected_values
     
    Rcpp::NumericVector dims
     
    Rcpp::NumericVector lpdf_vec
     
    Rcpp::IntegerVector x
     
    Rcpp::NumericVector p
     
    - Public Attributes inherited from DistributionsInterfaceBase
    uint32_t id_m
     
    std::vector< uint32_t > key_m
     
    std::string input_type_m
     
    uint32_t interface_observed_data_id_m
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    uint32_t id
     
    @@ -156,10 +129,10 @@

    Additional Inherited Members

     

    Detailed Description

    -

    Rcpp interface for Dmultinom as an S4 object. To instantiate from R: dmultinom_ <- new(DmultinomDistribution)

    +

    Rcpp interface for Dmultinom as an S4 object. To instantiate from R: dmultinom_ <- new(TMBDmultinomDistribution)

    Member Function Documentation

    - -

    ◆ evaluate()

    + +

    ◆ evaluate()

    @@ -170,7 +143,8 @@

    virtual double DmultinomDistributionsInterface::evaluate ( - ) + bool  + do_log) @@ -190,117 +164,19 @@

    Returns
    log pdf
    -

    Implements DistributionsInterfaceBase.

    - -

    -
    - -

    ◆ set_distribution_links()

    - -
    -
    - - - - - -
    - - - - - - - - - - - - - - - - - - -
    virtual bool DmultinomDistributionsInterface::set_distribution_links (std::string input_type,
    Rcpp::IntegerVector ids 
    )
    -     		-inlinevirtual
    -
    - -

    set_distribution_links sets pointers for data observations, random effects, or priors

    -
    Parameters
    - - - -
    input_typeString that sets whether the distribution type is: priors, random_effects, or data.
    idsVector of unique ids for each linked parameter/s, derived value/s, or observed data vector
    -
    -
    - -

    Reimplemented from DistributionsInterfaceBase.

    - -
    -
    - -

    ◆ set_observed_data()

    - -
    -
    - - - - - -
    - - - - - - - - -
    virtual bool DmultinomDistributionsInterface::set_observed_data (int observed_data_id)
    -     		-inlinevirtual
    -
    - -

    Set the unique id for the Observed Data object.

    -
    Parameters
    - - -
    observed_data_idUnique id for the Observed Age Comp Data object
    -
    -
    - -

    Reimplemented from DistributionsInterfaceBase.

    +

    Implements DistributionsInterfaceBase.

    Member Data Documentation

    - -

    ◆ dims

    + +

    ◆ p

    - - -
    Rcpp::NumericVector DmultinomDistributionsInterface::dims
    -
    -

    Dimensions of the number of rows and columns of the multivariate dataset

    - -
    -
    - -

    ◆ expected_values

    - -
    -
    - - - +
    ParameterVector DmultinomDistributionsInterface::expected_valuesRcpp::NumericVector DmultinomDistributionsInterface::p
    @@ -308,29 +184,14 @@

    -

    ◆ lpdf_vec

    - -
    -
    - - - - -
    Rcpp::NumericVector DmultinomDistributionsInterface::lpdf_vec
    -
    -

    The vector

    - -
    -
    - -

    ◆ x

    + +

    ◆ x

    - +
    ParameterVector DmultinomDistributionsInterface::xRcpp::IntegerVector DmultinomDistributionsInterface::x
    @@ -339,7 +200,7 @@

    rcpp_distribution.hpp +
  • inst/include/interface/rcpp/rcpp_objects/rcpp_tmb_distribution.hpp

    • diff --git a/docs/classDnormDistributionsInterface-members.html b/docs/classDnormDistributionsInterface-members.html index 6ce6c2e..04aecf6 100644 --- a/docs/classDnormDistributionsInterface-members.html +++ b/docs/classDnormDistributionsInterface-members.html @@ -78,26 +78,17 @@ add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual DistributionsInterfaceBase() (defined in DistributionsInterfaceBase)DistributionsInterfaceBaseinline DnormDistributionsInterface() (defined in DnormDistributionsInterface)DnormDistributionsInterfaceinline - evaluate()DnormDistributionsInterfaceinlinevirtual - expected_valuesDnormDistributionsInterface - fims_interface_objectsFIMSRcppInterfaceBasestatic - finalize()DnormDistributionsInterfaceinlinevirtual - finalizedFIMSRcppInterfaceBase - get_id()DnormDistributionsInterfaceinlinevirtual + evaluate(bool do_log)DnormDistributionsInterfaceinlinevirtual + fims_interface_objectsFIMSRcppInterfaceBasestatic + get_id()DnormDistributionsInterfaceinlinevirtual + idDistributionsInterfaceBase id_gDistributionsInterfaceBasestatic - id_mDistributionsInterfaceBase - input_type_mDistributionsInterfaceBase - interface_observed_data_id_mDistributionsInterfaceBase - key_mDistributionsInterfaceBase live_objectsDistributionsInterfaceBasestatic - log_sdDnormDistributionsInterface - lpdf_vecDnormDistributionsInterface - set_distribution_links(std::string input_type, Rcpp::IntegerVector ids)DnormDistributionsInterfaceinlinevirtual - set_observed_data(int observed_data_id)DnormDistributionsInterfaceinlinevirtual - to_json()DnormDistributionsInterfaceinlinevirtual - xDnormDistributionsInterface - ~DistributionsInterfaceBase() (defined in DistributionsInterfaceBase)DistributionsInterfaceBaseinlinevirtual - ~DnormDistributionsInterface() (defined in DnormDistributionsInterface)DnormDistributionsInterfaceinlinevirtual + meanDnormDistributionsInterface + sdDnormDistributionsInterface + xDnormDistributionsInterface + ~DistributionsInterfaceBase() (defined in DistributionsInterfaceBase)DistributionsInterfaceBaseinlinevirtual + ~DnormDistributionsInterface() (defined in DnormDistributionsInterface)DnormDistributionsInterfaceinlinevirtual
    diff --git a/docs/classDnormDistributionsInterface.html b/docs/classDnormDistributionsInterface.html index d91a508..5fa1ec2 100644 --- a/docs/classDnormDistributionsInterface.html +++ b/docs/classDnormDistributionsInterface.html @@ -77,10 +77,10 @@

    -

    Rcpp interface for Dnorm as an S4 object. To instantiate from R: dnorm_ <- new(DnormDistribution) +

    Rcpp interface for Dnorm as an S4 object. To instantiate from R: dnorm_ <- new(TMBDnormDistribution) More...

    -

    #include <rcpp_distribution.hpp>

    +

    #include <rcpp_tmb_distribution.hpp>

    Inheritance diagram for DnormDistributionsInterface:
    @@ -98,23 +98,9 @@ virtual uint32_t get_id ()  get_id method for child distribution interface objects to inherit
      -virtual bool set_observed_data (int observed_data_id) - Set the unique id for the Observed Data object. More...
    -  -virtual bool set_distribution_links (std::string input_type, Rcpp::IntegerVector ids) - set_distribution_links sets pointers for data observations, random effects, or priors More...
    -  -virtual double evaluate () - Evaluate normal probability density function, default returns the log of the pdf. More...
    -  - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  +virtual double evaluate (bool do_log) + Evaluate normal probability density function, default returns the log of the pdf. More...
    +  - Public Member Functions inherited from FIMSRcppInterfaceBase virtual bool add_to_fims_tmb () @@ -123,26 +109,15 @@ - - - - - - - - + + + + + + - - - - - - - - - - - + +

    Public Attributes

    ParameterVector x
     
    ParameterVector expected_values
     
    ParameterVector log_sd
     
    Rcpp::NumericVector lpdf_vec
     
    Parameter x
     
    Parameter mean
     
    Parameter sd
     
    - Public Attributes inherited from DistributionsInterfaceBase
    uint32_t id_m
     
    std::vector< uint32_t > key_m
     
    std::string input_type_m
     
    uint32_t interface_observed_data_id_m
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    uint32_t id
     
    @@ -156,10 +131,10 @@

    Additional Inherited Members

     

    Detailed Description

    -

    Rcpp interface for Dnorm as an S4 object. To instantiate from R: dnorm_ <- new(DnormDistribution)

    +

    Rcpp interface for Dnorm as an S4 object. To instantiate from R: dnorm_ <- new(TMBDnormDistribution)

    Member Function Documentation

    - -

    ◆ evaluate()

    + +

    ◆ evaluate()

    @@ -170,7 +145,8 @@

    virtual double DnormDistributionsInterface::evaluate ( - ) + bool  + do_log) @@ -190,102 +166,19 @@

    Returns
    log pdf
    -

    Implements DistributionsInterfaceBase.

    - -

    -
    - -

    ◆ set_distribution_links()

    - -
    -
    - - - - - -
    - - - - - - - - - - - - - - - - - - -
    virtual bool DnormDistributionsInterface::set_distribution_links (std::string input_type,
    Rcpp::IntegerVector ids 
    )
    -     		-inlinevirtual
    -
    - -

    set_distribution_links sets pointers for data observations, random effects, or priors

    -
    Parameters
    - - - -
    input_typeString that sets whether the distribution type is: priors, random_effects, or data.
    idsVector of unique ids for each linked parameter/s, derived value/s, or observed data vector
    -
    -
    - -

    Reimplemented from DistributionsInterfaceBase.

    - -
    -
    - -

    ◆ set_observed_data()

    - -
    -
    - - - - - -
    - - - - - - - - -
    virtual bool DnormDistributionsInterface::set_observed_data (int observed_data_id)
    -     		-inlinevirtual
    -
    - -

    Set the unique id for the Observed Data object.

    -
    Parameters
    - - -
    observed_data_idUnique id for the Observed Age Comp Data object
    -
    -
    - -

    Reimplemented from DistributionsInterfaceBase.

    +

    Implements DistributionsInterfaceBase.

    Member Data Documentation

    - -

    ◆ expected_values

    + +

    ◆ mean

    - +
    ParameterVector DnormDistributionsInterface::expected_valuesParameter DnormDistributionsInterface::mean
    @@ -293,14 +186,14 @@

    -

    ◆ log_sd

    + +

    ◆ sd

    - +
    ParameterVector DnormDistributionsInterface::log_sdParameter DnormDistributionsInterface::sd
    @@ -308,29 +201,14 @@

    -

    ◆ lpdf_vec

    - -
    -
    - - - - -
    Rcpp::NumericVector DnormDistributionsInterface::lpdf_vec
    -
    -

    The vector

    - -
    -
    - -

    ◆ x

    + +

    ◆ x

    - +
    ParameterVector DnormDistributionsInterface::xParameter DnormDistributionsInterface::x
    @@ -339,7 +217,7 @@

    rcpp_distribution.hpp +
  • inst/include/interface/rcpp/rcpp_objects/rcpp_tmb_distribution.hpp

    • diff --git a/docs/classDoubleLogisticSelectivityInterface-members.html b/docs/classDoubleLogisticSelectivityInterface-members.html index 5b1e9ff..a128d0f 100644 --- a/docs/classDoubleLogisticSelectivityInterface-members.html +++ b/docs/classDoubleLogisticSelectivityInterface-members.html @@ -79,20 +79,17 @@ DoubleLogisticSelectivityInterface() (defined in DoubleLogisticSelectivityInterface)DoubleLogisticSelectivityInterfaceinline evaluate(double x)DoubleLogisticSelectivityInterfaceinlinevirtual fims_interface_objectsFIMSRcppInterfaceBasestatic - finalize()DoubleLogisticSelectivityInterfaceinlinevirtual - finalizedFIMSRcppInterfaceBase get_id()DoubleLogisticSelectivityInterfaceinlinevirtual idSelectivityInterfaceBase id_gSelectivityInterfaceBasestatic - inflection_point_ascDoubleLogisticSelectivityInterface - inflection_point_descDoubleLogisticSelectivityInterface + inflection_point_ascDoubleLogisticSelectivityInterface + inflection_point_descDoubleLogisticSelectivityInterface live_objectsSelectivityInterfaceBasestatic SelectivityInterfaceBase() (defined in SelectivityInterfaceBase)SelectivityInterfaceBaseinline - slope_ascDoubleLogisticSelectivityInterface - slope_descDoubleLogisticSelectivityInterface - to_json()DoubleLogisticSelectivityInterfaceinlinevirtual - ~DoubleLogisticSelectivityInterface() (defined in DoubleLogisticSelectivityInterface)DoubleLogisticSelectivityInterfaceinlinevirtual - ~SelectivityInterfaceBase() (defined in SelectivityInterfaceBase)SelectivityInterfaceBaseinlinevirtual + slope_ascDoubleLogisticSelectivityInterface + slope_descDoubleLogisticSelectivityInterface + ~DoubleLogisticSelectivityInterface() (defined in DoubleLogisticSelectivityInterface)DoubleLogisticSelectivityInterfaceinlinevirtual + ~SelectivityInterfaceBase() (defined in SelectivityInterfaceBase)SelectivityInterfaceBaseinlinevirtual
    diff --git a/docs/classDoubleLogisticSelectivityInterface.html b/docs/classDoubleLogisticSelectivityInterface.html index 62747db..fbfe205 100644 --- a/docs/classDoubleLogisticSelectivityInterface.html +++ b/docs/classDoubleLogisticSelectivityInterface.html @@ -101,14 +101,6 @@ virtual double evaluate (double x)  evaluate the double logistic selectivity function More...
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - Public Member Functions inherited from FIMSRcppInterfaceBase virtual bool add_to_fims_tmb () @@ -117,20 +109,17 @@ - - - - - - - - + + + + + + + + - - -

    Public Attributes

    ParameterVector inflection_point_asc
     
    ParameterVector slope_asc
     
    ParameterVector inflection_point_desc
     
    ParameterVector slope_desc
     
    Parameter inflection_point_asc
     
    Parameter slope_asc
     
    Parameter inflection_point_desc
     
    Parameter slope_desc
     
    - Public Attributes inherited from SelectivityInterfaceBase
    uint32_t id
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    @@ -183,14 +172,14 @@

    Member Data Documentation

    - -

    ◆ inflection_point_asc

    + +

    ◆ inflection_point_asc

    Additional Inherited Members

    - +
    ParameterVector DoubleLogisticSelectivityInterface::inflection_point_ascParameter DoubleLogisticSelectivityInterface::inflection_point_asc

    @@ -198,14 +187,14 @@

    -

    ◆ inflection_point_desc

    + +

    ◆ inflection_point_desc

    - +
    ParameterVector DoubleLogisticSelectivityInterface::inflection_point_descParameter DoubleLogisticSelectivityInterface::inflection_point_desc
    @@ -213,14 +202,14 @@

    -

    ◆ slope_asc

    + +

    ◆ slope_asc

    - +
    ParameterVector DoubleLogisticSelectivityInterface::slope_ascParameter DoubleLogisticSelectivityInterface::slope_asc
    @@ -228,14 +217,14 @@

    -

    ◆ slope_desc

    + +

    ◆ slope_desc

    - +
    ParameterVector DoubleLogisticSelectivityInterface::slope_descParameter DoubleLogisticSelectivityInterface::slope_desc
    diff --git a/docs/classEWAAGrowthInterface-members.html b/docs/classEWAAGrowthInterface-members.html index 51f118e..a9fc789 100644 --- a/docs/classEWAAGrowthInterface-members.html +++ b/docs/classEWAAGrowthInterface-members.html @@ -81,8 +81,6 @@ ewaaEWAAGrowthInterface EWAAGrowthInterface() (defined in EWAAGrowthInterface)EWAAGrowthInterfaceinline fims_interface_objectsFIMSRcppInterfaceBasestatic - finalize()FIMSRcppInterfaceBaseinlinevirtual - finalizedFIMSRcppInterfaceBase get_id()EWAAGrowthInterfaceinlinevirtual GrowthInterfaceBase() (defined in GrowthInterfaceBase)GrowthInterfaceBaseinline idGrowthInterfaceBase @@ -90,10 +88,9 @@ initializedEWAAGrowthInterface live_objectsGrowthInterfaceBasestatic make_map(std::vector< double > ages, std::vector< double > weights)EWAAGrowthInterfaceinline - to_json()EWAAGrowthInterfaceinlinevirtual - weightsEWAAGrowthInterface - ~EWAAGrowthInterface() (defined in EWAAGrowthInterface)EWAAGrowthInterfaceinlinevirtual - ~GrowthInterfaceBase() (defined in GrowthInterfaceBase)GrowthInterfaceBaseinlinevirtual + weightsEWAAGrowthInterface + ~EWAAGrowthInterface() (defined in EWAAGrowthInterface)EWAAGrowthInterfaceinlinevirtual + ~GrowthInterfaceBase() (defined in GrowthInterfaceBase)GrowthInterfaceBaseinlinevirtual
    diff --git a/docs/classEWAAGrowthInterface.html b/docs/classEWAAGrowthInterface.html index eed6713..7b80b08 100644 --- a/docs/classEWAAGrowthInterface.html +++ b/docs/classEWAAGrowthInterface.html @@ -105,19 +105,11 @@ virtual double evaluate (double age)  Rcpp interface to the EWAAgrowth evaluate method you can call from R using ewaagrowth.evaluate(age)
      - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - Public Member Functions inherited from FIMSRcppInterfaceBase virtual bool add_to_fims_tmb ()  virtual method to inherit to add objects to the TMB model
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  @@ -132,9 +124,6 @@ - - -

    Public Attributes

    - Public Attributes inherited from GrowthInterfaceBase
    uint32_t id
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    diff --git a/docs/classFIMSRcppInterfaceBase-members.html b/docs/classFIMSRcppInterfaceBase-members.html index ddd7a78..9963c1e 100644 --- a/docs/classFIMSRcppInterfaceBase-members.html +++ b/docs/classFIMSRcppInterfaceBase-members.html @@ -77,9 +77,6 @@

    Additional Inherited Members

    - - -
    add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual
    fims_interface_objectsFIMSRcppInterfaceBasestatic
    finalize()FIMSRcppInterfaceBaseinlinevirtual
    finalizedFIMSRcppInterfaceBase
    to_json()FIMSRcppInterfaceBaseinlinevirtual
    diff --git a/docs/classFIMSRcppInterfaceBase.html b/docs/classFIMSRcppInterfaceBase.html index 62e791c..0df3dd2 100644 --- a/docs/classFIMSRcppInterfaceBase.html +++ b/docs/classFIMSRcppInterfaceBase.html @@ -70,7 +70,6 @@
    Public Member Functions | -Public Attributes | Static Public Attributes | List of all members
    @@ -92,8 +91,8 @@ DistributionsInterfaceBase FleetInterfaceBase GrowthInterfaceBase -LPDFInterfaceBase -MaturityInterfaceBase +MaturityInterfaceBase +NLLInterfaceBase PopulationInterfaceBase RecruitmentInterfaceBase SelectivityInterfaceBase @@ -106,19 +105,6 @@ virtual bool add_to_fims_tmb ()  virtual method to inherit to add objects to the TMB model
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - - - -

    -Public Attributes

    bool finalized = false
     
    @@ -147,22 +133,7 @@

    -

    FIMS interface object vectors

    - - - -     -

    ◆ finalized

    - -
    -
    -

    Static Public Attributes

    - - - -
    bool FIMSRcppInterfaceBase::finalized = false
    -
    -

    If already finalized

    +

    < FIMS interface object vectors

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    This is the complete list of members for FleetInterface, including all inherited members.

    - - - - - - - - - - - - - - - - - + + + + + + + - - - + + + - - - - - - - - + + + + + + - - - + +
    add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual
    age_length_conversion_matrixFleetInterface
    derived_age_compositionFleetInterface
    derived_cnaaFleetInterface
    derived_cnalFleetInterface
    derived_cwaaFleetInterface
    derived_indexFleetInterface
    derived_length_compositionFleetInterface
    estimate_qFleetInterface
    fims_interface_objectsFIMSRcppInterfaceBasestatic
    finalize()FleetInterfaceinlinevirtual
    finalizedFIMSRcppInterfaceBase
    FleetInterface() (defined in FleetInterface)FleetInterfaceinline
    FleetInterfaceBase() (defined in FleetInterfaceBase)FleetInterfaceBaseinline
    get_id()FleetInterfaceinlinevirtual
    GetObservedAgeCompDataID()FleetInterfaceinline
    GetObservedIndexDataID()FleetInterfaceinline
    GetObservedLengthCompDataID()FleetInterfaceinline
    estimate_FFleetInterface
    estimate_obs_errorFleetInterface
    estimate_qFleetInterface
    fims_interface_objectsFIMSRcppInterfaceBasestatic
    FleetInterface() (defined in FleetInterface)FleetInterfaceinline
    FleetInterfaceBase() (defined in FleetInterfaceBase)FleetInterfaceBaseinline
    get_id()FleetInterfaceinlinevirtual
    idFleetInterfaceBase
    id_gFleetInterfaceBasestatic
    is_surveyFleetInterface
    live_objectsFleetInterfaceBasestatic
    log_expected_indexFleetInterface
    log_FmortFleetInterface
    log_qFleetInterface
    log_FmortFleetInterface
    log_obs_errorFleetInterface
    log_qFleetInterface
    nagesFleetInterface
    nameFleetInterface
    nlengthsFleetInterface
    nyearsFleetInterface
    proportion_catch_numbers_at_ageFleetInterface
    proportion_catch_numbers_at_lengthFleetInterface
    random_qFleetInterface
    SetObservedAgeCompData(int observed_agecomp_data_id)FleetInterfaceinline
    SetObservedIndexData(int observed_index_data_id)FleetInterfaceinline
    SetObservedLengthCompData(int observed_lengthcomp_data_id)FleetInterfaceinline
    random_FFleetInterface
    random_qFleetInterface
    SetAgeCompLikelihood(int agecomp_likelihood_id)FleetInterfaceinline
    SetIndexLikelihood(int index_likelihood_id)FleetInterfaceinline
    SetObservedAgeCompData(int observed_agecomp_data_id)FleetInterfaceinline
    SetObservedIndexData(int observed_index_data_id)FleetInterfaceinline
    SetSelectivity(int selectivity_id)FleetInterfaceinline
    to_json()FleetInterfaceinlinevirtual
    ~FleetInterface() (defined in FleetInterface)FleetInterfaceinlinevirtual
    ~FleetInterfaceBase() (defined in FleetInterfaceBase)FleetInterfaceBaseinlinevirtual
    ~FleetInterface() (defined in FleetInterface)FleetInterfaceinlinevirtual
    ~FleetInterfaceBase() (defined in FleetInterfaceBase)FleetInterfaceBaseinlinevirtual

    diff --git a/docs/classFleetInterface.html b/docs/classFleetInterface.html index 8192261..3dcab32 100644 --- a/docs/classFleetInterface.html +++ b/docs/classFleetInterface.html @@ -98,38 +98,21 @@ virtual uint32_t get_id ()  returns the id for the fleet interface
      +void SetAgeCompLikelihood (int agecomp_likelihood_id) + Set the unique id for the Age Comp Likelihood object. More...
    +  +void SetIndexLikelihood (int index_likelihood_id) + Set the unique id for the Index Likelihood object. More...
    +  void SetObservedAgeCompData (int observed_agecomp_data_id)  Set the unique id for the Observed Age Comp Data object. More...
      -void SetObservedLengthCompData (int observed_lengthcomp_data_id) - Set the unique id for the Observed Length Comp Data object. More...
    -  - -int GetObservedAgeCompDataID () - Return the unique id for the Observed Age Comp Data object.
    -  - -int GetObservedLengthCompDataID () - Return the unique id for the Observed Length Comp Data object.
    -  void SetObservedIndexData (int observed_index_data_id)  Set the unique id for the Observed Index Data object. More...
      - -int GetObservedIndexDataID () - Return the unique id for the Observed Index Data object.
    -  void SetSelectivity (int selectivity_id)  Set the unique id for the Selectivity object. More...
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - Public Member Functions inherited from FIMSRcppInterfaceBase virtual bool add_to_fims_tmb () @@ -138,50 +121,31 @@ - - - - - - - - - - - - - - - - + + + + + + + + - - - - - - - - - - - - + + + + - - -

    Public Attributes

    std::string name = "NA"
     
    bool is_survey = false
     
    int nages
     
    int nlengths = 0
     
    int nyears
     
    ParameterVector log_q
     
    ParameterVector log_Fmort
     
    ParameterVector log_expected_index
     
    ParameterVector proportion_catch_numbers_at_age
     
    ParameterVector proportion_catch_numbers_at_length
     
    ParameterVector age_length_conversion_matrix
     
    double log_q
     
    Rcpp::NumericVector log_Fmort
     
    bool estimate_F = false
     
    bool estimate_q = false
     
    bool estimate_obs_error = false
     
    bool random_q = false
     
    Rcpp::NumericVector derived_cnaa
     
    Rcpp::NumericVector derived_cnal
     
    Rcpp::NumericVector derived_cwaa
     
    Rcpp::NumericVector derived_index
     
    Rcpp::NumericVector derived_age_composition
     
    Rcpp::NumericVector derived_length_composition
     
    bool random_F = false
     
    Rcpp::NumericVector log_obs_error
     
    - Public Attributes inherited from FleetInterfaceBase
    uint32_t id
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    @@ -197,8 +161,8 @@

    Detailed Description

    Rcpp interface for Fleet as an S4 object. To instantiate from R: fleet <- new(Fleet)

    Member Function Documentation

    - -

    ◆ SetObservedAgeCompData()

    + +

    ◆ SetAgeCompLikelihood()

    @@ -207,10 +171,10 @@

    Additional Inherited Members

    - + - +
    void FleetInterface::SetObservedAgeCompData void FleetInterface::SetAgeCompLikelihood ( int observed_agecomp_data_id)agecomp_likelihood_id)
    @@ -221,18 +185,18 @@

    -

    Set the unique id for the Observed Age Comp Data object.

    +

    Set the unique id for the Age Comp Likelihood object.

    Parameters
    - +
    observed_agecomp_data_idUnique id for the Observed Age Comp Data object
    agecomp_likelihood_idUnique id for the Age Comp Likelihood object

    - -

    ◆ SetObservedIndexData()

    + +

    ◆ SetIndexLikelihood()

    @@ -241,10 +205,10 @@

    - + - +
    void FleetInterface::SetObservedIndexData void FleetInterface::SetIndexLikelihood ( int observed_index_data_id)index_likelihood_id)
    @@ -255,18 +219,18 @@

    -

    Set the unique id for the Observed Index Data object.

    +

    Set the unique id for the Index Likelihood object.

    Parameters
    - +
    observed_index_data_idUnique id for the Observed Index Data object
    index_likelihood_idUnique id for the Index Likelihood object

    - -

    ◆ SetObservedLengthCompData()

    + +

    ◆ SetObservedAgeCompData()

    @@ -275,10 +239,10 @@

    - + - +
    void FleetInterface::SetObservedLengthCompData void FleetInterface::SetObservedAgeCompData ( int observed_lengthcomp_data_id)observed_agecomp_data_id)
    @@ -289,18 +253,18 @@

    -

    Set the unique id for the Observed Length Comp Data object.

    +

    Set the unique id for the Observed Age Comp Data object.

    Parameters
    - +
    observed_lengthcomp_data_idUnique id for the Observed Length Comp Data object
    observed_agecomp_data_idUnique id for the Observed Age Comp Data object

    - -

    ◆ SetSelectivity()

    + +

    ◆ SetObservedIndexData()

    @@ -309,10 +273,10 @@

    - + - +
    void FleetInterface::SetSelectivity void FleetInterface::SetObservedIndexData ( int selectivity_id)observed_index_data_id)
    @@ -323,119 +287,78 @@

    -

    Set the unique id for the Selectivity object.

    +

    Set the unique id for the Observed Index Data object.

    Parameters
    - +
    selectivity_idUnique id for the Selectivity object
    observed_index_data_idUnique id for the Observed Index Data object

    -

    Member Data Documentation

    -     -

    ◆ age_length_conversion_matrix

    - -
    -
    - - - - -
    ParameterVector FleetInterface::age_length_conversion_matrix
    -
    -

    matrix to convert ages to lengths

    - -
    -
    - -

    ◆ derived_age_composition

    - -
    -
    - - - - -
    Rcpp::NumericVector FleetInterface::derived_age_composition
    -
    -

    derived quantity: expected age composition

    - -
    -
    - -

    ◆ derived_cnaa

    - -
    -
    - - - - -
    Rcpp::NumericVector FleetInterface::derived_cnaa
    -
    -

    derived quantity: catch numbers at age

    - -
    -
    - -

    ◆ derived_cnal

    + +

    ◆ SetSelectivity()

    + + + + + +
    - + + + + +
    Rcpp::NumericVector FleetInterface::derived_cnalvoid FleetInterface::SetSelectivity (int selectivity_id)
    +     		+inline
    -

    derived quantity: catch numbers at length

    -
    -
    - -

    ◆ derived_cwaa

    - -
    -
    - - - - -
    Rcpp::NumericVector FleetInterface::derived_cwaa
    -
    -

    derived quantity: catch weight at age

    +

    Set the unique id for the Selectivity object.

    +
    Parameters
    + + +
    selectivity_idUnique id for the Selectivity object
    +
    +
    - -

    ◆ derived_index

    +

    Member Data Documentation

    + +

    ◆ estimate_F

    - +
    Rcpp::NumericVector FleetInterface::derived_indexbool FleetInterface::estimate_F = false
    -

    derived quantity: expected index

    +

    whether the parameter F should be estimated

    - -

    ◆ derived_length_composition

    + +

    ◆ estimate_obs_error

    - +
    Rcpp::NumericVector FleetInterface::derived_length_compositionbool FleetInterface::estimate_obs_error = false
    -

    derived quantity: expected length composition

    +

    whether the parameter log_obs_error should be estimated

    @@ -469,44 +392,44 @@

    -

    ◆ log_expected_index

    + +

    ◆ log_Fmort

    - +
    ParameterVector FleetInterface::log_expected_indexRcpp::NumericVector FleetInterface::log_Fmort
    -

    expected index of abundance for the survey

    +

    log of fishing mortality rate for the fleet

    - -

    ◆ log_Fmort

    + +

    ◆ log_obs_error

    - +
    ParameterVector FleetInterface::log_FmortRcpp::NumericVector FleetInterface::log_obs_error
    -

    log of fishing mortality rate for the fleet

    +

    the log of the observation error

    - -

    ◆ log_q

    + +

    ◆ log_q

    - +
    ParameterVector FleetInterface::log_qdouble FleetInterface::log_q
    @@ -527,36 +450,6 @@

    number of ages in the fleet data

    -

    -
    - -

    ◆ name

    - -
    -
    - - - - -
    std::string FleetInterface::name = "NA"
    -
    -

    the name of the fleet

    - -
    -
    - -

    ◆ nlengths

    - -
    -
    - - - - -
    int FleetInterface::nlengths = 0
    -
    -

    number of length bins in the fleet data

    -
    @@ -574,33 +467,18 @@

    -

    ◆ proportion_catch_numbers_at_age

    - -
    -
    - - - - -
    ParameterVector FleetInterface::proportion_catch_numbers_at_age
    -
    -

    expected catch numbers at age for the fleet

    - -
    -
    - -

    ◆ proportion_catch_numbers_at_length

    + +

    ◆ random_F

    - +
    ParameterVector FleetInterface::proportion_catch_numbers_at_lengthbool FleetInterface::random_F = false
    -

    expected catch numbers at length for the fleet

    +

    whether F should be a random effect

    diff --git a/docs/classFleetInterfaceBase-members.html b/docs/classFleetInterfaceBase-members.html index 11be812..51f533f 100644 --- a/docs/classFleetInterfaceBase-members.html +++ b/docs/classFleetInterfaceBase-members.html @@ -77,15 +77,12 @@ - - - - +
    add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual
    fims_interface_objectsFIMSRcppInterfaceBasestatic
    finalize()FIMSRcppInterfaceBaseinlinevirtual
    finalizedFIMSRcppInterfaceBase
    FleetInterfaceBase() (defined in FleetInterfaceBase)FleetInterfaceBaseinline
    get_id()=0FleetInterfaceBasepure virtual
    idFleetInterfaceBase
    id_gFleetInterfaceBasestatic
    live_objectsFleetInterfaceBasestatic
    to_json()FIMSRcppInterfaceBaseinlinevirtual
    ~FleetInterfaceBase() (defined in FleetInterfaceBase)FleetInterfaceBaseinlinevirtual
    ~FleetInterfaceBase() (defined in FleetInterfaceBase)FleetInterfaceBaseinlinevirtual

    diff --git a/docs/classFleetInterfaceBase.html b/docs/classFleetInterfaceBase.html index 7fcf2c2..2d69d13 100644 --- a/docs/classFleetInterfaceBase.html +++ b/docs/classFleetInterfaceBase.html @@ -104,22 +104,11 @@ virtual bool add_to_fims_tmb ()  virtual method to inherit to add objects to the TMB model
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - - -

    Public Attributes

    uint32_t id
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    diff --git a/docs/classGrowthInterfaceBase-members.html b/docs/classGrowthInterfaceBase-members.html index bca7c3b..2a37fe4 100644 --- a/docs/classGrowthInterfaceBase-members.html +++ b/docs/classGrowthInterfaceBase-members.html @@ -78,15 +78,12 @@ - - - - +

    Static Public Attributes

    add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual
    evaluate(double age)=0GrowthInterfaceBasepure virtual
    fims_interface_objectsFIMSRcppInterfaceBasestatic
    finalize()FIMSRcppInterfaceBaseinlinevirtual
    finalizedFIMSRcppInterfaceBase
    get_id()=0GrowthInterfaceBasepure virtual
    GrowthInterfaceBase() (defined in GrowthInterfaceBase)GrowthInterfaceBaseinline
    idGrowthInterfaceBase
    id_gGrowthInterfaceBasestatic
    live_objectsGrowthInterfaceBasestatic
    to_json()FIMSRcppInterfaceBaseinlinevirtual
    ~GrowthInterfaceBase() (defined in GrowthInterfaceBase)GrowthInterfaceBaseinlinevirtual
    ~GrowthInterfaceBase() (defined in GrowthInterfaceBase)GrowthInterfaceBaseinlinevirtual

    diff --git a/docs/classGrowthInterfaceBase.html b/docs/classGrowthInterfaceBase.html index 580722f..e241ce8 100644 --- a/docs/classGrowthInterfaceBase.html +++ b/docs/classGrowthInterfaceBase.html @@ -108,22 +108,11 @@ virtual bool add_to_fims_tmb ()  virtual method to inherit to add objects to the TMB model
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - - -

    Public Attributes

    uint32_t id
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    diff --git a/docs/classIndexDataInterface-members.html b/docs/classIndexDataInterface-members.html index f769ede..faced86 100644 --- a/docs/classIndexDataInterface-members.html +++ b/docs/classIndexDataInterface-members.html @@ -78,8 +78,6 @@ - - @@ -87,10 +85,9 @@ - - - - + + +

    Static Public Attributes

    add_to_fims_tmb()DataInterfaceBaseinlinevirtual
    DataInterfaceBase()DataInterfaceBaseinline
    fims_interface_objectsFIMSRcppInterfaceBasestatic
    finalize()FIMSRcppInterfaceBaseinlinevirtual
    finalizedFIMSRcppInterfaceBase
    get_id()IndexDataInterfaceinlinevirtual
    idDataInterfaceBase
    id_gDataInterfaceBasestatic
    IndexDataInterface(int ymax=0)IndexDataInterfaceinline
    live_objectsDataInterfaceBasestatic
    observed_dataDataInterfaceBase
    to_json()IndexDataInterfaceinlinevirtual
    ymaxIndexDataInterface
    ~DataInterfaceBase()DataInterfaceBaseinlinevirtual
    ~IndexDataInterface()IndexDataInterfaceinlinevirtual
    ymaxIndexDataInterface
    ~DataInterfaceBase()DataInterfaceBaseinlinevirtual
    ~IndexDataInterface()IndexDataInterfaceinlinevirtual
    diff --git a/docs/classIndexDataInterface.html b/docs/classIndexDataInterface.html index 7d7258d..9f67339 100644 --- a/docs/classIndexDataInterface.html +++ b/docs/classIndexDataInterface.html @@ -106,10 +106,6 @@ virtual uint32_t get_id ()  get the ID of the interface base object
      - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - Public Member Functions inherited from DataInterfaceBase  DataInterfaceBase () @@ -123,11 +119,6 @@ virtual bool add_to_fims_tmb ()  add_to_fims_tmb dummy method
      -- Public Member Functions inherited from FIMSRcppInterfaceBase - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  @@ -140,9 +131,6 @@ - - -

    Public Attributes

     
    uint32_t id
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    diff --git a/docs/classLogisticMaturityInterface-members.html b/docs/classLogisticMaturityInterface-members.html index 0fe223e..5b16a07 100644 --- a/docs/classLogisticMaturityInterface-members.html +++ b/docs/classLogisticMaturityInterface-members.html @@ -78,19 +78,16 @@ - - - + - - - - + + +

    Additional Inherited Members

    add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual
    evaluate(double x)LogisticMaturityInterfaceinlinevirtual
    fims_interface_objectsFIMSRcppInterfaceBasestatic
    finalize()LogisticMaturityInterfaceinlinevirtual
    finalizedFIMSRcppInterfaceBase
    get_id()LogisticMaturityInterfaceinlinevirtual
    idMaturityInterfaceBase
    id_gMaturityInterfaceBasestatic
    inflection_pointLogisticMaturityInterface
    inflection_pointLogisticMaturityInterface
    live_objectsMaturityInterfaceBasestatic
    LogisticMaturityInterface() (defined in LogisticMaturityInterface)LogisticMaturityInterfaceinline
    MaturityInterfaceBase() (defined in MaturityInterfaceBase)MaturityInterfaceBaseinline
    slopeLogisticMaturityInterface
    to_json()LogisticMaturityInterfaceinlinevirtual
    ~LogisticMaturityInterface() (defined in LogisticMaturityInterface)LogisticMaturityInterfaceinlinevirtual
    ~MaturityInterfaceBase() (defined in MaturityInterfaceBase)MaturityInterfaceBaseinlinevirtual
    slopeLogisticMaturityInterface
    ~LogisticMaturityInterface() (defined in LogisticMaturityInterface)LogisticMaturityInterfaceinlinevirtual
    ~MaturityInterfaceBase() (defined in MaturityInterfaceBase)MaturityInterfaceBaseinlinevirtual

    diff --git a/docs/classLogisticMaturityInterface.html b/docs/classLogisticMaturityInterface.html index 6347bf0..4a2de18 100644 --- a/docs/classLogisticMaturityInterface.html +++ b/docs/classLogisticMaturityInterface.html @@ -101,14 +101,6 @@ virtual double evaluate (double x)  evaluate the logistic maturity function More...
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - Public Member Functions inherited from FIMSRcppInterfaceBase virtual bool add_to_fims_tmb () @@ -117,16 +109,13 @@ - - - - + + + + - - -

    Public Attributes

    ParameterVector inflection_point
     
    ParameterVector slope
     
    Parameter inflection_point
     
    Parameter slope
     
    - Public Attributes inherited from MaturityInterfaceBase
    uint32_t id
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    @@ -179,14 +168,14 @@

    Member Data Documentation

    - -

    ◆ inflection_point

    + +

    ◆ inflection_point

    Additional Inherited Members

    - +
    ParameterVector LogisticMaturityInterface::inflection_pointParameter LogisticMaturityInterface::inflection_point
    @@ -194,14 +183,14 @@

    -

    ◆ slope

    + +

    ◆ slope

    - +
    ParameterVector LogisticMaturityInterface::slopeParameter LogisticMaturityInterface::slope
    diff --git a/docs/classLogisticSelectivityInterface-members.html b/docs/classLogisticSelectivityInterface-members.html index c0f46ab..3de690c 100644 --- a/docs/classLogisticSelectivityInterface-members.html +++ b/docs/classLogisticSelectivityInterface-members.html @@ -78,19 +78,16 @@ add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual evaluate(double x)LogisticSelectivityInterfaceinlinevirtual fims_interface_objectsFIMSRcppInterfaceBasestatic - finalize()LogisticSelectivityInterfaceinlinevirtual - finalizedFIMSRcppInterfaceBase get_id()LogisticSelectivityInterfaceinlinevirtual idSelectivityInterfaceBase id_gSelectivityInterfaceBasestatic - inflection_pointLogisticSelectivityInterface + inflection_pointLogisticSelectivityInterface live_objectsSelectivityInterfaceBasestatic LogisticSelectivityInterface() (defined in LogisticSelectivityInterface)LogisticSelectivityInterfaceinline SelectivityInterfaceBase() (defined in SelectivityInterfaceBase)SelectivityInterfaceBaseinline - slopeLogisticSelectivityInterface - to_json()LogisticSelectivityInterfaceinlinevirtual - ~LogisticSelectivityInterface() (defined in LogisticSelectivityInterface)LogisticSelectivityInterfaceinlinevirtual - ~SelectivityInterfaceBase() (defined in SelectivityInterfaceBase)SelectivityInterfaceBaseinlinevirtual + slopeLogisticSelectivityInterface + ~LogisticSelectivityInterface() (defined in LogisticSelectivityInterface)LogisticSelectivityInterfaceinlinevirtual + ~SelectivityInterfaceBase() (defined in SelectivityInterfaceBase)SelectivityInterfaceBaseinlinevirtual
    diff --git a/docs/classLogisticSelectivityInterface.html b/docs/classLogisticSelectivityInterface.html index 2e0974b..54a122a 100644 --- a/docs/classLogisticSelectivityInterface.html +++ b/docs/classLogisticSelectivityInterface.html @@ -101,14 +101,6 @@ virtual double evaluate (double x)  evaluate the logistic selectivity function More...
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - Public Member Functions inherited from FIMSRcppInterfaceBase virtual bool add_to_fims_tmb () @@ -117,16 +109,13 @@ - - - - + + + + - - -

    Public Attributes

    ParameterVector inflection_point
     
    ParameterVector slope
     
    Parameter inflection_point
     
    Parameter slope
     
    - Public Attributes inherited from SelectivityInterfaceBase
    uint32_t id
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    @@ -179,14 +168,14 @@

    Member Data Documentation

    - -

    ◆ inflection_point

    + +

    ◆ inflection_point

    Additional Inherited Members

    - +
    ParameterVector LogisticSelectivityInterface::inflection_pointParameter LogisticSelectivityInterface::inflection_point
    @@ -194,14 +183,14 @@

    -

    ◆ slope

    + +

    ◆ slope

    - +
    ParameterVector LogisticSelectivityInterface::slopeParameter LogisticSelectivityInterface::slope
    diff --git a/docs/classMaturityInterfaceBase-members.html b/docs/classMaturityInterfaceBase-members.html index 2e64dc9..03548f6 100644 --- a/docs/classMaturityInterfaceBase-members.html +++ b/docs/classMaturityInterfaceBase-members.html @@ -78,15 +78,12 @@ add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual evaluate(double x)=0MaturityInterfaceBasepure virtual fims_interface_objectsFIMSRcppInterfaceBasestatic - finalize()FIMSRcppInterfaceBaseinlinevirtual - finalizedFIMSRcppInterfaceBase get_id()=0MaturityInterfaceBasepure virtual idMaturityInterfaceBase id_gMaturityInterfaceBasestatic live_objectsMaturityInterfaceBasestatic MaturityInterfaceBase() (defined in MaturityInterfaceBase)MaturityInterfaceBaseinline - to_json()FIMSRcppInterfaceBaseinlinevirtual - ~MaturityInterfaceBase() (defined in MaturityInterfaceBase)MaturityInterfaceBaseinlinevirtual + ~MaturityInterfaceBase() (defined in MaturityInterfaceBase)MaturityInterfaceBaseinlinevirtual
    diff --git a/docs/classMaturityInterfaceBase.html b/docs/classMaturityInterfaceBase.html index 9ee8abd..94db030 100644 --- a/docs/classMaturityInterfaceBase.html +++ b/docs/classMaturityInterfaceBase.html @@ -108,22 +108,11 @@ virtual bool add_to_fims_tmb ()  virtual method to inherit to add objects to the TMB model
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - - -

    Public Attributes

    uint32_t id
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    diff --git a/docs/classParameter-members.html b/docs/classParameter-members.html index 0f4d7a3..435f679 100644 --- a/docs/classParameter-members.html +++ b/docs/classParameter-members.html @@ -76,19 +76,13 @@

    This is the complete list of members for Parameter, including all inherited members.

    Static Public Attributes

    - - - - - - - + - +
    estimated_mParameter
    final_value_mParameter
    id_gParameterstatic
    id_mParameter
    initial_value_mParameter
    is_random_effect_mParameter
    max_mParameter
    min_mParameter
    operator=(const Parameter &right)Parameterinline
    Parameter(double value, double min, double max, bool estimated)Parameterinline
    Parameter(const Parameter &other)Parameterinline
    Parameter(double value, double min, double max, bool estimated)Parameterinline
    Parameter(double value)Parameterinline
    Parameter()Parameterinline
    random_mParameter
    value_mParameter
    diff --git a/docs/classParameter.html b/docs/classParameter.html index 0376cbd..b3c0277 100644 --- a/docs/classParameter.html +++ b/docs/classParameter.html @@ -71,7 +71,6 @@
    Public Member Functions | Public Attributes | -Static Public Attributes | List of all members
    Parameter Class Reference
    @@ -88,14 +87,6 @@  Parameter (double value, double min, double max, bool estimated)  Constructor for initializing Parameter. More...
      - - Parameter (const Parameter &other) - Constructor for initializing Parameter.
    -  - -Parameter & operator= (const Parameter &right) - Constructor for initializing Parameter.
    -   Parameter (double value)  Constructor for initializing Parameter. More...
      @@ -105,12 +96,8 @@ - - - - - - + + @@ -119,13 +106,6 @@ - - -

    Public Attributes

    uint32_t id_m
     
    double initial_value_m = 0.0
     
    double final_value_m = 0.0
     
    double value_m
     
    double min_m
     
    double max_m
     
    bool estimated_m
     
    bool random_m
     
    - - -

    -Static Public Attributes

    static uint32_t id_g = 0
     

    Detailed Description

    RcppInterface class that defines the interface between R and C++ for parameter types.

    @@ -254,74 +234,6 @@

    false

    Is the parameter estimated? Default value is false.

    -

    -
    - -

    ◆ final_value_m

    - -
    -
    - - - - -
    double Parameter::final_value_m = 0.0
    -
    -

    final value of the parameter

    - -
    -
    - -

    ◆ id_g

    - -
    -
    - - - - - -
    - - - - -
    uint32_t Parameter::id_g = 0
    -     		-static
    -
    -

    global id of the parameter

    - -
    -
    - -

    ◆ id_m

    - -
    -
    - - - - -
    uint32_t Parameter::id_m
    -
    -

    id of the parameter

    - -
    -
    - -

    ◆ initial_value_m

    - -
    -
    - - - - -
    double Parameter::initial_value_m = 0.0
    -
    -

    initial value of the parameter

    -
    @@ -351,8 +263,8 @@

    Initial value:
    =
    -
    std::numeric_limits<double>::infinity()
    -

    max value of the parameter; default is positive infinity

    +
    std::numeric_limits<double>::max()
    +

    max value of the parameter

    @@ -368,25 +280,23 @@

    Initial value:
    =
    -
    -std::numeric_limits<double>::infinity()
    -

    min value of the parameter; default is negative infinity

    +
    std::numeric_limits<double>::min()
    +

    min value of the parameter

    - -

    ◆ random_m

    + +

    ◆ value_m

    - +
    bool Parameter::random_mdouble Parameter::value_m
    -Initial value:
    =
    -
    false
    -

    is the parameter random? Default value is false.

    +

    initial value of the parameter

    diff --git a/docs/classPopulationInterface-members.html b/docs/classPopulationInterface-members.html index 444df5c..43941ae 100644 --- a/docs/classPopulationInterface-members.html +++ b/docs/classPopulationInterface-members.html @@ -77,32 +77,22 @@ - - - - + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + - - - + @@ -111,9 +101,8 @@ - - - + +
    add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual
    agesPopulationInterface
    derived_biomassPopulationInterface
    derived_naaPopulationInterface
    derived_recruitmentPopulationInterface
    derived_ssbPopulationInterface
    estimate_initNAAPopulationInterface
    estimate_MPopulationInterface
    estimate_prop_femalePopulationInterface
    estimated_log_init_naaPopulationInterface
    estimated_log_MPopulationInterface
    estimated_proportion_femalePopulationInterface
    evaluate()PopulationInterfaceinlinevirtual
    fims_interface_objectsFIMSRcppInterfaceBasestatic
    finalize()PopulationInterfaceinlinevirtual
    finalizedFIMSRcppInterfaceBase
    get_id()PopulationInterfaceinlinevirtual
    growth_idPopulationInterface
    idPopulationInterfaceBase
    id_gPopulationInterfaceBasestatic
    live_objectsPopulationInterfaceBasestatic
    log_init_naaPopulationInterface
    log_MPopulationInterface
    maturity_idPopulationInterface
    nagesPopulationInterface
    namePopulationInterface
    evaluate()PopulationInterfaceinlinevirtual
    fims_interface_objectsFIMSRcppInterfaceBasestatic
    get_id()PopulationInterfaceinlinevirtual
    growth_idPopulationInterface
    idPopulationInterfaceBase
    id_gPopulationInterfaceBasestatic
    live_objectsPopulationInterfaceBasestatic
    log_init_naaPopulationInterface
    log_MPopulationInterface
    maturity_idPopulationInterface
    nagesPopulationInterface
    nfleetsPopulationInterface
    nlengthsPopulationInterface
    nseasonsPopulationInterface
    numbers_at_agePopulationInterface
    nseasonsPopulationInterface
    nyearsPopulationInterface
    PopulationInterface() (defined in PopulationInterface)PopulationInterfaceinline
    PopulationInterfaceBase() (defined in PopulationInterfaceBase)PopulationInterfaceBaseinline
    SetGrowth(uint32_t growth_id)PopulationInterfaceinline
    SetMaturity(uint32_t maturity_id)PopulationInterfaceinline
    SetRecruitment(uint32_t recruitment_id)PopulationInterfaceinline
    to_json()PopulationInterfaceinlinevirtual
    ~PopulationInterface() (defined in PopulationInterface)PopulationInterfaceinlinevirtual
    ~PopulationInterfaceBase() (defined in PopulationInterfaceBase)PopulationInterfaceBaseinlinevirtual
    ~PopulationInterface() (defined in PopulationInterface)PopulationInterfaceinlinevirtual
    ~PopulationInterfaceBase() (defined in PopulationInterfaceBase)PopulationInterfaceBaseinlinevirtual
    diff --git a/docs/classPopulationInterface.html b/docs/classPopulationInterface.html index c24fc0e..12eaaa1 100644 --- a/docs/classPopulationInterface.html +++ b/docs/classPopulationInterface.html @@ -111,14 +111,6 @@ virtual void evaluate ()  evaluate the population function
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - Public Member Functions inherited from FIMSRcppInterfaceBase virtual bool add_to_fims_tmb () @@ -135,48 +127,29 @@   uint32_t nyears   -uint32_t nlengths -  uint32_t maturity_id   uint32_t growth_id   uint32_t recruitment_id   -ParameterVector log_M -  -ParameterVector log_init_naa -  -ParameterVector numbers_at_age -  +Rcpp::NumericVector log_M +  +Rcpp::NumericVector log_init_naa +  Rcpp::NumericVector ages   Rcpp::NumericVector proportion_female   +bool estimate_M +  +bool estimate_initNAA +  bool estimate_prop_female   -Rcpp::NumericVector derived_ssb -  -Rcpp::NumericVector derived_naa -  -Rcpp::NumericVector derived_biomass -  -Rcpp::NumericVector derived_recruitment -  -Rcpp::NumericVector estimated_log_M -  -Rcpp::NumericVector estimated_log_init_naa -  -Rcpp::NumericVector estimated_proportion_female -  -std::string name -  - Public Attributes inherited from PopulationInterfaceBase uint32_t id   -- Public Attributes inherited from FIMSRcppInterfaceBase -bool finalized = false -  @@ -310,63 +283,33 @@

    -

    ◆ derived_biomass

    + +

    ◆ estimate_initNAA

    Additional Inherited Members

    - +
    Rcpp::NumericVector PopulationInterface::derived_biomassbool PopulationInterface::estimate_initNAA
    -

    derived quantity: biomass

    +

    whether parameter should be estimated

    - -

    ◆ derived_naa

    + +

    ◆ estimate_M

    - +
    Rcpp::NumericVector PopulationInterface::derived_naabool PopulationInterface::estimate_M
    -

    derived quantity: numbers at age

    - -
    -
    - -

    ◆ derived_recruitment

    - -
    -
    - - - - -
    Rcpp::NumericVector PopulationInterface::derived_recruitment
    -
    -

    derived quantity: recruitment

    - -
    -
    - -

    ◆ derived_ssb

    - -
    -
    - - - - -
    Rcpp::NumericVector PopulationInterface::derived_ssb
    -
    -

    derived quantity: spawning stock biomass

    +

    whether parameter should be estimated

    @@ -383,51 +326,6 @@

    whether proportion female should be estimated

    -

    - - -

    ◆ estimated_log_init_naa

    - -
    -
    - - - - -
    Rcpp::NumericVector PopulationInterface::estimated_log_init_naa
    -
    -

    derived quantity: natural log initial numbers at age

    - -
    -
    - -

    ◆ estimated_log_M

    - -
    -
    - - - - -
    Rcpp::NumericVector PopulationInterface::estimated_log_M
    -
    -

    derived quantity: natural log mortality

    - -
    -
    - -

    ◆ estimated_proportion_female

    - -
    -
    - - - - -
    Rcpp::NumericVector PopulationInterface::estimated_proportion_female
    -
    -

    TODO: delete

    -
    @@ -445,14 +343,14 @@

    -

    ◆ log_init_naa

    + +

    ◆ log_init_naa

    - +
    ParameterVector PopulationInterface::log_init_naaRcpp::NumericVector PopulationInterface::log_init_naa
    @@ -460,14 +358,14 @@

    -

    ◆ log_M

    + +

    ◆ log_M

    - +
    ParameterVector PopulationInterface::log_MRcpp::NumericVector PopulationInterface::log_M
    @@ -503,21 +401,6 @@

    number of ages

    -

    -
    - -

    ◆ name

    - -
    -
    - - - - -
    std::string PopulationInterface::name
    -
    -

    TODO: document

    -
    @@ -533,21 +416,6 @@

    number of fleets

    -

    -
    - -

    ◆ nlengths

    - -
    -
    - - - - -
    uint32_t PopulationInterface::nlengths
    -
    -

    number of lengths

    -
    @@ -563,21 +431,6 @@

    number of seasons

    - - -     -

    ◆ numbers_at_age

    - -
    -
    - - - - -
    ParameterVector PopulationInterface::numbers_at_age
    -
    -

    log of the initial numbers at age

    -
    diff --git a/docs/classPopulationInterfaceBase-members.html b/docs/classPopulationInterfaceBase-members.html index 3422cfd..cf280dd 100644 --- a/docs/classPopulationInterfaceBase-members.html +++ b/docs/classPopulationInterfaceBase-members.html @@ -77,15 +77,12 @@ - - - - +
    add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual
    fims_interface_objectsFIMSRcppInterfaceBasestatic
    finalize()FIMSRcppInterfaceBaseinlinevirtual
    finalizedFIMSRcppInterfaceBase
    get_id()=0PopulationInterfaceBasepure virtual
    idPopulationInterfaceBase
    id_gPopulationInterfaceBasestatic
    live_objectsPopulationInterfaceBasestatic
    PopulationInterfaceBase() (defined in PopulationInterfaceBase)PopulationInterfaceBaseinline
    to_json()FIMSRcppInterfaceBaseinlinevirtual
    ~PopulationInterfaceBase() (defined in PopulationInterfaceBase)PopulationInterfaceBaseinlinevirtual
    ~PopulationInterfaceBase() (defined in PopulationInterfaceBase)PopulationInterfaceBaseinlinevirtual
    diff --git a/docs/classPopulationInterfaceBase.html b/docs/classPopulationInterfaceBase.html index b1b0816..56e62e1 100644 --- a/docs/classPopulationInterfaceBase.html +++ b/docs/classPopulationInterfaceBase.html @@ -104,22 +104,11 @@ virtual bool add_to_fims_tmb ()  virtual method to inherit to add objects to the TMB model
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - - -

    Public Attributes

    uint32_t id
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    diff --git a/docs/classRecruitmentInterfaceBase-members.html b/docs/classRecruitmentInterfaceBase-members.html index b9150d2..cea405f 100644 --- a/docs/classRecruitmentInterfaceBase-members.html +++ b/docs/classRecruitmentInterfaceBase-members.html @@ -77,15 +77,13 @@

    Static Public Attributes

    - - - - - - - - - + + + + + + +
    add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual
    evaluate(double spawners, double ssbzero)=0RecruitmentInterfaceBasepure virtual
    fims_interface_objectsFIMSRcppInterfaceBasestatic
    finalize()FIMSRcppInterfaceBaseinlinevirtual
    finalizedFIMSRcppInterfaceBase
    get_id()=0RecruitmentInterfaceBasepure virtual
    idRecruitmentInterfaceBase
    id_gRecruitmentInterfaceBasestatic
    live_objectsRecruitmentInterfaceBasestatic
    RecruitmentInterfaceBase() (defined in RecruitmentInterfaceBase)RecruitmentInterfaceBaseinline
    to_json()FIMSRcppInterfaceBaseinlinevirtual
    evaluate_nll()=0RecruitmentInterfaceBasepure virtual
    fims_interface_objectsFIMSRcppInterfaceBasestatic
    get_id()=0RecruitmentInterfaceBasepure virtual
    idRecruitmentInterfaceBase
    id_gRecruitmentInterfaceBasestatic
    live_objectsRecruitmentInterfaceBasestatic
    RecruitmentInterfaceBase() (defined in RecruitmentInterfaceBase)RecruitmentInterfaceBaseinline
    ~RecruitmentInterfaceBase() (defined in RecruitmentInterfaceBase)RecruitmentInterfaceBaseinlinevirtual
    diff --git a/docs/classRecruitmentInterfaceBase.html b/docs/classRecruitmentInterfaceBase.html index 20e7cdd..645537a 100644 --- a/docs/classRecruitmentInterfaceBase.html +++ b/docs/classRecruitmentInterfaceBase.html @@ -103,27 +103,19 @@ virtual double evaluate (double spawners, double ssbzero)=0  evaluate method for child recruitment interface objects to inherit
      +virtual double evaluate_nll ()=0 + evaluate recruitment nll More...
    +  - Public Member Functions inherited from FIMSRcppInterfaceBase virtual bool add_to_fims_tmb ()  virtual method to inherit to add objects to the TMB model
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - - -

    Public Attributes

    uint32_t id
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    @@ -138,7 +130,38 @@

    Detailed Description

    RecruitmentInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Recruitment function.

    Recruitment Rcpp interface

    -

    Member Data Documentation

    +

    Member Function Documentation

    + +

    ◆ evaluate_nll()

    + +
    +
    +

    Static Public Attributes

    + + + + +
    + + + + + + + +
    virtual double RecruitmentInterfaceBase::evaluate_nll ()
    +     		+pure virtual
    +
    + +

    evaluate recruitment nll

    +
    Returns
    double
    + +

    Implemented in BevertonHoltRecruitmentInterface.

    + +
    + +

    Member Data Documentation

    ◆ id

    diff --git a/docs/classSelectivityInterfaceBase-members.html b/docs/classSelectivityInterfaceBase-members.html index 6d67dd5..5a243dc 100644 --- a/docs/classSelectivityInterfaceBase-members.html +++ b/docs/classSelectivityInterfaceBase-members.html @@ -78,15 +78,12 @@ add_to_fims_tmb()FIMSRcppInterfaceBaseinlinevirtual evaluate(double x)=0SelectivityInterfaceBasepure virtual fims_interface_objectsFIMSRcppInterfaceBasestatic - finalize()FIMSRcppInterfaceBaseinlinevirtual - finalizedFIMSRcppInterfaceBase get_id()=0SelectivityInterfaceBasepure virtual idSelectivityInterfaceBase id_gSelectivityInterfaceBasestatic live_objectsSelectivityInterfaceBasestatic SelectivityInterfaceBase() (defined in SelectivityInterfaceBase)SelectivityInterfaceBaseinline - to_json()FIMSRcppInterfaceBaseinlinevirtual - ~SelectivityInterfaceBase() (defined in SelectivityInterfaceBase)SelectivityInterfaceBaseinlinevirtual + ~SelectivityInterfaceBase() (defined in SelectivityInterfaceBase)SelectivityInterfaceBaseinlinevirtual
    diff --git a/docs/classSelectivityInterfaceBase.html b/docs/classSelectivityInterfaceBase.html index 9456639..88258c2 100644 --- a/docs/classSelectivityInterfaceBase.html +++ b/docs/classSelectivityInterfaceBase.html @@ -109,22 +109,11 @@ virtual bool add_to_fims_tmb ()  virtual method to inherit to add objects to the TMB model
      - -virtual void finalize () - finalize function. Extracts derived quantities back to the Rcpp interface object from the Information object.
    -  - -virtual std::string to_json () - Convert the data to json representation for the output.
    -  - - -

    Public Attributes

    uint32_t id
     
    - Public Attributes inherited from FIMSRcppInterfaceBase
    bool finalized = false
     
    diff --git a/docs/classes.html b/docs/classes.html index 256a5c5..1d9a325 100644 --- a/docs/classes.html +++ b/docs/classes.html @@ -82,13 +82,13 @@
    BevertonHoltRecruitmentInterface
    D
    -
    DataInterfaceBase
    DataObject (fims_data_object)
    DensityComponentBase (fims_distributions)
    DistributionsInterfaceBase
    DlnormDistributionsInterface
    DmultinomDistributionsInterface
    DnormDistributionsInterface
    DoubleLogisticSelectivity (fims_popdy)
    DoubleLogisticSelectivityInterface
    +
    DataInterfaceBase
    DataObject (fims_data_object)
    DistributionsBase (fims_distributions)
    DistributionsInterfaceBase
    DlnormDistributionsInterface
    DmultinomDistributionsInterface
    DnormDistributionsInterface
    DoubleLogisticSelectivity (fims_popdy)
    DoubleLogisticSelectivityInterface
    E
    EWAAgrowth (fims_popdy)
    EWAAGrowthInterface
    F
    -
    FIMSLog (fims)
    FIMSObject (fims_model_object)
    FIMSRcppInterfaceBase
    Fleet (fims_popdy)
    FleetInterface
    FleetInterfaceBase
    +
    fims_log (fims)
    FIMSObject (fims_model_object)
    FIMSRcppInterfaceBase
    Fleet (fims_popdy)
    FleetInterface
    FleetInterfaceBase
    G
    GrowthBase (fims_popdy)
    GrowthInterfaceBase
    @@ -97,19 +97,19 @@
    IndexDataInterface
    Information (fims_info)
    J
    -
    JsonParser (fims)
    JsonValue (fims)
    +
    JsonParser
    JsonValue
    L
    -
    LengthCompDataInterface
    LogEntry (fims)
    LogisticMaturity (fims_popdy)
    LogisticMaturityInterface
    LogisticSelectivity (fims_popdy)
    LogisticSelectivityInterface
    LogNormalLPDF (fims_distributions)
    LPDFInterfaceBase
    +
    LogisticMaturity (fims_popdy)
    LogisticMaturityInterface
    LogisticSelectivity (fims_popdy)
    LogisticSelectivityInterface
    M
    -
    MaturityBase (fims_popdy)
    MaturityInterfaceBase
    Model (fims_model)
    MultinomialLPMF (fims_distributions)
    +
    MaturityBase (fims_popdy)
    MaturityInterfaceBase
    Model (fims_model)
    N
    -
    NormalLPDF (fims_distributions)
    +
    NLLInterfaceBase
    P
    -
    Parameter
    ParameterVector
    Population (fims_popdy)
    PopulationInterface
    PopulationInterfaceBase
    +
    Parameter
    Population (fims_popdy)
    PopulationInterface
    PopulationInterfaceBase
    R
    RecruitmentBase (fims_popdy)
    RecruitmentInterfaceBase
    diff --git a/docs/classfims_1_1Vector-members.html b/docs/classfims_1_1Vector-members.html index b001475..646017d 100644 --- a/docs/classfims_1_1Vector-members.html +++ b/docs/classfims_1_1Vector-members.html @@ -102,37 +102,36 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

    Static Public Attributes

    erase(iterator first, iterator last)fims::Vector< Type >inline
    front()fims::Vector< Type >inline
    front() constfims::Vector< Type >inline
    get_force_scalar(size_t pos)fims::Vector< Type >inline
    insert(const_iterator pos, const Type &value)fims::Vector< Type >inline
    insert(const_iterator pos, size_type count, const Type &value)fims::Vector< Type >inline
    insert(const_iterator pos, InputIt first, InputIt last)fims::Vector< Type >inline
    insert(const_iterator pos, std::initializer_list< Type > ilist)fims::Vector< Type >inline
    iterator typedeffims::Vector< Type >
    max_size() constfims::Vector< Type >inline
    operator std::vector< Type >()fims::Vector< Type >inline
    operator==(const fims::Vector< T > &lhs, const fims::Vector< T > &rhs)fims::Vector< Type >friend
    operator[](size_t pos)fims::Vector< Type >inline
    operator[](size_t n) constfims::Vector< Type >inline
    pointer typedeffims::Vector< Type >
    pop_back()fims::Vector< Type >inline
    push_back(const Type &&value)fims::Vector< Type >inline
    rbegin()fims::Vector< Type >inline
    rbegin() constfims::Vector< Type >inline
    reference typedeffims::Vector< Type >
    rend()fims::Vector< Type >inline
    rend() constfims::Vector< Type >inline
    reserve(size_type cap)fims::Vector< Type >inline
    resize(size_t s)fims::Vector< Type >inline
    reverse_iterator typedeffims::Vector< Type >
    shrink_to_fit()fims::Vector< Type >inline
    size() constfims::Vector< Type >inline
    size_type typedeffims::Vector< Type >
    swap(Vector &other)fims::Vector< Type >inline
    value_type typedeffims::Vector< Type >
    Vector()fims::Vector< Type >inline
    Vector(size_t size, const Type &value=Type())fims::Vector< Type >inline
    Vector(const Vector< Type > &other)fims::Vector< Type >inline
    Vector(const std::vector< Type > &other)fims::Vector< Type >inline
    insert(const_iterator pos, const Type &value)fims::Vector< Type >inline
    insert(const_iterator pos, size_type count, const Type &value)fims::Vector< Type >inline
    insert(const_iterator pos, InputIt first, InputIt last)fims::Vector< Type >inline
    insert(const_iterator pos, std::initializer_list< Type > ilist)fims::Vector< Type >inline
    iterator typedeffims::Vector< Type >
    max_size() constfims::Vector< Type >inline
    operator std::vector< Type >()fims::Vector< Type >inline
    operator==(const fims::Vector< T > &lhs, const fims::Vector< T > &rhs)fims::Vector< Type >friend
    operator[](size_t pos)fims::Vector< Type >inline
    operator[](size_t n) constfims::Vector< Type >inline
    pointer typedeffims::Vector< Type >
    pop_back()fims::Vector< Type >inline
    push_back(const Type &&value)fims::Vector< Type >inline
    rbegin()fims::Vector< Type >inline
    rbegin() constfims::Vector< Type >inline
    reference typedeffims::Vector< Type >
    rend()fims::Vector< Type >inline
    rend() constfims::Vector< Type >inline
    reserve(size_type cap)fims::Vector< Type >inline
    resize(size_t s)fims::Vector< Type >inline
    reverse_iterator typedeffims::Vector< Type >
    shrink_to_fit()fims::Vector< Type >inline
    size() constfims::Vector< Type >inline
    size_type typedeffims::Vector< Type >
    swap(Vector &other)fims::Vector< Type >inline
    value_type typedeffims::Vector< Type >
    Vector()fims::Vector< Type >inline
    Vector(size_t size, const Type &value=Type())fims::Vector< Type >inline
    Vector(const Vector< Type > &other)fims::Vector< Type >inline
    Vector(const std::vector< Type > &other)fims::Vector< Type >inline
    diff --git a/docs/classfims_1_1Vector.html b/docs/classfims_1_1Vector.html index 0fba0ee..0ee5ca3 100644 --- a/docs/classfims_1_1Vector.html +++ b/docs/classfims_1_1Vector.html @@ -142,9 +142,6 @@ const Type & at (size_t n) const  Returns a constant reference to the element at specified location pos. Bounds checking is performed.
      -Type & get_force_scalar (size_t pos) - If this vector is size 1 and pos is greater than zero, the first index is returned. If this vector has size greater than 1 and pos is greater than size, a invalid_argument exception is thrown. Otherwise, the value at index pos is returned. More...
    -  reference front ()  Returns a reference to the first element in the container.
    @@ -552,43 +549,6 @@

    -

    ◆ get_force_scalar()

    - -
    -
    -
    -template<typename Type >
    - - - - - -
    - - - - - - - - -
    Type& fims::Vector< Type >::get_force_scalar (size_t pos)
    -     		-inline
    -
    - -

    If this vector is size 1 and pos is greater than zero, the first index is returned. If this vector has size greater than 1 and pos is greater than size, a invalid_argument exception is thrown. Otherwise, the value at index pos is returned.

    -
    Parameters
    - - -
    pos
    -
    -
    -
    Returns
    a constant reference to the element at specified location
    -
    diff --git a/docs/classfims__info_1_1Information-members.html b/docs/classfims__info_1_1Information-members.html index e761663..f4fdbcf 100644 --- a/docs/classfims__info_1_1Information-members.html +++ b/docs/classfims__info_1_1Information-members.html @@ -82,8 +82,8 @@ CreateModel()fims_info::Information< Type >inline data_iterator typedeffims_info::Information< Type > data_objectsfims_info::Information< Type > - density_componentsfims_info::Information< Type > - density_components_iterator typedeffims_info::Information< Type > + distribution_modelsfims_info::Information< Type > + distribution_models_iterator typedeffims_info::Information< Type > fims_informationfims_info::Information< Type >static fixed_effects_parametersfims_info::Information< Type > fleet_iterator typedeffims_info::Information< Type > @@ -103,27 +103,20 @@ nagesfims_info::Information< Type > nseasonsfims_info::Information< Type > nyearsfims_info::Information< Type > - parameter_namesfims_info::Information< Type > - parametersfims_info::Information< Type > - population_iterator typedeffims_info::Information< Type > - populationsfims_info::Information< Type > - random_effects_parametersfims_info::Information< Type > - recruitment_modelsfims_info::Information< Type > - recruitment_models_iterator typedeffims_info::Information< Type > - RegisterParameter(Type &p)fims_info::Information< Type >inline - RegisterParameterName(std::string p_name)fims_info::Information< Type >inline + parametersfims_info::Information< Type > + population_iterator typedeffims_info::Information< Type > + populationsfims_info::Information< Type > + random_effects_parametersfims_info::Information< Type > + recruitment_modelsfims_info::Information< Type > + recruitment_models_iterator typedeffims_info::Information< Type > + RegisterParameter(Type &p)fims_info::Information< Type >inline RegisterRandomEffect(Type &re)fims_info::Information< Type >inline selectivity_modelsfims_info::Information< Type > selectivity_models_iterator typedeffims_info::Information< Type > SetNages(size_t nages)fims_info::Information< Type >inline SetNseasons(size_t nseasons)fims_info::Information< Type >inline SetNyears(size_t nyears)fims_info::Information< Type >inline - setup_data()fims_info::Information< Type >inline - setup_priors()fims_info::Information< Type >inline - setup_random_effects()fims_info::Information< Type >inline - variable_mapfims_info::Information< Type > - variable_map_iterator typedeffims_info::Information< Type > - ~Information() (defined in fims_info::Information< Type >)fims_info::Information< Type >inlinevirtual + ~Information() (defined in fims_info::Information< Type >)fims_info::Information< Type >inlinevirtual
    diff --git a/docs/classfims__info_1_1Information.html b/docs/classfims__info_1_1Information.html index 42a1a1a..39ca39e 100644 --- a/docs/classfims__info_1_1Information.html +++ b/docs/classfims__info_1_1Information.html @@ -105,10 +105,8 @@   typedef std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > >::iterator population_iterator   -typedef std::map< uint32_t, std::shared_ptr< fims_distributions::DensityComponentBase< Type > > >::iterator density_components_iterator -  -typedef std::unordered_map< uint32_t, fims::Vector< Type > * >::iterator variable_map_iterator -  +typedef std::map< uint32_t, std::shared_ptr< fims_distributions::DistributionsBase< Type > > >::iterator distribution_models_iterator +  @@ -116,14 +114,6 @@ - - - - - - - - @@ -161,11 +151,11 @@

    Public Member Functions

     
    void RegisterRandomEffect (Type &re)
     
    void RegisterParameterName (std::string p_name)
     
    void setup_priors ()
     
    void setup_random_effects ()
     
    void setup_data ()
     
    bool CreateModel ()
     
    size_t GetNages () const
    - + - + @@ -173,8 +163,6 @@ - - @@ -189,10 +177,8 @@ - - - - + +

    Public Attributes

    size_t nyears = 0
    size_t nyears
     
    size_t nseasons = 1
     
    size_t nages = 0
    size_t nages
     
    std::vector< Type * > parameters
     
     
    std::vector< Type * > fixed_effects_parameters
     
    std::vector< std::string > parameter_names
     
    std::map< uint32_t, std::shared_ptr< fims_data_object::DataObject< Type > > > data_objects
     
    std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > > recruitment_models
     
    std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > > populations
     
    std::map< uint32_t, std::shared_ptr< fims_distributions::DensityComponentBase< Type > > > density_components
     
    std::unordered_map< uint32_t, fims::Vector< Type > * > variable_map
     
    std::map< uint32_t, std::shared_ptr< fims_distributions::DistributionsBase< Type > > > distribution_models
     
    @@ -222,8 +208,8 @@

    -

    ◆ density_components_iterator

    + +

    ◆ distribution_models_iterator

    @@ -231,7 +217,7 @@

    - +

    Static Public Attributes

    typedef std::map< uint32_t, std::shared_ptr<fims_distributions::DensityComponentBase<Type> > >::iterator fims_info::Information< Type >::density_components_iteratortypedef std::map< uint32_t, std::shared_ptr<fims_distributions::DistributionsBase<Type> > >::iterator fims_info::Information< Type >::distribution_models_iterator
    @@ -339,23 +325,6 @@

    iterator for selectivity objects>

    -

    - - -

    ◆ variable_map_iterator

    - -
    -
    -
    -template<typename Type >
    - - - - -
    typedef std::unordered_map<uint32_t, fims::Vector<Type>* >::iterator fims_info::Information< Type >::variable_map_iterator
    -
    -

    iterator for variable map>

    -

    Member Function Documentation

    @@ -630,41 +599,6 @@

    -

    ◆ RegisterParameterName()

    - -
    -
    -
    -template<typename Type >
    - - - - - -
    - - - - - - - - -
    void fims_info::Information< Type >::RegisterParameterName (std::string p_name)
    -     		-inline
    -
    -

    Register a parameter name.

    -
    Parameters
    - - -
    p_name
    -
    -
    -
    @@ -808,90 +742,6 @@

    -

    ◆ setup_data()

    - -
    -
    -
    -template<typename Type >
    - - - - - -
    - - - - - - - -
    void fims_info::Information< Type >::setup_data ()
    -     		-inline
    -
    -

    Loop over distributions and set links to distribution expected value if distribution is a data type.

    - -
    -
    - -

    ◆ setup_priors()

    - -
    -
    -
    -template<typename Type >
    - - - - - -
    - - - - - - - -
    void fims_info::Information< Type >::setup_priors ()
    -     		-inline
    -
    -

    Loop over distributions and set links to distribution x value if distribution is a prior type.

    - -
    -
    - -

    ◆ setup_random_effects()

    - -
    -
    -
    -template<typename Type >
    - - - - - -
    - - - - - - - -
    void fims_info::Information< Type >::setup_random_effects ()
    -     		-inline
    -
    -

    Loop over distributions and set links to distribution x value if distribution is a random effects type.

    -

    Member Data Documentation

    @@ -912,8 +762,8 @@

    -

    ◆ density_components

    + +

    ◆ distribution_models

    @@ -921,7 +771,7 @@

    - std::map<uint32_t, std::shared_ptr<fims_distributions::DensityComponentBase<Type> > > fims_info::Information< Type >::density_components + std::map<uint32_t, std::shared_ptr<fims_distributions::DistributionsBase<Type> > > fims_info::Information< Type >::distribution_models

    @@ -1033,7 +883,7 @@

    - size_t fims_info::Information< Type >::nages = 0 + size_t fims_info::Information< Type >::nages

    @@ -1067,29 +917,12 @@

    - size_t fims_info::Information< Type >::nyears = 0 + size_t fims_info::Information< Type >::nyears

    number of years >

    -
    -
    - -

    ◆ parameter_names

    - -
    -
    -
    -template<typename Type >
    - - - - -
    std::vector<std::string> fims_info::Information< Type >::parameter_names
    -
    -

    list of all parameter names estimated in the model

    -
    @@ -1175,23 +1008,6 @@

    hash map to link each object to its shared location in memory

    - - -     -

    ◆ variable_map

    - -
    -
    -
    -template<typename Type >
    - - - - -
    std::unordered_map<uint32_t, fims::Vector<Type>* > fims_info::Information< Type >::variable_map
    -
    -

    hash map to link a parameter, derived value, or observation to its shared location in memory

    -
    The documentation for this class was generated from the following file:
      diff --git a/docs/data__object_8hpp_source.html b/docs/data__object_8hpp_source.html index 5209394..9396801 100644 --- a/docs/data__object_8hpp_source.html +++ b/docs/data__object_8hpp_source.html @@ -76,142 +76,167 @@
      data_object.hpp
      -Go to the documentation of this file.
      1 
      -
      8 #ifndef FIMS_COMMON_DATA_OBJECT_HPP
      -
      9 #define FIMS_COMMON_DATA_OBJECT_HPP
      -
      10 
      -
      11 #include <exception>
      -
      12 #include <vector>
      -
      13 
      -
      14 #include "model_object.hpp"
      -
      15 #include "fims_vector.hpp"
      -
      16 
      -
      17 namespace fims_data_object {
      -
      18 
      -
      22 template <typename Type>
      -
      23 struct DataObject : public fims_model_object::FIMSObject<Type> {
      -
      24  static uint32_t id_g;
      -
      25  fims::Vector<Type> data;
      -
      26  size_t dimensions;
      -
      27  size_t imax;
      -
      28  size_t jmax;
      -
      29  size_t kmax;
      -
      30  size_t lmax;
      -
      31  Type na_value = -999;
      -
      36  DataObject(size_t imax) : dimensions(1), imax(imax) {
      -
      37  data.resize(imax);
      -
      38 
      -
      39  this->id = DataObject<Type>::id_g++;
      -
      40  }
      +
      1 /*
      +
      2  * File: data_object.hpp
      +
      3  *
      +
      4  * Author: Matthew Supernaw
      +
      5  * National Oceanic and Atmospheric Administration
      +
      6  * National Marine Fisheries Service
      +
      7  * Email: matthew.supernaw@noaa.gov, andrea.havron@noaa.gov
      +
      8  *
      +
      9  * Created on March 24, 2022, 2:37 PM
      +
      10  *
      +
      11  * This File is part of the NOAA, National Marine Fisheries Service
      +
      12  * Fisheries Integrated Modeling System project.
      +
      13  *
      +
      14  * This software is a "United States Government Work" under the terms of the
      +
      15  * United States Copyright Act. It was written as part of the author's official
      +
      16  * duties as a United States Government employee and thus cannot be copyrighted.
      +
      17  * This software is freely available to the public for use. The National Oceanic
      +
      18  * And Atmospheric Administration and the U.S. Government have not placed any
      +
      19  * restriction on its use or reproduction. Although all reasonable efforts have
      +
      20  * been taken to ensure the accuracy and reliability of the software and data,
      +
      21  * the National Oceanic And Atmospheric Administration and the U.S. Government
      +
      22  * do not and cannot warrant the performance or results that may be obtained by
      +
      23  * using this software or data. The National Oceanic And Atmospheric
      +
      24  * Administration and the U.S. Government disclaim all warranties, express or
      +
      25  * implied, including warranties of performance, merchantability or fitness
      +
      26  * for any particular purpose.
      +
      27  *
      +
      28  * Please cite the author(s) in any work or product based on this material.
      +
      29  *
      +
      30  */
      +
      31 
      +
      32 #ifndef FIMS_COMMON_DATA_OBJECT_HPP
      +
      33 #define FIMS_COMMON_DATA_OBJECT_HPP
      +
      34 
      +
      35 #include <exception>
      +
      36 #include <vector>
      +
      37 
      +
      38 #include "model_object.hpp"
      +
      39 
      +
      40 namespace fims_data_object {
      41 
      -
      45  DataObject(size_t imax, size_t jmax) : dimensions(2), imax(imax), jmax(jmax) {
      -
      46  data.resize(imax * jmax);
      -
      47  this->id = DataObject<Type>::id_g++;
      -
      48  }
      -
      49 
      -
      53  DataObject(size_t imax, size_t jmax, size_t kmax)
      -
      54  : dimensions(3), imax(imax), jmax(jmax), kmax(kmax) {
      -
      55  data.resize(imax * jmax * kmax);
      -
      56  this->id = DataObject<Type>::id_g++;
      -
      57  }
      -
      58 
      -
      62  DataObject(size_t imax, size_t jmax, size_t kmax, size_t lmax)
      -
      63  : dimensions(4), imax(imax), jmax(jmax), kmax(kmax), lmax(lmax) {
      -
      64  data.resize(imax * jmax * kmax * lmax);
      -
      65  this->id = DataObject<Type>::id_g++;
      -
      66  }
      -
      67 
      -
      73  inline Type operator()(size_t i) { return data[i]; }
      -
      74 
      -
      81  inline Type& at(size_t i) {
      -
      82  if (i >= this->data.size()) {
      -
      83  throw std::overflow_error("DataObject error:i index out of bounds");
      -
      84  }
      -
      85  return data[i];
      -
      86  }
      -
      87 
      -
      94  inline const Type operator()(size_t i, size_t j) {
      -
      95  return data[i * jmax + j];
      -
      96  }
      +
      45 template <typename Type>
      +
      46 struct DataObject : public fims_model_object::FIMSObject<Type> {
      +
      47  static uint32_t id_g;
      +
      48  std::vector<Type> data;
      +
      49  size_t dimensions;
      +
      50  size_t imax;
      +
      51  size_t jmax;
      +
      52  size_t kmax;
      +
      53  size_t lmax;
      +
      54  Type na_value = -999;
      +
      59  DataObject(size_t imax) : dimensions(1), imax(imax) {
      +
      60  data.resize(imax);
      +
      61 
      +
      62  this->id = DataObject<Type>::id_g++;
      +
      63  }
      +
      64 
      +
      68  DataObject(size_t imax, size_t jmax) : dimensions(2), imax(imax), jmax(jmax) {
      +
      69  data.resize(imax * jmax);
      +
      70  this->id = DataObject<Type>::id_g++;
      +
      71  }
      +
      72 
      +
      76  DataObject(size_t imax, size_t jmax, size_t kmax)
      +
      77  : dimensions(3), imax(imax), jmax(jmax), kmax(kmax) {
      +
      78  data.resize(imax * jmax * kmax);
      +
      79  this->id = DataObject<Type>::id_g++;
      +
      80  }
      +
      81 
      +
      85  DataObject(size_t imax, size_t jmax, size_t kmax, size_t lmax)
      +
      86  : dimensions(4), imax(imax), jmax(jmax), kmax(kmax), lmax(lmax) {
      +
      87  data.resize(imax * jmax * kmax * lmax);
      +
      88  this->id = DataObject<Type>::id_g++;
      +
      89  }
      +
      90 
      +
      96  inline Type operator()(size_t i) { return data[i]; }
      97 
      -
      105  inline Type& at(size_t i, size_t j) {
      -
      106  if ((i * jmax + j) >= this->data.size()) {
      -
      107  throw std::overflow_error("DataObject error: index out of bounds");
      -
      108  }
      -
      109  return data[i * jmax + j];
      -
      110  }
      -
      111 
      -
      119  inline const Type operator()(size_t i, size_t j, size_t k) {
      -
      120  return data[i * jmax * kmax + j * kmax + k];
      -
      121  }
      -
      122 
      -
      131  inline Type& at(size_t i, size_t j, size_t k) {
      -
      132  if ((i * jmax * kmax + j * kmax + k) >= this->data.size()) {
      -
      133  throw std::overflow_error("DataObject error: index out of bounds");
      -
      134  }
      -
      135  return data[i * jmax * kmax + j * kmax + k];
      -
      136  }
      -
      137 
      -
      146  inline const Type operator()(size_t i, size_t j, size_t k, size_t l) {
      -
      147  return data[i * jmax * kmax * lmax + j * kmax * lmax + k * lmax + l];
      -
      148  }
      -
      149 
      -
      159  inline Type& at(size_t i, size_t j, size_t k, size_t l) {
      -
      160  if ((i * jmax * kmax * lmax + j * kmax * lmax + k * lmax + l) >=
      -
      161  this->data.size()) {
      -
      162  throw std::overflow_error("DataObject error: index out of bounds");
      -
      163  }
      -
      164  return data[i * jmax * kmax * lmax + j * kmax * lmax + k * lmax + l];
      -
      165  }
      -
      166 
      -
      172  size_t get_dimensions() const { return dimensions; }
      -
      173 
      -
      179  size_t get_imax() const { return imax; }
      -
      180 
      -
      186  size_t get_jmax() const { return jmax; }
      -
      187 
      -
      193  size_t get_kmax() const { return kmax; }
      -
      194 
      -
      200  size_t get_lmax() const { return lmax; }
      -
      201 };
      -
      202 
      -
      203 template <typename Type>
      -
      204 uint32_t DataObject<Type>::id_g = 0;
      -
      205 
      -
      206 } // namespace fims_data_object
      -
      207 
      -
      208 #endif
      -
      fims::Vector
      Definition: fims_vector.hpp:25
      -
      fims::Vector::size
      size_type size() const
      Returns the number of elements.
      Definition: fims_vector.hpp:295
      -
      fims_vector.hpp
      TODO: provide a brief description.
      -
      model_object.hpp
      TODO: provide a brief description.
      -
      fims_data_object::DataObject
      Definition: data_object.hpp:23
      -
      fims_data_object::DataObject::get_dimensions
      size_t get_dimensions() const
      Get the dimensions object.
      Definition: data_object.hpp:172
      -
      fims_data_object::DataObject::lmax
      size_t lmax
      Definition: data_object.hpp:30
      -
      fims_data_object::DataObject::operator()
      Type operator()(size_t i)
      Definition: data_object.hpp:73
      -
      fims_data_object::DataObject::get_imax
      size_t get_imax() const
      Get the imax object.
      Definition: data_object.hpp:179
      -
      fims_data_object::DataObject::at
      Type & at(size_t i)
      Definition: data_object.hpp:81
      -
      fims_data_object::DataObject::at
      Type & at(size_t i, size_t j)
      Definition: data_object.hpp:105
      -
      fims_data_object::DataObject::kmax
      size_t kmax
      Definition: data_object.hpp:29
      -
      fims_data_object::DataObject::operator()
      const Type operator()(size_t i, size_t j)
      Definition: data_object.hpp:94
      -
      fims_data_object::DataObject::DataObject
      DataObject(size_t imax, size_t jmax, size_t kmax)
      Definition: data_object.hpp:53
      -
      fims_data_object::DataObject::operator()
      const Type operator()(size_t i, size_t j, size_t k)
      Definition: data_object.hpp:119
      -
      fims_data_object::DataObject::get_jmax
      size_t get_jmax() const
      Get the jmax object.
      Definition: data_object.hpp:186
      -
      fims_data_object::DataObject::data
      fims::Vector< Type > data
      Definition: data_object.hpp:25
      -
      fims_data_object::DataObject::get_lmax
      size_t get_lmax() const
      Get the lmax object.
      Definition: data_object.hpp:200
      -
      fims_data_object::DataObject::na_value
      Type na_value
      Definition: data_object.hpp:31
      -
      fims_data_object::DataObject::DataObject
      DataObject(size_t imax)
      Definition: data_object.hpp:36
      -
      fims_data_object::DataObject::imax
      size_t imax
      Definition: data_object.hpp:27
      -
      fims_data_object::DataObject::DataObject
      DataObject(size_t imax, size_t jmax, size_t kmax, size_t lmax)
      Definition: data_object.hpp:62
      -
      fims_data_object::DataObject::DataObject
      DataObject(size_t imax, size_t jmax)
      Definition: data_object.hpp:45
      -
      fims_data_object::DataObject::operator()
      const Type operator()(size_t i, size_t j, size_t k, size_t l)
      Definition: data_object.hpp:146
      -
      fims_data_object::DataObject::at
      Type & at(size_t i, size_t j, size_t k)
      Definition: data_object.hpp:131
      -
      fims_data_object::DataObject::get_kmax
      size_t get_kmax() const
      Get the kmax object.
      Definition: data_object.hpp:193
      -
      fims_data_object::DataObject::dimensions
      size_t dimensions
      Definition: data_object.hpp:26
      -
      fims_data_object::DataObject::at
      Type & at(size_t i, size_t j, size_t k, size_t l)
      Definition: data_object.hpp:159
      -
      fims_data_object::DataObject::jmax
      size_t jmax
      Definition: data_object.hpp:28
      -
      fims_data_object::DataObject::id_g
      static uint32_t id_g
      Definition: data_object.hpp:24
      -
      fims_model_object::FIMSObject
      FIMSObject struct that defines member types and returns the unique id.
      Definition: model_object.hpp:24
      +
      104  inline Type& at(size_t i) {
      +
      105  if (i >= this->data.size()) {
      +
      106  throw std::overflow_error("DataObject error:i index out of bounds");
      +
      107  }
      +
      108  return data[i];
      +
      109  }
      +
      110 
      +
      117  inline const Type operator()(size_t i, size_t j) {
      +
      118  return data[i * jmax + j];
      +
      119  }
      +
      120 
      +
      128  inline Type& at(size_t i, size_t j) {
      +
      129  if ((i * jmax + j) >= this->data.size()) {
      +
      130  throw std::overflow_error("DataObject error: index out of bounds");
      +
      131  }
      +
      132  return data[i * jmax + j];
      +
      133  }
      +
      134 
      +
      142  inline const Type operator()(size_t i, size_t j, size_t k) {
      +
      143  return data[i * jmax * kmax + j * kmax + k];
      +
      144  }
      +
      145 
      +
      154  inline Type& at(size_t i, size_t j, size_t k) {
      +
      155  if ((i * jmax * kmax + j * kmax + k) >= this->data.size()) {
      +
      156  throw std::overflow_error("DataObject error: index out of bounds");
      +
      157  }
      +
      158  return data[i * jmax * kmax + j * kmax + k];
      +
      159  }
      +
      160 
      +
      169  inline const Type operator()(size_t i, size_t j, size_t k, size_t l) {
      +
      170  return data[i * jmax * kmax * lmax + j * kmax * lmax + k * lmax + l];
      +
      171  }
      +
      172 
      +
      182  inline Type& at(size_t i, size_t j, size_t k, size_t l) {
      +
      183  if ((i * jmax * kmax * lmax + j * kmax * lmax + k * lmax + l) >=
      +
      184  this->data.size()) {
      +
      185  throw std::overflow_error("DataObject error: index out of bounds");
      +
      186  }
      +
      187  return data[i * jmax * kmax * lmax + j * kmax * lmax + k * lmax + l];
      +
      188  }
      +
      189 
      +
      195  size_t get_dimensions() const { return dimensions; }
      +
      196 
      +
      202  size_t get_imax() const { return imax; }
      +
      203 
      +
      209  size_t get_jmax() const { return jmax; }
      +
      210 
      +
      216  size_t get_kmax() const { return kmax; }
      +
      217 
      +
      223  size_t get_lmax() const { return lmax; }
      +
      224 };
      +
      225 
      +
      226 template <typename Type>
      +
      227 uint32_t DataObject<Type>::id_g = 0;
      +
      228 
      +
      229 } // namespace fims_data_object
      +
      230 
      +
      231 #endif
      +
      fims_data_object::DataObject
      Definition: data_object.hpp:46
      +
      fims_data_object::DataObject::get_dimensions
      size_t get_dimensions() const
      Get the dimensions object.
      Definition: data_object.hpp:195
      +
      fims_data_object::DataObject::lmax
      size_t lmax
      Definition: data_object.hpp:53
      +
      fims_data_object::DataObject::operator()
      Type operator()(size_t i)
      Definition: data_object.hpp:96
      +
      fims_data_object::DataObject::get_imax
      size_t get_imax() const
      Get the imax object.
      Definition: data_object.hpp:202
      +
      fims_data_object::DataObject::at
      Type & at(size_t i)
      Definition: data_object.hpp:104
      +
      fims_data_object::DataObject::at
      Type & at(size_t i, size_t j)
      Definition: data_object.hpp:128
      +
      fims_data_object::DataObject::kmax
      size_t kmax
      Definition: data_object.hpp:52
      +
      fims_data_object::DataObject::operator()
      const Type operator()(size_t i, size_t j)
      Definition: data_object.hpp:117
      +
      fims_data_object::DataObject::DataObject
      DataObject(size_t imax, size_t jmax, size_t kmax)
      Definition: data_object.hpp:76
      +
      fims_data_object::DataObject::data
      std::vector< Type > data
      Definition: data_object.hpp:48
      +
      fims_data_object::DataObject::operator()
      const Type operator()(size_t i, size_t j, size_t k)
      Definition: data_object.hpp:142
      +
      fims_data_object::DataObject::get_jmax
      size_t get_jmax() const
      Get the jmax object.
      Definition: data_object.hpp:209
      +
      fims_data_object::DataObject::get_lmax
      size_t get_lmax() const
      Get the lmax object.
      Definition: data_object.hpp:223
      +
      fims_data_object::DataObject::na_value
      Type na_value
      Definition: data_object.hpp:54
      +
      fims_data_object::DataObject::DataObject
      DataObject(size_t imax)
      Definition: data_object.hpp:59
      +
      fims_data_object::DataObject::imax
      size_t imax
      Definition: data_object.hpp:50
      +
      fims_data_object::DataObject::DataObject
      DataObject(size_t imax, size_t jmax, size_t kmax, size_t lmax)
      Definition: data_object.hpp:85
      +
      fims_data_object::DataObject::DataObject
      DataObject(size_t imax, size_t jmax)
      Definition: data_object.hpp:68
      +
      fims_data_object::DataObject::operator()
      const Type operator()(size_t i, size_t j, size_t k, size_t l)
      Definition: data_object.hpp:169
      +
      fims_data_object::DataObject::at
      Type & at(size_t i, size_t j, size_t k)
      Definition: data_object.hpp:154
      +
      fims_data_object::DataObject::get_kmax
      size_t get_kmax() const
      Get the kmax object.
      Definition: data_object.hpp:216
      +
      fims_data_object::DataObject::dimensions
      size_t dimensions
      Definition: data_object.hpp:49
      +
      fims_data_object::DataObject::at
      Type & at(size_t i, size_t j, size_t k, size_t l)
      Definition: data_object.hpp:182
      +
      fims_data_object::DataObject::jmax
      size_t jmax
      Definition: data_object.hpp:51
      +
      fims_data_object::DataObject::id_g
      static uint32_t id_g
      Definition: data_object.hpp:47
      +
      fims_model_object::FIMSObject
      FIMSObject struct that defines member types and returns the unique id.
      Definition: model_object.hpp:25
      diff --git a/docs/def_8hpp.html b/docs/def_8hpp.html index a098961..17a8315 100644 --- a/docs/def_8hpp.html +++ b/docs/def_8hpp.html @@ -74,212 +74,276 @@
      Classes | -Macros | Functions
      def.hpp File Reference
      - -

      TODO: provide a brief description. -More...

      #include <fstream>
      #include <map>
      #include <memory>
      #include <vector>
      -#include <string>
      -#include <unordered_map>
      -#include <cstdlib>
      -#include <chrono>
      -#include <sstream>
      -#include <iostream>
      -#include <filesystem>
      -#include <stdlib.h>
      -#include <signal.h>
      -#include <csignal>
      -#include <cstring>
      -#include <stdexcept>

      Go to the source code of this file.

      - - - +

      Classes

      struct  fims::LogEntry
       
      class  fims::FIMSLog
      class  fims::fims_log
       
      - - - - - - - - - - - -

      -Macros

      #define FIMS_DEBUG_LOG(MESSAGE)
       
      #define FIMS_INFO_LOG(MESSAGE)   fims::FIMSLog::fims_log->info_message(MESSAGE, __LINE__, __FILE__, __PRETTY_FUNCTION__);
       
      #define FIMS_WARNING_LOG(MESSAGE)   fims::FIMSLog::fims_log->warning_message(MESSAGE, __LINE__, __FILE__, __PRETTY_FUNCTION__);
       
      #define FIMS_ERROR_LOG(MESSAGE)   fims::FIMSLog::fims_log->error_message(MESSAGE, __LINE__, __FILE__, __PRETTY_FUNCTION__);
       
      #define FIMS_STR(s)   #s
       
      - - - - - + + + + + + + + + + + + + + + + + + + + + + + +

      Functions

      void fims::WriteAtExit (int sig)
       
      template<typename T >
      std::string fims::to_string (T v)
       
      std::ofstream FIMS_LOG ("logs/fims.log")
       
      std::ofstream INFO_LOG ("logs/info.log")
       
      std::ofstream ERROR_LOG ("logs/error.log")
       
      std::ofstream DATA_LOG ("logs/data.log")
       
      std::ofstream MODEL_LOG ("logs/model.log")
       
      std::ofstream FLEET_LOG ("logs/fleet.log")
       
      std::ofstream POPULATION_LOG ("logs/population.log")
       
      std::ofstream RECRUITMENT_LOG ("logs/recruitment.log")
       
      std::ofstream GROWTH_LOG ("logs/growth.log")
       
      std::ofstream MATURITY_LOG ("logs/maturity.log")
       
      std::ofstream SELECTIVITY_LOG ("logs/selectivity.log")
       
      std::ofstream DEBUG_LOG ("logs/debug/debug.log")
       
      -

      Detailed Description

      -

      TODO: provide a brief description.

      -
      Copyright
      This file is part of the NOAA, National Marine Fisheries Service Fisheries Integrated Modeling System project. See LICENSE in the source folder for reuse information.
      -

      Macro Definition Documentation

      - -

      ◆ FIMS_DEBUG_LOG

      +

      Function Documentation

      + +

      ◆ DATA_LOG()

      - + - - + +
      #define FIMS_DEBUG_LOGstd::ofstream DATA_LOG ( MESSAGE)"logs/data.log" )
      -

      Print MESSAGE to debug log

      +

      Data input tracking log file

      - -

      ◆ FIMS_ERROR_LOG

      + +

      ◆ DEBUG_LOG()

      - + - - - + + +
      #define FIMS_ERROR_LOGstd::ofstream DEBUG_LOG ( MESSAGE)   fims::FIMSLog::fims_log->error_message(MESSAGE, __LINE__, __FILE__, __PRETTY_FUNCTION__);"logs/debug/debug.log" )
      -

      Print MESSAGE to error log

      +

      Development debugging log file

      - -

      ◆ FIMS_INFO_LOG

      + +

      ◆ ERROR_LOG()

      - + - - - + + +
      #define FIMS_INFO_LOGstd::ofstream ERROR_LOG ( MESSAGE)   fims::FIMSLog::fims_log->info_message(MESSAGE, __LINE__, __FILE__, __PRETTY_FUNCTION__);"logs/error.log" )
      -

      Print MESSAGE to info log

      +

      Error tracking log file

      - -

      ◆ FIMS_STR

      + +

      ◆ FIMS_LOG()

      - + - - - + + +
      #define FIMS_STRstd::ofstream FIMS_LOG ( s)   #s"logs/fims.log" )
      -

      String of s

      +

      Generic log file

      - -

      ◆ FIMS_WARNING_LOG

      + +

      ◆ FLEET_LOG()

      - + - - - + + +
      #define FIMS_WARNING_LOGstd::ofstream FLEET_LOG ( MESSAGE)   fims::FIMSLog::fims_log->warning_message(MESSAGE, __LINE__, __FILE__, __PRETTY_FUNCTION__);"logs/fleet.log" )
      -

      Print MESSAGE to warning log

      +

      Fleet module log file

      -

      Function Documentation

      - -

      ◆ to_string()

      + +

      ◆ GROWTH_LOG()

      + +
      +
      + + + + + + + + +
      std::ofstream GROWTH_LOG ("logs/growth.log" )
      +
      +

      Growth module log file

      + +
      +
      + +

      ◆ INFO_LOG()

      + +
      +
      + + + + + + + + +
      std::ofstream INFO_LOG ("logs/info.log" )
      +
      +

      Information.hpp log file

      + +
      +
      + +

      ◆ MATURITY_LOG()

      + +
      +
      + + + + + + + + +
      std::ofstream MATURITY_LOG ("logs/maturity.log" )
      +
      +

      Maturity module log file

      + +
      +
      + +

      ◆ MODEL_LOG()

      + +
      +
      + + + + + + + + +
      std::ofstream MODEL_LOG ("logs/model.log" )
      +
      +

      Model.hpp log file

      + +
      +
      + +

      ◆ POPULATION_LOG()

      + +
      +
      + + + + + + + + +
      std::ofstream POPULATION_LOG ("logs/population.log" )
      +
      +

      Populations module log file

      + +
      +
      + +

      ◆ RECRUITMENT_LOG()

      -
      -template<typename T >
      - + - - + +
      std::string fims::to_string std::ofstream RECRUITMENT_LOG (T v)"logs/recruitment.log" )
      -

      Converts an object T to a string.

      -
      Parameters
      - - -
      v
      -
      -
      -
      Returns
      +

      Recruitment module log file

      - -

      ◆ WriteAtExit()

      + +

      ◆ SELECTIVITY_LOG()

      - + - - + +
      void fims::WriteAtExit std::ofstream SELECTIVITY_LOG (int sig)"logs/selectivity.log" )
      -

      Signal intercept function. Writes the log to the disk before a crash occurs.

      -
      Parameters
      - - -
      sig
      -
      -
      +

      Selectivity module log file

      diff --git a/docs/def_8hpp_source.html b/docs/def_8hpp_source.html index c37f2fa..881f017 100644 --- a/docs/def_8hpp_source.html +++ b/docs/def_8hpp_source.html @@ -77,526 +77,87 @@
      Go to the documentation of this file.
      1 
      -
      8 #ifndef DEF_HPP
      -
      9 #define DEF_HPP
      -
      10 #include <fstream>
      -
      11 #include <map>
      -
      12 #include <memory>
      -
      13 #include <vector>
      -
      14 #include <string>
      -
      15 #include <unordered_map>
      -
      16 
      +
      4 /*
      +
      5  * File: def.hpp
      +
      6  *
      +
      7  * This File is part of the NOAA, National Marine Fisheries Service
      +
      8  * Fisheries Integrated Modeling System project. See LICENSE in the
      +
      9  * source folder for reuse information.
      +
      10  */
      +
      11 #ifndef DEF_HPP
      +
      12 #define DEF_HPP
      +
      13 #include <fstream>
      +
      14 #include <map>
      +
      15 #include <memory>
      +
      16 #include <vector>
      17 
      -
      18 #include <cstdlib>
      -
      19 #include <chrono>
      -
      20 #include <sstream>
      -
      21 #include <iostream>
      -
      22 #include <filesystem>
      -
      23 #include <stdlib.h>
      -
      24 #include <fstream>
      -
      25 #include <signal.h>
      -
      26 #include <csignal>
      -
      27 #include <cstring>
      -
      28 
      -
      29 #include <stdexcept>
      -
      30 
      -
      31 
      -
      32 #if defined(linux) || defined(__linux) || defined(__linux__)
      -
      33 #define FIMS_LINUX
      -
      34 #elif defined(__FreeBSD__) || defined(__NetBSD__) || defined(__OpenBSD__) || defined(__DragonFly__)
      -
      35 #define FIMS_BSD
      -
      36 #elif defined(sun) || defined(__sun)
      -
      37 #define FIMS_SOLARIS
      -
      38 #elif defined(__sgi)
      -
      39 #define FIMS_IRIX
      -
      40 #elif defined(__hpux)
      -
      41 #define FIMS_HPUX
      -
      42 #elif defined(__CYGWIN__)
      -
      43 #define FIMS_CYGWIN
      -
      44 #elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
      -
      45 #define FIMS_WIN32
      -
      46 #elif defined(_WIN64) || defined(__WIN64__) || defined(WIN64)
      -
      47 #define FIMS_WIN64
      -
      48 #elif defined(__BEOS__)
      -
      49 #define FIMS_BEOS
      -
      50 #elif defined(macintosh) || defined(__APPLE__) || defined(__APPLE_CC__)
      -
      51 #define FIMS_MACOS
      -
      52 #elif defined(__IBMCPP__) || defined(_AIX)
      -
      53 #define FIMS_AIX
      -
      54 #elif defined(__amigaos__)
      -
      55 #define FIMS_AMIGAOS
      -
      56 #elif defined(__QNXNTO__)
      -
      57 #define FIMS_QNXNTO
      -
      58 #endif
      -
      59 
      -
      60 #if defined(FIMS_WIN32) || defined(FIMS_WIN64)
      -
      61 #define FIMS_WINDOWS
      -
      62 #endif
      -
      63 
      -
      64 #ifdef FIMS_WINDOWS
      -
      65 #include <Windows.h>
      -
      66 //#define __PRETTY_FUNCTION__ __FUNCSIG__
      -
      67 #endif
      +
      18 // The following rows initialize default log files for outputing model progress
      +
      19 // comments used to assist in diagnosing model issues and tracking progress.
      +
      20 // These files will only be created if a logs folder is added to the root model
      +
      21 // directory.
      +
      22 std::ofstream FIMS_LOG("logs/fims.log");
      +
      23 std::ofstream INFO_LOG("logs/info.log");
      +
      24 std::ofstream ERROR_LOG("logs/error.log");
      +
      25 std::ofstream DATA_LOG("logs/data.log");
      +
      26 std::ofstream MODEL_LOG("logs/model.log");
      +
      27 std::ofstream FLEET_LOG("logs/fleet.log");
      +
      28 std::ofstream POPULATION_LOG(
      +
      29  "logs/population.log");
      +
      30 std::ofstream RECRUITMENT_LOG(
      +
      31  "logs/recruitment.log");
      +
      32 std::ofstream GROWTH_LOG("logs/growth.log");
      +
      33 std::ofstream MATURITY_LOG(
      +
      34  "logs/maturity.log");
      +
      35 std::ofstream SELECTIVITY_LOG(
      +
      36  "logs/selectivity.log");
      +
      37 std::ofstream DEBUG_LOG(
      +
      38  "logs/debug/debug.log");
      +
      40 #ifdef TMB_MODEL
      +
      41 // simplify access to singletons
      +
      42 #define TMB_FIMS_REAL_TYPE double
      +
      43 #define TMB_FIMS_FIRST_ORDER AD<TMB_FIMS_REAL_TYPE>
      +
      44 #define TMB_FIMS_SECOND_ORDER AD<TMB_FIMS_FIRST_ORDER>
      +
      45 #define TMB_FIMS_THIRD_ORDER AD<TMB_FIMS_SECOND_ORDER>
      +
      46 #endif
      +
      47 
      +
      48 namespace fims {
      +
      49 
      +
      54 class fims_log {
      +
      55  public:
      +
      56  static std::map<std::string, std::ofstream>
      +
      57  FIMS_LOGS;
      +
      61  static std::ofstream& get(const std::string& l) {
      +
      62  typename std::map<std::string, std::ofstream>::iterator it;
      +
      63  it = fims_log::FIMS_LOGS.find(l);
      +
      64  if (it == fims_log::FIMS_LOGS.end()) {
      +
      65  std::ofstream& of = fims_log::FIMS_LOGS[l];
      +
      66  of.open(l.c_str());
      +
      67  }
      68 
      -
      69 #if !defined(__PRETTY_FUNCTION__) && !defined(__GNUC__)
      -
      70 #ifdef FIMS_WINDOWS
      -
      71 #define __PRETTY_FUNCTION__ __FUNCTION__
      -
      72 #endif
      -
      73 #endif
      +
      69  return fims_log::FIMS_LOGS[l];
      +
      70  }
      +
      71 };
      +
      72 
      +
      73 std::map<std::string, std::ofstream> fims_log::FIMS_LOGS;
      74 
      -
      75 // The following rows initialize default log files for outputing model progress
      -
      76 // comments used to assist in diagnosing model issues and tracking progress.
      -
      77 // These files will only be created if a logs folder is added to the root model
      -
      78 // directory.
      -
      79 
      -
      80 #ifdef TMB_MODEL
      -
      81 // simplify access to singletons
      -
      82 #define TMB_FIMS_REAL_TYPE double
      -
      83 #define TMB_FIMS_FIRST_ORDER AD<TMB_FIMS_REAL_TYPE>
      -
      84 #define TMB_FIMS_SECOND_ORDER AD<TMB_FIMS_FIRST_ORDER>
      -
      85 #define TMB_FIMS_THIRD_ORDER AD<TMB_FIMS_SECOND_ORDER>
      -
      86 #endif
      -
      87 
      -
      88 namespace fims {
      -
      89 
      -
      93  struct LogEntry {
      -
      95  std::string timestamp;
      -
      97  std::string message;
      -
      99  std::string level;
      -
      101  size_t rank;
      -
      103  std::string user;
      -
      105  std::string wd;
      -
      107  std::string file;
      -
      109  std::string routine;
      -
      111  int line;
      -
      112 
      -
      116  std::string to_string() {
      -
      117  std::stringstream ss;
      -
      118  ss << "\"timestamp\" : " << "\"" << this->timestamp << "\"" << ",\n";
      -
      119  ss << "\"level\" : " << "\"" << this->level << "\",\n";
      -
      120  ss << "\"message\" : " << "\"" << this->message << "\",\n";
      -
      121  ss << "\"id\" : " << "\"" << this->rank << "\",\n";
      -
      122  ss << "\"user\" : " << "\"" << this->user << "\",\n";
      -
      123  ss << "\"wd\" : " << "\"" << this->wd << "\",\n";
      -
      124  ss << "\"file\" : " << "\"" << this->file << "\",\n";
      -
      125  ss << "\"routine\" : " << "\"" << this->routine << "\",\n";
      -
      126  ss << "\"line\" : " << "\"" << this->line << "\"\n";
      -
      127  return ss.str();
      -
      128  }
      -
      129 
      -
      130  };
      -
      131 
      -
      135  class FIMSLog {
      -
      136  std::vector<std::string> entries;
      -
      137  std::vector<LogEntry> log_entries;
      -
      138  size_t entry_number = 0;
      -
      139  std::string path = "fims.log";
      -
      140  size_t warning_count = 0;
      -
      141  size_t error_count = 0;
      -
      142 
      -
      148  std::string get_user() {
      -
      149  char * user;
      -
      150  std::string user_ret = "UNKOWN_USER";
      -
      151 
      -
      152 #ifdef FIMS_WINDOWS
      -
      153  user = getenv("username");
      -
      154  user_ret = std::string(user);
      -
      155 #endif
      -
      156 #ifdef FIMS_LINUX
      -
      157  user = getenv("USER");
      -
      158  user_ret = std::string(user);
      -
      159 #endif
      -
      160 
      -
      161 #ifdef FIMS_MACOS
      -
      162  user = getenv("USER");
      -
      163  user_ret = std::string(user);
      -
      164 #endif
      -
      165 
      -
      166  return user_ret;
      -
      167  }
      -
      168  public:
      -
      169  bool write_on_exit = true;
      -
      170  bool throw_on_error = false;
      -
      171  static std::shared_ptr<FIMSLog> fims_log;
      -
      176  FIMSLog() {
      -
      177 
      -
      178  }
      -
      179 
      -
      184  ~FIMSLog() {
      -
      185  if (this->write_on_exit) {
      -
      186  std::ofstream log(this->path);
      -
      187  log << this->get_log();
      -
      188  log.close();
      -
      189  }
      -
      190  }
      -
      191 
      -
      201  std::filesystem::path getAbsolutePathWithoutDotDot(const std::filesystem::path& relativePath) {
      -
      202  std::filesystem::path absolutePath = std::filesystem::absolute(relativePath);
      -
      203 
      -
      204  std::filesystem::path result;
      -
      205  for (const auto& part : absolutePath) {
      -
      206  if (part == "..") {
      -
      207  if (!result.empty()) {
      -
      208  result = result.parent_path();
      -
      209  }
      -
      210  } else {
      -
      211  result /= part;
      -
      212  }
      -
      213  }
      -
      214 
      -
      215  return result.generic_string();
      -
      216  }
      -
      217 
      -
      223  void set_path(std::string path) {
      -
      224  this->path = path;
      -
      225  }
      -
      226 
      -
      232  std::string get_path() {
      -
      233  return this->path;
      -
      234  }
      -
      235 
      -
      244  void info_message(std::string str, int line, const char* file, const char* func) {
      -
      245  std::filesystem::path relativePath = file;
      -
      246  std::filesystem::path absolutePath = getAbsolutePathWithoutDotDot(relativePath);
      -
      247  std::filesystem::path cwd = std::filesystem::current_path();
      -
      248  std::stringstream ss;
      -
      249  auto now = std::chrono::system_clock::now();
      -
      250  std::time_t now_time = std::chrono::system_clock::to_time_t(now);
      -
      251  std::string ctime_no_newline = strtok(ctime(&now_time), "\n");
      -
      252 
      -
      253  LogEntry l;
      -
      254  l.timestamp = ctime_no_newline;
      -
      255  l.message = str;
      -
      256  l.level = "info";
      -
      257  l.rank = this->log_entries.size();
      -
      258  l.user = this->get_user();
      -
      259  l.wd = cwd.generic_string();
      -
      260  l.file = absolutePath.string();
      -
      261  l.line = line;
      -
      262  l.routine = func;
      -
      263  this->log_entries.push_back(l);
      -
      264 
      -
      265  }
      -
      266 
      -
      275  void debug_message(std::string str, int line, const char* file, const char* func) {
      -
      276  std::filesystem::path relativePath = file;
      -
      277  std::filesystem::path absolutePath = getAbsolutePathWithoutDotDot(relativePath);
      -
      278  std::filesystem::path cwd = std::filesystem::current_path();
      -
      279  std::stringstream ss;
      -
      280  auto now = std::chrono::system_clock::now();
      -
      281  std::time_t now_time = std::chrono::system_clock::to_time_t(now);
      -
      282  std::string ctime_no_newline = strtok(ctime(&now_time), "\n");
      -
      283 
      -
      284  LogEntry l;
      -
      285  l.timestamp = ctime_no_newline;
      -
      286  l.message = str;
      -
      287  l.level = "debug";
      -
      288  l.rank = this->log_entries.size();
      -
      289  l.user = this->get_user();
      -
      290  l.wd = cwd.generic_string();
      -
      291  l.file = absolutePath.string();
      -
      292  l.line = line;
      -
      293  l.routine = func;
      -
      294  this->log_entries.push_back(l);
      -
      295 
      -
      296  }
      -
      297 
      -
      306  void error_message(std::string str, int line, const char* file, const char* func) {
      -
      307  this->error_count++;
      -
      308  std::filesystem::path relativePath = file;
      -
      309  std::filesystem::path absolutePath = getAbsolutePathWithoutDotDot(relativePath);
      -
      310  std::filesystem::path cwd = std::filesystem::current_path();
      -
      311 
      -
      312  std::stringstream ss;
      -
      313  auto now = std::chrono::system_clock::now();
      -
      314  std::time_t now_time = std::chrono::system_clock::to_time_t(now);
      -
      315  std::string ctime_no_newline = strtok(ctime(&now_time), "\n");
      -
      316 
      -
      317  LogEntry l;
      -
      318  l.timestamp = ctime_no_newline;
      -
      319  l.message = str;
      -
      320  l.level = "error";
      -
      321  l.rank = this->log_entries.size();
      -
      322  l.user = this->get_user();
      -
      323  l.wd = cwd.generic_string();
      -
      324  l.file = absolutePath.string();
      -
      325  l.line = line;
      -
      326  l.routine = func;
      -
      327  this->log_entries.push_back(l);
      -
      328 
      -
      329  if (this->throw_on_error) {
      -
      330  std::stringstream ss;
      -
      331  ss << "\n\n" << l.to_string() << "\n\n";
      -
      332  throw std::runtime_error(ss.str().c_str());
      -
      333  }
      -
      334 
      -
      335  }
      -
      336 
      -
      345  void warning_message(std::string str, int line, const char* file, const char* func) {
      -
      346  this->warning_count++;
      -
      347  std::filesystem::path relativePath = file;
      -
      348  std::filesystem::path absolutePath = getAbsolutePathWithoutDotDot(relativePath);
      -
      349  std::filesystem::path cwd = std::filesystem::current_path();
      -
      350 
      -
      351  std::stringstream ss;
      -
      352  auto now = std::chrono::system_clock::now();
      -
      353  std::time_t now_time = std::chrono::system_clock::to_time_t(now);
      -
      354  std::string ctime_no_newline = strtok(ctime(&now_time), "\n");
      -
      355 
      -
      356  LogEntry l;
      -
      357  l.timestamp = ctime_no_newline;
      -
      358  l.message = str;
      -
      359  l.level = "warning";
      -
      360  l.rank = this->log_entries.size();
      -
      361  l.user = this->get_user();
      -
      362  l.wd = cwd.generic_string();
      -
      363  l.file = absolutePath.string();
      -
      364  l.line = line;
      -
      365  l.routine = func;
      -
      366  this->log_entries.push_back(l);
      -
      367 
      -
      368  }
      -
      369 
      -
      375  std::string get_log() {
      -
      376  std::stringstream ss;
      -
      377  if (log_entries.size() == 0) {
      -
      378  ss << "[\n]";
      -
      379  } else {
      -
      380  ss << "[\n";
      -
      381  for (size_t i = 0; i < log_entries.size() - 1; i++) {
      -
      382  ss << "{\n" << this->log_entries[i].to_string() << "},\n";
      -
      383 
      -
      384  }
      -
      385  ss << "{\n" << this->log_entries[log_entries.size() - 1].to_string() << "}\n]";
      -
      386  }
      -
      387  return ss.str();
      -
      388  }
      -
      389 
      -
      395  std::string get_errors() {
      -
      396  std::stringstream ss;
      -
      397  std::vector<LogEntry> errors;
      -
      398  for (size_t i = 0; i < log_entries.size(); i++) {
      -
      399  if (log_entries[i].level == "error") {
      -
      400  errors.push_back(this->log_entries[i]);
      -
      401  }
      -
      402  }
      -
      403 
      -
      404  if (errors.size() == 0) {
      -
      405  ss << "[\n]";
      -
      406  } else {
      -
      407  ss << "[\n";
      -
      408  for (size_t i = 0; i < errors.size() - 1; i++) {
      -
      409 
      -
      410  ss << "{\n" << errors[i].to_string() << "},\n";
      -
      411 
      -
      412  }
      -
      413 
      -
      414  ss << "{\n" << errors[errors.size() - 1].to_string() << "}\n]";
      -
      415 
      -
      416  }
      -
      417  return ss.str();
      -
      418  }
      -
      419 
      -
      425  std::string get_warnings() {
      -
      426  std::stringstream ss;
      -
      427  std::vector<LogEntry> warnings;
      -
      428  for (size_t i = 0; i < log_entries.size(); i++) {
      -
      429  if (log_entries[i].level == "warning") {
      -
      430  warnings.push_back(this->log_entries[i]);
      -
      431  }
      -
      432  }
      -
      433 
      -
      434  if (warnings.size() == 0) {
      -
      435  ss << "[\n]";
      -
      436  } else {
      -
      437  ss << "[\n";
      -
      438  for (size_t i = 0; i < warnings.size() - 1; i++) {
      -
      439 
      -
      440  ss << "{\n" << warnings[i].to_string() << "},\n";
      -
      441 
      -
      442  }
      -
      443 
      -
      444  ss << "{\n" << warnings[warnings.size() - 1].to_string() << "}\n]";
      -
      445 
      -
      446  }
      -
      447  return ss.str();
      -
      448  }
      -
      449 
      -
      455  std::string get_info() {
      -
      456  std::stringstream ss;
      -
      457  std::vector<LogEntry> info;
      -
      458  for (size_t i = 0; i < log_entries.size(); i++) {
      -
      459  if (log_entries[i].level == "info") {
      -
      460  info.push_back(this->log_entries[i]);
      -
      461  }
      -
      462  }
      -
      463 
      -
      464  if (info.size() == 0) {
      -
      465  ss << "[\n]";
      -
      466  } else {
      -
      467  ss << "[\n";
      -
      468  for (size_t i = 0; i < info.size() - 1; i++) {
      -
      469 
      -
      470  ss << "{\n" << info[i].to_string() << "},\n";
      -
      471 
      -
      472  }
      -
      473 
      -
      474  ss << "{\n" << info[info.size() - 1].to_string() << "}\n]";
      -
      475 
      -
      476  }
      -
      477  return ss.str();
      -
      478  }
      -
      479 
      -
      486  std::string get_module(const std::string& module) {
      -
      487  std::stringstream ss;
      -
      488  std::vector<LogEntry> info;
      -
      489  for (size_t i = 0; i < log_entries.size(); i++) {
      -
      490  if (log_entries[i].file.find(module) != std::string::npos) {
      -
      491  info.push_back(this->log_entries[i]);
      -
      492  }
      -
      493  }
      -
      494 
      -
      495  if (info.size() == 0) {
      -
      496  ss << "[\n]";
      -
      497  } else {
      -
      498  ss << "[\n";
      -
      499  for (size_t i = 0; i < info.size() - 1; i++) {
      -
      500 
      -
      501  ss << "{\n" << info[i].to_string() << "},\n";
      -
      502 
      -
      503  }
      -
      504 
      -
      505  ss << "{\n" << info[info.size() - 1].to_string() << "}\n]";
      -
      506 
      -
      507  }
      -
      508  return ss.str();
      -
      509  }
      -
      510 
      -
      514  size_t get_error_count() const {
      -
      515  return error_count;
      -
      516  }
      -
      517 
      -
      521  size_t get_warning_count() const {
      -
      522  return warning_count;
      -
      523  }
      -
      524 
      -
      529  void clear() {
      -
      530  this->entries.clear();
      -
      531  this->log_entries.clear();
      -
      532  this->warning_count = 0;
      -
      533  this->entry_number = 0;
      -
      534  }
      -
      535 
      -
      536  };
      -
      537 
      -
      538 
      -
      539  std::shared_ptr<FIMSLog> FIMSLog::fims_log = std::make_shared<FIMSLog>();
      -
      540 
      -
      541 } // namespace fims
      -
      542 
      -
      543 
      -
      544 
      -
      545 
      -
      546 
      -
      547 #ifdef FIMS_DEBUG
      -
      548 
      -
      549 #define FIMS_DEBUG_LOG(MESSAGE) FIMSLog::fims_log->debug_message(MESSAGE, __LINE__, __FILE__, __PRETTY_FUNCTION__);
      -
      550 
      -
      551 #else
      -
      552 
      -
      553 #define FIMS_DEBUG_LOG(MESSAGE)
      -
      555 #endif
      -
      556 
      -
      557 #define FIMS_INFO_LOG(MESSAGE) fims::FIMSLog::fims_log->info_message(MESSAGE, __LINE__, __FILE__, __PRETTY_FUNCTION__);
      -
      559 #define FIMS_WARNING_LOG(MESSAGE) fims::FIMSLog::fims_log->warning_message(MESSAGE, __LINE__, __FILE__, __PRETTY_FUNCTION__);
      -
      561 #define FIMS_ERROR_LOG(MESSAGE) fims::FIMSLog::fims_log->error_message(MESSAGE, __LINE__, __FILE__, __PRETTY_FUNCTION__);
      -
      563 #define FIMS_STR(s) #s
      -
      566 namespace fims {
      -
      567 
      -
      574  void WriteAtExit(int sig) {
      -
      575 
      -
      576  std::string signal_error = "NA";
      -
      577  switch (sig) {
      -
      578  case SIGSEGV:
      -
      579  signal_error = "Invalid memory access (segmentation fault)";
      -
      580  break;
      -
      581  case SIGINT:
      -
      582  signal_error = "External interrupt, possibly initiated by the user.";
      -
      583  break;
      -
      584  case SIGABRT:
      -
      585  signal_error = "Abnormal termination condition, possible call to std::abort.";
      -
      586  break;
      -
      587  case SIGFPE:
      -
      588  signal_error = "Erroneous arithmetic operation.";
      -
      589  break;
      -
      590  case SIGILL:
      -
      591  signal_error = "Invalid program image or invalid instruction";
      -
      592  break;
      -
      593  case SIGTERM:
      -
      594  signal_error = "Termination request, sent to the program.";
      -
      595  break;
      -
      596  default:
      -
      597  signal_error = "Unknown signal thrown";
      -
      598 
      -
      599  }
      -
      600 
      -
      601  FIMSLog::fims_log->error_message(signal_error, -999, "?", "?");
      -
      602 
      -
      603 
      -
      604  if (FIMSLog::fims_log->write_on_exit) {
      -
      605 
      -
      606  std::ofstream log(FIMSLog::fims_log->get_path());
      -
      607  log << FIMSLog::fims_log->get_log();
      -
      608  log.close();
      -
      609  }
      -
      610  std::signal(sig, SIG_DFL);
      -
      611  raise(sig);
      -
      612  }
      -
      613 
      -
      620  template<typename T>
      -
      621  std::string to_string(T v) {
      -
      622  std::stringstream ss;
      -
      623  ss << v;
      -
      624  return ss.str();
      -
      625  }
      -
      626 
      -
      627 }
      -
      628 
      -
      629 #endif /* TRAITS_HPP */
      -
      fims::FIMSLog
      Definition: def.hpp:135
      -
      fims::FIMSLog::debug_message
      void debug_message(std::string str, int line, const char *file, const char *func)
      Definition: def.hpp:275
      -
      fims::FIMSLog::error_message
      void error_message(std::string str, int line, const char *file, const char *func)
      Definition: def.hpp:306
      -
      fims::FIMSLog::clear
      void clear()
      Clear all pointers/references of a FIMS model.
      Definition: def.hpp:529
      -
      fims::FIMSLog::write_on_exit
      bool write_on_exit
      Definition: def.hpp:169
      -
      fims::FIMSLog::throw_on_error
      bool throw_on_error
      Definition: def.hpp:170
      -
      fims::FIMSLog::get_log
      std::string get_log()
      Definition: def.hpp:375
      -
      fims::FIMSLog::warning_message
      void warning_message(std::string str, int line, const char *file, const char *func)
      Definition: def.hpp:345
      -
      fims::FIMSLog::get_warning_count
      size_t get_warning_count() const
      Get the counts of the number of warnings.
      Definition: def.hpp:521
      -
      fims::FIMSLog::get_module
      std::string get_module(const std::string &module)
      Definition: def.hpp:486
      -
      fims::FIMSLog::get_warnings
      std::string get_warnings()
      Definition: def.hpp:425
      -
      fims::FIMSLog::get_path
      std::string get_path()
      Definition: def.hpp:232
      -
      fims::FIMSLog::fims_log
      static std::shared_ptr< FIMSLog > fims_log
      Definition: def.hpp:171
      -
      fims::FIMSLog::FIMSLog
      FIMSLog()
      Definition: def.hpp:176
      -
      fims::FIMSLog::get_errors
      std::string get_errors()
      Definition: def.hpp:395
      -
      fims::FIMSLog::set_path
      void set_path(std::string path)
      Definition: def.hpp:223
      -
      fims::FIMSLog::~FIMSLog
      ~FIMSLog()
      Definition: def.hpp:184
      -
      fims::FIMSLog::getAbsolutePathWithoutDotDot
      std::filesystem::path getAbsolutePathWithoutDotDot(const std::filesystem::path &relativePath)
      Get the Absolute Path Without Dot Dot object.
      Definition: def.hpp:201
      -
      fims::FIMSLog::get_error_count
      size_t get_error_count() const
      Get the counts of the number of errors.
      Definition: def.hpp:514
      -
      fims::FIMSLog::info_message
      void info_message(std::string str, int line, const char *file, const char *func)
      Definition: def.hpp:244
      -
      fims::FIMSLog::get_info
      std::string get_info()
      Definition: def.hpp:455
      -
      fims::WriteAtExit
      void WriteAtExit(int sig)
      Definition: def.hpp:574
      -
      fims::to_string
      std::string to_string(T v)
      Definition: def.hpp:621
      -
      fims::LogEntry
      Definition: def.hpp:93
      -
      fims::LogEntry::wd
      std::string wd
      Definition: def.hpp:105
      -
      fims::LogEntry::rank
      size_t rank
      Definition: def.hpp:101
      -
      fims::LogEntry::file
      std::string file
      Definition: def.hpp:107
      -
      fims::LogEntry::routine
      std::string routine
      Definition: def.hpp:109
      -
      fims::LogEntry::level
      std::string level
      Definition: def.hpp:99
      -
      fims::LogEntry::message
      std::string message
      Definition: def.hpp:97
      -
      fims::LogEntry::line
      int line
      Definition: def.hpp:111
      -
      fims::LogEntry::timestamp
      std::string timestamp
      Definition: def.hpp:95
      -
      fims::LogEntry::to_string
      std::string to_string()
      Definition: def.hpp:116
      -
      fims::LogEntry::user
      std::string user
      Definition: def.hpp:103
      +
      75 } // namespace fims
      +
      76 
      +
      77 #endif /* TRAITS_HPP */
      +
      fims::fims_log
      Definition: def.hpp:54
      +
      fims::fims_log::FIMS_LOGS
      static std::map< std::string, std::ofstream > FIMS_LOGS
      Definition: def.hpp:57
      +
      fims::fims_log::get
      static std::ofstream & get(const std::string &l)
      Definition: def.hpp:61
      +
      MODEL_LOG
      std::ofstream MODEL_LOG("logs/model.log")
      +
      GROWTH_LOG
      std::ofstream GROWTH_LOG("logs/growth.log")
      +
      ERROR_LOG
      std::ofstream ERROR_LOG("logs/error.log")
      +
      SELECTIVITY_LOG
      std::ofstream SELECTIVITY_LOG("logs/selectivity.log")
      +
      DATA_LOG
      std::ofstream DATA_LOG("logs/data.log")
      +
      FLEET_LOG
      std::ofstream FLEET_LOG("logs/fleet.log")
      +
      DEBUG_LOG
      std::ofstream DEBUG_LOG("logs/debug/debug.log")
      +
      MATURITY_LOG
      std::ofstream MATURITY_LOG("logs/maturity.log")
      +
      FIMS_LOG
      std::ofstream FIMS_LOG("logs/fims.log")
      +
      RECRUITMENT_LOG
      std::ofstream RECRUITMENT_LOG("logs/recruitment.log")
      +
      POPULATION_LOG
      std::ofstream POPULATION_LOG("logs/population.log")
      +
      INFO_LOG
      std::ofstream INFO_LOG("logs/info.log")
      diff --git a/docs/dir_1678aebb33bcc66091bafb58a771ebcc.html b/docs/dir_1678aebb33bcc66091bafb58a771ebcc.html index 3c411ad..6409005 100644 --- a/docs/dir_1678aebb33bcc66091bafb58a771ebcc.html +++ b/docs/dir_1678aebb33bcc66091bafb58a771ebcc.html @@ -79,17 +79,9 @@ - - + - - - - - - - - +

      Files

      file  density_components_base.hpp [code]
       Declares the DensityComponentBase class, which is the base class for all distribution functors.
      file  distributions_base.hpp [code]
       
      file  lognormal_lpdf.hpp [code]
       Lognormal Log Probability Density Function (LPDF) defines the Lognormal LPDF class and its fields and returns the log probability density function.
       
      file  multinomial_lpmf.hpp [code]
       Multinomial Log Probability Mass Function (LPMF) module file defines the Multinomial LPMF class and its fields and returns the log probability mass function.
       
      file  normal_lpdf.hpp [code]
       Normal Log Probability Density Function (LPDF) module file defines the Normal LPDF class and its fields and returns the log probability density function.
      file  tmb_distributions.hpp [code]
       
      diff --git a/docs/dir_18d7dde31df7be29ff6228ae177c21fd.html b/docs/dir_18d7dde31df7be29ff6228ae177c21fd.html index bfdf14e..e7b8083 100644 --- a/docs/dir_18d7dde31df7be29ff6228ae177c21fd.html +++ b/docs/dir_18d7dde31df7be29ff6228ae177c21fd.html @@ -79,12 +79,6 @@ -

      Directories

      - - - -

      -Files

      file  distributions.hpp [code]
       This distributions module includes any .hpp files within the subfolders so that only this file needs to included in the model.hpp file.
       
      diff --git a/docs/dir_1e91ec27400c96ae80a632ccfbdcb525.html b/docs/dir_1e91ec27400c96ae80a632ccfbdcb525.html index 908da56..4c8ae11 100644 --- a/docs/dir_1e91ec27400c96ae80a632ccfbdcb525.html +++ b/docs/dir_1e91ec27400c96ae80a632ccfbdcb525.html @@ -79,12 +79,6 @@ -

      Directories

      - - - -

      -Files

      file  selectivity.hpp [code]
       Includes any .hpp files within the subfolders so that only this file needs to included in the model.hpp file.
       
      diff --git a/docs/dir_2e8bd4230d2fd1bf70799e5d0f1b5e4a.html b/docs/dir_2e8bd4230d2fd1bf70799e5d0f1b5e4a.html index d8ddd59..e8818e2 100644 --- a/docs/dir_2e8bd4230d2fd1bf70799e5d0f1b5e4a.html +++ b/docs/dir_2e8bd4230d2fd1bf70799e5d0f1b5e4a.html @@ -76,16 +76,6 @@
      functors Directory Reference
      - - - - - - - - -

      -Files

      file  logistic.hpp [code]
       Defines the LogisticMaturity class, which inherits from the MaturityBase class.
       
      file  maturity_base.hpp [code]
       Declares the MaturityBase class which is the base class for all maturity functors.
       
      diff --git a/docs/dir_33e0024dd00b9ce79198d783b7c2b2ff.html b/docs/dir_33e0024dd00b9ce79198d783b7c2b2ff.html index c33d235..94c9dc6 100644 --- a/docs/dir_33e0024dd00b9ce79198d783b7c2b2ff.html +++ b/docs/dir_33e0024dd00b9ce79198d783b7c2b2ff.html @@ -79,12 +79,6 @@ -

      Directories

      - - - -

      -Files

      file  maturity.hpp [code]
       Includes any .hpp files within the subfolders so that only this file needs to included in the model.hpp file.
       
      diff --git a/docs/dir_37bdea9fff2fdc698227d6fda51b8784.html b/docs/dir_37bdea9fff2fdc698227d6fda51b8784.html index 1f528dd..9ce2119 100644 --- a/docs/dir_37bdea9fff2fdc698227d6fda51b8784.html +++ b/docs/dir_37bdea9fff2fdc698227d6fda51b8784.html @@ -79,12 +79,6 @@ -

      Directories

      - - - -

      -Files

      file  growth.hpp [code]
       Includes any .hpp files within the subfolders so that only this file needs to included in the model.hpp file.
       
      diff --git a/docs/dir_393b99a6ba686a4e9d8893eeed28f446.html b/docs/dir_393b99a6ba686a4e9d8893eeed28f446.html index c5eb5b0..05a2af4 100644 --- a/docs/dir_393b99a6ba686a4e9d8893eeed28f446.html +++ b/docs/dir_393b99a6ba686a4e9d8893eeed28f446.html @@ -76,16 +76,6 @@
      functors Directory Reference
      - - - - - - - - -

      -Files

      file  logistic.hpp [code]
       Declares the DoubleLogisticSelectivity class which implements the logistic function from fims_math in the selectivity module.
       
      file  selectivity_base.hpp [code]
       Declares the SelectivityBase class which is the base class for all selectivity functors.
       
      diff --git a/docs/dir_4061a19dc6288bb60d0da2c821ead74b.html b/docs/dir_4061a19dc6288bb60d0da2c821ead74b.html index c89ccba..8013c6c 100644 --- a/docs/dir_4061a19dc6288bb60d0da2c821ead74b.html +++ b/docs/dir_4061a19dc6288bb60d0da2c821ead74b.html @@ -76,40 +76,6 @@
      rcpp_objects Directory Reference
      - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

      -Files

      file  rcpp_distribution.hpp [code]
       TODO: provide a brief description.
       
      file  rcpp_fleet.hpp [code]
       TODO: provide a brief description.
       
      file  rcpp_growth.hpp [code]
       TODO: provide a brief description.
       
      file  rcpp_interface_base.hpp [code]
       TODO: provide a brief description.
       
      file  rcpp_lpdf.hpp [code]
       TODO: provide a brief description.
       
      file  rcpp_maturity.hpp [code]
       TODO: provide a brief description.
       
      file  rcpp_natural_mortality.hpp [code]
       TODO: provide a brief description.
       
      file  rcpp_population.hpp [code]
       TODO: provide a brief description.
       
      file  rcpp_recruitment.hpp [code]
       TODO: provide a brief description.
       
      file  rcpp_selectivity.hpp [code]
       TODO: provide a brief description.
       
      diff --git a/docs/dir_4b06d3d22876e8a9de795c0a16cf36db.html b/docs/dir_4b06d3d22876e8a9de795c0a16cf36db.html index 5fa00f3..9f5d634 100644 --- a/docs/dir_4b06d3d22876e8a9de795c0a16cf36db.html +++ b/docs/dir_4b06d3d22876e8a9de795c0a16cf36db.html @@ -80,10 +80,6 @@

      Files

      file  recruitment_base.hpp [code] - Serves as the parent class where recruitment functions are called.
      -  -file  sr_beverton_holt.hpp [code] - Calls the Beverton–Holt stock–recruitment function from fims_math and does the calculation.
        diff --git a/docs/dir_6315be8a572b87c2bcef063caabfa549.html b/docs/dir_6315be8a572b87c2bcef063caabfa549.html index 7e20520..9e61f42 100644 --- a/docs/dir_6315be8a572b87c2bcef063caabfa549.html +++ b/docs/dir_6315be8a572b87c2bcef063caabfa549.html @@ -76,15 +76,6 @@
      population Directory Reference
      - - - - - - - -

      -Files

      file  population.hpp [code]
       Defines the Population class and its fields and methods.
       
      file  subpopulation.hpp [code]
       
      diff --git a/docs/dir_78bab4de0b210d1f38696a0ee50fd3de.html b/docs/dir_78bab4de0b210d1f38696a0ee50fd3de.html index 038121e..2a868ba 100644 --- a/docs/dir_78bab4de0b210d1f38696a0ee50fd3de.html +++ b/docs/dir_78bab4de0b210d1f38696a0ee50fd3de.html @@ -79,15 +79,6 @@ -

      Directories

      - - - - - - -

      -Files

      file  init.hpp [code]
       TODO: provide a brief description.
       
      file  interface.hpp [code]
       TODO: provide a brief description.
       
      diff --git a/docs/dir_825acd3dee85b944c8adc67f8f95c8cb.html b/docs/dir_825acd3dee85b944c8adc67f8f95c8cb.html index 0ebe6ee..21e3340 100644 --- a/docs/dir_825acd3dee85b944c8adc67f8f95c8cb.html +++ b/docs/dir_825acd3dee85b944c8adc67f8f95c8cb.html @@ -79,26 +79,11 @@ - - - - - - - - - - - - - - -

      Files

      file  data_object.hpp [code]
       TODO: provide a brief description.
       
      file  def.hpp [code]
       TODO: provide a brief description.
       
      file  fims_math.hpp [code]
       TODO: provide a brief description.
       
      file  fims_vector.hpp [code]
       TODO: provide a brief description.
       
      file  information.hpp [code]
       TODO: provide a brief description.
       
      file  model.hpp [code]
       TODO: provide a brief description.
       
      file  model_object.hpp [code]
       TODO: provide a brief description.
       
      diff --git a/docs/dir_cf9876eeb8486b9ec32ec52ea9e00fbd.html b/docs/dir_cf9876eeb8486b9ec32ec52ea9e00fbd.html index ec033c5..ccd5595 100644 --- a/docs/dir_cf9876eeb8486b9ec32ec52ea9e00fbd.html +++ b/docs/dir_cf9876eeb8486b9ec32ec52ea9e00fbd.html @@ -79,12 +79,6 @@ -

      Directories

      - - - -

      -Files

      file  rcpp_interface.hpp [code]
       TODO: provide a brief description.
       
      diff --git a/docs/dir_dc730c142f9595d227ed6282d167d643.html b/docs/dir_dc730c142f9595d227ed6282d167d643.html index d95de68..70f6c68 100644 --- a/docs/dir_dc730c142f9595d227ed6282d167d643.html +++ b/docs/dir_dc730c142f9595d227ed6282d167d643.html @@ -80,7 +80,6 @@

      Files

      file  fleet.hpp [code] - Declare the fleet functor class which is the base class for all fleet functors.
        diff --git a/docs/dir_e37de6988527f326a4d5f60f689d8e02.html b/docs/dir_e37de6988527f326a4d5f60f689d8e02.html index fe3c21c..bcfe0d9 100644 --- a/docs/dir_e37de6988527f326a4d5f60f689d8e02.html +++ b/docs/dir_e37de6988527f326a4d5f60f689d8e02.html @@ -79,12 +79,6 @@ -

      Directories

      - - - -

      -Files

      file  recruitment.hpp [code]
       Includes any .hpp files within the subfolders so that only this file needs to included in the model.hpp file.
       
      diff --git a/docs/dir_ec7d59b9ad424ffe7f0c26e992e91d44.html b/docs/dir_ec7d59b9ad424ffe7f0c26e992e91d44.html index 0dd6da2..1c684a9 100644 --- a/docs/dir_ec7d59b9ad424ffe7f0c26e992e91d44.html +++ b/docs/dir_ec7d59b9ad424ffe7f0c26e992e91d44.html @@ -76,16 +76,6 @@
      functors Directory Reference
      - - - - - - - - -

      -Files

      file  ewaa.hpp [code]
       Declares the growth functor class which is the base class for all growth functors.
       
      file  growth_base.hpp [code]
       Includes any .hpp files within the subfolders so that only this file needs to included in the model.hpp file.
       
      diff --git a/docs/distributions_8hpp_source.html b/docs/distributions_8hpp_source.html index 5c059e7..8220ec4 100644 --- a/docs/distributions_8hpp_source.html +++ b/docs/distributions_8hpp_source.html @@ -76,20 +76,28 @@
      distributions.hpp
      -Go to the documentation of this file.
      1 
      -
      11 #ifndef FIMS_DISTRIBUTIONS_HPP
      -
      12 #define FIMS_DISTRIBUTIONS_HPP
      -
      13 
      -
      14 #include "functors/density_components_base.hpp"
      -
      15 #include "functors/lognormal_lpdf.hpp"
      -
      16 #include "functors/multinomial_lpmf.hpp"
      -
      17 #include "functors/normal_lpdf.hpp"
      -
      18 
      -
      19 #endif /* FIMS_DISTRIBUTIONS_HPP */
      -
      density_components_base.hpp
      Declares the DensityComponentBase class, which is the base class for all distribution functors.
      -
      lognormal_lpdf.hpp
      Lognormal Log Probability Density Function (LPDF) defines the Lognormal LPDF class and its fields and...
      -
      multinomial_lpmf.hpp
      Multinomial Log Probability Mass Function (LPMF) module file defines the Multinomial LPMF class and i...
      -
      normal_lpdf.hpp
      Normal Log Probability Density Function (LPDF) module file defines the Normal LPDF class and its fiel...
      +
      1 /*
      +
      2  *
      +
      3  * This File is part of the NOAA, National Marine Fisheries Service
      +
      4  * Fisheries Integrated Modeling System project. See LICENSE in the
      +
      5  * source folder for reuse information.
      +
      6  *
      +
      7  * Distributions module file
      +
      8  * The purpose of this file is to include any .hpp files within the
      +
      9  * subfolders so that only this file needs to included in the model.hpp file.
      +
      10  *
      +
      11  * DEFINE guards for distributions module outline to define the
      +
      12  * distributions hpp file if not already defined.
      +
      13  */
      +
      14 #ifndef FIMS_DISTRIBUTIONS_HPP
      +
      15 #define FIMS_DISTRIBUTIONS_HPP
      +
      16 
      +
      17 #include "functors/distributions_base.hpp"
      +
      18 #include "functors/tmb_distributions.hpp"
      +
      19 
      +
      20 #endif /* FIMS_DISTRIBUTIONS_HPP */
      +
      distributions_base.hpp
      +
      tmb_distributions.hpp
      diff --git a/docs/double__logistic_8hpp_source.html b/docs/double__logistic_8hpp_source.html index 0ccafed..c2bd6f2 100644 --- a/docs/double__logistic_8hpp_source.html +++ b/docs/double__logistic_8hpp_source.html @@ -76,58 +76,46 @@
      double_logistic.hpp
      -
      1 
      -
      9 #ifndef POPULATION_DYNAMICS_SELECTIVITY_DOUBLE_LOGISTIC_HPP
      -
      10 #define POPULATION_DYNAMICS_SELECTIVITY_DOUBLE_LOGISTIC_HPP
      -
      11 
      -
      12 //#include "../../../interface/interface.hpp"
      -
      13 #include "../../../common/fims_math.hpp"
      -
      14 #include "../../../common/fims_vector.hpp"
      -
      15 #include "selectivity_base.hpp"
      -
      16 
      -
      17 namespace fims_popdy {
      -
      18 
      -
      23 template <typename Type>
      -
      24 struct DoubleLogisticSelectivity : public SelectivityBase<Type> {
      -
      25  fims::Vector<Type> inflection_point_asc;
      -
      28  fims::Vector<Type> slope_asc;
      -
      31  fims::Vector<Type> inflection_point_desc;
      -
      34  fims::Vector<Type> slope_desc;
      -
      38  DoubleLogisticSelectivity() : SelectivityBase<Type>()
      -
      39  {
      -
      40  }
      -
      41 
      -
      42  virtual ~DoubleLogisticSelectivity()
      -
      43  {
      -
      44  }
      -
      45 
      -
      57  virtual const Type evaluate(const Type &x)
      -
      58  {
      -
      59  return fims_math::double_logistic<Type>(
      -
      60  inflection_point_asc[0], slope_asc[0], inflection_point_desc[0], slope_desc[0], x);
      -
      61  }
      -
      62 
      -
      75  virtual const Type evaluate(const Type &x, size_t pos)
      -
      76  {
      -
      77  return fims_math::double_logistic<Type>(
      -
      78  inflection_point_asc.get_force_scalar(pos), slope_asc.get_force_scalar(pos),
      -
      79  inflection_point_desc.get_force_scalar(pos), slope_desc.get_force_scalar(pos), x);
      -
      80  }
      -
      81 };
      -
      82 
      -
      83 } // namespace fims_popdy
      -
      84 
      -
      85 #endif /* POPULATION_DYNAMICS_SELECTIVITY_DOUBLE_LOGISTIC_HPP */
      -
      fims::Vector
      Definition: fims_vector.hpp:25
      -
      selectivity_base.hpp
      Declares the SelectivityBase class which is the base class for all selectivity functors.
      -
      fims_popdy::DoubleLogisticSelectivity
      DoubleLogisticSelectivity class that returns the double logistic function value from fims_math.
      Definition: double_logistic.hpp:24
      -
      fims_popdy::DoubleLogisticSelectivity::evaluate
      virtual const Type evaluate(const Type &x, size_t pos)
      Method of the double logistic selectivity class that implements the double logistic function from FIM...
      Definition: double_logistic.hpp:75
      -
      fims_popdy::DoubleLogisticSelectivity::inflection_point_asc
      fims::Vector< Type > inflection_point_asc
      Definition: double_logistic.hpp:25
      -
      fims_popdy::DoubleLogisticSelectivity::slope_asc
      fims::Vector< Type > slope_asc
      Definition: double_logistic.hpp:28
      -
      fims_popdy::DoubleLogisticSelectivity::slope_desc
      fims::Vector< Type > slope_desc
      Definition: double_logistic.hpp:34
      -
      fims_popdy::DoubleLogisticSelectivity::inflection_point_desc
      fims::Vector< Type > inflection_point_desc
      Definition: double_logistic.hpp:31
      -
      fims_popdy::DoubleLogisticSelectivity::evaluate
      virtual const Type evaluate(const Type &x)
      Method of the double logistic selectivity class that implements the double logistic function from FIM...
      Definition: double_logistic.hpp:57
      -
      fims_popdy::SelectivityBase
      Base class for all selectivity functors.
      Definition: selectivity_base.hpp:24
      +
      1 /*
      +
      2  * This File is part of the NOAA, National Marine Fisheries Service
      +
      3  * Fisheries Integrated Modeling System project.
      +
      4  * Refer to the LICENSE file for reuse information.
      +
      5  *
      +
      6  */
      +
      7 #ifndef POPULATION_DYNAMICS_SELECTIVITY_DOUBLE_LOGISTIC_HPP
      +
      8 #define POPULATION_DYNAMICS_SELECTIVITY_DOUBLE_LOGISTIC_HPP
      +
      9 
      +
      10 //#include "../../../interface/interface.hpp"
      +
      11 #include "../../../common/fims_math.hpp"
      +
      12 #include "selectivity_base.hpp"
      +
      13 
      +
      14 namespace fims_popdy {
      +
      15 
      +
      20 template <typename Type>
      +
      21 struct DoubleLogisticSelectivity : public SelectivityBase<Type> {
      +
      22  Type inflection_point_asc;
      +
      25  Type slope_asc;
      +
      28  Type inflection_point_desc;
      +
      31  Type slope_desc;
      +
      35  DoubleLogisticSelectivity() : SelectivityBase<Type>() {}
      +
      36 
      +
      37  virtual ~DoubleLogisticSelectivity() {}
      +
      49  virtual const Type evaluate(const Type &x) {
      +
      50  return fims_math::double_logistic<Type>(
      +
      51  inflection_point_asc, slope_asc, inflection_point_desc, slope_desc, x);
      +
      52  }
      +
      53 };
      +
      54 
      +
      55 } // namespace fims_popdy
      +
      56 
      +
      57 #endif /* POPULATION_DYNAMICS_SELECTIVITY_DOUBLE_LOGISTIC_HPP */
      +
      fims_popdy::DoubleLogisticSelectivity
      DoubleLogisticSelectivity class that returns the double logistic function value from fims_math.
      Definition: double_logistic.hpp:21
      +
      fims_popdy::DoubleLogisticSelectivity::inflection_point_asc
      Type inflection_point_asc
      Definition: double_logistic.hpp:22
      +
      fims_popdy::DoubleLogisticSelectivity::inflection_point_desc
      Type inflection_point_desc
      Definition: double_logistic.hpp:28
      +
      fims_popdy::DoubleLogisticSelectivity::slope_asc
      Type slope_asc
      Definition: double_logistic.hpp:25
      +
      fims_popdy::DoubleLogisticSelectivity::slope_desc
      Type slope_desc
      Definition: double_logistic.hpp:31
      +
      fims_popdy::DoubleLogisticSelectivity::evaluate
      virtual const Type evaluate(const Type &x)
      Method of the double logistic selectivity class that implements the double logistic function from FIM...
      Definition: double_logistic.hpp:49
      +
      fims_popdy::SelectivityBase
      Base class for all selectivity functors.
      Definition: selectivity_base.hpp:27
      diff --git a/docs/ewaa_8hpp_source.html b/docs/ewaa_8hpp_source.html index f616cad..292ee0f 100644 --- a/docs/ewaa_8hpp_source.html +++ b/docs/ewaa_8hpp_source.html @@ -76,14 +76,21 @@
      ewaa.hpp
      -Go to the documentation of this file.
      1 
      +
      1 /*
      +
      2  * This File is part of the NOAA, National Marine Fisheries Service
      +
      3  * Fisheries Integrated Modeling System project.
      +
      4  * Refer to the LICENSE file for reuse information.
      +
      5  *
      +
      6  * The purpose of this file is to declare the growth functor class
      +
      7  * which is the base class for all growth functors.
      +
      8  */
      9 #ifndef POPULATION_DYNAMICS_GROWTH_EWAA_HPP
      10 #define POPULATION_DYNAMICS_GROWTH_EWAA_HPP
      11 
      12 //#include "../../../interface/interface.hpp"
      13 #include <map>
      14 
      -
      15 #include "growth_base.hpp"
      +
      15 #include "growth_base.hpp"
      16 
      17 namespace fims_popdy {
      18 
      @@ -95,28 +102,21 @@
      27  // in this case, our key is age (first double), and
      28  // the value is the weight at that age (second double)
      29  std::map<double, double> ewaa;
      -
      31  typedef typename std::map<double, double>::iterator weight_iterator;
      -
      33  EWAAgrowth() : GrowthBase<Type>() {}
      -
      34 
      -
      35  virtual ~EWAAgrowth() {}
      -
      36 
      -
      42  virtual const Type evaluate(const double& a) {
      -
      43  weight_iterator it = this->ewaa.find(a);
      -
      44  if(it == this->ewaa.end() ){
      -
      45  return 0.0;
      -
      46  }
      -
      47  Type ret = (*it).second;//itewaa[a];
      -
      48  return ret;
      -
      49  }
      -
      50 };
      -
      51 } // namespace fims_popdy
      -
      52 #endif /* POPULATION_DYNAMICS_GROWTH_EWAA_HPP */
      -
      growth_base.hpp
      Includes any .hpp files within the subfolders so that only this file needs to included in the model....
      +
      32  EWAAgrowth() : GrowthBase<Type>() {}
      +
      33 
      +
      34  virtual ~EWAAgrowth() {}
      +
      35 
      +
      41  virtual const Type evaluate(const double& a) {
      +
      42  Type ret = ewaa[a];
      +
      43  return ret;
      +
      44  }
      +
      45 };
      +
      46 } // namespace fims_popdy
      +
      47 #endif /* POPULATION_DYNAMICS_GROWTH_EWAA_HPP */
      fims_popdy::EWAAgrowth
      EWAAgrowth class that returns the EWAA function value.
      Definition: ewaa.hpp:23
      fims_popdy::EWAAgrowth::ewaa
      std::map< double, double > ewaa
      Definition: ewaa.hpp:29
      -
      fims_popdy::EWAAgrowth::evaluate
      virtual const Type evaluate(const double &a)
      Returns the weight at age a (in kg) from the input vector.
      Definition: ewaa.hpp:42
      -
      fims_popdy::EWAAgrowth::weight_iterator
      std::map< double, double >::iterator weight_iterator
      Definition: ewaa.hpp:31
      -
      fims_popdy::GrowthBase
      Base class for all growth functors.
      Definition: growth_base.hpp:24
      +
      fims_popdy::EWAAgrowth::evaluate
      virtual const Type evaluate(const double &a)
      Returns the weight at age a (in kg) from the input vector.
      Definition: ewaa.hpp:41
      +
      fims_popdy::GrowthBase
      Base class for all growth functors.
      Definition: growth_base.hpp:27
      diff --git a/docs/files.html b/docs/files.html index 6c59020..dc03825 100644 --- a/docs/files.html +++ b/docs/files.html @@ -77,64 +77,62 @@  ▼ inst  ▼ include  ▼ common - data_object.hppTODO: provide a brief description - def.hppTODO: provide a brief description - fims_math.hppTODO: provide a brief description - fims_vector.hppTODO: provide a brief description - information.hppTODO: provide a brief description - model.hppTODO: provide a brief description - model_object.hppTODO: provide a brief description + data_object.hpp + def.hpp + fims_math.hpp + fims_vector.hpp + information.hpp + model.hpp + model_object.hpp  ▼ distributions  ▼ functors - density_components_base.hppDeclares the DensityComponentBase class, which is the base class for all distribution functors - lognormal_lpdf.hppLognormal Log Probability Density Function (LPDF) defines the Lognormal LPDF class and its fields and returns the log probability density function - multinomial_lpmf.hppMultinomial Log Probability Mass Function (LPMF) module file defines the Multinomial LPMF class and its fields and returns the log probability mass function - normal_lpdf.hppNormal Log Probability Density Function (LPDF) module file defines the Normal LPDF class and its fields and returns the log probability density function - distributions.hppThis distributions module includes any .hpp files within the subfolders so that only this file needs to included in the model.hpp file + distributions_base.hpp + tmb_distributions.hpp + distributions.hpp  ▼ interface  ▼ rcpp  ▼ rcpp_objects  rcpp_data.hpp - rcpp_distribution.hppTODO: provide a brief description - rcpp_fleet.hppTODO: provide a brief description - rcpp_growth.hppTODO: provide a brief description - rcpp_interface_base.hppTODO: provide a brief description - rcpp_lpdf.hppTODO: provide a brief description - rcpp_maturity.hppTODO: provide a brief description - rcpp_natural_mortality.hppTODO: provide a brief description - rcpp_population.hppTODO: provide a brief description - rcpp_recruitment.hppTODO: provide a brief description - rcpp_selectivity.hppTODO: provide a brief description - rcpp_interface.hppTODO: provide a brief description - init.hppTODO: provide a brief description - interface.hppTODO: provide a brief description + rcpp_fleet.hpp + rcpp_growth.hpp + rcpp_interface_base.hpp + rcpp_maturity.hpp + rcpp_natural_mortality.hpp + rcpp_nll.hpp + rcpp_population.hpp + rcpp_recruitment.hpp + rcpp_selectivity.hpp + rcpp_tmb_distribution.hpp + rcpp_interface.hpp + init.hpp + interface.hpp  ▼ population_dynamics  ▼ fleet - fleet.hppDeclare the fleet functor class which is the base class for all fleet functors + fleet.hpp  ▼ growth  ▼ functors - ewaa.hppDeclares the growth functor class which is the base class for all growth functors - growth_base.hppIncludes any .hpp files within the subfolders so that only this file needs to included in the model.hpp file - growth.hppIncludes any .hpp files within the subfolders so that only this file needs to included in the model.hpp file + ewaa.hpp + growth_base.hpp + growth.hpp  ▼ maturity  ▼ functors - logistic.hppDefines the LogisticMaturity class, which inherits from the MaturityBase class - maturity_base.hppDeclares the MaturityBase class which is the base class for all maturity functors - maturity.hppIncludes any .hpp files within the subfolders so that only this file needs to included in the model.hpp file + logistic.hpp + maturity_base.hpp + maturity.hpp  ▼ population - population.hppDefines the Population class and its fields and methods - subpopulation.hpp + population.hpp + subpopulation.hpp  ▼ recruitment  ▼ functors - recruitment_base.hppServes as the parent class where recruitment functions are called - sr_beverton_holt.hppCalls the Beverton–Holt stock–recruitment function from fims_math and does the calculation - recruitment.hppIncludes any .hpp files within the subfolders so that only this file needs to included in the model.hpp file + recruitment_base.hpp + sr_beverton_holt.hpp + recruitment.hpp  ▼ selectivity  ▼ functors  double_logistic.hpp - logistic.hppDeclares the DoubleLogisticSelectivity class which implements the logistic function from fims_math in the selectivity module - selectivity_base.hppDeclares the SelectivityBase class which is the base class for all selectivity functors - selectivity.hppIncludes any .hpp files within the subfolders so that only this file needs to included in the model.hpp file + logistic.hpp + selectivity_base.hpp + selectivity.hpp  ▼ utilities  fims_json.hppA simple JSON parsing and generation library diff --git a/docs/fims__json_8hpp.html b/docs/fims__json_8hpp.html index cda4935..903f0cb 100644 --- a/docs/fims__json_8hpp.html +++ b/docs/fims__json_8hpp.html @@ -94,44 +94,44 @@ - + - +

      Classes

      class  fims::JsonValue
      class  JsonValue
       
      class  fims::JsonParser
      class  JsonParser
       
      - - - - + + + +

      Typedefs

      using fims::JsonObject = std::map< std::string, JsonValue >
       
      using fims::JsonArray = std::vector< JsonValue >
       
      using JsonObject = std::map< std::string, JsonValue >
       
      using JsonArray = std::vector< JsonValue >
       
      - - +

      Enumerations

      enum  fims::JsonValueType {
      -  fims::Null = 0 -, fims::Number -, fims::String -, fims::Bool +
      enum  JsonValueType {
      +  Null = 0 +, Number +, String +, Bool ,
      -  fims::Object -, fims::JArray +  Object +, Array
      }
       
       

      Detailed Description

      A simple JSON parsing and generation library.

      -

      This library provides classes and functions for parsing JSON strings and generating JSON data structures.

      Copyright
      This file is part of the NOAA, National Marine Fisheries Service Fisheries Integrated Modeling System project. See LICENSE in the source folder for reuse information.
      +

      This library provides classes and functions for parsing JSON strings and generating JSON data structures.

      Typedef Documentation

      - -

      ◆ JsonArray

      + +

      ◆ JsonArray

      - +
      using fims::JsonArray = typedef std::vector<JsonValue>using JsonArray = std::vector<JsonValue>
      @@ -139,14 +139,14 @@

      -

      ◆ JsonObject

      + +

      ◆ JsonObject

      - +
      using fims::JsonObject = typedef std::map<std::string, JsonValue>using JsonObject = std::map<std::string, JsonValue>
      @@ -155,30 +155,30 @@

      Enumeration Type Documentation

      - -

      ◆ JsonValueType

      + +

      ◆ JsonValueType

      - +
      enum fims::JsonValueTypeenum JsonValueType

      Represents different types of JSON values.

      - - - - - -
      Enumerator
      Null 

      Null JSON value.

      +
      Enumerator
      Null 

      Null JSON value.

      Number 

      Numeric JSON value.

      +
      Number 

      Numeric JSON value.

      String 

      String JSON value.

      +
      String 

      String JSON value.

      Bool 

      Boolean JSON value.

      +
      Bool 

      Boolean JSON value.

      Object 

      JSON object.

      +
      Object 

      JSON object.

      JArray 

      JSON array.

      +
      Array 

      JSON array.

      diff --git a/docs/fims__json_8hpp_source.html b/docs/fims__json_8hpp_source.html index 3f7b59c..1ae1663 100644 --- a/docs/fims__json_8hpp_source.html +++ b/docs/fims__json_8hpp_source.html @@ -77,453 +77,353 @@
      Go to the documentation of this file.
      1 
      -
      10 #include <cctype>
      -
      11 #include <iostream>
      -
      12 #include <map>
      -
      13 #include <sstream>
      -
      14 #include <string>
      -
      15 #include <vector>
      -
      16 
      -
      17 
      -
      18 namespace fims {
      -
      19  class JsonValue;
      +
      7 #include <cctype>
      +
      8 #include <iostream>
      +
      9 #include <map>
      +
      10 #include <sstream>
      +
      11 #include <string>
      +
      12 #include <vector>
      +
      13 
      +
      14 class JsonValue;
      +
      15 
      +
      19 using JsonObject = std::map<std::string, JsonValue>;
      20 
      -
      24  using JsonObject = std::map<std::string, JsonValue>;
      +
      24 using JsonArray = std::vector<JsonValue>;
      25 
      -
      29  using JsonArray = std::vector<JsonValue>;
      -
      30 
      -
      34  enum JsonValueType {
      -
      35  Null = 0,
      -
      36  Number,
      -
      37  String,
      -
      38  Bool,
      -
      39  Object,
      -
      40  JArray
      -
      41  };
      -
      42 
      -
      46  class JsonValue {
      -
      47  public:
      +
      29 enum JsonValueType {
      +
      30  Null = 0,
      +
      31  Number,
      +
      32  String,
      +
      33  Bool,
      +
      34  Object,
      +
      35  Array
      +
      36 };
      +
      37 
      +
      41 class JsonValue {
      +
      42  public:
      +
      44  JsonValue() : type(JsonValueType::Null) {}
      +
      45 
      +
      47  JsonValue(int num) : type(JsonValueType::Number), number(num) {}
      48 
      -
      50  JsonValue() : type(JsonValueType::Null) {
      -
      51  }
      -
      52 
      -
      54  JsonValue(int num) : type(JsonValueType::Number), number(num) {
      -
      55  }
      -
      56 
      -
      58  JsonValue(double num) : type(JsonValueType::Number), number(num) {
      -
      59  }
      +
      50  JsonValue(double num) : type(JsonValueType::Number), number(num) {}
      +
      51 
      +
      53  JsonValue(const std::string& str) : type(JsonValueType::String), str(str) {}
      +
      54 
      +
      56  JsonValue(bool b) : type(JsonValueType::Bool), boolean(b) {}
      +
      57 
      +
      59  JsonValue(const JsonObject& obj) : type(JsonValueType::Object), object(obj) {}
      60 
      -
      62  JsonValue(const std::string& str) : type(JsonValueType::String), str(str) {
      -
      63  }
      -
      64 
      -
      66  JsonValue(bool b) : type(JsonValueType::Bool), boolean(b) {
      -
      67  }
      -
      68 
      -
      70  JsonValue(const JsonObject& obj) : type(JsonValueType::Object), object(obj) {
      -
      71  }
      +
      62  JsonValue(const JsonArray& arr) : type(JsonValueType::Array), array(arr) {}
      +
      63 
      +
      65  JsonValueType GetType() const { return type; }
      +
      66 
      +
      68  int GetInt() const { return static_cast<int>(number); }
      +
      69 
      +
      71  double GetDouble() const { return number; }
      72 
      -
      74  JsonValue(const JsonArray& arr) : type(JsonValueType::JArray), array(arr) {
      -
      75  }
      -
      76 
      -
      78  JsonValueType GetType() const {
      -
      79  return type;
      -
      80  }
      +
      74  const std::string& GetString() const { return str; }
      +
      75 
      +
      77  bool GetBool() const { return boolean; }
      +
      78 
      +
      80  JsonObject& GetObject() { return object; }
      81 
      -
      83  int GetInt() const {
      -
      84  return static_cast<int> (number);
      -
      85  }
      -
      86 
      -
      88  double GetDouble() const {
      -
      89  return number;
      -
      90  }
      -
      91 
      -
      93  const std::string& GetString() const {
      -
      94  return str;
      -
      95  }
      -
      96 
      -
      98  bool GetBool() const {
      -
      99  return boolean;
      -
      100  }
      -
      101 
      -
      103  JsonObject& GetObject() {
      -
      104  return object;
      -
      105  }
      -
      106 
      -
      108  JsonArray& GetArray() {
      -
      109  return array;
      -
      110  }
      -
      111 
      -
      112  private:
      -
      113  JsonValueType type;
      -
      114  double number;
      -
      115  std::string str;
      -
      116  bool boolean;
      -
      117  JsonObject object;
      -
      118  JsonArray array;
      -
      119  };
      -
      120 
      -
      124  class JsonParser {
      -
      125  public:
      -
      127  JsonValue Parse(const std::string& json);
      -
      129  void WriteToFile(const std::string& filename, JsonValue jsonValue);
      -
      131  void Show(JsonValue jsonValue);
      -
      132 
      -
      134  static std::string removeWhitespace(const std::string& input) {
      -
      135  std::string result = input;
      -
      136  result.erase(std::remove_if(result.begin(), result.end(), ::isspace), result.end());
      -
      137  return result;
      -
      138  }
      -
      139 
      -
      145  static std::string PrettyFormatJSON(const std::string& json) {
      -
      146  std::string result;
      -
      147  std::string input = JsonParser::removeWhitespace(json);
      -
      148  int indentLevel = 0;
      -
      149  bool inQuotes = false;
      -
      150 
      -
      151  for (size_t i = 0; i < input.size(); ++i) {
      -
      152  char current = input[i];
      -
      153 
      -
      154  switch (current) {
      -
      155  case '{':
      -
      156  case '[':
      -
      157  result += current;
      -
      158  if (!inQuotes) {
      -
      159  result += '\n';
      -
      160  indentLevel++;
      -
      161  result += std::string(indentLevel * 4, ' ');
      -
      162  }
      -
      163  break;
      -
      164 
      -
      165  case '}':
      -
      166  case ']':
      -
      167  if (!inQuotes) {
      -
      168  result += '\n';
      -
      169  indentLevel--;
      -
      170  result += std::string(indentLevel * 4, ' ');
      -
      171  }
      -
      172  result += current;
      -
      173  break;
      -
      174 
      -
      175  case ',':
      -
      176  result += current;
      -
      177  if (!inQuotes) {
      -
      178  result += '\n';
      -
      179  result += std::string(indentLevel * 4, ' ');
      -
      180  }
      -
      181  break;
      -
      182 
      -
      183  case ':':
      -
      184  result += current;
      -
      185  if (!inQuotes) result += " ";
      -
      186  break;
      -
      187 
      -
      188  case '"':
      -
      189  result += current;
      -
      190  // Toggle inQuotes when we encounter a double-quote
      -
      191  if (i == 0 || input[i - 1] != '\\') {
      -
      192  inQuotes = !inQuotes;
      -
      193  }
      -
      194  break;
      +
      83  JsonArray& GetArray() { return array; }
      +
      84 
      +
      85  private:
      +
      86  JsonValueType type;
      +
      87  double number;
      +
      88  std::string str;
      +
      89  bool boolean;
      +
      90  JsonObject object;
      +
      91  JsonArray array;
      +
      92 };
      +
      93 
      +
      97 class JsonParser {
      +
      98  public:
      +
      100  JsonValue Parse(const std::string& json);
      +
      102  void WriteToFile(const std::string& filename, JsonValue jsonValue);
      +
      104  void Show(JsonValue jsonValue);
      +
      105 
      +
      106  private:
      +
      108  void SkipWhitespace();
      +
      110  JsonValue ParseValue();
      +
      112  JsonValue ParseNumber();
      +
      114  JsonValue ParseString();
      +
      116  JsonValue ParseBool();
      +
      118  JsonValue ParseNull();
      +
      120  JsonValue ParseObject();
      +
      122  JsonValue ParseArray();
      +
      124  void WriteJsonValue(std::ofstream& outputFile, JsonValue jsonValue);
      +
      126  void PrintJsonValue(std::ostream& outputFile, JsonValue jsonValue);
      +
      128  void Indent(std::ostream& outputFile, int level);
      +
      130  void Indent(std::ofstream& outputFile, int level);
      +
      131 
      +
      132  std::string data;
      +
      133  size_t position;
      +
      134 };
      +
      135 
      +
      141 JsonValue JsonParser::Parse(const std::string& json) {
      +
      142  data = json;
      +
      143  position = 0;
      +
      144  return ParseValue();
      +
      145 }
      +
      146 
      +
      147 void JsonParser::SkipWhitespace() {
      +
      148  while (position < data.length() && std::isspace(data[position])) {
      +
      149  position++;
      +
      150  }
      +
      151 }
      +
      152 
      +
      157 JsonValue JsonParser::ParseValue() {
      +
      159  SkipWhitespace();
      +
      160  char current = data[position];
      +
      161  if (current == '{') {
      +
      162  return ParseObject();
      +
      163  } else if (current == '[') {
      +
      164  return ParseArray();
      +
      165  } else if (current == '"') {
      +
      166  return ParseString();
      +
      167  } else if (current == 't' || current == 'f') {
      +
      168  return ParseBool();
      +
      169  } else if (current == 'n') {
      +
      170  return ParseNull();
      +
      171  } else {
      +
      172  return ParseNumber();
      +
      173  }
      +
      174 }
      +
      175 
      +
      180 JsonValue JsonParser::ParseNumber() {
      +
      181  size_t end_pos = position;
      +
      182  bool is_float = false;
      +
      183  while (end_pos < data.length() &&
      +
      184  (std::isdigit(data[end_pos]) || data[end_pos] == '.' ||
      +
      185  data[end_pos] == '-' || data[end_pos] == 'e' ||
      +
      186  data[end_pos] == 'E')) {
      +
      187  if (data[end_pos] == '.' || data[end_pos] == 'e' || data[end_pos] == 'E') {
      +
      188  is_float = true;
      +
      189  }
      +
      190  end_pos++;
      +
      191  }
      +
      192 
      +
      193  std::string num_str = data.substr(position, end_pos - position);
      +
      194  position = end_pos;
      195 
      -
      196  default:
      -
      197  result += current;
      -
      198  break;
      -
      199  }
      -
      200  }
      -
      201  return result;
      -
      202  }
      -
      203 
      -
      204  private:
      -
      206  void SkipWhitespace();
      -
      208  JsonValue ParseValue();
      -
      210  JsonValue ParseNumber();
      -
      212  JsonValue ParseString();
      -
      214  JsonValue ParseBool();
      -
      216  JsonValue ParseNull();
      -
      218  JsonValue ParseObject();
      -
      220  JsonValue ParseArray();
      -
      222  void WriteJsonValue(std::ofstream& outputFile, JsonValue jsonValue);
      -
      224  void PrintJsonValue(std::ostream& outputFile, JsonValue jsonValue);
      -
      226  void Indent(std::ostream& outputFile, int level);
      -
      228  void Indent(std::ofstream& outputFile, int level);
      -
      229 
      -
      230  std::string data;
      -
      231  size_t position;
      -
      232  };
      -
      233 
      -
      239  JsonValue JsonParser::Parse(const std::string& json) {
      -
      240  data = json;
      -
      241  position = 0;
      -
      242  return ParseValue();
      -
      243  }
      -
      244 
      -
      249  void JsonParser::SkipWhitespace() {
      -
      250  while (position < data.size() && std::isspace(data[position])) {
      -
      251  position++;
      -
      252  }
      -
      253  }
      -
      254 
      -
      259  JsonValue JsonParser::ParseValue() {
      -
      261  SkipWhitespace();
      -
      262  char current = data[position];
      -
      263  if (current == '{') {
      -
      264  return ParseObject();
      -
      265  } else if (current == '[') {
      -
      266  return ParseArray();
      -
      267  } else if (current == '"') {
      -
      268  return ParseString();
      -
      269  } else if (current == 't' || current == 'f') {
      -
      270  return ParseBool();
      -
      271  } else if (current == 'n') {
      -
      272  return ParseNull();
      -
      273  } else {
      -
      274  return ParseNumber();
      -
      275  }
      -
      276  }
      -
      277 
      -
      282  JsonValue JsonParser::ParseNumber() {
      -
      283  size_t end_pos = position;
      -
      284  bool is_float = false;
      -
      285  while (end_pos < data.size() &&
      -
      286  (std::isdigit(data[end_pos]) || data[end_pos] == '.' ||
      -
      287  data[end_pos] == '-' || data[end_pos] == 'e' ||
      -
      288  data[end_pos] == 'E')) {
      -
      289  if (data[end_pos] == '.' || data[end_pos] == 'e' || data[end_pos] == 'E') {
      -
      290  is_float = true;
      -
      291  }
      -
      292  end_pos++;
      -
      293  }
      -
      294 
      -
      295  std::string num_str = data.substr(position, end_pos - position);
      -
      296  position = end_pos;
      -
      297 
      -
      298  if (is_float) {
      -
      299  double num;
      -
      300  std::istringstream(num_str) >> num;
      -
      301  return JsonValue(num);
      -
      302  } else {
      -
      303  int num;
      -
      304  std::istringstream(num_str) >> num;
      -
      305  return JsonValue(num);
      -
      306  }
      -
      307  }
      -
      308 
      -
      313  JsonValue JsonParser::ParseString() {
      -
      314  position++; // Skip the initial '"'
      -
      315  size_t end_pos = data.find('"', position);
      -
      316  std::string str = data.substr(position, end_pos - position);
      -
      317  position = end_pos + 1;
      -
      318  return JsonValue(str);
      -
      319  }
      -
      320 
      -
      325  JsonValue JsonParser::ParseBool() {
      -
      326  if (data.compare(position, 4, "true") == 0) {
      -
      327  position += 4;
      -
      328  return JsonValue(true);
      -
      329  } else if (data.compare(position, 5, "false") == 0) {
      -
      330  position += 5;
      -
      331  return JsonValue(false);
      -
      332  } else {
      -
      333  // Invalid boolean value
      -
      334  return JsonValue();
      -
      335  }
      -
      336  }
      -
      337 
      -
      342  JsonValue JsonParser::ParseNull() {
      -
      343  if (data.compare(position, 4, "null") == 0) {
      -
      344  position += 4;
      -
      345  return JsonValue();
      -
      346  } else {
      -
      347  // Invalid null value
      -
      348  return JsonValue();
      -
      349  }
      -
      350  }
      -
      351 
      -
      356  JsonValue JsonParser::ParseObject() {
      -
      357  JsonObject obj;
      -
      358  position++; // Skip the initial '{'
      -
      359 
      -
      360  while (data[position] != '}') {
      -
      361  SkipWhitespace();
      -
      362  std::string key = ParseString().GetString();
      -
      363 
      -
      364  position++; // Skip the ':'
      -
      365  SkipWhitespace();
      -
      366  JsonValue value = ParseValue();
      -
      367  obj[key] = value;
      -
      368 
      -
      369  SkipWhitespace();
      -
      370  if (data[position] == ',') {
      -
      371  position++;
      -
      372  }
      -
      373  }
      -
      374 
      -
      375  position++; // Skip the trailing '}'
      -
      376  return JsonValue(obj);
      -
      377  }
      -
      378 
      -
      383  JsonValue JsonParser::ParseArray() {
      -
      384  JsonArray arr;
      -
      385  position++; // Skip the initial '['
      -
      386 
      -
      387  while (data[position] != ']') {
      -
      388  SkipWhitespace();
      -
      389  JsonValue value = ParseValue();
      -
      390  arr.push_back(value);
      -
      391 
      -
      392  SkipWhitespace();
      -
      393  if (data[position] == ',') {
      -
      394  position++;
      -
      395  }
      -
      396  }
      -
      397 
      -
      398  position++; // Skip the trailing ']'
      -
      399  return JsonValue(arr);
      -
      400  }
      -
      401 
      -
      407  void JsonParser::WriteToFile(const std::string& filename, JsonValue jsonValue) {
      -
      408  std::ofstream outputFile(filename);
      -
      409  if (!outputFile) {
      -
      410  std::cerr << "Error: Unable to open file " << filename << " for writing."
      -
      411  << std::endl;
      -
      412  return;
      -
      413  }
      -
      414 
      -
      416  WriteJsonValue(outputFile, jsonValue);
      -
      417  }
      -
      418 
      -
      425  void JsonParser::WriteJsonValue(std::ofstream& outputFile,
      -
      426  JsonValue jsonValue) {
      -
      427  switch (jsonValue.GetType()) {
      -
      428  case JsonValueType::Null:
      -
      429  outputFile << "null";
      -
      430  break;
      -
      431  case JsonValueType::Number:
      -
      432  outputFile << jsonValue.GetDouble();
      -
      433  break;
      -
      434  case JsonValueType::String:
      -
      435  outputFile << "\"" << jsonValue.GetString() << "\"";
      -
      436  break;
      -
      437  case JsonValueType::Bool:
      -
      438  outputFile << (jsonValue.GetBool() ? "true" : "false");
      -
      439  break;
      -
      440  case JsonValueType::Object:
      -
      441  {
      -
      442  JsonObject& obj = jsonValue.GetObject();
      -
      443  outputFile << "{";
      -
      444  bool first = true;
      -
      445  for (const auto& pair : obj) {
      -
      446  if (!first) {
      -
      447  outputFile << ",";
      -
      448  }
      -
      449  first = false;
      -
      450  outputFile << "\"" << pair.first << "\":";
      -
      451  WriteJsonValue(outputFile, pair.second);
      -
      452  }
      -
      453  outputFile << "}";
      -
      454  }
      -
      455  break;
      -
      456  case JsonValueType::JArray:
      -
      457  {
      -
      458  JsonArray& arr = jsonValue.GetArray();
      -
      459  outputFile << "[";
      -
      460  bool first = true;
      -
      461  for (const auto& value : arr) {
      -
      462  if (!first) {
      -
      463  outputFile << ",";
      -
      464  }
      -
      465  first = false;
      -
      466  WriteJsonValue(outputFile, value);
      -
      467  }
      -
      468  outputFile << "]";
      -
      469  }
      -
      470  break;
      -
      471  }
      -
      472  }
      -
      473 
      -
      478  void JsonParser::Show(JsonValue jsonValue) {
      -
      479  this->PrintJsonValue(std::cout, jsonValue);
      -
      480  std::cout << std::endl;
      -
      481  }
      -
      482 
      -
      488  void JsonParser::PrintJsonValue(std::ostream& output, JsonValue jsonValue) {
      -
      489  switch (jsonValue.GetType()) {
      -
      490  case JsonValueType::Null:
      -
      491  output << "null";
      -
      492  break;
      -
      493  case JsonValueType::Number:
      -
      494  output << jsonValue.GetDouble();
      -
      495  break;
      -
      496  case JsonValueType::String:
      -
      497  output << "\"" << jsonValue.GetString() << "\"";
      -
      498  break;
      -
      499  case JsonValueType::Bool:
      -
      500  output << (jsonValue.GetBool() ? "true" : "false");
      -
      501  break;
      -
      502  case JsonValueType::Object:
      -
      503  {
      -
      504  JsonObject& obj = jsonValue.GetObject();
      -
      505  output << "{";
      -
      506  bool first = true;
      -
      507  for (const auto& pair : obj) {
      -
      508  if (!first) {
      -
      509  output << ",";
      -
      510  }
      -
      511  first = false;
      -
      512  output << "\"" << pair.first << "\":";
      -
      513  PrintJsonValue(output, pair.second);
      -
      514  }
      -
      515  output << "}";
      -
      516  }
      -
      517  break;
      -
      518  case JsonValueType::JArray:
      -
      519  {
      -
      520  JsonArray& arr = jsonValue.GetArray();
      -
      521  output << "[";
      -
      522  bool first = true;
      -
      523  for (const auto& value : arr) {
      -
      524  if (!first) {
      -
      525  output << ",";
      -
      526  }
      -
      527  first = false;
      -
      528  PrintJsonValue(output, value);
      -
      529  }
      -
      530  output << "]";
      -
      531  }
      -
      532  break;
      -
      533  }
      -
      534  }
      -
      535 }
      -
      fims::JsonParser
      Definition: fims_json.hpp:124
      -
      fims::JsonParser::Show
      void Show(JsonValue jsonValue)
      Definition: fims_json.hpp:478
      -
      fims::JsonParser::WriteToFile
      void WriteToFile(const std::string &filename, JsonValue jsonValue)
      Definition: fims_json.hpp:407
      -
      fims::JsonParser::PrettyFormatJSON
      static std::string PrettyFormatJSON(const std::string &json)
      Formats a JSON string.
      Definition: fims_json.hpp:145
      -
      fims::JsonParser::Parse
      JsonValue Parse(const std::string &json)
      Definition: fims_json.hpp:239
      -
      fims::JsonParser::removeWhitespace
      static std::string removeWhitespace(const std::string &input)
      Definition: fims_json.hpp:134
      -
      fims::JsonValue
      Definition: fims_json.hpp:46
      -
      fims::JsonValue::JsonValue
      JsonValue(bool b)
      Definition: fims_json.hpp:66
      -
      fims::JsonValue::JsonValue
      JsonValue()
      Definition: fims_json.hpp:50
      -
      fims::JsonValue::JsonValue
      JsonValue(const JsonArray &arr)
      Definition: fims_json.hpp:74
      -
      fims::JsonValue::GetDouble
      double GetDouble() const
      Definition: fims_json.hpp:88
      -
      fims::JsonValue::GetObject
      JsonObject & GetObject()
      Definition: fims_json.hpp:103
      -
      fims::JsonValue::JsonValue
      JsonValue(const JsonObject &obj)
      Definition: fims_json.hpp:70
      -
      fims::JsonValue::JsonValue
      JsonValue(double num)
      Definition: fims_json.hpp:58
      -
      fims::JsonValue::GetArray
      JsonArray & GetArray()
      Definition: fims_json.hpp:108
      -
      fims::JsonValue::GetInt
      int GetInt() const
      Definition: fims_json.hpp:83
      -
      fims::JsonValue::GetBool
      bool GetBool() const
      Definition: fims_json.hpp:98
      -
      fims::JsonValue::JsonValue
      JsonValue(const std::string &str)
      Definition: fims_json.hpp:62
      -
      fims::JsonValue::GetType
      JsonValueType GetType() const
      Definition: fims_json.hpp:78
      -
      fims::JsonValue::JsonValue
      JsonValue(int num)
      Definition: fims_json.hpp:54
      -
      fims::JsonValue::GetString
      const std::string & GetString() const
      Definition: fims_json.hpp:93
      -
      fims::JsonArray
      std::vector< JsonValue > JsonArray
      Definition: fims_json.hpp:29
      -
      fims::JsonValueType
      JsonValueType
      Definition: fims_json.hpp:34
      -
      fims::Bool
      @ Bool
      Definition: fims_json.hpp:38
      -
      fims::Number
      @ Number
      Definition: fims_json.hpp:36
      -
      fims::String
      @ String
      Definition: fims_json.hpp:37
      -
      fims::Object
      @ Object
      Definition: fims_json.hpp:39
      -
      fims::Null
      @ Null
      Definition: fims_json.hpp:35
      -
      fims::JArray
      @ JArray
      Definition: fims_json.hpp:40
      -
      fims::JsonObject
      std::map< std::string, JsonValue > JsonObject
      Definition: fims_json.hpp:24
      +
      196  if (is_float) {
      +
      197  double num;
      +
      198  std::istringstream(num_str) >> num;
      +
      199  return JsonValue(num);
      +
      200  } else {
      +
      201  int num;
      +
      202  std::istringstream(num_str) >> num;
      +
      203  return JsonValue(num);
      +
      204  }
      +
      205 }
      +
      206 
      +
      211 JsonValue JsonParser::ParseString() {
      +
      212  position++; // Skip the initial '"'
      +
      213  size_t end_pos = data.find('"', position);
      +
      214  std::string str = data.substr(position, end_pos - position);
      +
      215  position = end_pos + 1;
      +
      216  return JsonValue(str);
      +
      217 }
      +
      218 
      +
      223 JsonValue JsonParser::ParseBool() {
      +
      224  if (data.compare(position, 4, "true") == 0) {
      +
      225  position += 4;
      +
      226  return JsonValue(true);
      +
      227  } else if (data.compare(position, 5, "false") == 0) {
      +
      228  position += 5;
      +
      229  return JsonValue(false);
      +
      230  } else {
      +
      231  // Invalid boolean value
      +
      232  return JsonValue();
      +
      233  }
      +
      234 }
      +
      235 
      +
      240 JsonValue JsonParser::ParseNull() {
      +
      241  if (data.compare(position, 4, "null") == 0) {
      +
      242  position += 4;
      +
      243  return JsonValue();
      +
      244  } else {
      +
      245  // Invalid null value
      +
      246  return JsonValue();
      +
      247  }
      +
      248 }
      +
      249 
      +
      254 JsonValue JsonParser::ParseObject() {
      +
      255  JsonObject obj;
      +
      256  position++; // Skip the initial '{'
      +
      257 
      +
      258  while (data[position] != '}') {
      +
      259  SkipWhitespace();
      +
      260  std::string key = ParseString().GetString();
      +
      261 
      +
      262  position++; // Skip the ':'
      +
      263  SkipWhitespace();
      +
      264  JsonValue value = ParseValue();
      +
      265  obj[key] = value;
      +
      266 
      +
      267  SkipWhitespace();
      +
      268  if (data[position] == ',') {
      +
      269  position++;
      +
      270  }
      +
      271  }
      +
      272 
      +
      273  position++; // Skip the trailing '}'
      +
      274  return JsonValue(obj);
      +
      275 }
      +
      276 
      +
      281 JsonValue JsonParser::ParseArray() {
      +
      282  JsonArray arr;
      +
      283  position++; // Skip the initial '['
      +
      284 
      +
      285  while (data[position] != ']') {
      +
      286  SkipWhitespace();
      +
      287  JsonValue value = ParseValue();
      +
      288  arr.push_back(value);
      +
      289 
      +
      290  SkipWhitespace();
      +
      291  if (data[position] == ',') {
      +
      292  position++;
      +
      293  }
      +
      294  }
      +
      295 
      +
      296  position++; // Skip the trailing ']'
      +
      297  return JsonValue(arr);
      +
      298 }
      +
      299 
      +
      305 void JsonParser::WriteToFile(const std::string& filename, JsonValue jsonValue) {
      +
      306  std::ofstream outputFile(filename);
      +
      307  if (!outputFile) {
      +
      308  std::cerr << "Error: Unable to open file " << filename << " for writing."
      +
      309  << std::endl;
      +
      310  return;
      +
      311  }
      +
      312 
      +
      314  WriteJsonValue(outputFile, jsonValue);
      +
      315 }
      +
      316 
      +
      323 void JsonParser::WriteJsonValue(std::ofstream& outputFile,
      +
      324  JsonValue jsonValue) {
      +
      325  switch (jsonValue.GetType()) {
      +
      326  case JsonValueType::Null:
      +
      327  outputFile << "null";
      +
      328  break;
      +
      329  case JsonValueType::Number:
      +
      330  outputFile << jsonValue.GetDouble();
      +
      331  break;
      +
      332  case JsonValueType::String:
      +
      333  outputFile << "\"" << jsonValue.GetString() << "\"";
      +
      334  break;
      +
      335  case JsonValueType::Bool:
      +
      336  outputFile << (jsonValue.GetBool() ? "true" : "false");
      +
      337  break;
      +
      338  case JsonValueType::Object: {
      +
      339  JsonObject& obj = jsonValue.GetObject();
      +
      340  outputFile << "{";
      +
      341  bool first = true;
      +
      342  for (const auto& pair : obj) {
      +
      343  if (!first) {
      +
      344  outputFile << ",";
      +
      345  }
      +
      346  first = false;
      +
      347  outputFile << "\"" << pair.first << "\":";
      +
      348  WriteJsonValue(outputFile, pair.second);
      +
      349  }
      +
      350  outputFile << "}";
      +
      351  } break;
      +
      352  case JsonValueType::Array: {
      +
      353  JsonArray& arr = jsonValue.GetArray();
      +
      354  outputFile << "[";
      +
      355  bool first = true;
      +
      356  for (const auto& value : arr) {
      +
      357  if (!first) {
      +
      358  outputFile << ",";
      +
      359  }
      +
      360  first = false;
      +
      361  WriteJsonValue(outputFile, value);
      +
      362  }
      +
      363  outputFile << "]";
      +
      364  } break;
      +
      365  }
      +
      366 }
      +
      367 
      +
      372 void JsonParser::Show(JsonValue jsonValue) {
      +
      373  this->PrintJsonValue(std::cout, jsonValue);
      +
      374  std::cout << std::endl;
      +
      375 }
      +
      376 
      +
      382 void JsonParser::PrintJsonValue(std::ostream& output, JsonValue jsonValue) {
      +
      383  switch (jsonValue.GetType()) {
      +
      384  case JsonValueType::Null:
      +
      385  output << "null";
      +
      386  break;
      +
      387  case JsonValueType::Number:
      +
      388  output << jsonValue.GetDouble();
      +
      389  break;
      +
      390  case JsonValueType::String:
      +
      391  output << "\"" << jsonValue.GetString() << "\"";
      +
      392  break;
      +
      393  case JsonValueType::Bool:
      +
      394  output << (jsonValue.GetBool() ? "true" : "false");
      +
      395  break;
      +
      396  case JsonValueType::Object: {
      +
      397  JsonObject& obj = jsonValue.GetObject();
      +
      398  output << "{";
      +
      399  bool first = true;
      +
      400  for (const auto& pair : obj) {
      +
      401  if (!first) {
      +
      402  output << ",";
      +
      403  }
      +
      404  first = false;
      +
      405  output << "\"" << pair.first << "\":";
      +
      406  PrintJsonValue(output, pair.second);
      +
      407  }
      +
      408  output << "}";
      +
      409  } break;
      +
      410  case JsonValueType::Array: {
      +
      411  JsonArray& arr = jsonValue.GetArray();
      +
      412  output << "[";
      +
      413  bool first = true;
      +
      414  for (const auto& value : arr) {
      +
      415  if (!first) {
      +
      416  output << ",";
      +
      417  }
      +
      418  first = false;
      +
      419  PrintJsonValue(output, value);
      +
      420  }
      +
      421  output << "]";
      +
      422  } break;
      +
      423  }
      +
      424 }
      +
      JsonParser
      Definition: fims_json.hpp:97
      +
      JsonParser::Parse
      JsonValue Parse(const std::string &json)
      Definition: fims_json.hpp:141
      +
      JsonParser::Show
      void Show(JsonValue jsonValue)
      Definition: fims_json.hpp:372
      +
      JsonParser::WriteToFile
      void WriteToFile(const std::string &filename, JsonValue jsonValue)
      Definition: fims_json.hpp:305
      +
      JsonValue
      Definition: fims_json.hpp:41
      +
      JsonValue::GetDouble
      double GetDouble() const
      Definition: fims_json.hpp:71
      +
      JsonValue::JsonValue
      JsonValue(double num)
      Definition: fims_json.hpp:50
      +
      JsonValue::GetType
      JsonValueType GetType() const
      Definition: fims_json.hpp:65
      +
      JsonValue::JsonValue
      JsonValue(int num)
      Definition: fims_json.hpp:47
      +
      JsonValue::GetBool
      bool GetBool() const
      Definition: fims_json.hpp:77
      +
      JsonValue::JsonValue
      JsonValue(bool b)
      Definition: fims_json.hpp:56
      +
      JsonValue::GetObject
      JsonObject & GetObject()
      Definition: fims_json.hpp:80
      +
      JsonValue::GetArray
      JsonArray & GetArray()
      Definition: fims_json.hpp:83
      +
      JsonValue::JsonValue
      JsonValue()
      Definition: fims_json.hpp:44
      +
      JsonValue::GetInt
      int GetInt() const
      Definition: fims_json.hpp:68
      +
      JsonValue::GetString
      const std::string & GetString() const
      Definition: fims_json.hpp:74
      +
      JsonValue::JsonValue
      JsonValue(const JsonObject &obj)
      Definition: fims_json.hpp:59
      +
      JsonValue::JsonValue
      JsonValue(const JsonArray &arr)
      Definition: fims_json.hpp:62
      +
      JsonValue::JsonValue
      JsonValue(const std::string &str)
      Definition: fims_json.hpp:53
      +
      JsonArray
      std::vector< JsonValue > JsonArray
      Definition: fims_json.hpp:24
      +
      JsonObject
      std::map< std::string, JsonValue > JsonObject
      Definition: fims_json.hpp:19
      +
      JsonValueType
      JsonValueType
      Definition: fims_json.hpp:29
      +
      Bool
      @ Bool
      Definition: fims_json.hpp:33
      +
      Object
      @ Object
      Definition: fims_json.hpp:34
      +
      Null
      @ Null
      Definition: fims_json.hpp:30
      +
      String
      @ String
      Definition: fims_json.hpp:32
      +
      Array
      @ Array
      Definition: fims_json.hpp:35
      +
      Number
      @ Number
      Definition: fims_json.hpp:31
      diff --git a/docs/fims__math_8hpp.html b/docs/fims__math_8hpp.html index d6d3404..3a3f877 100644 --- a/docs/fims__math_8hpp.html +++ b/docs/fims__math_8hpp.html @@ -78,14 +78,8 @@
      fims_math.hpp File Reference
      - -

      TODO: provide a brief description. -More...

      #include <cmath>
      -#include <random>
      -#include <sstream>
      -#include "../interface/interface.hpp"
      -#include "fims_vector.hpp"
      +#include "../interface/interface.hpp"

      Go to the source code of this file.

      @@ -116,17 +110,8 @@ - - - - - -
      template<typename Type >
      const Type fims_math::ad_max (const Type &a, const Type &b, Type C=1e-5)
       
      template<class T >
      T fims_math::sum (const std::vector< T > &v)
       
      template<class T >
      T fims_math::sum (const fims::Vector< T > &v)
       
      -

      Detailed Description

      -

      TODO: provide a brief description.

      -
      Copyright
      This file is part of the NOAA, National Marine Fisheries Service Fisheries Integrated Modeling System project. See LICENSE in the source folder for reuse information.
      -

      Function Documentation

      +

      Function Documentation

      ◆ ad_fabs()

      @@ -513,62 +498,6 @@

      Returns
      the parameter in real space
      -

      -
      - -

      ◆ sum() [1/2]

      - -
      -
      -
      -template<class T >
      - - - - - - - - -
      T fims_math::sum (const fims::Vector< T > & v)
      -
      -

      Sum elements of a vector

      -
      Parameters
      - - -
      vA vector of constants.
      -
      -
      -
      Returns
      A single numeric value.
      - -
      -
      - -

      ◆ sum() [2/2]

      - -
      -
      -
      -template<class T >
      - - - - - - - - -
      T fims_math::sum (const std::vector< T > & v)
      -
      -

      Sum elements of a vector

      -
      Parameters
      - - -
      vA vector of constants.
      -
      -
      -
      Returns
      A single numeric value.
      -

      diff --git a/docs/fims__math_8hpp_source.html b/docs/fims__math_8hpp_source.html index 471d9a3..43a8817 100644 --- a/docs/fims__math_8hpp_source.html +++ b/docs/fims__math_8hpp_source.html @@ -77,177 +77,117 @@
      Go to the documentation of this file.
      1 
      -
      8 #ifndef FIMS_MATH_HPP
      -
      9 #define FIMS_MATH_HPP
      -
      10 
      -
      11 // note: this is modeling platform specific, must be controlled by
      -
      12 // preprocessing macros
      -
      13 //#include "def.hpp"
      -
      14 #include <cmath>
      -
      15 #include <random>
      -
      16 #include <sstream>
      -
      17 
      -
      18 #include "../interface/interface.hpp"
      -
      19 #include "fims_vector.hpp"
      -
      20 
      -
      21 namespace fims_math {
      -
      22 #ifdef STD_LIB
      +
      3 // note: To document a global C function, typedef, enum or preprocessor
      +
      4 // definition you must first document the file that contains it
      +
      5 
      +
      6 /*
      +
      7  * File: fims_math.hpp
      +
      8  *
      +
      9  * This File is part of the NOAA, National Marine Fisheries Service
      +
      10  * Fisheries Integrated Modeling System project. See LICENSE in the
      +
      11  * source folder for reuse information.
      +
      12  *
      +
      13  */
      +
      14 #ifndef FIMS_MATH_HPP
      +
      15 #define FIMS_MATH_HPP
      +
      16 
      +
      17 // note: this is modeling platform specific, must be controlled by
      +
      18 // preprocessing macros
      +
      19 //#include "def.hpp"
      +
      20 #include <cmath>
      +
      21 
      +
      22 #include "../interface/interface.hpp"
      23 
      -
      31 template <class Type>
      -
      32 inline const Type exp(const Type &x) {
      -
      33  return std::exp(x);
      -
      34 }
      -
      35 
      -
      42 template <class Type>
      -
      43 inline const Type log(const Type &x) {
      -
      44  return std::log(x);
      -
      45 }
      -
      46 
      -
      47 template <class Type>
      -
      48 inline const Type cos(const Type &x) {
      -
      49  return std::cos(x);
      -
      50 }
      -
      51 
      -
      52 template <class Type>
      -
      53 inline const Type sqrt(const Type &x) {
      -
      54  return std::sqrt(x);
      -
      55 }
      -
      56 
      -
      57 template <class Type>
      -
      58 inline const Type pow(const Type &x, const Type &y) {
      -
      59  return std::pow(x, y);
      -
      60 }
      -
      61 #endif
      -
      62 
      -
      63 #ifdef TMB_MODEL
      -
      64 // #include <TMB.hpp>
      -
      65 
      -
      74 template <class Type>
      -
      75 inline const Type exp(const Type &x) {
      -
      76  using ::exp;
      -
      77  return exp(x);
      -
      78 }
      -
      79 
      -
      80 template <>
      -
      81 inline const double exp(const double &x) {
      -
      82  return std::exp(x);
      +
      24 namespace fims_math {
      +
      25 #ifdef STD_LIB
      +
      33 template <class Type>
      +
      34 inline const Type exp(const Type &x) {
      +
      35  return std::exp(x);
      +
      36 }
      +
      37 
      +
      44 template <class Type>
      +
      45 inline const Type log(const Type &x) {
      +
      46  return std::log(x);
      +
      47 }
      +
      48 #endif
      +
      49 
      +
      50 #ifdef TMB_MODEL
      +
      51 // #include <TMB.hpp>
      +
      52 
      +
      61 template <class Type>
      +
      62 inline const Type exp(const Type &x) {
      +
      63  using ::exp;
      +
      64  return exp(x);
      +
      65 }
      +
      66 
      +
      67 template <>
      +
      68 inline const double exp(const double &x) {
      +
      69  return std::exp(x);
      +
      70 }
      +
      71 
      +
      80 template <class Type>
      +
      81 inline const Type log(const Type &x) {
      +
      82  return log(x);
      83 }
      84 
      -
      93 template <class Type>
      -
      94 inline const Type log(const Type &x) {
      -
      95  return log(x);
      -
      96 }
      -
      97 
      -
      98 template <>
      -
      99 inline const double log(const double &x) {
      -
      100  return std::log(x);
      -
      101 }
      -
      102 
      -
      103 template <class Type>
      -
      104 inline const Type cos(const Type &x) {
      -
      105  return cos(x);
      +
      85 template <>
      +
      86 inline const double log(const double &x) {
      +
      87  return std::log(x);
      +
      88 }
      +
      89 
      +
      90 #endif
      +
      91 
      +
      102 template <class Type>
      +
      103 inline const Type logistic(const Type &inflection_point, const Type &slope,
      +
      104  const Type &x) {
      +
      105  return (1.0) / (1.0 + exp(-1.0 * slope * (x - inflection_point)));
      106 }
      107 
      -
      108 template <>
      -
      109 inline const double cos(const double &x) {
      -
      110  return std::cos(x);
      -
      111 }
      -
      112 
      -
      113 template <class Type>
      -
      114 inline const Type sqrt(const Type &x) {
      -
      115  return sqrt(x);
      -
      116 }
      -
      117 
      -
      118 template <>
      -
      119 inline const double sqrt(const double &x) {
      -
      120  return std::sqrt(x);
      +
      118 template <class Type>
      +
      119 inline const Type logit(const Type &a, const Type &b, const Type &x) {
      +
      120  return -fims_math::log(b - x) + fims_math::log(x - a);
      121 }
      122 
      -
      123 template <class Type>
      -
      124 inline const Type pow(const Type &x, const Type &y) {
      -
      125  return pow(x, y);
      -
      126 }
      -
      127 
      -
      128 template <>
      -
      129 inline const double pow(const double &x, const double &y) {
      -
      130  return std::pow(x, y);
      -
      131 }
      -
      132 
      -
      133 #endif
      -
      134 
      -
      145 template <class Type>
      -
      146 inline const Type logistic(const Type &inflection_point, const Type &slope,
      -
      147  const Type &x) {
      -
      148  return (1.0) / (1.0 + exp(-1.0 * slope * (x - inflection_point)));
      -
      149 }
      -
      150 
      -
      161 template <class Type>
      -
      162 inline const Type logit(const Type &a, const Type &b, const Type &x) {
      -
      163  return -fims_math::log(b - x) + fims_math::log(x - a);
      -
      164 }
      -
      165 
      -
      176 template <class Type>
      -
      177 inline const Type inv_logit(const Type &a, const Type &b, const Type &logit_x) {
      -
      178  return a + (b - a) / (1.0 + fims_math::exp(-logit_x));
      -
      179 }
      -
      180 
      -
      201 template <class Type>
      -
      202 inline const Type double_logistic(const Type &inflection_point_asc,
      -
      203  const Type &slope_asc,
      -
      204  const Type &inflection_point_desc,
      -
      205  const Type &slope_desc, const Type &x) {
      -
      206  return (1.0) / (1.0 + exp(-1.0 * slope_asc * (x - inflection_point_asc))) *
      -
      207  (1.0 -
      -
      208  (1.0) / (1.0 + exp(-1.0 * slope_desc * (x - inflection_point_desc))));
      -
      209 }
      -
      210 
      -
      224 template <class Type>
      -
      225 const Type ad_fabs(const Type &x, Type C = 1e-5) {
      -
      226  return sqrt((x * x) + C);
      -
      227 }
      -
      228 
      -
      244 template <typename Type>
      -
      245 inline const Type ad_min(const Type &a, const Type &b, Type C = 1e-5) {
      -
      246  return (a + b - fims_math::ad_fabs(a - b, C)) * 0.5;
      -
      247 }
      -
      248 
      -
      261 template <typename Type>
      -
      262 inline const Type ad_max(const Type &a, const Type &b, Type C = 1e-5) {
      -
      263  return (a + b + fims_math::ad_fabs(a - b, C)) * static_cast<Type>(.5);
      -
      264 }
      -
      265 
      -
      274  template<class T>
      -
      275  T sum(const std::vector<T>& v) {
      -
      276  T ret = 0.0;
      -
      277  for (int i = 0; i < v.size(); i++) {
      -
      278  ret += v[i];
      -
      279  }
      -
      280  return ret;
      -
      281  }
      -
      282 
      -
      291  template<class T>
      -
      292  T sum(const fims::Vector<T>& v) {
      -
      293  T ret = 0.0;
      -
      294  for (int i = 0; i < v.size(); i++) {
      -
      295  ret += v[i];
      -
      296  }
      -
      297  return ret;
      -
      298  }
      -
      299 
      -
      300 } // namespace fims_math
      -
      301 
      -
      302 #endif /* FIMS_MATH_HPP */
      -
      fims::Vector
      Definition: fims_vector.hpp:25
      -
      fims::Vector::size
      size_type size() const
      Returns the number of elements.
      Definition: fims_vector.hpp:295
      -
      fims_math::logit
      const Type logit(const Type &a, const Type &b, const Type &x)
      A logit function for bounding of parameters.
      Definition: fims_math.hpp:162
      -
      fims_math::sum
      T sum(const std::vector< T > &v)
      Definition: fims_math.hpp:275
      -
      fims_math::ad_min
      const Type ad_min(const Type &a, const Type &b, Type C=1e-5)
      Definition: fims_math.hpp:245
      -
      fims_math::double_logistic
      const Type double_logistic(const Type &inflection_point_asc, const Type &slope_asc, const Type &inflection_point_desc, const Type &slope_desc, const Type &x)
      The general double logistic function.
      Definition: fims_math.hpp:202
      -
      fims_math::ad_max
      const Type ad_max(const Type &a, const Type &b, Type C=1e-5)
      Definition: fims_math.hpp:262
      -
      fims_math::inv_logit
      const Type inv_logit(const Type &a, const Type &b, const Type &logit_x)
      An inverse logit function for bounding of parameters.
      Definition: fims_math.hpp:177
      -
      fims_math::ad_fabs
      const Type ad_fabs(const Type &x, Type C=1e-5)
      Definition: fims_math.hpp:225
      -
      fims_math::logistic
      const Type logistic(const Type &inflection_point, const Type &slope, const Type &x)
      The general logistic function.
      Definition: fims_math.hpp:146
      -
      fims_vector.hpp
      TODO: provide a brief description.
      +
      133 template <class Type>
      +
      134 inline const Type inv_logit(const Type &a, const Type &b, const Type &logit_x) {
      +
      135  return a + (b - a) / (1.0 + fims_math::exp(-logit_x));
      +
      136 }
      +
      137 
      +
      158 template <class Type>
      +
      159 inline const Type double_logistic(const Type &inflection_point_asc,
      +
      160  const Type &slope_asc,
      +
      161  const Type &inflection_point_desc,
      +
      162  const Type &slope_desc, const Type &x) {
      +
      163  return (1.0) / (1.0 + exp(-1.0 * slope_asc * (x - inflection_point_asc))) *
      +
      164  (1.0 -
      +
      165  (1.0) / (1.0 + exp(-1.0 * slope_desc * (x - inflection_point_desc))));
      +
      166 }
      +
      167 
      +
      181 template <class Type>
      +
      182 const Type ad_fabs(const Type &x, Type C = 1e-5) {
      +
      183  return sqrt((x * x) + C); //, .5);
      +
      184 }
      +
      185 
      +
      201 template <typename Type>
      +
      202 inline const Type ad_min(const Type &a, const Type &b, Type C = 1e-5) {
      +
      203  return (a + b - fims_math::ad_fabs(a - b, C)) * 0.5;
      +
      204 }
      +
      205 
      +
      218 template <typename Type>
      +
      219 inline const Type ad_max(const Type &a, const Type &b, Type C = 1e-5) {
      +
      220  return (a + b + fims_math::ad_fabs(a - b, C)) * static_cast<Type>(.5);
      +
      221 }
      +
      222 
      +
      223 } // namespace fims_math
      +
      224 
      +
      225 #endif /* FIMS_MATH_HPP */
      +
      fims_math::logit
      const Type logit(const Type &a, const Type &b, const Type &x)
      A logit function for bounding of parameters.
      Definition: fims_math.hpp:119
      +
      fims_math::ad_min
      const Type ad_min(const Type &a, const Type &b, Type C=1e-5)
      Definition: fims_math.hpp:202
      +
      fims_math::double_logistic
      const Type double_logistic(const Type &inflection_point_asc, const Type &slope_asc, const Type &inflection_point_desc, const Type &slope_desc, const Type &x)
      The general double logistic function.
      Definition: fims_math.hpp:159
      +
      fims_math::ad_max
      const Type ad_max(const Type &a, const Type &b, Type C=1e-5)
      Definition: fims_math.hpp:219
      +
      fims_math::inv_logit
      const Type inv_logit(const Type &a, const Type &b, const Type &logit_x)
      An inverse logit function for bounding of parameters.
      Definition: fims_math.hpp:134
      +
      fims_math::ad_fabs
      const Type ad_fabs(const Type &x, Type C=1e-5)
      Definition: fims_math.hpp:182
      +
      fims_math::logistic
      const Type logistic(const Type &inflection_point, const Type &slope, const Type &x)
      The general logistic function.
      Definition: fims_math.hpp:103
      diff --git a/docs/fims__vector_8hpp_source.html b/docs/fims__vector_8hpp_source.html index 53ad170..844a018 100644 --- a/docs/fims__vector_8hpp_source.html +++ b/docs/fims__vector_8hpp_source.html @@ -76,396 +76,256 @@
      fims_vector.hpp
      -Go to the documentation of this file.
      1 
      -
      8 #ifndef FIMS_VECTOR_HPP
      -
      9 #define FIMS_VECTOR_HPP
      -
      10 
      -
      11 #include "../interface/interface.hpp"
      -
      12 #include <ostream>
      -
      13 namespace fims {
      -
      14 
      -
      24 template <typename Type>
      -
      25 class Vector {
      -
      26  std::vector<Type> vec_m;
      -
      27 
      -
      32  template <typename T>
      -
      33  friend bool operator==(const fims::Vector<T>& lhs,
      -
      34  const fims::Vector<T>& rhs);
      -
      35 
      -
      36 public:
      -
      37  // Member Types
      -
      38 
      -
      39  typedef
      -
      40  typename std::vector<Type>::value_type value_type;
      -
      41  typedef typename std::vector<Type>::allocator_type
      -
      42  allocator_type;
      -
      43  typedef typename std::vector<Type>::size_type size_type;
      -
      44  typedef typename std::vector<Type>::difference_type
      -
      45  difference_type;
      -
      46  typedef typename std::vector<Type>::reference
      -
      47  reference;
      -
      48  typedef typename std::vector<Type>::const_reference
      -
      49  const_reference;
      -
      50  typedef typename std::vector<Type>::pointer pointer;
      -
      51  typedef typename std::vector<Type>::const_pointer
      -
      52  const_pointer;
      -
      53  typedef typename std::vector<Type>::iterator iterator;
      -
      54  typedef typename std::vector<Type>::const_iterator
      -
      55  const_iterator;
      -
      56  typedef typename std::vector<Type>::reverse_iterator
      -
      57  reverse_iterator;
      -
      58  typedef typename std::vector<Type>::const_reverse_iterator
      -
      59  const_reverse_iterator;
      -
      61  // Constructors
      -
      62 
      -
      66  Vector()
      -
      67  {
      -
      68  }
      -
      69 
      -
      74  Vector(size_t size, const Type& value = Type())
      -
      75  {
      -
      76  this->vec_m.resize(size, value);
      -
      77  }
      -
      78 
      -
      82  Vector(const Vector<Type>& other)
      -
      83  {
      -
      84  this->vec_m.resize(other.size());
      -
      85  for (size_t i = 0; i < this->vec_m.size(); i++) {
      -
      86  this->vec_m[i] = other[i];
      -
      87  }
      -
      88  }
      -
      89 
      -
      93  Vector(const std::vector<Type>& other)
      -
      94  {
      -
      95  this->vec_m = other;
      -
      96  }
      +
      1 #ifndef FIMS_VECTOR_HPP
      +
      2 #define FIMS_VECTOR_HPP
      +
      3 
      +
      4 #include "../interface/interface.hpp"
      +
      5 
      +
      6 namespace fims {
      +
      7 
      +
      17 template <typename Type>
      +
      18 class Vector {
      +
      19  std::vector<Type> vec_m;
      +
      20 
      +
      25  template <typename T>
      +
      26  friend bool operator==(const fims::Vector<T>& lhs,
      +
      27  const fims::Vector<T>& rhs);
      +
      28 
      +
      29  public:
      +
      30  // Member Types
      +
      31 
      +
      32  typedef
      +
      33  typename std::vector<Type>::value_type value_type;
      +
      34  typedef typename std::vector<Type>::allocator_type
      +
      35  allocator_type;
      +
      36  typedef typename std::vector<Type>::size_type size_type;
      +
      37  typedef typename std::vector<Type>::difference_type
      +
      38  difference_type;
      +
      39  typedef typename std::vector<Type>::reference
      +
      40  reference;
      +
      41  typedef typename std::vector<Type>::const_reference
      +
      42  const_reference;
      +
      43  typedef typename std::vector<Type>::pointer pointer;
      +
      44  typedef typename std::vector<Type>::const_pointer
      +
      45  const_pointer;
      +
      46  typedef typename std::vector<Type>::iterator iterator;
      +
      47  typedef typename std::vector<Type>::const_iterator
      +
      48  const_iterator;
      +
      49  typedef typename std::vector<Type>::reverse_iterator
      +
      50  reverse_iterator;
      +
      51  typedef typename std::vector<Type>::const_reverse_iterator
      +
      52  const_reverse_iterator;
      +
      54  // Constructors
      +
      58  Vector() {}
      +
      59 
      +
      64  Vector(size_t size, const Type& value = Type()) {
      +
      65  this->vec_m.resize(size, value);
      +
      66  }
      +
      67 
      +
      71  Vector(const Vector<Type>& other) {
      +
      72  this->vec_m.resize(other.size());
      +
      73  for (size_t i = 0; i < this->vec_m.size(); i++) {
      +
      74  this->vec_m[i] = other[i];
      +
      75  }
      +
      76  }
      +
      77 
      +
      81  Vector(const std::vector<Type>& other) { this->vec_m = other; }
      +
      82 
      +
      83  // TMB specific constructor
      +
      84 #ifdef TMB_MODEL
      +
      85 
      +
      89  Vector(const tmbutils::vector<Type>& other) {
      +
      90  this->vec_m.resize(other.size());
      +
      91  for (size_t i = 0; i < this->vec_m.size(); i++) {
      +
      92  this->vec_m[i] = other[i];
      +
      93  }
      +
      94  }
      +
      95 
      +
      96 #endif
      97 
      -
      98  // TMB specific constructor
      -
      99 #ifdef TMB_MODEL
      -
      100 
      -
      104  Vector(const tmbutils::vector<Type>& other)
      -
      105  {
      -
      106  this->vec_m.resize(other.size());
      -
      107  for (size_t i = 0; i < this->vec_m.size(); i++) {
      -
      108  this->vec_m[i] = other[i];
      -
      109  }
      -
      110  }
      -
      111 
      -
      112 #endif
      -
      113 
      -
      124  inline Type& operator[](size_t pos)
      -
      125  {
      -
      126  return this->vec_m[pos];
      -
      127  }
      -
      128 
      -
      133  inline const Type& operator[](size_t n) const
      -
      134  {
      -
      135  return this->vec_m[n];
      -
      136  }
      +
      108  inline Type& operator[](size_t pos) { return this->vec_m[pos]; }
      +
      109 
      +
      114  inline const Type& operator[](size_t n) const { return this->vec_m[n]; }
      +
      115 
      +
      120  inline Type& at(size_t n) { return this->vec_m.at(n); }
      +
      121 
      +
      126  inline const Type& at(size_t n) const { return this->vec_m.at(n); }
      +
      127 
      +
      131  inline reference front() { return this->vec_m.front(); }
      +
      132 
      +
      136  inline const_reference front() const { return this->vec_m.front(); }
      137 
      -
      142  inline Type& at(size_t n)
      -
      143  {
      -
      144  return this->vec_m.at(n);
      -
      145  }
      -
      146 
      -
      151  inline const Type& at(size_t n) const
      -
      152  {
      -
      153  return this->vec_m.at(n);
      -
      154  }
      -
      155 
      -
      165  inline Type& get_force_scalar(size_t pos)
      -
      166  {
      -
      167  if (this->size() == 1 && pos > 0) {
      -
      168  return this->at(0);
      -
      169  } else if (this->size() > 1 && pos >= this->size()) {
      -
      170  throw std::invalid_argument("force_get fims::Vector index out of bounds.");
      -
      171  } else {
      -
      172  return this->at(pos);
      -
      173  }
      -
      174  }
      -
      175 
      -
      179  inline reference front()
      -
      180  {
      -
      181  return this->vec_m.front();
      -
      182  }
      +
      141  inline reference back() { return this->vec_m.back(); }
      +
      142 
      +
      146  inline const_reference back() const { return this->vec_m.back(); }
      +
      147 
      +
      151  inline pointer data() { return this->vec_m.data(); }
      +
      152 
      +
      156  inline const_pointer data() const { return this->vec_m.data(); }
      +
      157 
      +
      158  // iterators
      +
      159 
      +
      163  inline iterator begin() { return this->vec_m.begin(); }
      +
      164 
      +
      169  inline iterator end() { return this->vec_m.end(); }
      +
      170 
      +
      175  inline reverse_iterator rbegin() { return this->vec_m.rbegin(); }
      +
      176 
      +
      182  inline reverse_iterator rend() { return this->vec_m.rend(); }
      183 
      -
      187  inline const_reference front() const
      -
      188  {
      -
      189  return this->vec_m.front();
      -
      190  }
      -
      191 
      -
      195  inline reference back()
      -
      196  {
      -
      197  return this->vec_m.back();
      -
      198  }
      +
      189  inline const_reverse_iterator rbegin() const { return this->vec_m.rbegin(); }
      +
      190 
      +
      196  inline const_reverse_iterator rend() const { return this->vec_m.rend(); }
      +
      197 
      +
      198  // capacity
      199 
      -
      203  inline const_reference back() const
      -
      204  {
      -
      205  return this->vec_m.back();
      -
      206  }
      -
      207 
      -
      211  inline pointer data()
      -
      212  {
      -
      213  return this->vec_m.data();
      -
      214  }
      -
      215 
      -
      219  inline const_pointer data() const
      -
      220  {
      -
      221  return this->vec_m.data();
      -
      222  }
      -
      223 
      -
      224  // iterators
      +
      203  inline bool empty() { return this->vec_m.empty(); }
      +
      204 
      +
      208  inline size_type size() const { return this->vec_m.size(); }
      +
      209 
      +
      213  inline size_type max_size() const { return this->vec_m.max_size(); }
      +
      214 
      +
      218  inline void reserve(size_type cap) { this->vec_m.reserve(cap); }
      +
      219 
      +
      224  inline size_type capacity() { return this->vec_m.capacity(); }
      225 
      -
      229  inline iterator begin()
      -
      230  {
      -
      231  return this->vec_m.begin();
      -
      232  }
      -
      233 
      -
      238  inline iterator end()
      -
      239  {
      -
      240  return this->vec_m.end();
      -
      241  }
      -
      242 
      -
      247  inline reverse_iterator rbegin()
      -
      248  {
      -
      249  return this->vec_m.rbegin();
      -
      250  }
      -
      251 
      -
      257  inline reverse_iterator rend()
      -
      258  {
      -
      259  return this->vec_m.rend();
      -
      260  }
      -
      261 
      -
      267  inline const_reverse_iterator rbegin() const
      -
      268  {
      -
      269  return this->vec_m.rbegin();
      -
      270  }
      -
      271 
      -
      277  inline const_reverse_iterator rend() const
      -
      278  {
      -
      279  return this->vec_m.rend();
      -
      280  }
      +
      229  inline void shrink_to_fit() { this->vec_m.shrink_to_fit(); }
      +
      230 
      +
      231  // modifiers
      +
      232 
      +
      236  inline void clear() { this->vec_m.clear(); }
      +
      237 
      +
      241  inline iterator insert(const_iterator pos, const Type& value) {
      +
      242  return this->vec_m.insert(pos, value);
      +
      243  }
      +
      244 
      +
      248  inline iterator insert(const_iterator pos, size_type count,
      +
      249  const Type& value) {
      +
      250  return this->vec_m.insert(pos, count, value);
      +
      251  }
      +
      252 
      +
      256  template <class InputIt>
      +
      257  iterator insert(const_iterator pos, InputIt first, InputIt last) {
      +
      258  return this->vec_m.insert(pos, first, last);
      +
      259  }
      +
      260 
      +
      265  iterator insert(const_iterator pos, std::initializer_list<Type> ilist) {
      +
      266  return this->vec_m.insert(pos, ilist);
      +
      267  }
      +
      268 
      +
      272  template <class... Args>
      +
      273  iterator emplace(const_iterator pos, Args&&... args) {
      +
      274  return this->vec_m.emplace(pos, std::forward<Args>(args)...);
      +
      275  }
      +
      276 
      +
      280  inline iterator erase(iterator pos) { return this->vec_m.erase(pos); }
      281 
      -
      282  // capacity
      -
      283 
      -
      287  inline bool empty()
      -
      288  {
      -
      289  return this->vec_m.empty();
      -
      290  }
      -
      291 
      -
      295  inline size_type size() const
      -
      296  {
      -
      297  return this->vec_m.size();
      -
      298  }
      -
      299 
      -
      303  inline size_type max_size() const
      -
      304  {
      -
      305  return this->vec_m.max_size();
      -
      306  }
      -
      307 
      -
      311  inline void reserve(size_type cap)
      -
      312  {
      -
      313  this->vec_m.reserve(cap);
      -
      314  }
      -
      315 
      -
      320  inline size_type capacity()
      -
      321  {
      -
      322  return this->vec_m.capacity();
      -
      323  }
      -
      324 
      -
      328  inline void shrink_to_fit()
      -
      329  {
      -
      330  this->vec_m.shrink_to_fit();
      -
      331  }
      -
      332 
      -
      333  // modifiers
      -
      334 
      -
      338  inline void clear()
      -
      339  {
      -
      340  this->vec_m.clear();
      -
      341  }
      -
      342 
      -
      346  inline iterator insert(const_iterator pos, const Type& value)
      -
      347  {
      -
      348  return this->vec_m.insert(pos, value);
      +
      285  inline iterator erase(iterator first, iterator last) {
      +
      286  return this->vec_m.erase(first, last);
      +
      287  }
      +
      288 
      +
      292  inline void push_back(const Type&& value) { this->vec_m.push_back(value); }
      +
      293 
      +
      297  template <class... Args>
      +
      298  void emplace_back(Args&&... args) {
      +
      299  this->vec_m.emplace_back(std::forward<Args>(args)...);
      +
      300  }
      +
      301 
      +
      305  inline void pop_back() { this->vec_m.pop_back(); }
      +
      306 
      +
      310  inline void resize(size_t s) { this->vec_m.resize(s); }
      +
      311 
      +
      315  inline void swap(Vector& other) { this->vec_m.swap(other.vec_m); }
      +
      316 
      +
      317  // end std::vector functions
      +
      318 
      +
      326  inline operator std::vector<Type>() { return this->vec_m; }
      +
      327 
      +
      328 #ifdef TMB_MODEL
      +
      332  operator tmbutils::vector<Type>() const {
      +
      333  tmbutils::vector<Type> ret;
      +
      334  ret.resize(this->vec_m.size());
      +
      335  for (size_t i = 0; i < this->vec_m.size(); i++) {
      +
      336  ret[i] = this->vec_m[i];
      +
      337  }
      +
      338  return ret;
      +
      339  }
      +
      340 
      +
      344  operator tmbutils::vector<Type>() {
      +
      345  tmbutils::vector<Type> ret;
      +
      346  ret.resize(this->vec_m.size());
      +
      347  for (size_t i = 0; i < this->vec_m.size(); i++) {
      +
      348  ret[i] = this->vec_m[i];
      349  }
      -
      350 
      -
      354  inline iterator insert(const_iterator pos, size_type count,
      -
      355  const Type& value)
      -
      356  {
      -
      357  return this->vec_m.insert(pos, count, value);
      -
      358  }
      -
      359 
      -
      363  template <class InputIt>
      -
      364  iterator insert(const_iterator pos, InputIt first, InputIt last)
      -
      365  {
      -
      366  return this->vec_m.insert(pos, first, last);
      -
      367  }
      -
      368 
      -
      373  iterator insert(const_iterator pos, std::initializer_list<Type> ilist)
      -
      374  {
      -
      375  return this->vec_m.insert(pos, ilist);
      -
      376  }
      -
      377 
      -
      381  template <class... Args>
      -
      382  iterator emplace(const_iterator pos, Args&&... args)
      -
      383  {
      -
      384  return this->vec_m.emplace(pos, std::forward<Args>(args)...);
      -
      385  }
      -
      386 
      -
      390  inline iterator erase(iterator pos)
      -
      391  {
      -
      392  return this->vec_m.erase(pos);
      -
      393  }
      -
      394 
      -
      398  inline iterator erase(iterator first, iterator last)
      -
      399  {
      -
      400  return this->vec_m.erase(first, last);
      -
      401  }
      -
      402 
      -
      406  inline void push_back(const Type&& value)
      -
      407  {
      -
      408  this->vec_m.push_back(value);
      -
      409  }
      -
      410 
      -
      414  template <class... Args>
      -
      415  void emplace_back(Args&&... args)
      -
      416  {
      -
      417  this->vec_m.emplace_back(std::forward<Args>(args)...);
      -
      418  }
      -
      419 
      -
      423  inline void pop_back()
      -
      424  {
      -
      425  this->vec_m.pop_back();
      -
      426  }
      -
      427 
      -
      431  inline void resize(size_t s)
      -
      432  {
      -
      433  this->vec_m.resize(s);
      -
      434  }
      -
      435 
      -
      439  inline void swap(Vector& other)
      -
      440  {
      -
      441  this->vec_m.swap(other.vec_m);
      -
      442  }
      -
      443 
      -
      444  // end std::vector functions
      -
      445 
      -
      453  inline operator std::vector<Type>()
      -
      454  {
      -
      455  return this->vec_m;
      -
      456  }
      -
      457 
      -
      458 #ifdef TMB_MODEL
      -
      459 
      -
      463  operator tmbutils::vector<Type>() const
      -
      464  {
      -
      465  tmbutils::vector<Type> ret;
      -
      466  ret.resize(this->vec_m.size());
      -
      467  for (size_t i = 0; i < this->vec_m.size(); i++) {
      -
      468  ret[i] = this->vec_m[i];
      -
      469  }
      -
      470  return ret;
      -
      471  }
      -
      472 
      -
      476  operator tmbutils::vector<Type>()
      -
      477  {
      -
      478  tmbutils::vector<Type> ret;
      -
      479  ret.resize(this->vec_m.size());
      -
      480  for (size_t i = 0; i < this->vec_m.size(); i++) {
      -
      481  ret[i] = this->vec_m[i];
      -
      482  }
      -
      483  return ret;
      -
      484  }
      -
      485 
      -
      486 #endif
      -
      487 
      -
      488 private:
      -
      489 }; // end fims::Vector class
      -
      490 
      -
      494 template <class T>
      -
      495 bool operator==(const fims::Vector<T>& lhs, const fims::Vector<T>& rhs)
      -
      496 {
      -
      497  return lhs.vec_m == rhs.vec_m;
      -
      498 }
      -
      499 
      -
      500 } // namespace fims
      -
      501 
      -
      510 template<typename Type>
      -
      511 std::ostream& operator<<(std::ostream& out, fims::Vector<Type>& v)
      -
      512 {
      -
      513  out << "[";
      -
      514 
      -
      515  if (v.size() == 0) {
      -
      516  out << "]";
      -
      517  return out;
      -
      518  }
      -
      519  for (size_t i = 0; i < v.size() - 1; i++) {
      -
      520  out << v[i] << ",";
      -
      521  }
      -
      522 
      -
      523  out << v[v.size() - 1] << "]";
      -
      524  return out;
      -
      525 }
      -
      526 
      -
      527 
      -
      528 #endif
      -
      fims::Vector
      Definition: fims_vector.hpp:25
      -
      fims::Vector::emplace_back
      void emplace_back(Args &&... args)
      Constructs an element in-place at the end.
      Definition: fims_vector.hpp:415
      -
      fims::Vector::pointer
      std::vector< Type >::pointer pointer
      Definition: fims_vector.hpp:50
      -
      fims::Vector::const_iterator
      std::vector< Type >::const_iterator const_iterator
      Definition: fims_vector.hpp:55
      -
      fims::Vector::max_size
      size_type max_size() const
      Returns the maximum possible number of elements.
      Definition: fims_vector.hpp:303
      -
      fims::Vector::rend
      reverse_iterator rend()
      Returns a reverse iterator to the element following the last element of the reversed vector....
      Definition: fims_vector.hpp:257
      -
      fims::Vector::front
      const_reference front() const
      Returns a constant reference to the first element in the container.
      Definition: fims_vector.hpp:187
      -
      fims::Vector::const_reverse_iterator
      std::vector< Type >::const_reverse_iterator const_reverse_iterator
      Definition: fims_vector.hpp:59
      -
      fims::Vector::Vector
      Vector(const Vector< Type > &other)
      Copy constructor.
      Definition: fims_vector.hpp:82
      -
      fims::Vector::reserve
      void reserve(size_type cap)
      Reserves storage.
      Definition: fims_vector.hpp:311
      -
      fims::Vector::begin
      iterator begin()
      Returns an iterator to the first element of the vector.
      Definition: fims_vector.hpp:229
      -
      fims::Vector::reference
      std::vector< Type >::reference reference
      Definition: fims_vector.hpp:47
      -
      fims::Vector::end
      iterator end()
      Returns an iterator to the element following the last element of the vector.
      Definition: fims_vector.hpp:238
      -
      fims::Vector::at
      Type & at(size_t n)
      Returns a reference to the element at specified location pos. Bounds checking is performed.
      Definition: fims_vector.hpp:142
      -
      fims::Vector::shrink_to_fit
      void shrink_to_fit()
      Reduces memory usage by freeing unused memory.
      Definition: fims_vector.hpp:328
      -
      fims::Vector::at
      const Type & at(size_t n) const
      Returns a constant reference to the element at specified location pos. Bounds checking is performed.
      Definition: fims_vector.hpp:151
      -
      fims::Vector::capacity
      size_type capacity()
      Returns the number of elements that can be held in currently allocated storage.
      Definition: fims_vector.hpp:320
      -
      fims::Vector::get_force_scalar
      Type & get_force_scalar(size_t pos)
      If this vector is size 1 and pos is greater than zero, the first index is returned....
      Definition: fims_vector.hpp:165
      -
      fims::Vector::front
      reference front()
      Returns a reference to the first element in the container.
      Definition: fims_vector.hpp:179
      -
      fims::Vector::value_type
      std::vector< Type >::value_type value_type
      Definition: fims_vector.hpp:40
      -
      fims::Vector::swap
      void swap(Vector &other)
      Swaps the contents.
      Definition: fims_vector.hpp:439
      -
      fims::Vector::operator[]
      Type & operator[](size_t pos)
      Returns a reference to the element at specified location pos. No bounds checking is performed.
      Definition: fims_vector.hpp:124
      -
      fims::Vector::push_back
      void push_back(const Type &&value)
      Adds an element to the end.
      Definition: fims_vector.hpp:406
      -
      fims::Vector::insert
      iterator insert(const_iterator pos, InputIt first, InputIt last)
      Inserts elements from range [first, last) before pos.
      Definition: fims_vector.hpp:364
      -
      fims::Vector::empty
      bool empty()
      Checks whether the container is empty.
      Definition: fims_vector.hpp:287
      -
      fims::Vector::erase
      iterator erase(iterator pos)
      Removes the element at pos.
      Definition: fims_vector.hpp:390
      -
      fims::Vector::const_reference
      std::vector< Type >::const_reference const_reference
      Definition: fims_vector.hpp:49
      -
      fims::Vector::Vector
      Vector(size_t size, const Type &value=Type())
      Constructs a Vector of length "size" and sets the elements with the value from input "value".
      Definition: fims_vector.hpp:74
      -
      fims::Vector::data
      pointer data()
      Returns a pointer to the underlying data array.
      Definition: fims_vector.hpp:211
      -
      fims::Vector::back
      reference back()
      Returns a reference to the last element in the container.
      Definition: fims_vector.hpp:195
      -
      fims::Vector::rend
      const_reverse_iterator rend() const
      Returns a constant reverse iterator to the element following the last element of the reversed vector....
      Definition: fims_vector.hpp:277
      -
      fims::Vector::pop_back
      void pop_back()
      Removes the last element.
      Definition: fims_vector.hpp:423
      -
      fims::Vector::resize
      void resize(size_t s)
      Changes the number of elements stored.
      Definition: fims_vector.hpp:431
      -
      fims::Vector::erase
      iterator erase(iterator first, iterator last)
      Removes the elements in the range [first, last).
      Definition: fims_vector.hpp:398
      -
      fims::Vector::rbegin
      const_reverse_iterator rbegin() const
      Returns a constant reverse iterator to the first element of the reversed vector. It corresponds to th...
      Definition: fims_vector.hpp:267
      -
      fims::Vector::insert
      iterator insert(const_iterator pos, const Type &value)
      Inserts value before pos.
      Definition: fims_vector.hpp:346
      -
      fims::Vector::allocator_type
      std::vector< Type >::allocator_type allocator_type
      Definition: fims_vector.hpp:42
      -
      fims::Vector::insert
      iterator insert(const_iterator pos, std::initializer_list< Type > ilist)
      Inserts elements from initializer list ilist before pos.
      Definition: fims_vector.hpp:373
      -
      fims::Vector::rbegin
      reverse_iterator rbegin()
      Returns a reverse iterator to the first element of the reversed vector. It corresponds to the last el...
      Definition: fims_vector.hpp:247
      -
      fims::Vector::data
      const_pointer data() const
      Returns a constant pointer to the underlying data array.
      Definition: fims_vector.hpp:219
      -
      fims::Vector::size
      size_type size() const
      Returns the number of elements.
      Definition: fims_vector.hpp:295
      -
      fims::Vector::Vector
      Vector()
      Definition: fims_vector.hpp:66
      -
      fims::Vector::operator[]
      const Type & operator[](size_t n) const
      Returns a constant reference to the element at specified location pos. No bounds checking is performe...
      Definition: fims_vector.hpp:133
      -
      fims::Vector::difference_type
      std::vector< Type >::difference_type difference_type
      Definition: fims_vector.hpp:45
      -
      fims::Vector::const_pointer
      std::vector< Type >::const_pointer const_pointer
      Definition: fims_vector.hpp:52
      -
      fims::Vector::iterator
      std::vector< Type >::iterator iterator
      Definition: fims_vector.hpp:53
      -
      fims::Vector::Vector
      Vector(const std::vector< Type > &other)
      Initialization constructor from std::vector<Type> type.
      Definition: fims_vector.hpp:93
      -
      fims::Vector::clear
      void clear()
      Clears the contents.
      Definition: fims_vector.hpp:338
      -
      fims::Vector::size_type
      std::vector< Type >::size_type size_type
      Definition: fims_vector.hpp:43
      -
      fims::Vector::emplace
      iterator emplace(const_iterator pos, Args &&... args)
      Constructs element in-place.
      Definition: fims_vector.hpp:382
      -
      fims::Vector::back
      const_reference back() const
      Returns a constant reference to the last element in the container.
      Definition: fims_vector.hpp:203
      -
      fims::Vector::operator==
      friend bool operator==(const fims::Vector< T > &lhs, const fims::Vector< T > &rhs)
      friend comparison operator. Allows the operartor to see private members of fims::Vector<Type>.
      Definition: fims_vector.hpp:495
      -
      fims::Vector::reverse_iterator
      std::vector< Type >::reverse_iterator reverse_iterator
      Definition: fims_vector.hpp:57
      -
      fims::Vector::insert
      iterator insert(const_iterator pos, size_type count, const Type &value)
      Inserts count copies of the value before pos.
      Definition: fims_vector.hpp:354
      -
      fims::operator==
      bool operator==(const fims::Vector< T > &lhs, const fims::Vector< T > &rhs)
      Comparison operator.
      Definition: fims_vector.hpp:495
      -
      operator<<
      std::ostream & operator<<(std::ostream &out, fims::Vector< Type > &v)
      TODO: provide a brief description.
      Definition: fims_vector.hpp:511
      +
      350  return ret;
      +
      351  }
      +
      352 
      +
      353 #endif
      +
      354 
      +
      355  private:
      +
      356 }; // end fims::Vector class
      +
      357 
      +
      361 template <class T>
      +
      362 bool operator==(const fims::Vector<T>& lhs, const fims::Vector<T>& rhs) {
      +
      363  return lhs.vec_m == rhs.vec_m;
      +
      364 }
      +
      365 
      +
      366 } // namespace fims
      +
      367 
      +
      368 #endif
      +
      fims::Vector
      Definition: fims_vector.hpp:18
      +
      fims::Vector::emplace_back
      void emplace_back(Args &&... args)
      Constructs an element in-place at the end.
      Definition: fims_vector.hpp:298
      +
      fims::Vector::pointer
      std::vector< Type >::pointer pointer
      Definition: fims_vector.hpp:43
      +
      fims::Vector::const_iterator
      std::vector< Type >::const_iterator const_iterator
      Definition: fims_vector.hpp:48
      +
      fims::Vector::max_size
      size_type max_size() const
      Returns the maximum possible number of elements.
      Definition: fims_vector.hpp:213
      +
      fims::Vector::rend
      reverse_iterator rend()
      Returns a reverse iterator to the element following the last element of the reversed vector....
      Definition: fims_vector.hpp:182
      +
      fims::Vector::front
      const_reference front() const
      Returns a constant reference to the first element in the container.
      Definition: fims_vector.hpp:136
      +
      fims::Vector::const_reverse_iterator
      std::vector< Type >::const_reverse_iterator const_reverse_iterator
      Definition: fims_vector.hpp:52
      +
      fims::Vector::Vector
      Vector(const Vector< Type > &other)
      Copy constructor.
      Definition: fims_vector.hpp:71
      +
      fims::Vector::reserve
      void reserve(size_type cap)
      Reserves storage.
      Definition: fims_vector.hpp:218
      +
      fims::Vector::begin
      iterator begin()
      Returns an iterator to the first element of the vector.
      Definition: fims_vector.hpp:163
      +
      fims::Vector::reference
      std::vector< Type >::reference reference
      Definition: fims_vector.hpp:40
      +
      fims::Vector::end
      iterator end()
      Returns an iterator to the element following the last element of the vector.
      Definition: fims_vector.hpp:169
      +
      fims::Vector::at
      Type & at(size_t n)
      Returns a reference to the element at specified location pos. Bounds checking is performed.
      Definition: fims_vector.hpp:120
      +
      fims::Vector::shrink_to_fit
      void shrink_to_fit()
      Reduces memory usage by freeing unused memory.
      Definition: fims_vector.hpp:229
      +
      fims::Vector::at
      const Type & at(size_t n) const
      Returns a constant reference to the element at specified location pos. Bounds checking is performed.
      Definition: fims_vector.hpp:126
      +
      fims::Vector::capacity
      size_type capacity()
      Returns the number of elements that can be held in currently allocated storage.
      Definition: fims_vector.hpp:224
      +
      fims::Vector::front
      reference front()
      Returns a reference to the first element in the container.
      Definition: fims_vector.hpp:131
      +
      fims::Vector::value_type
      std::vector< Type >::value_type value_type
      Definition: fims_vector.hpp:33
      +
      fims::Vector::swap
      void swap(Vector &other)
      Swaps the contents.
      Definition: fims_vector.hpp:315
      +
      fims::Vector::operator[]
      Type & operator[](size_t pos)
      Returns a reference to the element at specified location pos. No bounds checking is performed.
      Definition: fims_vector.hpp:108
      +
      fims::Vector::push_back
      void push_back(const Type &&value)
      Adds an element to the end.
      Definition: fims_vector.hpp:292
      +
      fims::Vector::insert
      iterator insert(const_iterator pos, InputIt first, InputIt last)
      Inserts elements from range [first, last) before pos.
      Definition: fims_vector.hpp:257
      +
      fims::Vector::empty
      bool empty()
      Checks whether the container is empty.
      Definition: fims_vector.hpp:203
      +
      fims::Vector::erase
      iterator erase(iterator pos)
      Removes the element at pos.
      Definition: fims_vector.hpp:280
      +
      fims::Vector::const_reference
      std::vector< Type >::const_reference const_reference
      Definition: fims_vector.hpp:42
      +
      fims::Vector::Vector
      Vector(size_t size, const Type &value=Type())
      Constructs a Vector of length "size" and sets the elements with the value from input "value".
      Definition: fims_vector.hpp:64
      +
      fims::Vector::data
      pointer data()
      Returns a pointer to the underlying data array.
      Definition: fims_vector.hpp:151
      +
      fims::Vector::back
      reference back()
      Returns a reference to the last element in the container.
      Definition: fims_vector.hpp:141
      +
      fims::Vector::rend
      const_reverse_iterator rend() const
      Returns a constant reverse iterator to the element following the last element of the reversed vector....
      Definition: fims_vector.hpp:196
      +
      fims::Vector::pop_back
      void pop_back()
      Removes the last element.
      Definition: fims_vector.hpp:305
      +
      fims::Vector::resize
      void resize(size_t s)
      Changes the number of elements stored.
      Definition: fims_vector.hpp:310
      +
      fims::Vector::erase
      iterator erase(iterator first, iterator last)
      Removes the elements in the range [first, last).
      Definition: fims_vector.hpp:285
      +
      fims::Vector::rbegin
      const_reverse_iterator rbegin() const
      Returns a constant reverse iterator to the first element of the reversed vector. It corresponds to th...
      Definition: fims_vector.hpp:189
      +
      fims::Vector::insert
      iterator insert(const_iterator pos, const Type &value)
      Inserts value before pos.
      Definition: fims_vector.hpp:241
      +
      fims::Vector::allocator_type
      std::vector< Type >::allocator_type allocator_type
      Definition: fims_vector.hpp:35
      +
      fims::Vector::insert
      iterator insert(const_iterator pos, std::initializer_list< Type > ilist)
      Inserts elements from initializer list ilist before pos.
      Definition: fims_vector.hpp:265
      +
      fims::Vector::rbegin
      reverse_iterator rbegin()
      Returns a reverse iterator to the first element of the reversed vector. It corresponds to the last el...
      Definition: fims_vector.hpp:175
      +
      fims::Vector::data
      const_pointer data() const
      Returns a constant pointer to the underlying data array.
      Definition: fims_vector.hpp:156
      +
      fims::Vector::size
      size_type size() const
      Returns the number of elements.
      Definition: fims_vector.hpp:208
      +
      fims::Vector::Vector
      Vector()
      Definition: fims_vector.hpp:58
      +
      fims::Vector::operator[]
      const Type & operator[](size_t n) const
      Returns a constant reference to the element at specified location pos. No bounds checking is performe...
      Definition: fims_vector.hpp:114
      +
      fims::Vector::difference_type
      std::vector< Type >::difference_type difference_type
      Definition: fims_vector.hpp:38
      +
      fims::Vector::const_pointer
      std::vector< Type >::const_pointer const_pointer
      Definition: fims_vector.hpp:45
      +
      fims::Vector::iterator
      std::vector< Type >::iterator iterator
      Definition: fims_vector.hpp:46
      +
      fims::Vector::Vector
      Vector(const std::vector< Type > &other)
      Initialization constructor from std::vector<Type> type.
      Definition: fims_vector.hpp:81
      +
      fims::Vector::clear
      void clear()
      Clears the contents.
      Definition: fims_vector.hpp:236
      +
      fims::Vector::size_type
      std::vector< Type >::size_type size_type
      Definition: fims_vector.hpp:36
      +
      fims::Vector::emplace
      iterator emplace(const_iterator pos, Args &&... args)
      Constructs element in-place.
      Definition: fims_vector.hpp:273
      +
      fims::Vector::back
      const_reference back() const
      Returns a constant reference to the last element in the container.
      Definition: fims_vector.hpp:146
      +
      fims::Vector::operator==
      friend bool operator==(const fims::Vector< T > &lhs, const fims::Vector< T > &rhs)
      friend comparison operator. Allows the operartor to see private members of fims::Vector<Type>.
      Definition: fims_vector.hpp:362
      +
      fims::Vector::reverse_iterator
      std::vector< Type >::reverse_iterator reverse_iterator
      Definition: fims_vector.hpp:50
      +
      fims::Vector::insert
      iterator insert(const_iterator pos, size_type count, const Type &value)
      Inserts count copies of the value before pos.
      Definition: fims_vector.hpp:248
      diff --git a/docs/fleet_8hpp.html b/docs/fleet_8hpp.html index 9bedddb..afaaa5b 100644 --- a/docs/fleet_8hpp.html +++ b/docs/fleet_8hpp.html @@ -78,14 +78,11 @@
      fleet.hpp File Reference
      - -

      Declare the fleet functor class which is the base class for all fleet functors. -More...

      -
      #include "../../common/data_object.hpp"
      -#include "../../common/fims_vector.hpp"
      -#include "../../common/model_object.hpp"
      -#include "../../distributions/distributions.hpp"
      -#include "../selectivity/selectivity.hpp"
      +
      #include "../../common/data_object.hpp"
      +#include "../../common/fims_vector.hpp"
      +#include "../../common/model_object.hpp"
      +#include "../../distributions/distributions.hpp"
      +#include "../selectivity/selectivity.hpp"

      Go to the source code of this file.

      @@ -96,8 +93,8 @@
       

      Detailed Description

      -

      Declare the fleet functor class which is the base class for all fleet functors.

      -
      Copyright
      This file is part of the NOAA, National Marine Fisheries Service Fisheries Integrated Modeling System project. See LICENSE in the source folder for reuse information.
      +

      This File is part of the NOAA, National Marine Fisheries Service Fisheries Integrated Modeling System project. Refer to the LICENSE file for reuse information.

      +

      The purpose of this file is to declare the fleet functor class which is the base class for all fleet functors.

      diff --git a/docs/fleet_8hpp_source.html b/docs/fleet_8hpp_source.html index 21ded81..ecd5d3f 100644 --- a/docs/fleet_8hpp_source.html +++ b/docs/fleet_8hpp_source.html @@ -77,240 +77,242 @@
      Go to the documentation of this file.
      1 
      -
      9 #ifndef FIMS_POPULATION_DYNAMICS_FLEET_HPP
      -
      10 #define FIMS_POPULATION_DYNAMICS_FLEET_HPP
      -
      11 
      -
      12 #include "../../common/data_object.hpp"
      -
      13 #include "../../common/fims_vector.hpp"
      -
      14 #include "../../common/model_object.hpp"
      -
      15 #include "../../distributions/distributions.hpp"
      -
      16 #include "../selectivity/selectivity.hpp"
      -
      17 
      -
      18 namespace fims_popdy {
      -
      19 
      -
      24  template <class Type>
      -
      25  struct Fleet : public fims_model_object::FIMSObject<Type> {
      -
      26  static uint32_t id_g;
      -
      27  size_t nyears;
      -
      28  size_t nages;
      -
      29  size_t nlengths;
      -
      31  // selectivity
      -
      32  int fleet_selectivity_id_m = -999;
      -
      33  std::shared_ptr<SelectivityBase<Type>>
      -
      34  selectivity;
      -
      36  // index data
      -
      37  int fleet_observed_index_data_id_m = -999;
      -
      38  std::shared_ptr<fims_data_object::DataObject<Type>>
      -
      39  observed_index_data;
      -
      41  // age comp data
      -
      42  int fleet_observed_agecomp_data_id_m = -999;
      -
      43  std::shared_ptr<fims_data_object::DataObject<Type>>
      -
      44  observed_agecomp_data;
      -
      46  // length comp data
      -
      47  int fleet_observed_lengthcomp_data_id_m = -999;
      -
      48  std::shared_ptr<fims_data_object::DataObject<Type>>
      -
      49  observed_lengthcomp_data;
      -
      51  // Mortality and catchability
      -
      52  fims::Vector<Type>
      -
      53  log_Fmort;
      -
      54  fims::Vector<Type> log_q;
      -
      56  fims::Vector<Type> Fmort;
      -
      57  fims::Vector<Type> q;
      -
      59  // derived quantities
      -
      60  fims::Vector<Type> catch_at_age;
      -
      61  fims::Vector<Type> catch_index;
      -
      62  fims::Vector<Type> age_composition;
      -
      63  fims::Vector<Type> length_composition;
      -
      64  fims::Vector<Type> age_length_conversion_matrix;
      -
      66  // derived quantities
      -
      67  fims::Vector<Type> observed_catch_lpdf;
      -
      69  fims::Vector<Type> observed_index_lpdf;
      -
      71  fims::Vector<Type> expected_catch;
      -
      72  fims::Vector<Type> expected_index;
      -
      73  fims::Vector<Type> log_expected_index;
      -
      74  fims::Vector<Type> expected_catch_lpdf;
      -
      76  fims::Vector<Type> expected_index_lpdf;
      -
      78  fims::Vector<Type> catch_numbers_at_age;
      -
      79  fims::Vector<Type> catch_numbers_at_length;
      -
      80  fims::Vector<Type> proportion_catch_numbers_at_age;
      -
      81  fims::Vector<Type> proportion_catch_numbers_at_length;
      -
      82  fims::Vector<Type> catch_weight_at_age;
      -
      83  bool is_survey = false;
      -
      85 #ifdef TMB_MODEL
      -
      86  ::objective_function<Type> *of;
      -
      87 #endif
      -
      88 
      -
      92  Fleet() {
      -
      93  this->id = Fleet::id_g++;
      -
      94  }
      +
      10 #ifndef FIMS_POPULATION_DYNAMICS_FLEET_HPP
      +
      11 #define FIMS_POPULATION_DYNAMICS_FLEET_HPP
      +
      12 
      +
      13 #include "../../common/data_object.hpp"
      +
      14 #include "../../common/fims_vector.hpp"
      +
      15 #include "../../common/model_object.hpp"
      +
      16 #include "../../distributions/distributions.hpp"
      +
      17 #include "../selectivity/selectivity.hpp"
      +
      18 
      +
      19 namespace fims_popdy {
      +
      20 
      +
      25 template <class Type>
      +
      26 struct Fleet : public fims_model_object::FIMSObject<Type> {
      +
      27  static uint32_t id_g;
      +
      28  size_t nyears;
      +
      29  size_t nages;
      +
      31  // This likelihood index is not currently being used as only one likelihood
      +
      32  // distribution is available. These are for a future update M2+.
      +
      33  int fleet_index_likelihood_id_m =
      +
      34  -999;
      +
      37  std::shared_ptr<fims_distributions::DistributionsBase<Type>>
      +
      38  index_likelihood;
      +
      40  // This likelihood index is not currently being used as only one likelihood
      +
      41  // distribution is available. These are for a future update M2+.
      +
      42  int fleet_agecomp_likelihood_id_m =
      +
      43  -999;
      +
      44  std::shared_ptr<fims_distributions::DistributionsBase<Type>>
      +
      45  agecomp_likelihood;
      +
      47  // selectivity
      +
      48  int fleet_selectivity_id_m = -999;
      +
      49  std::shared_ptr<SelectivityBase<Type>>
      +
      50  selectivity;
      +
      52  int fleet_observed_index_data_id_m = -999;
      +
      53  std::shared_ptr<fims_data_object::DataObject<Type>>
      +
      54  observed_index_data;
      +
      56  int fleet_observed_agecomp_data_id_m = -999;
      +
      57  std::shared_ptr<fims_data_object::DataObject<Type>>
      +
      58  observed_agecomp_data;
      +
      60  // Mortality and catchability
      +
      61  fims::Vector<Type>
      +
      62  log_Fmort;
      +
      63  Type log_q;
      +
      65  fims::Vector<Type> log_obs_error;
      +
      67  fims::Vector<Type> Fmort;
      +
      68  Type q;
      +
      70  // derived quantities
      +
      71  fims::Vector<Type> catch_at_age;
      +
      72  fims::Vector<Type> catch_index;
      +
      73  fims::Vector<Type> age_composition;
      +
      75  // derived quantities
      +
      76  fims::Vector<Type> expected_catch;
      +
      77  fims::Vector<Type> expected_index;
      +
      78  fims::Vector<Type> catch_numbers_at_age;
      +
      79  fims::Vector<Type> catch_weight_at_age;
      +
      80  bool is_survey = false;
      +
      82 #ifdef TMB_MODEL
      +
      83  ::objective_function<Type> *of;
      +
      84 #endif
      +
      85 
      +
      89  Fleet() { this->id = Fleet::id_g++; }
      +
      90 
      +
      94  virtual ~Fleet() {}
      95 
      -
      99  virtual ~Fleet() {
      -
      100  }
      -
      101 
      -
      108  void Initialize(int nyears, int nages, int nlengths = 0) {
      -
      109  if (this->log_q.size() == 0) {
      -
      110  this->log_q.resize(1);
      -
      111  this->log_q[0] = 0.0;
      -
      112  }
      -
      113  this->nyears = nyears;
      -
      114  this->nages = nages;
      -
      115  this->nlengths = nlengths;
      -
      116 
      -
      117  catch_at_age.resize(nyears * nages);
      -
      118  catch_numbers_at_age.resize(nyears * nages);
      -
      119  catch_numbers_at_length.resize(nyears * nlengths);
      -
      120  proportion_catch_numbers_at_age.resize(nyears * nages);
      -
      121  proportion_catch_numbers_at_length.resize(nyears * nlengths);
      -
      122  age_length_conversion_matrix.resize(nages * nlengths);
      -
      123  catch_weight_at_age.resize(nyears * nages);
      -
      124  catch_index.resize(nyears); // assume index is for all ages.
      -
      125  expected_catch.resize(nyears);
      -
      126  expected_index.resize(nyears);
      -
      127  log_expected_index.resize(nyears);
      -
      128  age_composition.resize(nyears * nages);
      -
      129  length_composition.resize(nyears * nlengths);
      -
      130  q.resize(this->log_q.size());
      -
      131  log_Fmort.resize(nyears);
      -
      132  Fmort.resize(nyears);
      -
      133  }
      -
      134 
      -
      140  void Prepare() {
      -
      141  // for(size_t fleet_ = 0; fleet_ <= this->nfleets; fleet_++) {
      -
      142  // this -> Fmort[fleet_] = fims_math::exp(this -> log_Fmort[fleet_]);
      -
      143 
      -
      144  // derived quantities
      -
      145  std::fill(catch_at_age.begin(), catch_at_age.end(),
      -
      146  0);
      -
      147  std::fill(catch_index.begin(), catch_index.end(),
      -
      148  0);
      -
      149  std::fill(age_composition.begin(), age_composition.end(),
      -
      150  0);
      -
      151  std::fill(length_composition.begin(), length_composition.end(),
      -
      152  0);
      -
      153  std::fill(expected_catch.begin(), expected_catch.end(),
      -
      154  0);
      -
      155  std::fill(expected_index.begin(), expected_index.end(),
      -
      156  0);
      -
      157  std::fill(log_expected_index.begin(), log_expected_index.end(),
      -
      158  0);
      -
      159  std::fill(catch_numbers_at_age.begin(), catch_numbers_at_age.end(),
      -
      160  0);
      -
      161  std::fill(proportion_catch_numbers_at_age.begin(), proportion_catch_numbers_at_age.end(),
      -
      162  0);
      -
      163  std::fill(catch_numbers_at_length.begin(), catch_numbers_at_length.end(),
      -
      164  0);
      -
      165  std::fill(proportion_catch_numbers_at_length.begin(), proportion_catch_numbers_at_length.end(),
      -
      166  0);
      -
      167  std::fill(catch_weight_at_age.begin(), catch_weight_at_age.end(),
      -
      168  0);
      -
      170  for (size_t i = 0; i < this->log_q.size(); i++) {
      -
      171  this->q[i] = fims_math::exp(this->log_q[i]);
      -
      172  }
      -
      173 
      -
      174  for (size_t year = 0; year < this->nyears; year++) {
      -
      175  this->Fmort[year] = fims_math::exp(this->log_Fmort[year]);
      -
      176  }
      -
      177  }
      -
      178 
      -
      182  void evaluate_age_comp() {
      -
      183  for (size_t y = 0; y < this->nyears; y++) {
      -
      184  Type sum = 0.0;
      -
      185  for (size_t a = 0; a < this->nages; a++) {
      -
      186  size_t i_age_year = y * this->nages + a;
      -
      187  sum += this->catch_numbers_at_age[i_age_year];
      -
      188  }
      -
      189  for (size_t a = 0; a < this->nages; a++) {
      -
      190  size_t i_age_year = y * this->nages + a;
      -
      191  this->proportion_catch_numbers_at_age[i_age_year] = this->catch_numbers_at_age[i_age_year] / sum;
      -
      192 
      -
      193  }
      -
      194  }
      -
      195  }
      -
      196 
      -
      200  void evaluate_length_comp() {
      -
      201  if (this->nlengths > 0) {
      -
      202  for (size_t y = 0; y < this->nyears; y++) {
      -
      203  Type sum = 0.0;
      -
      204  for (size_t l = 0; l < this->nlengths; l++) {
      -
      205  size_t i_length_year = y * this->nlengths + l;
      -
      206  for(size_t a = 0; a < this->nages; a++) {
      -
      207  size_t i_age_year = y * this->nages + a;
      -
      208  size_t i_length_age = a * this->nlengths + l;
      -
      209  this->catch_numbers_at_length[i_length_year] +=
      -
      210  this->catch_numbers_at_age[i_age_year] *
      -
      211  this->age_length_conversion_matrix[i_length_age];
      -
      212  }
      -
      213  sum += this->catch_numbers_at_length[i_length_year];
      -
      214  }
      -
      215  for (size_t l = 0; l < this->nlengths; l++) {
      -
      216  size_t i_length_year = y * this->nlengths + l;
      -
      217  this->proportion_catch_numbers_at_length[i_length_year] =
      -
      218  this->catch_numbers_at_length[i_length_year] / sum;
      -
      219  }
      -
      220  }
      -
      221  }
      -
      222  }
      -
      223 
      -
      227  void evaluate_index() {
      -
      228  for (size_t i = 0; i<this->expected_index.size(); i++) {
      -
      229  log_expected_index[i] = log(this->expected_index[i]);
      -
      230  }
      -
      231  }
      -
      232  };
      +
      101  void Initialize(int nyears, int nages) {
      +
      102  this->nyears = nyears;
      +
      103  this->nages = nages;
      +
      104 
      +
      105  catch_at_age.resize(nyears * nages);
      +
      106  catch_weight_at_age.resize(nyears * nages);
      +
      107  catch_index.resize(nyears); // assume index is for all ages.
      +
      108  age_composition.resize(nyears * nages);
      +
      109  expected_catch.resize(nyears);
      +
      110  expected_index.resize(nyears); // assume index is for all ages.
      +
      111  catch_numbers_at_age.resize(nyears * nages);
      +
      112 
      +
      113  log_obs_error.resize(nyears);
      +
      114  log_Fmort.resize(nyears);
      +
      115  Fmort.resize(nyears);
      +
      116  }
      +
      117 
      +
      123  void Prepare() {
      +
      124  // for(size_t fleet_ = 0; fleet_ <= this->nfleets; fleet_++) {
      +
      125  // this -> Fmort[fleet_] = fims_math::exp(this -> log_Fmort[fleet_]);
      +
      126 
      +
      127  // derived quantities
      +
      128  std::fill(catch_at_age.begin(), catch_at_age.end(),
      +
      129  0);
      +
      130  std::fill(catch_index.begin(), catch_index.end(),
      +
      131  0);
      +
      132  std::fill(age_composition.begin(), age_composition.end(), 0);
      +
      133  std::fill(expected_catch.begin(), expected_catch.end(),
      +
      134  0);
      +
      135  std::fill(expected_index.begin(), expected_index.end(),
      +
      136  0);
      +
      137  std::fill(catch_numbers_at_age.begin(), catch_numbers_at_age.end(),
      +
      138  0);
      +
      139  std::fill(catch_weight_at_age.begin(), catch_weight_at_age.end(),
      +
      140  0);
      +
      141  this->q = fims_math::exp(this->log_q);
      +
      142  for (size_t year = 0; year < this->nyears; year++) {
      +
      143  FLEET_LOG << "input F mort " << this->log_Fmort[year] << std::endl;
      +
      144  FLEET_LOG << "input q " << this->log_q << std::endl;
      +
      145  FLEET_LOG << "input log_obs_error " << this->log_obs_error[year]
      +
      146  << std::endl;
      +
      147  this->Fmort[year] = fims_math::exp(this->log_Fmort[year]);
      +
      148  }
      +
      149  }
      +
      150 
      +
      151  virtual const Type evaluate_age_comp_nll() {
      +
      152  Type nll = 0.0;
      +
      153 #ifdef TMB_MODEL
      +
      154  fims_distributions::Dmultinom<Type> dmultinom;
      +
      155  size_t dims = this->observed_agecomp_data->get_imax() *
      +
      156  this->observed_agecomp_data->get_jmax();
      +
      157  if (dims != this->catch_numbers_at_age.size()) {
      +
      158  ERROR_LOG << "Error: observed age comp is of size " << dims
      +
      159  << " and expected is of size " << this->age_composition.size()
      +
      160  << std::endl;
      +
      161  exit(1);
      +
      162 
      +
      163  } else {
      +
      164  for (size_t y = 0; y < this->nyears; y++) {
      +
      165  fims::Vector<Type> observed_acomp;
      +
      166  fims::Vector<Type> expected_acomp;
      +
      167 
      +
      168  observed_acomp.resize(this->nages);
      +
      169  expected_acomp.resize(this->nages);
      +
      170  Type sum = 0.0;
      +
      171  bool containsNA =
      +
      172  false;
      +
      173  for (size_t a = 0; a < this->nages; a++) {
      +
      174  if (this->observed_agecomp_data->at(y, a) !=
      +
      175  this->observed_agecomp_data->na_value) {
      +
      176  size_t i_age_year = y * this->nages + a;
      +
      177  sum += this->catch_numbers_at_age[i_age_year];
      +
      178  } else {
      +
      179  containsNA = true;
      +
      180  break;
      +
      181  }
      +
      182  }
      +
      183  if (!containsNA) {
      +
      184  for (size_t a = 0; a < this->nages; a++) {
      +
      185  size_t i_age_year = y * this->nages + a;
      +
      186  expected_acomp[a] = this->catch_numbers_at_age[i_age_year] /
      +
      187  sum; // probabilities for ages
      +
      188 
      +
      189  observed_acomp[a] = this->observed_agecomp_data->at(y, a);
      +
      190 
      +
      191  FLEET_LOG << " age " << a << " in year " << y
      +
      192  << "has expected: " << expected_acomp[a]
      +
      193  << " and observed: " << observed_acomp[a] << std::endl;
      +
      194  }
      +
      195  dmultinom.x = observed_acomp;
      +
      196  dmultinom.p = expected_acomp;
      +
      197  nll -= dmultinom.evaluate(true);
      +
      198  }
      +
      199  }
      +
      200  }
      +
      201  FLEET_LOG << "Age comp negative log-likelihood for fleet," << this->id
      +
      202  << nll << std::endl;
      +
      203 #endif
      +
      204  return nll;
      +
      205  }
      +
      206 
      +
      207  virtual const Type evaluate_index_nll() {
      +
      208  Type nll = 0.0;
      +
      210 #ifdef TMB_MODEL
      +
      211  fims_distributions::Dnorm<Type> dnorm;
      +
      212  for (size_t i = 0; i < this->expected_index.size(); i++) {
      +
      213  if (this->observed_index_data->at(i) !=
      +
      214  this->observed_index_data->na_value) {
      +
      215  dnorm.x = fims_math::log(this->observed_index_data->at(i));
      +
      216  dnorm.mean = fims_math::log(this->expected_index[i]);
      +
      217  dnorm.sd = fims_math::exp(this->log_obs_error[i]);
      +
      218  nll -= dnorm.evaluate(true);
      +
      219  }
      +
      220 
      +
      221  FLEET_LOG << "observed index data: " << i << " is "
      +
      222  << this->observed_index_data->at(i)
      +
      223  << " and expected is: " << this->expected_index[i] << std::endl;
      +
      224  FLEET_LOG << " log obs error is: " << this->log_obs_error[i] << std::endl;
      +
      225  }
      +
      226  FLEET_LOG << " sd is: " << dnorm.sd << std::endl;
      +
      227  FLEET_LOG << " index nll: " << nll << std::endl;
      +
      228 
      +
      229 #endif
      +
      230  return nll;
      +
      231  }
      +
      232 };
      233 
      -
      234  // default id of the singleton fleet class
      -
      235  template <class Type>
      -
      236  uint32_t Fleet<Type>::id_g = 0;
      +
      234 // default id of the singleton fleet class
      +
      235 template <class Type>
      +
      236 uint32_t Fleet<Type>::id_g = 0;
      237 
      -
      238 } // end namespace fims_popdy
      +
      238 } // end namespace fims_popdy
      239 
      240 #endif /* FIMS_POPULATION_DYNAMICS_FLEET_HPP */
      -
      fims::Vector
      Definition: fims_vector.hpp:25
      -
      fims::Vector::resize
      void resize(size_t s)
      Changes the number of elements stored.
      Definition: fims_vector.hpp:431
      -
      fims::Vector::size
      size_type size() const
      Returns the number of elements.
      Definition: fims_vector.hpp:295
      -
      fims_model_object::FIMSObject
      FIMSObject struct that defines member types and returns the unique id.
      Definition: model_object.hpp:24
      -
      fims_popdy::Fleet
      Base class for all fleets.
      Definition: fleet.hpp:25
      -
      fims_popdy::Fleet::is_survey
      bool is_survey
      Definition: fleet.hpp:83
      -
      fims_popdy::Fleet::age_length_conversion_matrix
      fims::Vector< Type > age_length_conversion_matrix
      Definition: fleet.hpp:64
      -
      fims_popdy::Fleet::Fleet
      Fleet()
      Constructor.
      Definition: fleet.hpp:92
      -
      fims_popdy::Fleet::log_q
      fims::Vector< Type > log_q
      Definition: fleet.hpp:54
      -
      fims_popdy::Fleet::selectivity
      std::shared_ptr< SelectivityBase< Type > > selectivity
      Definition: fleet.hpp:34
      -
      fims_popdy::Fleet::id_g
      static uint32_t id_g
      Definition: fleet.hpp:26
      -
      fims_popdy::Fleet::nages
      size_t nages
      Definition: fleet.hpp:28
      -
      fims_popdy::Fleet::catch_at_age
      fims::Vector< Type > catch_at_age
      Definition: fleet.hpp:60
      -
      fims_popdy::Fleet::nlengths
      size_t nlengths
      Definition: fleet.hpp:29
      -
      fims_popdy::Fleet::fleet_observed_lengthcomp_data_id_m
      int fleet_observed_lengthcomp_data_id_m
      Definition: fleet.hpp:47
      -
      fims_popdy::Fleet::expected_catch
      fims::Vector< Type > expected_catch
      Definition: fleet.hpp:71
      -
      fims_popdy::Fleet::fleet_selectivity_id_m
      int fleet_selectivity_id_m
      Definition: fleet.hpp:32
      -
      fims_popdy::Fleet::observed_agecomp_data
      std::shared_ptr< fims_data_object::DataObject< Type > > observed_agecomp_data
      Definition: fleet.hpp:44
      -
      fims_popdy::Fleet::catch_weight_at_age
      fims::Vector< Type > catch_weight_at_age
      Definition: fleet.hpp:82
      -
      fims_popdy::Fleet::catch_index
      fims::Vector< Type > catch_index
      Definition: fleet.hpp:61
      -
      fims_popdy::Fleet::fleet_observed_agecomp_data_id_m
      int fleet_observed_agecomp_data_id_m
      Definition: fleet.hpp:42
      -
      fims_popdy::Fleet::observed_index_data
      std::shared_ptr< fims_data_object::DataObject< Type > > observed_index_data
      Definition: fleet.hpp:39
      -
      fims_popdy::Fleet::observed_catch_lpdf
      fims::Vector< Type > observed_catch_lpdf
      Definition: fleet.hpp:67
      -
      fims_popdy::Fleet::evaluate_age_comp
      void evaluate_age_comp()
      Definition: fleet.hpp:182
      -
      fims_popdy::Fleet::expected_catch_lpdf
      fims::Vector< Type > expected_catch_lpdf
      Definition: fleet.hpp:74
      -
      fims_popdy::Fleet::Fmort
      fims::Vector< Type > Fmort
      Definition: fleet.hpp:56
      -
      fims_popdy::Fleet::evaluate_index
      void evaluate_index()
      Definition: fleet.hpp:227
      -
      fims_popdy::Fleet::log_expected_index
      fims::Vector< Type > log_expected_index
      Definition: fleet.hpp:73
      -
      fims_popdy::Fleet::observed_index_lpdf
      fims::Vector< Type > observed_index_lpdf
      Definition: fleet.hpp:69
      -
      fims_popdy::Fleet::Prepare
      void Prepare()
      Prepare to run the fleet module. Called at each model iteration, and used to exponentiate the log q a...
      Definition: fleet.hpp:140
      -
      fims_popdy::Fleet::age_composition
      fims::Vector< Type > age_composition
      Definition: fleet.hpp:62
      -
      fims_popdy::Fleet::catch_numbers_at_length
      fims::Vector< Type > catch_numbers_at_length
      Definition: fleet.hpp:79
      -
      fims_popdy::Fleet::~Fleet
      virtual ~Fleet()
      Destructor.
      Definition: fleet.hpp:99
      -
      fims_popdy::Fleet::q
      fims::Vector< Type > q
      Definition: fleet.hpp:57
      +
      fims::Vector
      Definition: fims_vector.hpp:18
      +
      fims::Vector::resize
      void resize(size_t s)
      Changes the number of elements stored.
      Definition: fims_vector.hpp:310
      +
      fims::Vector::size
      size_type size() const
      Returns the number of elements.
      Definition: fims_vector.hpp:208
      +
      ERROR_LOG
      std::ofstream ERROR_LOG("logs/error.log")
      +
      FLEET_LOG
      std::ofstream FLEET_LOG("logs/fleet.log")
      +
      fims_model_object::FIMSObject
      FIMSObject struct that defines member types and returns the unique id.
      Definition: model_object.hpp:25
      +
      fims_popdy::Fleet
      Base class for all fleets.
      Definition: fleet.hpp:26
      +
      fims_popdy::Fleet::is_survey
      bool is_survey
      Definition: fleet.hpp:80
      +
      fims_popdy::Fleet::Fleet
      Fleet()
      Constructor.
      Definition: fleet.hpp:89
      +
      fims_popdy::Fleet::selectivity
      std::shared_ptr< SelectivityBase< Type > > selectivity
      Definition: fleet.hpp:50
      +
      fims_popdy::Fleet::id_g
      static uint32_t id_g
      Definition: fleet.hpp:27
      +
      fims_popdy::Fleet::nages
      size_t nages
      Definition: fleet.hpp:29
      +
      fims_popdy::Fleet::catch_at_age
      fims::Vector< Type > catch_at_age
      Definition: fleet.hpp:71
      +
      fims_popdy::Fleet::expected_catch
      fims::Vector< Type > expected_catch
      Definition: fleet.hpp:76
      +
      fims_popdy::Fleet::evaluate_index_nll
      virtual const Type evaluate_index_nll()
      Definition: fleet.hpp:207
      +
      fims_popdy::Fleet::fleet_selectivity_id_m
      int fleet_selectivity_id_m
      Definition: fleet.hpp:48
      +
      fims_popdy::Fleet::q
      Type q
      Definition: fleet.hpp:68
      +
      fims_popdy::Fleet::observed_agecomp_data
      std::shared_ptr< fims_data_object::DataObject< Type > > observed_agecomp_data
      Definition: fleet.hpp:58
      +
      fims_popdy::Fleet::catch_weight_at_age
      fims::Vector< Type > catch_weight_at_age
      Definition: fleet.hpp:79
      +
      fims_popdy::Fleet::catch_index
      fims::Vector< Type > catch_index
      Definition: fleet.hpp:72
      +
      fims_popdy::Fleet::log_q
      Type log_q
      Definition: fleet.hpp:63
      +
      fims_popdy::Fleet::fleet_observed_agecomp_data_id_m
      int fleet_observed_agecomp_data_id_m
      Definition: fleet.hpp:56
      +
      fims_popdy::Fleet::observed_index_data
      std::shared_ptr< fims_data_object::DataObject< Type > > observed_index_data
      Definition: fleet.hpp:54
      +
      fims_popdy::Fleet::index_likelihood
      std::shared_ptr< fims_distributions::DistributionsBase< Type > > index_likelihood
      Definition: fleet.hpp:38
      +
      fims_popdy::Fleet::Fmort
      fims::Vector< Type > Fmort
      Definition: fleet.hpp:67
      +
      fims_popdy::Fleet::evaluate_age_comp_nll
      virtual const Type evaluate_age_comp_nll()
      Definition: fleet.hpp:151
      +
      fims_popdy::Fleet::fleet_index_likelihood_id_m
      int fleet_index_likelihood_id_m
      Definition: fleet.hpp:33
      +
      fims_popdy::Fleet::Prepare
      void Prepare()
      Prepare to run the fleet module. Called at each model itartion, and used to exponentiate the log q an...
      Definition: fleet.hpp:123
      +
      fims_popdy::Fleet::age_composition
      fims::Vector< Type > age_composition
      Definition: fleet.hpp:73
      +
      fims_popdy::Fleet::~Fleet
      virtual ~Fleet()
      Destructor.
      Definition: fleet.hpp:94
      +
      fims_popdy::Fleet::Initialize
      void Initialize(int nyears, int nages)
      Intialize Fleet Class.
      Definition: fleet.hpp:101
      +
      fims_popdy::Fleet::agecomp_likelihood
      std::shared_ptr< fims_distributions::DistributionsBase< Type > > agecomp_likelihood
      Definition: fleet.hpp:45
      fims_popdy::Fleet::catch_numbers_at_age
      fims::Vector< Type > catch_numbers_at_age
      Definition: fleet.hpp:78
      -
      fims_popdy::Fleet::observed_lengthcomp_data
      std::shared_ptr< fims_data_object::DataObject< Type > > observed_lengthcomp_data
      Definition: fleet.hpp:49
      -
      fims_popdy::Fleet::expected_index
      fims::Vector< Type > expected_index
      Definition: fleet.hpp:72
      -
      fims_popdy::Fleet::expected_index_lpdf
      fims::Vector< Type > expected_index_lpdf
      Definition: fleet.hpp:76
      -
      fims_popdy::Fleet::nyears
      size_t nyears
      Definition: fleet.hpp:27
      -
      fims_popdy::Fleet::fleet_observed_index_data_id_m
      int fleet_observed_index_data_id_m
      Definition: fleet.hpp:37
      -
      fims_popdy::Fleet::Initialize
      void Initialize(int nyears, int nages, int nlengths=0)
      Intialize Fleet Class.
      Definition: fleet.hpp:108
      -
      fims_popdy::Fleet::proportion_catch_numbers_at_length
      fims::Vector< Type > proportion_catch_numbers_at_length
      Definition: fleet.hpp:81
      -
      fims_popdy::Fleet::log_Fmort
      fims::Vector< Type > log_Fmort
      Definition: fleet.hpp:53
      -
      fims_popdy::Fleet::evaluate_length_comp
      void evaluate_length_comp()
      Definition: fleet.hpp:200
      -
      fims_popdy::Fleet::length_composition
      fims::Vector< Type > length_composition
      Definition: fleet.hpp:63
      -
      fims_popdy::Fleet::proportion_catch_numbers_at_age
      fims::Vector< Type > proportion_catch_numbers_at_age
      Definition: fleet.hpp:80
      +
      fims_popdy::Fleet::log_obs_error
      fims::Vector< Type > log_obs_error
      Definition: fleet.hpp:65
      +
      fims_popdy::Fleet::expected_index
      fims::Vector< Type > expected_index
      Definition: fleet.hpp:77
      +
      fims_popdy::Fleet::nyears
      size_t nyears
      Definition: fleet.hpp:28
      +
      fims_popdy::Fleet::fleet_observed_index_data_id_m
      int fleet_observed_index_data_id_m
      Definition: fleet.hpp:52
      +
      fims_popdy::Fleet::log_Fmort
      fims::Vector< Type > log_Fmort
      Definition: fleet.hpp:62
      +
      fims_popdy::Fleet::fleet_agecomp_likelihood_id_m
      int fleet_agecomp_likelihood_id_m
      Definition: fleet.hpp:42
      diff --git a/docs/functions.html b/docs/functions.html index 82dde4e..a83477c 100644 --- a/docs/functions.html +++ b/docs/functions.html @@ -81,9 +81,8 @@

      - a -

      diff --git a/docs/functions_c.html b/docs/functions_c.html index 37f320c..e64d2d4 100644 --- a/docs/functions_c.html +++ b/docs/functions_c.html @@ -128,18 +128,11 @@

      - c -

      • catch_numbers_at_age : fims_popdy::Fleet< Type >
        • -
      • catch_numbers_at_length -: fims_popdy::Fleet< Type > -
      • catch_weight_at_age : fims_popdy::Fleet< Type >
        • -
      • CheckDimensions() -: fims_model_object::FIMSObject< Type > -
      • clear() -: fims::FIMSLog -, fims::Vector< Type > +: fims::Vector< Type >
      • const_iterator : fims::Vector< Type > diff --git a/docs/functions_d.html b/docs/functions_d.html index 67c690e..185cc73 100644 --- a/docs/functions_d.html +++ b/docs/functions_d.html @@ -73,7 +73,7 @@

        - d -

        • data() : fims::Vector< Type > -, fims_data_object::DataObject< Type > +, fims_data_object::DataObject< Type >
        • data_iterator : fims_info::Information< Type > @@ -87,57 +87,20 @@

          - d -

          diff --git a/docs/functions_e.html b/docs/functions_e.html index cea7366..47eb386 100644 --- a/docs/functions_e.html +++ b/docs/functions_e.html @@ -86,8 +86,11 @@

          - e -

          • erase() : fims::Vector< Type >
            • -
          • error_message() -: fims::FIMSLog +
          • estimate_F +: FleetInterface +
            • +
          • estimate_initNAA +: PopulationInterface
          • estimate_log_devs : BevertonHoltRecruitmentInterface @@ -95,55 +98,40 @@

            - e -

            • estimate_log_recruit_devs : fims_popdy::RecruitmentBase< Type >
              • +
            • estimate_M +: PopulationInterface +
              • +
            • estimate_obs_error +: FleetInterface +
            • estimate_prop_female : PopulationInterface
            • estimate_q : FleetInterface
              • -
            • estimated_log_devs -: BevertonHoltRecruitmentInterface -
              • -
            • estimated_log_init_naa -: PopulationInterface -
              • -
            • estimated_log_M -: PopulationInterface -
              • -
            • estimated_log_rzero -: BevertonHoltRecruitmentInterface -
              • -
            • estimated_logit_steep -: BevertonHoltRecruitmentInterface -
            • estimated_m : Parameter
              • -
            • estimated_proportion_female -: PopulationInterface -
            • evaluate() : BevertonHoltRecruitmentInterface -, DistributionsInterfaceBase -, DlnormDistributionsInterface -, DmultinomDistributionsInterface -, DnormDistributionsInterface +, DistributionsInterfaceBase +, DlnormDistributionsInterface +, DmultinomDistributionsInterface +, DnormDistributionsInterface , DoubleLogisticSelectivityInterface , EWAAGrowthInterface -, fims_distributions::DensityComponentBase< Type > -, fims_distributions::LogNormalLPDF< Type > -, fims_distributions::MultinomialLPMF< Type > -, fims_distributions::NormalLPDF< Type > +, fims_distributions::DistributionsBase< Type >
            • Evaluate() : fims_model::Model< Type >
            • evaluate() -: fims_popdy::DoubleLogisticSelectivity< Type > +: fims_popdy::DoubleLogisticSelectivity< Type > , fims_popdy::EWAAgrowth< Type > , fims_popdy::GrowthBase< Type > -, fims_popdy::LogisticMaturity< Type > -, fims_popdy::LogisticSelectivity< Type > +, fims_popdy::LogisticMaturity< Type > +, fims_popdy::LogisticSelectivity< Type > , fims_popdy::MaturityBase< Type >
            • Evaluate() @@ -161,17 +149,17 @@

              - e -

                , RecruitmentInterfaceBase , SelectivityInterfaceBase -
              • evaluate_age_comp() -: fims_popdy::Fleet< Type > -
                • -
              • evaluate_index() -: fims_popdy::Fleet< Type > +
              • evaluate_age_comp_nll() +: fims_popdy::Fleet< Type >
                • -
              • evaluate_length_comp() -: fims_popdy::Fleet< Type > +
              • evaluate_index_nll() +: fims_popdy::Fleet< Type >
                • -
              • evaluate_lpdf() -: LPDFInterfaceBase +
              • evaluate_nll() +: BevertonHoltRecruitmentInterface +, fims_popdy::RecruitmentBase< Type > +, NLLInterfaceBase +, RecruitmentInterfaceBase
              • ewaa : EWAAGrowthInterface @@ -181,27 +169,15 @@

                - e -

                diff --git a/docs/functions_f.html b/docs/functions_f.html index 7fe9a42..19ed38b 100644 --- a/docs/functions_f.html +++ b/docs/functions_f.html @@ -71,18 +71,6 @@
                Here is a list of all documented class members with links to the class documentation for each member:

                - f -

                  -
                • file -: fims::LogEntry -
                  • -
                • fill() -: ParameterVector -
                  • -
                • fill_max() -: ParameterVector -
                  • -
                • fill_min() -: ParameterVector -
                • fims_information : fims_info::Information< Type > , fims_model::Model< Type > @@ -90,32 +78,12 @@

                  - f -

                  • fims_interface_objects : FIMSRcppInterfaceBase
                    • -
                  • fims_log -: fims::FIMSLog +
                  • FIMS_LOGS +: fims::fims_log
                  • fims_model : fims_model::Model< Type >
                    • -
                  • FIMSLog() -: fims::FIMSLog -
                    • -
                  • final_value_m -: Parameter -
                    • -
                  • finalize() -: BevertonHoltRecruitmentInterface -, DlnormDistributionsInterface -, DnormDistributionsInterface -, DoubleLogisticSelectivityInterface -, FIMSRcppInterfaceBase -, FleetInterface -, LogisticMaturityInterface -, LogisticSelectivityInterface -, PopulationInterface -
                    • -
                  • finalized -: FIMSRcppInterfaceBase -
                  • fixed_effects_parameters : fims_info::Information< Type > , fims_model_object::FIMSObject< Type > @@ -123,9 +91,15 @@

                    - f -

                    • Fleet() : fims_popdy::Fleet< Type >
                      • +
                    • fleet_agecomp_likelihood_id_m +: fims_popdy::Fleet< Type > +
                    • fleet_id : fims_popdy::Population< Type >
                      • +
                    • fleet_index_likelihood_id_m +: fims_popdy::Fleet< Type > +
                    • fleet_iterator : fims_info::Information< Type >
                      • @@ -135,9 +109,6 @@

                      - f -

                      • fleet_observed_index_data_id_m : fims_popdy::Fleet< Type >
                        • -
                      • fleet_observed_lengthcomp_data_id_m -: fims_popdy::Fleet< Type > -
                      • fleet_selectivity_id_m : fims_popdy::Fleet< Type >
                        • diff --git a/docs/functions_func.html b/docs/functions_func.html index 0d047a6..bbf3d7b 100644 --- a/docs/functions_func.html +++ b/docs/functions_func.html @@ -81,7 +81,439 @@

                        - a -

                        + + +

                        - b -

                        + + +

                        - c -

                        + + +

                        - d -

                        + + +

                        - e -

                        + + +

                        - f -

                        + + +

                        - g -

                        + + +

                        - i -

                        + + +

                        - j -

                        + + +

                        - m -

                        + + +

                        - o -

                        + + +

                        - p -

                        + + +

                        - r -

                        + + +

                        - s -

                        + + +

                        - v -

                        + + +

                        - w -

                        + + +

                        - ~ -

                        diff --git a/docs/functions_g.html b/docs/functions_g.html index d49c479..cbad940 100644 --- a/docs/functions_g.html +++ b/docs/functions_g.html @@ -72,20 +72,11 @@

                        - g -

                        • get() -: ParameterVector +: fims::fims_log
                        • get_dimensions() : fims_data_object::DataObject< Type >
                          • -
                        • get_error_count() -: fims::FIMSLog -
                          • -
                        • get_errors() -: fims::FIMSLog -
                          • -
                        • get_force_scalar() -: fims::Vector< Type > -
                        • get_id() : AgeCompDataInterface , BevertonHoltRecruitmentInterface @@ -100,12 +91,10 @@

                          - g -

                            , FleetInterfaceBase , GrowthInterfaceBase , IndexDataInterface -, LengthCompDataInterface , LogisticMaturityInterface , LogisticSelectivityInterface -, LPDFInterfaceBase , MaturityInterfaceBase -, ParameterVector +, NLLInterfaceBase , PopulationInterface , PopulationInterfaceBase , RecruitmentInterfaceBase @@ -114,9 +103,6 @@

                            - g -

                            • get_imax() : fims_data_object::DataObject< Type >
                              • -
                            • get_info() -: fims::FIMSLog -
                            • get_jmax() : fims_data_object::DataObject< Type >
                              • @@ -126,32 +112,14 @@

                              - g -

                              • get_lmax() : fims_data_object::DataObject< Type >
                                • -
                              • get_log() -: fims::FIMSLog -
                                • -
                              • get_module() -: fims::FIMSLog -
                                • -
                              • get_path() -: fims::FIMSLog -
                                • -
                              • get_warning_count() -: fims::FIMSLog -
                                • -
                              • get_warnings() -: fims::FIMSLog -
                                • -
                              • getAbsolutePathWithoutDotDot() -: fims::FIMSLog -
                              • GetArray() -: fims::JsonValue +: JsonValue
                              • GetBool() -: fims::JsonValue +: JsonValue
                              • GetDouble() -: fims::JsonValue +: JsonValue
                              • GetFixedEffectsParameters() : fims_info::Information< Type > @@ -164,7 +132,7 @@

                                - g -

                                  , fims_model::Model< Type >
                                • GetInt() -: fims::JsonValue +: JsonValue
                                • GetNages() : fims_info::Information< Type > @@ -176,16 +144,7 @@

                                  - g -

                                    : fims_info::Information< Type >
                                  • GetObject() -: fims::JsonValue -
                                    • -
                                  • GetObservedAgeCompDataID() -: FleetInterface -
                                    • -
                                  • GetObservedIndexDataID() -: FleetInterface -
                                    • -
                                  • GetObservedLengthCompDataID() -: FleetInterface +: JsonValue
                                  • GetParameters() : fims_info::Information< Type > @@ -194,10 +153,10 @@

                                    - g -

                                      : fims_info::Information< Type >
                                    • GetString() -: fims::JsonValue +: JsonValue
                                    • GetType() -: fims::JsonValue +: JsonValue
                                    • growth : fims_popdy::Population< Type > diff --git a/docs/functions_i.html b/docs/functions_i.html index 26122b0..e5ecf1d 100644 --- a/docs/functions_i.html +++ b/docs/functions_i.html @@ -73,11 +73,12 @@

                                      - i -

                                      • id : DataInterfaceBase +, DistributionsInterfaceBase , fims_model_object::FIMSObject< Type > , FleetInterfaceBase , GrowthInterfaceBase -, LPDFInterfaceBase , MaturityInterfaceBase +, NLLInterfaceBase , PopulationInterfaceBase , RecruitmentInterfaceBase , SelectivityInterfaceBase @@ -86,7 +87,7 @@

                                        - i -

                                          : DataInterfaceBase , DistributionsInterfaceBase , fims_data_object::DataObject< Type > -, fims_distributions::DensityComponentBase< Type > +, fims_distributions::DistributionsBase< Type > , fims_popdy::Fleet< Type > , fims_popdy::GrowthBase< Type > , fims_popdy::MaturityBase< Type > @@ -95,67 +96,48 @@

                                          - i -

                                            , fims_popdy::SelectivityBase< Type > , FleetInterfaceBase , GrowthInterfaceBase -, LPDFInterfaceBase , MaturityInterfaceBase -, Parameter -, ParameterVector +, NLLInterfaceBase , PopulationInterfaceBase , RecruitmentInterfaceBase , SelectivityInterfaceBase -
                                          • id_m -: DistributionsInterfaceBase -, Parameter -, ParameterVector -
                                          • imax : fims_data_object::DataObject< Type >
                                          • index_data : IndexDataInterface
                                            • +
                                          • index_likelihood +: fims_popdy::Fleet< Type > +
                                          • IndexDataInterface() : IndexDataInterface
                                          • inflection_point -: fims_popdy::LogisticMaturity< Type > -, fims_popdy::LogisticSelectivity< Type > -, LogisticMaturityInterface -, LogisticSelectivityInterface +: fims_popdy::LogisticMaturity< Type > +, fims_popdy::LogisticSelectivity< Type > +, LogisticMaturityInterface +, LogisticSelectivityInterface
                                          • inflection_point_asc -: DoubleLogisticSelectivityInterface -, fims_popdy::DoubleLogisticSelectivity< Type > +: DoubleLogisticSelectivityInterface +, fims_popdy::DoubleLogisticSelectivity< Type >
                                          • inflection_point_desc -: DoubleLogisticSelectivityInterface -, fims_popdy::DoubleLogisticSelectivity< Type > -
                                            • -
                                          • info_message() -: fims::FIMSLog -
                                            • -
                                          • initial_value_m -: Parameter +: DoubleLogisticSelectivityInterface +, fims_popdy::DoubleLogisticSelectivity< Type >
                                          • Initialize() -: fims_popdy::Fleet< Type > +: fims_popdy::Fleet< Type > , fims_popdy::Population< Type >
                                          • initialized : EWAAGrowthInterface
                                            • -
                                          • input_type -: fims_distributions::DensityComponentBase< Type > -
                                            • -
                                          • input_type_m -: DistributionsInterfaceBase -
                                          • insert() : fims::Vector< Type >
                                            • -
                                          • interface_observed_data_id_m -: DistributionsInterfaceBase -
                                          • is_random_effect_m : Parameter
                                            • diff --git a/docs/functions_j.html b/docs/functions_j.html index 3f2b2ce..42203a4 100644 --- a/docs/functions_j.html +++ b/docs/functions_j.html @@ -75,7 +75,7 @@

                                            - j -

                                            diff --git a/docs/functions_k.html b/docs/functions_k.html index 16ba48c..8e2d877 100644 --- a/docs/functions_k.html +++ b/docs/functions_k.html @@ -71,12 +71,6 @@
                                            Here is a list of all documented class members with links to the class documentation for each member:

                                            - k -

                                              -
                                            • key -: fims_distributions::DensityComponentBase< Type > -
                                              • -
                                            • key_m -: DistributionsInterfaceBase -
                                            • kmax : fims_data_object::DataObject< Type >
                                              • diff --git a/docs/functions_l.html b/docs/functions_l.html index a23a28d..9b41984 100644 --- a/docs/functions_l.html +++ b/docs/functions_l.html @@ -71,89 +71,57 @@
                                              Here is a list of all documented class members with links to the class documentation for each member:

                                              - l -

                                              diff --git a/docs/functions_m.html b/docs/functions_m.html index 6639161..76df43e 100644 --- a/docs/functions_m.html +++ b/docs/functions_m.html @@ -99,8 +99,11 @@

                                              - m -

                                              • max_size() : fims::Vector< Type >
                                                • -
                                              • message -: fims::LogEntry +
                                              • mean +: DnormDistributionsInterface +
                                                • +
                                              • meanlog +: DlnormDistributionsInterface
                                              • min_m : Parameter @@ -111,9 +114,6 @@

                                                - m -

                                                diff --git a/docs/functions_n.html b/docs/functions_n.html index 70fd4cc..d4b831d 100644 --- a/docs/functions_n.html +++ b/docs/functions_n.html @@ -81,22 +81,10 @@

                                                - n -

                                                  , FleetInterface , PopulationInterface -
                                                • name -: FleetInterface -, PopulationInterface -
                                                • nfleets : fims_popdy::Population< Type > , PopulationInterface
                                                  • -
                                                • nlengths -: fims_popdy::Fleet< Type > -, FleetInterface -, PopulationInterface -
                                                  • -
                                                • NormalLPDF() -: fims_distributions::NormalLPDF< Type > -
                                                • nseasons : fims_info::Information< Type > , fims_popdy::Population< Type > @@ -104,7 +92,6 @@

                                                  - n -

                                                  • numbers_at_age : fims_popdy::Population< Type > -, PopulationInterface
                                                  • nyears : fims_info::Information< Type > diff --git a/docs/functions_o.html b/docs/functions_o.html index 4f0bbc2..4c4d1bf 100644 --- a/docs/functions_o.html +++ b/docs/functions_o.html @@ -74,45 +74,23 @@

                                                    - o -

                                                    diff --git a/docs/functions_p.html b/docs/functions_p.html index 4daec7a..a0dac2a 100644 --- a/docs/functions_p.html +++ b/docs/functions_p.html @@ -71,21 +71,18 @@
                                                    Here is a list of all documented class members with links to the class documentation for each member:

                                                    - p -

                                                      -
                                                    • Parameter() -: Parameter +
                                                    • p +: DmultinomDistributionsInterface
                                                      • -
                                                    • parameter_names -: fims_info::Information< Type > +
                                                    • Parameter() +: Parameter
                                                    • parameters : fims_info::Information< Type > , fims_model_object::FIMSObject< Type >
                                                      • -
                                                    • ParameterVector() -: ParameterVector -
                                                    • Parse() -: fims::JsonParser +: JsonParser
                                                    • pointer : fims::Vector< Type > @@ -107,17 +104,6 @@

                                                      - p -

                                                      • PrepareConstrainedDeviations() : fims_popdy::RecruitmentBase< Type >
                                                        • -
                                                      • PrettyFormatJSON() -: fims::JsonParser -
                                                        • -
                                                      • proportion_catch_numbers_at_age -: fims_popdy::Fleet< Type > -, FleetInterface -
                                                        • -
                                                      • proportion_catch_numbers_at_length -: fims_popdy::Fleet< Type > -, FleetInterface -
                                                      • proportion_female : fims_popdy::Population< Type > , PopulationInterface diff --git a/docs/functions_q.html b/docs/functions_q.html index 6344c4c..516e8d2 100644 --- a/docs/functions_q.html +++ b/docs/functions_q.html @@ -72,7 +72,7 @@

                                                        - q -

                                                        diff --git a/docs/functions_r.html b/docs/functions_r.html index 5822a2b..f74cf21 100644 --- a/docs/functions_r.html +++ b/docs/functions_r.html @@ -75,15 +75,12 @@

                                                        - r -

                                                          : fims_info::Information< Type > , fims_model_object::FIMSObject< Type > -
                                                        • random_m -: Parameter +
                                                        • random_F +: FleetInterface
                                                        • random_q : FleetInterface
                                                          • -
                                                        • rank -: fims::LogEntry -
                                                        • rbegin() : fims::Vector< Type >
                                                          • @@ -109,15 +106,9 @@

                                                          - r -

                                                          • RegisterParameter() : fims_info::Information< Type >
                                                            • -
                                                          • RegisterParameterName() -: fims_info::Information< Type > -
                                                          • RegisterRandomEffect() : fims_info::Information< Type >
                                                            • -
                                                          • removeWhitespace() -: fims::JsonParser -
                                                          • rend() : fims::Vector< Type >
                                                            • @@ -126,14 +117,10 @@

                                                            - r -

                                                            diff --git a/docs/functions_s.html b/docs/functions_s.html index 85477ed..8abf3b2 100644 --- a/docs/functions_s.html +++ b/docs/functions_s.html @@ -71,6 +71,12 @@
                                                            Here is a list of all documented class members with links to the class documentation for each member:

                                                            - s -

                                                              +
                                                            • sd +: DnormDistributionsInterface +
                                                              • +
                                                            • sdlog +: DlnormDistributionsInterface +
                                                            • selectivity : fims_popdy::Fleet< Type >
                                                              • @@ -83,33 +89,15 @@

                                                              - s -

                                                              • SelectivityBase() : fims_popdy::SelectivityBase< Type >
                                                                • -
                                                              • set() -: ParameterVector -
                                                                • -
                                                              • set_all_estimable() -: ParameterVector -
                                                                • -
                                                              • set_all_random() -: ParameterVector -
                                                                • -
                                                              • set_distribution_links() -: DistributionsInterfaceBase -, DlnormDistributionsInterface -, DmultinomDistributionsInterface -, DnormDistributionsInterface -
                                                                • -
                                                              • set_observed_data() -: DistributionsInterfaceBase -, DlnormDistributionsInterface -, DmultinomDistributionsInterface -, DnormDistributionsInterface -
                                                                • -
                                                              • set_path() -: fims::FIMSLog +
                                                              • SetAgeCompLikelihood() +: FleetInterface
                                                              • SetGrowth() : PopulationInterface
                                                                • +
                                                              • SetIndexLikelihood() +: FleetInterface +
                                                              • SetMaturity() : PopulationInterface
                                                                • @@ -128,63 +116,41 @@

                                                                - s -

                                                                diff --git a/docs/functions_u.html b/docs/functions_u.html index a3bfe6b..af045ce 100644 --- a/docs/functions_u.html +++ b/docs/functions_u.html @@ -80,9 +80,6 @@

                                                                - u -

                                                                diff --git a/docs/functions_v.html b/docs/functions_v.html index 6da31aa..e61de81 100644 --- a/docs/functions_v.html +++ b/docs/functions_v.html @@ -71,15 +71,12 @@
                                                                Here is a list of all documented class members with links to the class documentation for each member:

                                                                - v -

                                                                  +
                                                                • value_m +: Parameter +
                                                                • value_type : fims::Vector< Type >
                                                                  • -
                                                                • variable_map -: fims_info::Information< Type > -
                                                                  • -
                                                                • variable_map_iterator -: fims_info::Information< Type > -
                                                                • Vector() : fims::Vector< Type >
                                                                  • diff --git a/docs/functions_vars.html b/docs/functions_vars.html index d006066..365dcd9 100644 --- a/docs/functions_vars.html +++ b/docs/functions_vars.html @@ -77,9 +77,8 @@

                                                                  - a -

                                                                  • age_composition : fims_popdy::Fleet< Type >
                                                                    • -
                                                                  • age_length_conversion_matrix -: fims_popdy::Fleet< Type > -, FleetInterface +
                                                                  • agecomp_likelihood +: fims_popdy::Fleet< Type >
                                                                  • ages : EWAAGrowthInterface @@ -90,6 +89,510 @@

                                                                    - a -

                                                                    + + +

                                                                    - b -

                                                                    + + +

                                                                    - c -

                                                                    + + +

                                                                    - d -

                                                                    + + +

                                                                    - e -

                                                                    + + +

                                                                    - f -

                                                                    + + +

                                                                    - g -

                                                                    + + +

                                                                    - i -

                                                                    + + +

                                                                    - j -

                                                                    + + +

                                                                    - k -

                                                                    + + +

                                                                    - l -

                                                                    + + +

                                                                    - m -

                                                                    + + +

                                                                    - n -

                                                                    + + +

                                                                    - o -

                                                                    + + +

                                                                    - p -

                                                                    + + +

                                                                    - q -

                                                                    + + +

                                                                    - r -

                                                                    + + +

                                                                    - s -

                                                                    + + +

                                                                    - u -

                                                                    + + +

                                                                    - v -

                                                                    + + +

                                                                    - w -

                                                                    + + +

                                                                    - x -

                                                                    + + +

                                                                    - y -

                                                                    diff --git a/docs/functions_w.html b/docs/functions_w.html index b28c443..cfc45b8 100644 --- a/docs/functions_w.html +++ b/docs/functions_w.html @@ -71,26 +71,14 @@
                                                                    Here is a list of all documented class members with links to the class documentation for each member:

                                                                    - w -

                                                                    diff --git a/docs/functions_x.html b/docs/functions_x.html index fee9a10..ba40fc3 100644 --- a/docs/functions_x.html +++ b/docs/functions_x.html @@ -72,10 +72,9 @@

                                                                    - x -

                                                                    diff --git a/docs/functions_y.html b/docs/functions_y.html index 0abcce0..77b4e74 100644 --- a/docs/functions_y.html +++ b/docs/functions_y.html @@ -77,7 +77,6 @@

                                                                    - y -

                                                                    diff --git a/docs/functions_~.html b/docs/functions_~.html index 9ce96bf..3be2f99 100644 --- a/docs/functions_~.html +++ b/docs/functions_~.html @@ -77,27 +77,12 @@

                                                                    - ~ -

                                                                    diff --git a/docs/globals.html b/docs/globals.html index 05d4dd9..fa67e3f 100644 --- a/docs/globals.html +++ b/docs/globals.html @@ -68,201 +68,69 @@
                                                                    -
                                                                    Here is a list of all documented file members with links to the documentation:
                                                                    - -

                                                                    - _ -

                                                                      -
                                                                    • _rcpp_module_boot_fims() -: init.hpp -
                                                                      • -
                                                                    - - -

                                                                    - a -

                                                                    - - -

                                                                    - c -

                                                                    - - -

                                                                    - e -

                                                                    - - -

                                                                    - f -

                                                                    diff --git a/docs/globals_func.html b/docs/globals_func.html index 4cd4f9d..6063e3b 100644 --- a/docs/globals_func.html +++ b/docs/globals_func.html @@ -68,142 +68,42 @@
                                                                    -  - -

                                                                    - _ -

                                                                      -
                                                                    • _rcpp_module_boot_fims() -: init.hpp -
                                                                      • -
                                                                    - - -

                                                                    - c -

                                                                    - - -

                                                                    - e -

                                                                    - - -

                                                                    - f -

                                                                    - - -

                                                                    - g -

                                                                    diff --git a/docs/growth_8hpp_source.html b/docs/growth_8hpp_source.html index 0c5f517..a52014c 100644 --- a/docs/growth_8hpp_source.html +++ b/docs/growth_8hpp_source.html @@ -76,16 +76,26 @@
                                                                    growth.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    11 #ifndef FIMS_POPULATION_DYNAMICS_GROWTH_HPP
                                                                    -
                                                                    12 #define FIMS_POPULATION_DYNAMICS_GROWTH_HPP
                                                                    -
                                                                    13 
                                                                    -
                                                                    14 #include "functors/ewaa.hpp"
                                                                    -
                                                                    15 #include "functors/growth_base.hpp"
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  *
                                                                    +
                                                                    3  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    4  * Fisheries Integrated Modeling System project. See LICENSE in the
                                                                    +
                                                                    5  * source folder for reuse information.
                                                                    +
                                                                    6  *
                                                                    +
                                                                    7  * Growth module file
                                                                    +
                                                                    8  * The purpose of this file is to include any .hpp files within the
                                                                    +
                                                                    9  * subfolders so that only this file needs to included in the model.hpp file.
                                                                    +
                                                                    10  *
                                                                    +
                                                                    11  * DEFINE guards for growth module outline to define the
                                                                    +
                                                                    12  * growth hpp file if not already defined.
                                                                    +
                                                                    13  */
                                                                    +
                                                                    14 #ifndef FIMS_POPULATION_DYNAMICS_GROWTH_HPP
                                                                    +
                                                                    15 #define FIMS_POPULATION_DYNAMICS_GROWTH_HPP
                                                                    16 
                                                                    -
                                                                    17 #endif /* FIMS_POPULATION_DYNAMICS_GROWTH_HPP */
                                                                    -
                                                                    ewaa.hpp
                                                                    Declares the growth functor class which is the base class for all growth functors.
                                                                    -
                                                                    growth_base.hpp
                                                                    Includes any .hpp files within the subfolders so that only this file needs to included in the model....
                                                                    +
                                                                    17 #include "functors/ewaa.hpp"
                                                                    +
                                                                    18 #include "functors/growth_base.hpp"
                                                                    +
                                                                    19 
                                                                    +
                                                                    20 #endif /* FIMS_POPULATION_DYNAMICS_GROWTH_HPP */
                                                                    diff --git a/docs/growth__base_8hpp_source.html b/docs/growth__base_8hpp_source.html index ae00e05..bb67265 100644 --- a/docs/growth__base_8hpp_source.html +++ b/docs/growth__base_8hpp_source.html @@ -76,38 +76,50 @@
                                                                    growth_base.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    11 #ifndef POPULATION_DYNAMICS_GROWTH_BASE_HPP
                                                                    -
                                                                    12 #define POPULATION_DYNAMICS_GROWTH_BASE_HPP
                                                                    -
                                                                    13 
                                                                    -
                                                                    14 #include "../../../common/model_object.hpp"
                                                                    -
                                                                    15 
                                                                    -
                                                                    16 namespace fims_popdy {
                                                                    -
                                                                    17 
                                                                    -
                                                                    23 template <typename Type>
                                                                    -
                                                                    24 struct GrowthBase : public fims_model_object::FIMSObject<Type> {
                                                                    -
                                                                    25  // id_g is the ID of the instance of the growthBase class.
                                                                    -
                                                                    26  // this is like a memory tracker.
                                                                    -
                                                                    27  // Assigning each one its own ID is a way to keep track of
                                                                    -
                                                                    28  // all the instances of the growthBase class.
                                                                    -
                                                                    29  static uint32_t id_g;
                                                                    -
                                                                    34  GrowthBase() { this->id = GrowthBase::id_g++; }
                                                                    -
                                                                    35 
                                                                    -
                                                                    36  virtual ~GrowthBase() {}
                                                                    -
                                                                    37 
                                                                    -
                                                                    42  virtual const Type evaluate(const double& a) = 0;
                                                                    -
                                                                    43 };
                                                                    -
                                                                    44 
                                                                    -
                                                                    45 template <typename Type>
                                                                    -
                                                                    46 uint32_t GrowthBase<Type>::id_g = 0;
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    3  * Fisheries Integrated Modeling System project. See LICENSE in the
                                                                    +
                                                                    4  * source folder for reuse information.
                                                                    +
                                                                    5  *
                                                                    +
                                                                    6  *
                                                                    +
                                                                    7  * growth module_base file
                                                                    +
                                                                    8  * The purpose of this file is to include any .hpp files within the
                                                                    +
                                                                    9  * subfolders so that only this file needs to included in the model.hpp file.
                                                                    +
                                                                    10  *
                                                                    +
                                                                    11  * DEFINE guards for growth module outline to define the
                                                                    +
                                                                    12  * module_name_base hpp file if not already defined.
                                                                    +
                                                                    13  */
                                                                    +
                                                                    14 #ifndef POPULATION_DYNAMICS_GROWTH_BASE_HPP
                                                                    +
                                                                    15 #define POPULATION_DYNAMICS_GROWTH_BASE_HPP
                                                                    +
                                                                    16 
                                                                    +
                                                                    17 #include "../../../common/model_object.hpp"
                                                                    +
                                                                    18 
                                                                    +
                                                                    19 namespace fims_popdy {
                                                                    +
                                                                    20 
                                                                    +
                                                                    26 template <typename Type>
                                                                    +
                                                                    27 struct GrowthBase : public fims_model_object::FIMSObject<Type> {
                                                                    +
                                                                    28  // id_g is the ID of the instance of the growthBase class.
                                                                    +
                                                                    29  // this is like a memory tracker.
                                                                    +
                                                                    30  // Assigning each one its own ID is a way to keep track of
                                                                    +
                                                                    31  // all the instances of the growthBase class.
                                                                    +
                                                                    32  static uint32_t id_g;
                                                                    +
                                                                    37  GrowthBase() { this->id = GrowthBase::id_g++; }
                                                                    +
                                                                    38 
                                                                    +
                                                                    39  virtual ~GrowthBase() {}
                                                                    +
                                                                    40 
                                                                    +
                                                                    45  virtual const Type evaluate(const double& a) = 0;
                                                                    +
                                                                    46 };
                                                                    47 
                                                                    -
                                                                    48 } // namespace fims_popdy
                                                                    -
                                                                    49 
                                                                    -
                                                                    50 #endif /* POPULATION_DYNAMICS_GROWTH_BASE_HPP */
                                                                    -
                                                                    fims_model_object::FIMSObject
                                                                    FIMSObject struct that defines member types and returns the unique id.
                                                                    Definition: model_object.hpp:24
                                                                    -
                                                                    fims_popdy::GrowthBase
                                                                    Base class for all growth functors.
                                                                    Definition: growth_base.hpp:24
                                                                    -
                                                                    fims_popdy::GrowthBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: growth_base.hpp:29
                                                                    -
                                                                    fims_popdy::GrowthBase::GrowthBase
                                                                    GrowthBase()
                                                                    Constructor.
                                                                    Definition: growth_base.hpp:34
                                                                    +
                                                                    48 template <typename Type>
                                                                    +
                                                                    49 uint32_t GrowthBase<Type>::id_g = 0;
                                                                    +
                                                                    50 
                                                                    +
                                                                    51 } // namespace fims_popdy
                                                                    +
                                                                    52 
                                                                    +
                                                                    53 #endif /* POPULATION_DYNAMICS_GROWTH_BASE_HPP */
                                                                    +
                                                                    fims_model_object::FIMSObject
                                                                    FIMSObject struct that defines member types and returns the unique id.
                                                                    Definition: model_object.hpp:25
                                                                    +
                                                                    fims_popdy::GrowthBase
                                                                    Base class for all growth functors.
                                                                    Definition: growth_base.hpp:27
                                                                    +
                                                                    fims_popdy::GrowthBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: growth_base.hpp:32
                                                                    +
                                                                    fims_popdy::GrowthBase::GrowthBase
                                                                    GrowthBase()
                                                                    Constructor.
                                                                    Definition: growth_base.hpp:37
                                                                    fims_popdy::GrowthBase::evaluate
                                                                    virtual const Type evaluate(const double &a)=0
                                                                    Calculates the growth at the independent variable value.
                                                                    diff --git a/docs/hierarchy.html b/docs/hierarchy.html index 3d867b5..b7e1d25 100644 --- a/docs/hierarchy.html +++ b/docs/hierarchy.html @@ -74,40 +74,36 @@
                                                                    This inheritance list is sorted roughly, but not completely, alphabetically:
                                                                    [detail level 123]
                                                                    - + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - + + + - - - + + + @@ -116,16 +112,13 @@ - - - - - - - - - - + + + + + + +
                                                                     Cfims::FIMSLog
                                                                     Cfims::fims_log
                                                                     ▼Cfims_model_object::FIMSObject< Type >FIMSObject struct that defines member types and returns the unique id
                                                                     Cfims_data_object::DataObject< Type >
                                                                     ▼Cfims_distributions::DensityComponentBase< Type >Base class for all module_name functors
                                                                     Cfims_distributions::LogNormalLPDF< Type >
                                                                     Cfims_distributions::MultinomialLPMF< Type >
                                                                     Cfims_distributions::NormalLPDF< Type >
                                                                     Cfims_popdy::Fleet< Type >Base class for all fleets
                                                                     ▼Cfims_popdy::GrowthBase< Type >Base class for all growth functors
                                                                     Cfims_popdy::EWAAgrowth< Type >EWAAgrowth class that returns the EWAA function value
                                                                     ▼Cfims_popdy::MaturityBase< Type >Base class for all maturity functors
                                                                     Cfims_popdy::LogisticMaturity< Type >LogisticMaturity class that returns the logistic function value from fims_math
                                                                     Cfims_popdy::Population< Type >Population class. Contains subpopulations that are divided into generic partitions (eg. sex, area)
                                                                     ▼Cfims_popdy::RecruitmentBase< Type >Base class for all recruitment functors
                                                                     Cfims_popdy::SRBevertonHolt< Type >BevertonHolt class that returns the Beverton Holt SR from fims_math
                                                                     ▼Cfims_popdy::SelectivityBase< Type >Base class for all selectivity functors
                                                                     Cfims_popdy::DoubleLogisticSelectivity< Type >DoubleLogisticSelectivity class that returns the double logistic function value from fims_math
                                                                     Cfims_popdy::LogisticSelectivity< Type >LogisticSelectivity class that returns the logistic function value from fims_math
                                                                     ▼CFIMSRcppInterfaceBaseBase class for all interface objects
                                                                     ▼CDataInterfaceBaseRcpp interface for Data as an S4 object. To instantiate from R: fleet <- new(Data)
                                                                     CAgeCompDataInterfaceRcpp interface for age comp data as an S4 object. To instantiate from R: acomp <- new(AgeComp)
                                                                     CIndexDataInterfaceRcpp interface for data as an S4 object. To instantiate from R: fleet <- new(Index)
                                                                     CLengthCompDataInterfaceRcpp interface for length comp data as an S4 object. To instantiate from R: lcomp <- new(LengthComp)
                                                                     Cfims_distributions::DistributionsBase< Type >Base class for all module_name functors
                                                                     Cfims_popdy::Fleet< Type >Base class for all fleets
                                                                     ▼Cfims_popdy::GrowthBase< Type >Base class for all growth functors
                                                                     Cfims_popdy::EWAAgrowth< Type >EWAAgrowth class that returns the EWAA function value
                                                                     ▼Cfims_popdy::MaturityBase< Type >Base class for all maturity functors
                                                                     Cfims_popdy::LogisticMaturity< Type >LogisticMaturity class that returns the logistic function value from fims_math
                                                                     Cfims_popdy::Population< Type >Population class. Contains subpopulations that are divided into generic partitions (eg. sex, area)
                                                                     ▼Cfims_popdy::RecruitmentBase< Type >Base class for all recruitment functors
                                                                     Cfims_popdy::SRBevertonHolt< Type >BevertonHolt class that returns the Beverton Holt SR from fims_math
                                                                     ▼Cfims_popdy::SelectivityBase< Type >Base class for all selectivity functors
                                                                     Cfims_popdy::DoubleLogisticSelectivity< Type >DoubleLogisticSelectivity class that returns the double logistic function value from fims_math
                                                                     Cfims_popdy::LogisticSelectivity< Type >LogisticSelectivity class that returns the logistic function value from fims_math
                                                                     ▼CFIMSRcppInterfaceBaseBase class for all interface objects
                                                                     ▼CDataInterfaceBaseRcpp interface for Data as an S4 object. To instantiate from R: fleet <- new(Data)
                                                                     CAgeCompDataInterfaceRcpp interface for age comp data as an S4 object. To instantiate from R: acomp <- new(AgeComp)
                                                                     CIndexDataInterfaceRcpp interface for data as an S4 object. To instantiate from R: fleet <- new(Index)
                                                                     ▼CDistributionsInterfaceBaseDistributions Rcpp Interface
                                                                     CDlnormDistributionsInterfaceRcpp interface for Dlnorm as an S4 object. To instantiate from R: dlnorm_ <- new(DlnormDistribution)
                                                                     CDmultinomDistributionsInterfaceRcpp interface for Dmultinom as an S4 object. To instantiate from R: dmultinom_ <- new(DmultinomDistribution)
                                                                     CDnormDistributionsInterfaceRcpp interface for Dnorm as an S4 object. To instantiate from R: dnorm_ <- new(DnormDistribution)
                                                                     CDlnormDistributionsInterfaceRcpp interface for Dlnorm as an S4 object. To instantiate from R: dlnorm_ <- new(TMBDlnormDistribution)
                                                                     CDmultinomDistributionsInterfaceRcpp interface for Dmultinom as an S4 object. To instantiate from R: dmultinom_ <- new(TMBDmultinomDistribution)
                                                                     CDnormDistributionsInterfaceRcpp interface for Dnorm as an S4 object. To instantiate from R: dnorm_ <- new(TMBDnormDistribution)
                                                                     ▼CFleetInterfaceBaseRcpp interface that serves as the parent class for Rcpp fleet interfaces. This type should be inherited and not called from R directly
                                                                     CFleetInterfaceRcpp interface for Fleet as an S4 object. To instantiate from R: fleet <- new(Fleet)
                                                                     ▼CGrowthInterfaceBaseRcpp interface that serves as the parent class for Rcpp growth interfaces. This type should be inherited and not called from R directly
                                                                     CEWAAGrowthInterfaceRcpp interface for EWAAgrowth as an S4 object. To instantiate from R: ewaa <- new(EWAAgrowth)
                                                                     CLPDFInterfaceBaseLPDFInterfaceBase class should be inherited to define different Rcpp interfaces for each possible log probability density function
                                                                     ▼CMaturityInterfaceBaseMaturityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible maturity function
                                                                     CLogisticMaturityInterfaceRcpp interface for logistic maturity as an S4 object. To instantiate from R: logistic_maturity <- new(logistic_maturity)
                                                                     ▼CMaturityInterfaceBaseMaturityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible maturity function
                                                                     CLogisticMaturityInterfaceRcpp interface for logistic maturity as an S4 object. To instantiate from R: logistic_maturity <- new(logistic_maturity)
                                                                     CNLLInterfaceBaseNLLInterfaceBase class should be inherited to define different Rcpp interfaces for each possible negative log-likelihood function
                                                                     ▼CPopulationInterfaceBasePopulationInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Population function
                                                                     CPopulationInterfaceRcpp interface for a new Population. To instantiate from R: population <- new(population)
                                                                     ▼CRecruitmentInterfaceBaseRecruitmentInterfaceBase class should be inherited to define different Rcpp interfaces for each possible Recruitment function
                                                                     CDoubleLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(logistic_selectivity)
                                                                     CLogisticSelectivityInterfaceRcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity <- new(logistic_selectivity)
                                                                     Cfims_info::Information< Type >Stores FIMS model information and creates model. Contains all objects and data pre-model construction
                                                                     Cfims::JsonParser
                                                                     Cfims::JsonValue
                                                                     Cfims::LogEntry
                                                                     Cfims_model::Model< Type >Model class. FIMS objective function
                                                                     CParameterRcppInterface class that defines the interface between R and C++ for parameter types
                                                                     CParameterVectorRcpp representation of a Parameter vector interface between R and cpp
                                                                     Cfims_popdy::Subpopulation< Type >
                                                                     Cfims::Vector< Type >
                                                                     Cfims::Vector< double >
                                                                     Cfims::Vector< size_t >
                                                                     CJsonParser
                                                                     CJsonValue
                                                                     Cfims_model::Model< Type >Model class. FIMS objective function
                                                                     CParameterRcppInterface class that defines the interface between R and C++ for parameter types
                                                                     Cfims_popdy::Subpopulation< Type >
                                                                     Cfims::Vector< Type >
                                                                     Cfims::Vector< double >
                                                                    diff --git a/docs/index.html b/docs/index.html index 1731a70..7a41dab 100644 --- a/docs/index.html +++ b/docs/index.html @@ -5,7 +5,7 @@ -FIMS: C++ source code documentation +FIMS: Main Page @@ -67,13 +67,11 @@
                                                                    -
                                                                    +
                                                                    -
                                                                    C++ source code documentation
                                                                    +
                                                                    FIMS Documentation
                                                                    -

                                                                    This site contains C++ source code documenation for FIMS. Other forms of documentation are linked from the main documentation site at https://noaa-fims.github.io/FIMS/articles/fims-documentation.html

                                                                    -
                                                                    diff --git a/docs/information_8hpp.html b/docs/information_8hpp.html index 80f4b6b..5dd3daf 100644 --- a/docs/information_8hpp.html +++ b/docs/information_8hpp.html @@ -78,22 +78,18 @@
                                                                    information.hpp File Reference
                                                                    - -

                                                                    TODO: provide a brief description. -More...

                                                                    #include <map>
                                                                    #include <memory>
                                                                    #include <vector>
                                                                    -#include <algorithm>
                                                                    -#include "../distributions/distributions.hpp"
                                                                    +#include "../distributions/distributions.hpp"
                                                                    #include "../population_dynamics/fleet/fleet.hpp"
                                                                    -#include "../population_dynamics/growth/growth.hpp"
                                                                    -#include "../population_dynamics/population/population.hpp"
                                                                    -#include "../population_dynamics/recruitment/recruitment.hpp"
                                                                    -#include "../population_dynamics/selectivity/selectivity.hpp"
                                                                    +#include "../population_dynamics/growth/growth.hpp"
                                                                    +#include "../population_dynamics/population/population.hpp"
                                                                    +#include "../population_dynamics/recruitment/recruitment.hpp"
                                                                    +#include "../population_dynamics/selectivity/selectivity.hpp"
                                                                    #include "def.hpp"
                                                                    -#include "fims_vector.hpp"
                                                                    -#include "model_object.hpp"
                                                                    +#include "fims_vector.hpp"
                                                                    +#include "model_object.hpp"

                                                                    Go to the source code of this file.

                                                                    @@ -104,8 +100,7 @@
                                                                     

                                                                    Detailed Description

                                                                    -

                                                                    TODO: provide a brief description.

                                                                    -
                                                                    Copyright
                                                                    This file is part of the NOAA, National Marine Fisheries Service Fisheries Integrated Modeling System project. See LICENSE in the source folder for reuse information.
                                                                    +

                                                                    This File is part of the NOAA, National Marine Fisheries Service Fisheries Integrated Modeling System project. See LICENSE in the source folder for reuse information.

                                                                    diff --git a/docs/information_8hpp_source.html b/docs/information_8hpp_source.html index ae0a68c..4dac42e 100644 --- a/docs/information_8hpp_source.html +++ b/docs/information_8hpp_source.html @@ -83,525 +83,495 @@
                                                                    12 #include <map>
                                                                    13 #include <memory>
                                                                    14 #include <vector>
                                                                    -
                                                                    15 #include <algorithm>
                                                                    -
                                                                    16 
                                                                    -
                                                                    17 #include "../distributions/distributions.hpp"
                                                                    -
                                                                    18 #include "../population_dynamics/fleet/fleet.hpp"
                                                                    -
                                                                    19 #include "../population_dynamics/growth/growth.hpp"
                                                                    -
                                                                    20 #include "../population_dynamics/population/population.hpp"
                                                                    -
                                                                    21 #include "../population_dynamics/recruitment/recruitment.hpp"
                                                                    -
                                                                    22 #include "../population_dynamics/selectivity/selectivity.hpp"
                                                                    -
                                                                    23 #include "def.hpp"
                                                                    -
                                                                    24 #include "fims_vector.hpp"
                                                                    -
                                                                    25 #include "model_object.hpp"
                                                                    -
                                                                    26 
                                                                    -
                                                                    27 namespace fims_info {
                                                                    -
                                                                    28 
                                                                    -
                                                                    33  template <typename Type>
                                                                    -
                                                                    34  class Information {
                                                                    -
                                                                    35  public:
                                                                    -
                                                                    36  size_t nyears = 0;
                                                                    -
                                                                    37  size_t nseasons = 1;
                                                                    -
                                                                    38  size_t nages = 0;
                                                                    -
                                                                    40  static std::shared_ptr<Information<Type> >
                                                                    -
                                                                    41  fims_information;
                                                                    -
                                                                    42  std::vector<Type*> parameters;
                                                                    -
                                                                    43  std::vector<Type*>
                                                                    -
                                                                    44  random_effects_parameters;
                                                                    -
                                                                    45  std::vector<Type*>
                                                                    -
                                                                    46  fixed_effects_parameters;
                                                                    -
                                                                    47  std::vector<std::string>
                                                                    -
                                                                    48  parameter_names;
                                                                    -
                                                                    50  // data objects
                                                                    -
                                                                    51  std::map<uint32_t, std::shared_ptr<fims_data_object::DataObject<Type> > >
                                                                    -
                                                                    52  data_objects;
                                                                    -
                                                                    53  typedef typename std::map<
                                                                    -
                                                                    54  uint32_t, std::shared_ptr<fims_data_object::DataObject<Type> > >::iterator
                                                                    -
                                                                    55  data_iterator;
                                                                    -
                                                                    57  // life history modules
                                                                    -
                                                                    58  std::map<uint32_t, std::shared_ptr<fims_popdy::RecruitmentBase<Type> > >
                                                                    -
                                                                    59  recruitment_models;
                                                                    -
                                                                    61  typedef typename std::map<
                                                                    -
                                                                    62  uint32_t, std::shared_ptr<fims_popdy::RecruitmentBase<Type> > >::iterator
                                                                    -
                                                                    63  recruitment_models_iterator;
                                                                    -
                                                                    66  std::map<uint32_t, std::shared_ptr<fims_popdy::SelectivityBase<Type> > >
                                                                    -
                                                                    67  selectivity_models;
                                                                    -
                                                                    69  typedef typename std::map<
                                                                    -
                                                                    70  uint32_t, std::shared_ptr<fims_popdy::SelectivityBase<Type> > >::iterator
                                                                    -
                                                                    71  selectivity_models_iterator;
                                                                    -
                                                                    74  std::map<uint32_t, std::shared_ptr<fims_popdy::GrowthBase<Type> > >
                                                                    -
                                                                    75  growth_models;
                                                                    -
                                                                    77  typedef typename std::map<
                                                                    -
                                                                    78  uint32_t, std::shared_ptr<fims_popdy::GrowthBase<Type> > >::iterator
                                                                    -
                                                                    79  growth_models_iterator;
                                                                    -
                                                                    82  std::map<uint32_t, std::shared_ptr<fims_popdy::MaturityBase<Type> > >
                                                                    -
                                                                    83  maturity_models;
                                                                    -
                                                                    85  typedef typename std::map<
                                                                    -
                                                                    86  uint32_t, std::shared_ptr<fims_popdy::MaturityBase<Type> > >::iterator
                                                                    -
                                                                    87  maturity_models_iterator;
                                                                    -
                                                                    90  // fleet modules
                                                                    -
                                                                    91  std::map<uint32_t, std::shared_ptr<fims_popdy::Fleet<Type> > >
                                                                    -
                                                                    92  fleets;
                                                                    -
                                                                    94  typedef
                                                                    -
                                                                    95  typename std::map<uint32_t,
                                                                    -
                                                                    96  std::shared_ptr<fims_popdy::Fleet<Type> > >::iterator
                                                                    -
                                                                    97  fleet_iterator;
                                                                    -
                                                                    100  // populations
                                                                    -
                                                                    101  std::map<uint32_t, std::shared_ptr<fims_popdy::Population<Type> > >
                                                                    -
                                                                    102  populations;
                                                                    -
                                                                    104  typedef typename std::map<
                                                                    -
                                                                    105  uint32_t, std::shared_ptr<fims_popdy::Population<Type> > >::iterator
                                                                    -
                                                                    106  population_iterator;
                                                                    -
                                                                    109  // distributions
                                                                    -
                                                                    110  std::map<uint32_t,
                                                                    -
                                                                    111  std::shared_ptr<fims_distributions::DensityComponentBase<Type> > >
                                                                    -
                                                                    112  density_components;
                                                                    -
                                                                    114  typedef typename std::map<
                                                                    -
                                                                    115  uint32_t,
                                                                    -
                                                                    116  std::shared_ptr<fims_distributions::DensityComponentBase<Type> > >::iterator
                                                                    -
                                                                    117  density_components_iterator;
                                                                    -
                                                                    120  std::unordered_map<uint32_t, fims::Vector<Type>* >
                                                                    -
                                                                    121  variable_map;
                                                                    -
                                                                    123  typedef typename std::unordered_map<uint32_t, fims::Vector<Type>* >::iterator
                                                                    -
                                                                    124  variable_map_iterator;
                                                                    -
                                                                    126  Information() {}
                                                                    -
                                                                    127 
                                                                    -
                                                                    128  virtual ~Information() {}
                                                                    -
                                                                    129 
                                                                    -
                                                                    135  static std::shared_ptr<Information<Type> > GetInstance() {
                                                                    -
                                                                    136  if (Information<Type>::fims_information == nullptr) {
                                                                    -
                                                                    137  Information<Type>::fims_information =
                                                                    -
                                                                    138  std::make_shared<fims_info::Information<Type> >();
                                                                    -
                                                                    139  }
                                                                    -
                                                                    140  return Information<Type>::fims_information;
                                                                    +
                                                                    15 
                                                                    +
                                                                    16 #include "../distributions/distributions.hpp"
                                                                    +
                                                                    17 #include "../population_dynamics/fleet/fleet.hpp"
                                                                    +
                                                                    18 #include "../population_dynamics/growth/growth.hpp"
                                                                    +
                                                                    19 #include "../population_dynamics/population/population.hpp"
                                                                    +
                                                                    20 #include "../population_dynamics/recruitment/recruitment.hpp"
                                                                    +
                                                                    21 #include "../population_dynamics/selectivity/selectivity.hpp"
                                                                    +
                                                                    22 #include "def.hpp"
                                                                    +
                                                                    23 #include "fims_vector.hpp"
                                                                    +
                                                                    24 #include "model_object.hpp"
                                                                    +
                                                                    25 
                                                                    +
                                                                    26 namespace fims_info {
                                                                    +
                                                                    27 
                                                                    +
                                                                    32 template <typename Type>
                                                                    +
                                                                    33 class Information {
                                                                    +
                                                                    34  public:
                                                                    +
                                                                    35  size_t nyears;
                                                                    +
                                                                    36  size_t nseasons = 1;
                                                                    +
                                                                    37  size_t nages;
                                                                    +
                                                                    39  static std::shared_ptr<Information<Type> >
                                                                    +
                                                                    40  fims_information;
                                                                    +
                                                                    41  std::vector<Type*> parameters;
                                                                    +
                                                                    42  std::vector<Type*>
                                                                    +
                                                                    43  random_effects_parameters;
                                                                    +
                                                                    44  std::vector<Type*>
                                                                    +
                                                                    45  fixed_effects_parameters;
                                                                    +
                                                                    47  // data objects
                                                                    +
                                                                    48  std::map<uint32_t, std::shared_ptr<fims_data_object::DataObject<Type> > >
                                                                    +
                                                                    49  data_objects;
                                                                    +
                                                                    50  typedef typename std::map<
                                                                    +
                                                                    51  uint32_t, std::shared_ptr<fims_data_object::DataObject<Type> > >::iterator
                                                                    +
                                                                    52  data_iterator;
                                                                    +
                                                                    54  // life history modules
                                                                    +
                                                                    55  std::map<uint32_t, std::shared_ptr<fims_popdy::RecruitmentBase<Type> > >
                                                                    +
                                                                    56  recruitment_models;
                                                                    +
                                                                    58  typedef typename std::map<
                                                                    +
                                                                    59  uint32_t, std::shared_ptr<fims_popdy::RecruitmentBase<Type> > >::iterator
                                                                    +
                                                                    60  recruitment_models_iterator;
                                                                    +
                                                                    63  std::map<uint32_t, std::shared_ptr<fims_popdy::SelectivityBase<Type> > >
                                                                    +
                                                                    64  selectivity_models;
                                                                    +
                                                                    66  typedef typename std::map<
                                                                    +
                                                                    67  uint32_t, std::shared_ptr<fims_popdy::SelectivityBase<Type> > >::iterator
                                                                    +
                                                                    68  selectivity_models_iterator;
                                                                    +
                                                                    71  std::map<uint32_t, std::shared_ptr<fims_popdy::GrowthBase<Type> > >
                                                                    +
                                                                    72  growth_models;
                                                                    +
                                                                    74  typedef typename std::map<
                                                                    +
                                                                    75  uint32_t, std::shared_ptr<fims_popdy::GrowthBase<Type> > >::iterator
                                                                    +
                                                                    76  growth_models_iterator;
                                                                    +
                                                                    79  std::map<uint32_t, std::shared_ptr<fims_popdy::MaturityBase<Type> > >
                                                                    +
                                                                    80  maturity_models;
                                                                    +
                                                                    82  typedef typename std::map<
                                                                    +
                                                                    83  uint32_t, std::shared_ptr<fims_popdy::MaturityBase<Type> > >::iterator
                                                                    +
                                                                    84  maturity_models_iterator;
                                                                    +
                                                                    87  // fleet modules
                                                                    +
                                                                    88  std::map<uint32_t, std::shared_ptr<fims_popdy::Fleet<Type> > >
                                                                    +
                                                                    89  fleets;
                                                                    +
                                                                    91  typedef
                                                                    +
                                                                    92  typename std::map<uint32_t,
                                                                    +
                                                                    93  std::shared_ptr<fims_popdy::Fleet<Type> > >::iterator
                                                                    +
                                                                    94  fleet_iterator;
                                                                    +
                                                                    97  // populations
                                                                    +
                                                                    98  std::map<uint32_t, std::shared_ptr<fims_popdy::Population<Type> > >
                                                                    +
                                                                    99  populations;
                                                                    +
                                                                    101  typedef typename std::map<
                                                                    +
                                                                    102  uint32_t, std::shared_ptr<fims_popdy::Population<Type> > >::iterator
                                                                    +
                                                                    103  population_iterator;
                                                                    +
                                                                    106  // distributions
                                                                    +
                                                                    107  std::map<uint32_t,
                                                                    +
                                                                    108  std::shared_ptr<fims_distributions::DistributionsBase<Type> > >
                                                                    +
                                                                    109  distribution_models;
                                                                    +
                                                                    111  typedef typename std::map<
                                                                    +
                                                                    112  uint32_t,
                                                                    +
                                                                    113  std::shared_ptr<fims_distributions::DistributionsBase<Type> > >::iterator
                                                                    +
                                                                    114  distribution_models_iterator;
                                                                    +
                                                                    117  Information() {}
                                                                    +
                                                                    118 
                                                                    +
                                                                    119  virtual ~Information() {}
                                                                    +
                                                                    120 
                                                                    +
                                                                    126  static std::shared_ptr<Information<Type> > GetInstance() {
                                                                    +
                                                                    127  if (Information<Type>::fims_information == nullptr) {
                                                                    +
                                                                    128  Information<Type>::fims_information =
                                                                    +
                                                                    129  std::make_shared<fims_info::Information<Type> >();
                                                                    +
                                                                    130  }
                                                                    +
                                                                    131  return Information<Type>::fims_information;
                                                                    +
                                                                    132  }
                                                                    +
                                                                    133 
                                                                    +
                                                                    139  void RegisterParameter(Type& p) {
                                                                    +
                                                                    140  this->fixed_effects_parameters.push_back(&p);
                                                                    141  }
                                                                    142 
                                                                    -
                                                                    148  void RegisterParameter(Type& p) {
                                                                    -
                                                                    149  this->fixed_effects_parameters.push_back(&p);
                                                                    +
                                                                    148  void RegisterRandomEffect(Type& re) {
                                                                    +
                                                                    149  this->random_effects_parameters.push_back(&re);
                                                                    150  }
                                                                    151 
                                                                    -
                                                                    157  void RegisterRandomEffect(Type& re) {
                                                                    -
                                                                    158  this->random_effects_parameters.push_back(&re);
                                                                    -
                                                                    159  }
                                                                    -
                                                                    160 
                                                                    -
                                                                    166  void RegisterParameterName(std::string p_name) {
                                                                    -
                                                                    167  this->parameter_names.push_back(p_name);
                                                                    -
                                                                    168  }
                                                                    -
                                                                    169 
                                                                    -
                                                                    173  void setup_priors() {
                                                                    -
                                                                    174  for (density_components_iterator it = density_components.begin(); it != density_components.end(); ++it) {
                                                                    -
                                                                    175  std::shared_ptr<fims_distributions::DensityComponentBase<Type> > d = (*it).second;
                                                                    -
                                                                    176  if (d->input_type == "prior") {
                                                                    -
                                                                    177  FIMS_INFO_LOG("Setup prior for distribution " + fims::to_string(d->id));
                                                                    -
                                                                    178  variable_map_iterator vmit;
                                                                    -
                                                                    179  FIMS_INFO_LOG("Link prior from distribution " + fims::to_string(d->id) + " to parameter " + fims::to_string(d->key[0]));
                                                                    -
                                                                    180  vmit = this->variable_map.find(d->key[0]);
                                                                    -
                                                                    181  d->x = *(*vmit).second;
                                                                    -
                                                                    182  for (size_t i = 1; i < d->key.size(); i++) {
                                                                    -
                                                                    183  FIMS_INFO_LOG("Link prior from distribution " + fims::to_string(d->id)
                                                                    -
                                                                    184  + " to parameter " + fims::to_string(d->key[0]));
                                                                    -
                                                                    185  vmit = this->variable_map.find(d->key[i]);
                                                                    -
                                                                    186  d->x.insert(std::end(d->x),
                                                                    -
                                                                    187  std::begin(*(*vmit).second), std::end(*(*vmit).second));
                                                                    -
                                                                    188  }
                                                                    -
                                                                    189  FIMS_INFO_LOG("Prior size for distribution " + fims::to_string(d->id) + "is: " + fims::to_string(d->x.size()));
                                                                    -
                                                                    190  }
                                                                    -
                                                                    191  }
                                                                    -
                                                                    192  }
                                                                    -
                                                                    193 
                                                                    -
                                                                    197  void setup_random_effects() {
                                                                    -
                                                                    198  for (density_components_iterator it = this->density_components.begin(); it != this->density_components.end(); ++it) {
                                                                    -
                                                                    199  std::shared_ptr<fims_distributions::DensityComponentBase<Type> > d = (*it).second;
                                                                    -
                                                                    200  if (d->input_type == "random_effects") {
                                                                    -
                                                                    201  FIMS_INFO_LOG("Setup random effects for distribution " + fims::to_string(d->id));
                                                                    -
                                                                    202  variable_map_iterator vmit;
                                                                    -
                                                                    203  FIMS_INFO_LOG("Link random effects from distribution "
                                                                    -
                                                                    204  + fims::to_string(d->id) + " to derived value " + fims::to_string(d->key[0]));
                                                                    -
                                                                    205  vmit = this->variable_map.find(d->key[0]);
                                                                    -
                                                                    206  d->x = *(*vmit).second;
                                                                    -
                                                                    207  for (size_t i = 1; i < d->key.size(); i++) {
                                                                    -
                                                                    208  FIMS_INFO_LOG("Link random effects from distribution " + fims::to_string(d->id)
                                                                    -
                                                                    209  + " to derived value " + fims::to_string(d->key[0]));
                                                                    -
                                                                    210  vmit = this->variable_map.find(d->key[i]);
                                                                    -
                                                                    211  d->x.insert(std::end(d->x),
                                                                    -
                                                                    212  std::begin(*(*vmit).second), std::end(*(*vmit).second));
                                                                    -
                                                                    213  }
                                                                    -
                                                                    214  FIMS_INFO_LOG("Random effect size for distribution " + fims::to_string(d->id) + "is: " + fims::to_string(d->x.size()));
                                                                    -
                                                                    215  }
                                                                    -
                                                                    216  }
                                                                    -
                                                                    217  }
                                                                    -
                                                                    218 
                                                                    -
                                                                    222  void setup_data() {
                                                                    -
                                                                    223  for (density_components_iterator it = this->density_components.begin(); it != this->density_components.end(); ++it) {
                                                                    -
                                                                    224  std::shared_ptr<fims_distributions::DensityComponentBase<Type> > d = (*it).second;
                                                                    -
                                                                    225  if (d->input_type == "data") {
                                                                    -
                                                                    226  FIMS_INFO_LOG("Setup expected value for data distribution " + fims::to_string(d->id));
                                                                    -
                                                                    227  variable_map_iterator vmit;
                                                                    -
                                                                    228  FIMS_INFO_LOG("Link expected value from distribution " + fims::to_string(d->id)
                                                                    -
                                                                    229  + " to derived value " + fims::to_string(d->key[0]));
                                                                    -
                                                                    230  vmit = this->variable_map.find(d->key[0]);
                                                                    -
                                                                    231  d->expected_values = *(*vmit).second;
                                                                    -
                                                                    232 
                                                                    -
                                                                    233  for (size_t i = 1; i < d->key.size(); i++) {
                                                                    -
                                                                    234  vmit = this->variable_map.find(d->key[i]);
                                                                    -
                                                                    235  FIMS_INFO_LOG("Link expected value from distribution "
                                                                    -
                                                                    236  + fims::to_string(d->id) + " to derived value " + fims::to_string(d->key[i]));
                                                                    -
                                                                    237  d->expected_values.insert(std::end(d->expected_values),
                                                                    -
                                                                    238  std::begin(*(*vmit).second), std::end(*(*vmit).second));
                                                                    -
                                                                    239  }
                                                                    -
                                                                    240  FIMS_INFO_LOG("Expected value size for distribution " + fims::to_string(d->id)
                                                                    -
                                                                    241  + " is: " + fims::to_string(d->expected_values.size()));
                                                                    -
                                                                    242  }
                                                                    -
                                                                    243  }
                                                                    -
                                                                    244  }
                                                                    -
                                                                    245 
                                                                    -
                                                                    256  bool CreateModel() {
                                                                    -
                                                                    257  bool valid_model = true;
                                                                    +
                                                                    162  bool CreateModel() {
                                                                    +
                                                                    163  bool valid_model = true;
                                                                    +
                                                                    164  INFO_LOG << "" << std::endl;
                                                                    +
                                                                    165  INFO_LOG
                                                                    +
                                                                    166  << "Beginning to create FIMS model in information.hpp CreateModel(). "
                                                                    +
                                                                    167  << std::endl;
                                                                    +
                                                                    168  INFO_LOG << "Initializing fleet objects for " << this->fleets.size()
                                                                    +
                                                                    169  << " fleets." << std::endl;
                                                                    +
                                                                    170  for (fleet_iterator it = this->fleets.begin(); it != this->fleets.end();
                                                                    +
                                                                    171  ++it) {
                                                                    +
                                                                    172  // Initialize fleet object
                                                                    +
                                                                    173 
                                                                    +
                                                                    174  std::shared_ptr<fims_popdy::Fleet<Type> > f = (*it).second;
                                                                    +
                                                                    175  INFO_LOG << "Initializing fleet " << f->id << "." << std::endl;
                                                                    +
                                                                    176 
                                                                    +
                                                                    177  f->Initialize(f->nyears, f->nages);
                                                                    +
                                                                    178 
                                                                    +
                                                                    179  INFO_LOG << "Expecting to import " << this->data_objects.size()
                                                                    +
                                                                    180  << " data objects." << std::endl;
                                                                    +
                                                                    181 
                                                                    +
                                                                    182  INFO_LOG << "Checking for available fleet index data objects."
                                                                    +
                                                                    183  << std::endl;
                                                                    +
                                                                    184  // set index data
                                                                    +
                                                                    185  if (f->fleet_observed_index_data_id_m != -999) {
                                                                    +
                                                                    186  uint32_t observed_index_id =
                                                                    +
                                                                    187  static_cast<uint32_t>(f->fleet_observed_index_data_id_m);
                                                                    +
                                                                    188  data_iterator it = this->data_objects.find(observed_index_id);
                                                                    +
                                                                    189  INFO_LOG << "Input fleet index id = " << observed_index_id << "."
                                                                    +
                                                                    190  << std::endl;
                                                                    +
                                                                    191 
                                                                    +
                                                                    192  if (it != this->data_objects.end()) {
                                                                    +
                                                                    193  f->observed_index_data = (*it).second;
                                                                    +
                                                                    194  INFO_LOG << "Index data successfully set." << std::endl;
                                                                    +
                                                                    195  DATA_LOG << "" << std::endl;
                                                                    +
                                                                    196  DATA_LOG << "Observed input for fleet " << f->id << ", index "
                                                                    +
                                                                    197  << observed_index_id << ": \n "
                                                                    +
                                                                    198  << f->observed_index_data->at(1) << std::endl;
                                                                    +
                                                                    199  } else {
                                                                    +
                                                                    200  valid_model = false;
                                                                    +
                                                                    201  ERROR_LOG << "Error: Expected data observations not defined for fleet"
                                                                    +
                                                                    202  << f->id << ", index " << observed_index_id << std::endl;
                                                                    +
                                                                    203  exit(1);
                                                                    +
                                                                    204  }
                                                                    +
                                                                    205 
                                                                    +
                                                                    206  } else {
                                                                    +
                                                                    207  valid_model = false;
                                                                    +
                                                                    208  ERROR_LOG << "Error: No index data observed for fleet " << f->id
                                                                    +
                                                                    209  << ". FIMS requires index data for all fleets." << std::endl;
                                                                    +
                                                                    210  exit(1);
                                                                    +
                                                                    211  }
                                                                    +
                                                                    212  // end set index data
                                                                    +
                                                                    213 
                                                                    +
                                                                    214  INFO_LOG << "Checking for available fleet age comp data objects."
                                                                    +
                                                                    215  << std::endl;
                                                                    +
                                                                    216  // set age composition data
                                                                    +
                                                                    217  if (f->fleet_observed_agecomp_data_id_m != -999) {
                                                                    +
                                                                    218  uint32_t observed_agecomp_id =
                                                                    +
                                                                    219  static_cast<uint32_t>(f->fleet_observed_agecomp_data_id_m);
                                                                    +
                                                                    220  data_iterator it = this->data_objects.find(observed_agecomp_id);
                                                                    +
                                                                    221  INFO_LOG << "Input fleet age comp id = " << observed_agecomp_id << "."
                                                                    +
                                                                    222  << std::endl;
                                                                    +
                                                                    223 
                                                                    +
                                                                    224  if (it != this->data_objects.end()) {
                                                                    +
                                                                    225  f->observed_agecomp_data = (*it).second;
                                                                    +
                                                                    226  INFO_LOG << "Age comp data successfully set." << std::endl;
                                                                    +
                                                                    227  DATA_LOG << "" << std::endl;
                                                                    +
                                                                    228  DATA_LOG << "Observed input age comp for fleet " << f->id << ", comp "
                                                                    +
                                                                    229  << observed_agecomp_id << ": \n "
                                                                    +
                                                                    230  << f->observed_agecomp_data->at(1) << std::endl;
                                                                    +
                                                                    231  } else {
                                                                    +
                                                                    232  valid_model = false;
                                                                    +
                                                                    233  ERROR_LOG << "Error: Expected age comp data observations not defined "
                                                                    +
                                                                    234  "for fleet "
                                                                    +
                                                                    235  << f->id << ", index " << observed_agecomp_id << std::endl;
                                                                    +
                                                                    236  exit(1);
                                                                    +
                                                                    237  }
                                                                    +
                                                                    238 
                                                                    +
                                                                    239  } else {
                                                                    +
                                                                    240  valid_model = false;
                                                                    +
                                                                    241  ERROR_LOG << "Error: No age comp data observed for fleet " << f->id
                                                                    +
                                                                    242  << ". FIMS requires age comp data for all fleets."
                                                                    +
                                                                    243  << std::endl;
                                                                    +
                                                                    244  exit(1);
                                                                    +
                                                                    245  }
                                                                    +
                                                                    246  // end set composition data
                                                                    +
                                                                    247 
                                                                    +
                                                                    248  INFO_LOG << "Checking for available fleet selectivity pattern."
                                                                    +
                                                                    249  << std::endl;
                                                                    +
                                                                    250  // set selectivity model
                                                                    +
                                                                    251  if (f->fleet_selectivity_id_m != -999) {
                                                                    +
                                                                    252  uint32_t sel_id = static_cast<uint32_t>(
                                                                    +
                                                                    253  f->fleet_selectivity_id_m); // cast as unsigned integer
                                                                    +
                                                                    254  selectivity_models_iterator it = this->selectivity_models.find(
                                                                    +
                                                                    255  sel_id); // if find, set it, otherwise invalid
                                                                    +
                                                                    256  INFO_LOG << "Input fleet selectivity pattern id = " << sel_id << "."
                                                                    +
                                                                    257  << std::endl;
                                                                    258 
                                                                    -
                                                                    259  for (fleet_iterator it = this->fleets.begin(); it != this->fleets.end();
                                                                    -
                                                                    260  ++it) {
                                                                    -
                                                                    261 
                                                                    -
                                                                    262  std::shared_ptr<fims_popdy::Fleet<Type> > f = (*it).second;
                                                                    -
                                                                    263  FIMS_INFO_LOG("Initializing fleet " + fims::to_string(f->id));
                                                                    -
                                                                    264 
                                                                    -
                                                                    265  f->Initialize(f->nyears, f->nages, f->nlengths);
                                                                    -
                                                                    266 
                                                                    -
                                                                    267  // set index data
                                                                    -
                                                                    268  if (f->fleet_observed_index_data_id_m != -999) {
                                                                    -
                                                                    269  uint32_t observed_index_id =
                                                                    -
                                                                    270  static_cast<uint32_t>(f->fleet_observed_index_data_id_m);
                                                                    -
                                                                    271  data_iterator it = this->data_objects.find(observed_index_id);
                                                                    -
                                                                    272  if (it != this->data_objects.end()) {
                                                                    -
                                                                    273  f->observed_index_data = (*it).second;
                                                                    -
                                                                    274  FIMS_INFO_LOG("Index data for fleet "
                                                                    -
                                                                    275  + fims::to_string(f->id) + " successfully set to "
                                                                    -
                                                                    276  + fims::to_string(f->observed_index_data->at(1)));
                                                                    -
                                                                    277  } else {
                                                                    -
                                                                    278  valid_model = false;
                                                                    -
                                                                    279  FIMS_ERROR_LOG("Expected index data not defined for fleet "
                                                                    -
                                                                    280  + fims::to_string(f->id) + ", index "
                                                                    -
                                                                    281  + fims::to_string(observed_index_id));
                                                                    -
                                                                    282  }
                                                                    -
                                                                    283  } else {
                                                                    -
                                                                    284  valid_model = false;
                                                                    -
                                                                    285  // TODO: explore why index data is required because it should not be
                                                                    -
                                                                    286  FIMS_ERROR_LOG("No index data observed for fleet "
                                                                    -
                                                                    287  + fims::to_string(f->id) + ". FIMS requires index data for all fleets.");
                                                                    -
                                                                    288  }
                                                                    -
                                                                    289  // end set index data
                                                                    -
                                                                    290 
                                                                    -
                                                                    291  // set age-composition data
                                                                    -
                                                                    292  if (f->fleet_observed_agecomp_data_id_m != -999) {
                                                                    -
                                                                    293  uint32_t observed_agecomp_id =
                                                                    -
                                                                    294  static_cast<uint32_t>(f->fleet_observed_agecomp_data_id_m);
                                                                    -
                                                                    295  data_iterator it = this->data_objects.find(observed_agecomp_id);
                                                                    -
                                                                    296  if (it != this->data_objects.end()) {
                                                                    -
                                                                    297  f->observed_agecomp_data = (*it).second;
                                                                    -
                                                                    298  FIMS_INFO_LOG("Observed input age-composition data for fleet "
                                                                    -
                                                                    299  + fims::to_string(f->id) + " successfully set to "
                                                                    -
                                                                    300  + fims::to_string(f->observed_agecomp_data->at(1)));
                                                                    -
                                                                    301  } else {
                                                                    -
                                                                    302  valid_model = false;
                                                                    -
                                                                    303  FIMS_ERROR_LOG("Expected age-composition observations not defined for fleet "
                                                                    -
                                                                    304  + fims::to_string(f->id));
                                                                    -
                                                                    305  }
                                                                    -
                                                                    306  }
                                                                    -
                                                                    307  // end set age-composition data
                                                                    -
                                                                    308 
                                                                    -
                                                                    309  // set length-composition data
                                                                    -
                                                                    310  if (f->fleet_observed_lengthcomp_data_id_m != -999) {
                                                                    -
                                                                    311  uint32_t observed_lengthcomp_id =
                                                                    -
                                                                    312  static_cast<uint32_t>(f->fleet_observed_lengthcomp_data_id_m);
                                                                    -
                                                                    313  data_iterator it = this->data_objects.find(observed_lengthcomp_id);
                                                                    -
                                                                    314  if (it != this->data_objects.end()) {
                                                                    -
                                                                    315  f->observed_lengthcomp_data = (*it).second;
                                                                    -
                                                                    316  FIMS_INFO_LOG("Observed input length-composition data for fleet "
                                                                    -
                                                                    317  + fims::to_string(f->id) + " successfully set to "
                                                                    -
                                                                    318  + fims::to_string(f->observed_lengthcomp_data->at(1)));
                                                                    -
                                                                    319  } else {
                                                                    -
                                                                    320  valid_model = false;
                                                                    -
                                                                    321  FIMS_ERROR_LOG("Expected length-composition observations not defined for fleet "
                                                                    -
                                                                    322  + fims::to_string(f->id));
                                                                    -
                                                                    323  }
                                                                    -
                                                                    324  }
                                                                    -
                                                                    325  // end set length-composition data
                                                                    -
                                                                    326 
                                                                    -
                                                                    327  // set selectivity model
                                                                    -
                                                                    328  if (f->fleet_selectivity_id_m != -999) {
                                                                    -
                                                                    329  uint32_t sel_id = static_cast<uint32_t> (
                                                                    -
                                                                    330  f->fleet_selectivity_id_m); // cast as unsigned integer
                                                                    -
                                                                    331  selectivity_models_iterator it = this->selectivity_models.find(
                                                                    -
                                                                    332  sel_id); // if find, set it, otherwise invalid
                                                                    -
                                                                    333 
                                                                    -
                                                                    334  if (it != this->selectivity_models.end()) {
                                                                    -
                                                                    335  f->selectivity = (*it).second; // elements in container held in pair
                                                                    -
                                                                    336  FIMS_INFO_LOG("Selectivity model "
                                                                    -
                                                                    337  + fims::to_string(f->fleet_selectivity_id_m)
                                                                    -
                                                                    338  + " successfully set to fleet " + fims::to_string(f->id));
                                                                    -
                                                                    339 
                                                                    -
                                                                    340  } else {
                                                                    -
                                                                    341  valid_model = false;
                                                                    -
                                                                    342  FIMS_ERROR_LOG("Expected selectivity pattern not defined for fleet "
                                                                    -
                                                                    343  + fims::to_string(f->id) + ", selectivity pattern " + fims::to_string(sel_id));
                                                                    -
                                                                    344  }
                                                                    -
                                                                    345 
                                                                    -
                                                                    346  } else {
                                                                    -
                                                                    347  valid_model = false;
                                                                    -
                                                                    348  FIMS_ERROR_LOG("Error: No selectivity pattern defined for fleet " + fims::to_string(f->id)
                                                                    -
                                                                    349  + ". FIMS requires selectivity be defined for all fleets.");
                                                                    -
                                                                    350  }
                                                                    -
                                                                    351  // end set selectivity
                                                                    -
                                                                    352  }
                                                                    -
                                                                    353 
                                                                    -
                                                                    354  for (density_components_iterator it = this->density_components.begin();
                                                                    -
                                                                    355  it != this->density_components.end(); ++it) {
                                                                    -
                                                                    356  std::shared_ptr<fims_distributions::DensityComponentBase<Type> > d = (*it).second;
                                                                    +
                                                                    259  if (it != this->selectivity_models.end()) {
                                                                    +
                                                                    260  f->selectivity = (*it).second; // elements in container held in pair
                                                                    +
                                                                    261  // (first is id, second is object -
                                                                    +
                                                                    262  // shared pointer to distribution)
                                                                    +
                                                                    263  INFO_LOG << "Selectivity successfully set." << std::endl;
                                                                    +
                                                                    264  } else {
                                                                    +
                                                                    265  valid_model = false;
                                                                    +
                                                                    266  ERROR_LOG
                                                                    +
                                                                    267  << "Error: Expected selectivity pattern not defined for fleet "
                                                                    +
                                                                    268  << f->id << ", selectivity pattern " << sel_id << std::endl;
                                                                    +
                                                                    269  exit(1);
                                                                    +
                                                                    270  }
                                                                    +
                                                                    271 
                                                                    +
                                                                    272  } else {
                                                                    +
                                                                    273  valid_model = false;
                                                                    +
                                                                    274  ERROR_LOG << "Error: No selectivity pattern defined for fleet " << f->id
                                                                    +
                                                                    275  << ". FIMS requires selectivity be defined for all fleets."
                                                                    +
                                                                    276  << std::endl;
                                                                    +
                                                                    277  exit(1);
                                                                    +
                                                                    278  }
                                                                    +
                                                                    279  // end set selectivity
                                                                    +
                                                                    280 
                                                                    +
                                                                    281  INFO_LOG << "Checking for available index likelihood function."
                                                                    +
                                                                    282  << std::endl;
                                                                    +
                                                                    283  // set index likelihood
                                                                    +
                                                                    284  if (f->fleet_index_likelihood_id_m != -999) {
                                                                    +
                                                                    285  uint32_t ind_like_id = static_cast<uint32_t>(
                                                                    +
                                                                    286  f->fleet_index_likelihood_id_m); // cast as unsigned integer
                                                                    +
                                                                    287  distribution_models_iterator it = this->distribution_models.find(
                                                                    +
                                                                    288  ind_like_id); // if find, set it, otherwise invalid
                                                                    +
                                                                    289  INFO_LOG << "Input index likelihood function id = " << ind_like_id
                                                                    +
                                                                    290  << "." << std::endl;
                                                                    +
                                                                    291 
                                                                    +
                                                                    292  if (it != this->distribution_models.end()) {
                                                                    +
                                                                    293  f->index_likelihood =
                                                                    +
                                                                    294  (*it).second; // elements in container held in pair (first is
                                                                    +
                                                                    295  // id, second is object - shared pointer to
                                                                    +
                                                                    296  // distribution)
                                                                    +
                                                                    297  INFO_LOG << "Index likelihood function successfully set."
                                                                    +
                                                                    298  << std::endl;
                                                                    +
                                                                    299  } else {
                                                                    +
                                                                    300  // Commented out for now as code uses single likelihood function
                                                                    +
                                                                    301  // making this fail valid_model = false; ERROR_LOG << "Error: Expected
                                                                    +
                                                                    302  // index likelihood function not defined for fleet "
                                                                    +
                                                                    303  // << f->id << ", likelihood function " << ind_like_id <<
                                                                    +
                                                                    304  // std::endl;
                                                                    +
                                                                    305  // exit(1);
                                                                    +
                                                                    306  }
                                                                    +
                                                                    307 
                                                                    +
                                                                    308  } else {
                                                                    +
                                                                    309  // Commented out for now as code uses single likelihood function making
                                                                    +
                                                                    310  // this fail valid_model = false; ERROR_LOG << "Error: No index
                                                                    +
                                                                    311  // likelihood function defined for fleet " << f->id
                                                                    +
                                                                    312  // << ". FIMS requires likelihood functions be defined for all
                                                                    +
                                                                    313  // data." << std::endl;
                                                                    +
                                                                    314  // exit(1);
                                                                    +
                                                                    315  }
                                                                    +
                                                                    316  // end set index likelihood
                                                                    +
                                                                    317 
                                                                    +
                                                                    318  INFO_LOG << "Checking for available age comp likelihood function."
                                                                    +
                                                                    319  << std::endl;
                                                                    +
                                                                    320  // set agecomp likelihood
                                                                    +
                                                                    321  if (f->fleet_agecomp_likelihood_id_m != -999) {
                                                                    +
                                                                    322  uint32_t ac_like_id = static_cast<uint32_t>(
                                                                    +
                                                                    323  f->fleet_agecomp_likelihood_id_m); // cast as unsigned integer
                                                                    +
                                                                    324  distribution_models_iterator it = this->distribution_models.find(
                                                                    +
                                                                    325  ac_like_id); // if find, set it, otherwise invalid
                                                                    +
                                                                    326  INFO_LOG << "Input age comp likelihood function id = " << ac_like_id
                                                                    +
                                                                    327  << "." << std::endl;
                                                                    +
                                                                    328 
                                                                    +
                                                                    329  if (it != this->distribution_models.end()) {
                                                                    +
                                                                    330  f->agecomp_likelihood =
                                                                    +
                                                                    331  (*it).second; // elements in container held in pair (first is
                                                                    +
                                                                    332  // id, second is object - shared pointer to
                                                                    +
                                                                    333  // distribution)
                                                                    +
                                                                    334  INFO_LOG << "Age comp likelihood function successfully set."
                                                                    +
                                                                    335  << std::endl;
                                                                    +
                                                                    336  } else {
                                                                    +
                                                                    337  // Commented out for now as code uses single likelihood function
                                                                    +
                                                                    338  // making this fail valid_model = false; ERROR_LOG << "Error: Expected
                                                                    +
                                                                    339  // age comp likelihood function not defined for fleet "
                                                                    +
                                                                    340  // << f->id << ", likelihood function " << ac_like_id <<
                                                                    +
                                                                    341  // std::endl;
                                                                    +
                                                                    342  // exit(1);
                                                                    +
                                                                    343  }
                                                                    +
                                                                    344 
                                                                    +
                                                                    345  } else {
                                                                    +
                                                                    346  // Commented out for now as code uses single likelihood function making
                                                                    +
                                                                    347  // this fail valid_model = false; ERROR_LOG << "Error: No age comp
                                                                    +
                                                                    348  // likelihood function defined for fleet " << f->id
                                                                    +
                                                                    349  // << ". FIMS requires likelihood functions be defined for all
                                                                    +
                                                                    350  // data." << std::endl;
                                                                    +
                                                                    351  // exit(1);
                                                                    +
                                                                    352  }
                                                                    +
                                                                    353  // end set agecomp likelihood
                                                                    +
                                                                    354 
                                                                    +
                                                                    355  INFO_LOG << "Completed initialization for fleet " << f->id << "."
                                                                    +
                                                                    356  << std::endl;
                                                                    357 
                                                                    -
                                                                    358  //set data objects if distribution is a data type
                                                                    -
                                                                    359  if (d->input_type == "data") {
                                                                    -
                                                                    360  if (d->observed_data_id_m != -999) {
                                                                    -
                                                                    361  uint32_t observed_data_id = static_cast<uint32_t> (d->observed_data_id_m);
                                                                    -
                                                                    362  data_iterator it = this->data_objects.find(observed_data_id);
                                                                    -
                                                                    363 
                                                                    -
                                                                    364  if (it != this->data_objects.end()) {
                                                                    -
                                                                    365  d->observed_values = (*it).second;
                                                                    -
                                                                    366  FIMS_INFO_LOG("Observed data "
                                                                    -
                                                                    367  + fims::to_string(observed_data_id)
                                                                    -
                                                                    368  + " successfully set to density component " + fims::to_string(d->id));
                                                                    -
                                                                    369  } else {
                                                                    -
                                                                    370  valid_model = false;
                                                                    -
                                                                    371  FIMS_ERROR_LOG("Expected data observations not defined for density component "
                                                                    -
                                                                    372  + fims::to_string(d->id) + ", observed data " + fims::to_string(observed_data_id));
                                                                    -
                                                                    373  }
                                                                    -
                                                                    374 
                                                                    -
                                                                    375  } else {
                                                                    -
                                                                    376  valid_model = false;
                                                                    -
                                                                    377  FIMS_ERROR_LOG("No data input for density component" + fims::to_string(d->id));
                                                                    -
                                                                    378  }
                                                                    -
                                                                    379  }
                                                                    -
                                                                    380  // end set data
                                                                    -
                                                                    381  }
                                                                    +
                                                                    358  } // close fleet iterator loop
                                                                    +
                                                                    359  INFO_LOG << "Completed initialization of all fleets." << std::endl;
                                                                    +
                                                                    360 
                                                                    +
                                                                    361  INFO_LOG << "Initializing population objects for "
                                                                    +
                                                                    362  << this->populations.size() << " populations." << std::endl;
                                                                    +
                                                                    363  for (population_iterator it = this->populations.begin();
                                                                    +
                                                                    364  it != this->populations.end(); ++it) {
                                                                    +
                                                                    365  std::shared_ptr<fims_popdy::Population<Type> > p = (*it).second;
                                                                    +
                                                                    366 
                                                                    +
                                                                    367  INFO_LOG << "Setting up links from population " << p->id
                                                                    +
                                                                    368  << " to fleets [ " << std::flush;
                                                                    +
                                                                    369  // error check and set population elements
                                                                    +
                                                                    370  // check me - add another fleet iterator to push information from
                                                                    +
                                                                    371  for (fleet_iterator it = this->fleets.begin(); it != this->fleets.end();
                                                                    +
                                                                    372  ++it) {
                                                                    +
                                                                    373  // Initialize fleet object
                                                                    +
                                                                    374  std::shared_ptr<fims_popdy::Fleet<Type> > f = (*it).second;
                                                                    +
                                                                    375  // population to the individual fleets This is to pass catch at age
                                                                    +
                                                                    376  // from population to fleets?
                                                                    +
                                                                    377  // any shared member in p (population is pushed into fleets)
                                                                    +
                                                                    378  p->fleets.push_back(f);
                                                                    +
                                                                    379  INFO_LOG << f->id << " " << std::flush;
                                                                    +
                                                                    380  }
                                                                    +
                                                                    381  INFO_LOG << "]" << std::endl;
                                                                    382 
                                                                    -
                                                                    383 
                                                                    -
                                                                    384  for (population_iterator it = this->populations.begin();
                                                                    -
                                                                    385  it != this->populations.end(); ++it) {
                                                                    -
                                                                    386  std::shared_ptr<fims_popdy::Population<Type> > p = (*it).second;
                                                                    -
                                                                    387 
                                                                    -
                                                                    388  FIMS_INFO_LOG("Initializing population " + fims::to_string(p->id));
                                                                    -
                                                                    389  // error check and set population elements
                                                                    -
                                                                    390  // check me - add another fleet iterator to push information from
                                                                    -
                                                                    391  for (fleet_iterator it = this->fleets.begin(); it != this->fleets.end();
                                                                    -
                                                                    392  ++it) {
                                                                    -
                                                                    393  // Initialize fleet object
                                                                    -
                                                                    394  std::shared_ptr<fims_popdy::Fleet<Type> > f = (*it).second;
                                                                    -
                                                                    395  // population to the individual fleets This is to pass catch at age
                                                                    -
                                                                    396  // from population to fleets?
                                                                    -
                                                                    397  // any shared member in p (population is pushed into fleets)
                                                                    -
                                                                    398  p->fleets.push_back(f);
                                                                    -
                                                                    399  }
                                                                    -
                                                                    400 
                                                                    -
                                                                    401  p->Initialize(p->nyears, p->nseasons, p->nages);
                                                                    -
                                                                    402 
                                                                    -
                                                                    403  //set information dimensions
                                                                    -
                                                                    404  this->nyears = std::max(this->nyears, p->nyears);
                                                                    -
                                                                    405  this->nages = std::max(this->nages, p->nages);
                                                                    -
                                                                    406  this->nseasons = std::max(this->nseasons, p->nseasons);
                                                                    -
                                                                    407 
                                                                    -
                                                                    408  // set recruitment
                                                                    -
                                                                    409  if (p->recruitment_id != -999) {
                                                                    -
                                                                    410  uint32_t recruitment_uint = static_cast<uint32_t> (p->recruitment_id);
                                                                    -
                                                                    411  recruitment_models_iterator it =
                                                                    -
                                                                    412  this->recruitment_models.find(recruitment_uint);
                                                                    -
                                                                    413 
                                                                    -
                                                                    414  if (it != this->recruitment_models.end()) {
                                                                    -
                                                                    415  p->recruitment =
                                                                    -
                                                                    416  (*it).second; // recruitment defined in population.hpp
                                                                    -
                                                                    417  FIMS_INFO_LOG("Recruitment model "
                                                                    -
                                                                    418  + fims::to_string(recruitment_uint)
                                                                    -
                                                                    419  + " successfully set to population "
                                                                    -
                                                                    420  + fims::to_string(p->id));
                                                                    -
                                                                    421  } else {
                                                                    -
                                                                    422  valid_model = false;
                                                                    -
                                                                    423  FIMS_ERROR_LOG("Expected recruitment function not defined for "
                                                                    -
                                                                    424  "population "
                                                                    -
                                                                    425  + fims::to_string(p->id) + ", recruitment function "
                                                                    -
                                                                    426  + fims::to_string(recruitment_uint));
                                                                    -
                                                                    427  }
                                                                    -
                                                                    428 
                                                                    -
                                                                    429  } else {
                                                                    -
                                                                    430  valid_model = false;
                                                                    -
                                                                    431  FIMS_ERROR_LOG("No recruitment function defined for population "
                                                                    -
                                                                    432  + fims::to_string(p->id)
                                                                    -
                                                                    433  + ". FIMS requires recruitment functions be defined for all "
                                                                    -
                                                                    434  "populations.");
                                                                    -
                                                                    435  }
                                                                    -
                                                                    436 
                                                                    -
                                                                    437  // set growth
                                                                    -
                                                                    438  if (p->growth_id != -999) {
                                                                    -
                                                                    439  uint32_t growth_uint = static_cast<uint32_t> (p->growth_id);
                                                                    -
                                                                    440  growth_models_iterator it = this->growth_models.find(
                                                                    -
                                                                    441  growth_uint); // growth_models is specified in information.hpp
                                                                    -
                                                                    442  // and used in rcpp
                                                                    -
                                                                    443  // at the head of information.hpp; are the
                                                                    -
                                                                    444  // dimensions of ages defined in rcpp or where?
                                                                    -
                                                                    445  if (it != this->growth_models.end()) {
                                                                    -
                                                                    446  p->growth =
                                                                    -
                                                                    447  (*it).second; // growth defined in population.hpp (the object
                                                                    -
                                                                    448  // is called p, growth is within p)
                                                                    -
                                                                    449  FIMS_INFO_LOG("Growth model "
                                                                    -
                                                                    450  + fims::to_string(growth_uint)
                                                                    -
                                                                    451  + " successfully set to population " + fims::to_string(p->id));
                                                                    -
                                                                    452  } else {
                                                                    -
                                                                    453  valid_model = false;
                                                                    -
                                                                    454  FIMS_ERROR_LOG("Expected growth function not defined for population "
                                                                    -
                                                                    455  + fims::to_string(p->id) + ", growth function "
                                                                    -
                                                                    456  + fims::to_string(growth_uint));
                                                                    -
                                                                    457  }
                                                                    -
                                                                    458 
                                                                    -
                                                                    459  } else {
                                                                    -
                                                                    460  valid_model = false;
                                                                    -
                                                                    461  FIMS_ERROR_LOG("No growth function defined for population "
                                                                    -
                                                                    462  + fims::to_string(p->id)
                                                                    -
                                                                    463  + ". FIMS requires growth functions be defined for all "
                                                                    -
                                                                    464  "populations.");
                                                                    -
                                                                    465  }
                                                                    -
                                                                    466 
                                                                    -
                                                                    467  // set maturity
                                                                    -
                                                                    468  if (p->maturity_id != -999) {
                                                                    -
                                                                    469  uint32_t maturity_uint = static_cast<uint32_t> (p->maturity_id);
                                                                    -
                                                                    470  maturity_models_iterator it = this->maturity_models.find(
                                                                    -
                                                                    471  maturity_uint); // >maturity_models is specified in
                                                                    -
                                                                    472  // information.hpp and used in rcpp
                                                                    -
                                                                    473  if (it != this->maturity_models.end()) {
                                                                    -
                                                                    474  p->maturity = (*it).second; // >maturity defined in population.hpp
                                                                    -
                                                                    475  FIMS_INFO_LOG("Maturity model "
                                                                    -
                                                                    476  + fims::to_string(maturity_uint)
                                                                    -
                                                                    477  + " successfully set to population " + fims::to_string(p->id));
                                                                    -
                                                                    478  } else {
                                                                    -
                                                                    479  valid_model = false;
                                                                    -
                                                                    480  FIMS_ERROR_LOG("Expected maturity function not defined for population "
                                                                    -
                                                                    481  + fims::to_string(p->id) + ", maturity function "
                                                                    -
                                                                    482  + fims::to_string(maturity_uint));
                                                                    -
                                                                    483  }
                                                                    -
                                                                    484  } else {
                                                                    +
                                                                    383  INFO_LOG << "Initializing population " << p->id << "." << std::endl;
                                                                    +
                                                                    384  p->Initialize(p->nyears, p->nseasons, p->nages);
                                                                    +
                                                                    385 
                                                                    +
                                                                    386  INFO_LOG << "Checking for available recruitment function." << std::endl;
                                                                    +
                                                                    387  // set recruitment
                                                                    +
                                                                    388  if (p->recruitment_id != -999) {
                                                                    +
                                                                    389  uint32_t recruitment_uint = static_cast<uint32_t>(p->recruitment_id);
                                                                    +
                                                                    390  recruitment_models_iterator it =
                                                                    +
                                                                    391  this->recruitment_models.find(recruitment_uint);
                                                                    +
                                                                    392  INFO_LOG << "Input recruitment id = " << recruitment_uint << "."
                                                                    +
                                                                    393  << std::endl;
                                                                    +
                                                                    394  if (it != this->recruitment_models.end()) {
                                                                    +
                                                                    395  p->recruitment =
                                                                    +
                                                                    396  (*it).second; // recruitment defined in population.hpp
                                                                    +
                                                                    397  INFO_LOG << "Recruitment function successfully set." << std::endl;
                                                                    +
                                                                    398  } else {
                                                                    +
                                                                    399  valid_model = false;
                                                                    +
                                                                    400  ERROR_LOG << "Error: Expected recruitment function not defined for "
                                                                    +
                                                                    401  "population "
                                                                    +
                                                                    402  << p->id << ", recruitment function " << recruitment_uint
                                                                    +
                                                                    403  << std::endl;
                                                                    +
                                                                    404  exit(1);
                                                                    +
                                                                    405  }
                                                                    +
                                                                    406 
                                                                    +
                                                                    407  } else {
                                                                    +
                                                                    408  valid_model = false;
                                                                    +
                                                                    409  ERROR_LOG << "Error: No recruitment function defined for population "
                                                                    +
                                                                    410  << p->id
                                                                    +
                                                                    411  << ". FIMS requires recruitment functions be defined for all "
                                                                    +
                                                                    412  "populations."
                                                                    +
                                                                    413  << std::endl;
                                                                    +
                                                                    414  exit(1);
                                                                    +
                                                                    415  }
                                                                    +
                                                                    416 
                                                                    +
                                                                    417  INFO_LOG << "Checking for available growth function." << std::endl;
                                                                    +
                                                                    418  // set growth
                                                                    +
                                                                    419  if (p->growth_id != -999) {
                                                                    +
                                                                    420  uint32_t growth_uint = static_cast<uint32_t>(p->growth_id);
                                                                    +
                                                                    421  growth_models_iterator it = this->growth_models.find(
                                                                    +
                                                                    422  growth_uint); // growth_models is specified in information.hpp
                                                                    +
                                                                    423  // and used in rcpp
                                                                    +
                                                                    424  // at the head of information.hpp; are the
                                                                    +
                                                                    425  // dimensions of ages defined in rcpp or where?
                                                                    +
                                                                    426  INFO_LOG << "Input growth id = " << growth_uint << "." << std::endl;
                                                                    +
                                                                    427  if (it != this->growth_models.end()) {
                                                                    +
                                                                    428  p->growth =
                                                                    +
                                                                    429  (*it).second; // growth defined in population.hpp (the object
                                                                    +
                                                                    430  // is called p, growth is within p)
                                                                    +
                                                                    431  INFO_LOG << "Growth function successfully set." << std::endl;
                                                                    +
                                                                    432  } else {
                                                                    +
                                                                    433  valid_model = false;
                                                                    +
                                                                    434  ERROR_LOG
                                                                    +
                                                                    435  << "Error: Expected growth function not defined for population "
                                                                    +
                                                                    436  << p->id << ", growth function " << growth_uint << std::endl;
                                                                    +
                                                                    437  exit(1);
                                                                    +
                                                                    438  }
                                                                    +
                                                                    439 
                                                                    +
                                                                    440  } else {
                                                                    +
                                                                    441  valid_model = false;
                                                                    +
                                                                    442  ERROR_LOG << "Error: No growth function defined for population "
                                                                    +
                                                                    443  << p->id
                                                                    +
                                                                    444  << ". FIMS requires growth functions be defined for all "
                                                                    +
                                                                    445  "populations."
                                                                    +
                                                                    446  << std::endl;
                                                                    +
                                                                    447  exit(1);
                                                                    +
                                                                    448  }
                                                                    +
                                                                    449 
                                                                    +
                                                                    450  INFO_LOG << "Checking for available maturity function." << std::endl;
                                                                    +
                                                                    451  // set maturity
                                                                    +
                                                                    452  if (p->maturity_id != -999) {
                                                                    +
                                                                    453  uint32_t maturity_uint = static_cast<uint32_t>(p->maturity_id);
                                                                    +
                                                                    454  maturity_models_iterator it = this->maturity_models.find(
                                                                    +
                                                                    455  maturity_uint); // >maturity_models is specified in
                                                                    +
                                                                    456  // information.hpp and used in rcpp
                                                                    +
                                                                    457  INFO_LOG << "Input maturity id = " << maturity_uint << "." << std::endl;
                                                                    +
                                                                    458  if (it != this->maturity_models.end()) {
                                                                    +
                                                                    459  p->maturity = (*it).second; // >maturity defined in population.hpp
                                                                    +
                                                                    460  INFO_LOG << "Maturity function successfully set." << std::endl;
                                                                    +
                                                                    461  } else {
                                                                    +
                                                                    462  valid_model = false;
                                                                    +
                                                                    463  ERROR_LOG
                                                                    +
                                                                    464  << "Error: Expected maturity function not defined for population "
                                                                    +
                                                                    465  << p->id << ", maturity function " << maturity_uint << std::endl;
                                                                    +
                                                                    466  exit(1);
                                                                    +
                                                                    467  }
                                                                    +
                                                                    468 
                                                                    +
                                                                    469  } else {
                                                                    +
                                                                    470  valid_model = false;
                                                                    +
                                                                    471  ERROR_LOG << "Error: No maturity function defined for population "
                                                                    +
                                                                    472  << p->id
                                                                    +
                                                                    473  << ". FIMS requires maturity functions be defined for all "
                                                                    +
                                                                    474  "populations."
                                                                    +
                                                                    475  << std::endl;
                                                                    +
                                                                    476  exit(1);
                                                                    +
                                                                    477  }
                                                                    +
                                                                    478  INFO_LOG << "Completed initialization for population " << p->id << "."
                                                                    +
                                                                    479  << std::endl;
                                                                    +
                                                                    480  }
                                                                    +
                                                                    481  INFO_LOG << "Completed initialization of all populations." << std::endl;
                                                                    +
                                                                    482  INFO_LOG << "Completed FIMS model creation." << std::endl;
                                                                    +
                                                                    483  return valid_model;
                                                                    +
                                                                    484  }
                                                                    485 
                                                                    -
                                                                    486  valid_model = false;
                                                                    -
                                                                    487  FIMS_ERROR_LOG("No maturity function defined for population "
                                                                    -
                                                                    488  + fims::to_string(p->id)
                                                                    -
                                                                    489  + ". FIMS requires maturity functions be defined for all "
                                                                    -
                                                                    490  "populations.");
                                                                    -
                                                                    491  }
                                                                    +
                                                                    491  size_t GetNages() const { return nages; }
                                                                    492 
                                                                    -
                                                                    493  }
                                                                    -
                                                                    494 
                                                                    -
                                                                    495  //setup priors, random effect, and data density components
                                                                    -
                                                                    496  setup_priors();
                                                                    -
                                                                    497 
                                                                    -
                                                                    498 
                                                                    -
                                                                    499  return valid_model;
                                                                    -
                                                                    500  }
                                                                    -
                                                                    501 
                                                                    -
                                                                    507  size_t GetNages() const {
                                                                    -
                                                                    508 
                                                                    -
                                                                    509  return nages;
                                                                    -
                                                                    510  }
                                                                    -
                                                                    511 
                                                                    -
                                                                    517  void SetNages(size_t nages) {
                                                                    -
                                                                    518 
                                                                    -
                                                                    519  this->nages = nages;
                                                                    -
                                                                    520  }
                                                                    -
                                                                    521 
                                                                    -
                                                                    527  size_t GetNseasons() const {
                                                                    -
                                                                    528 
                                                                    -
                                                                    529  return nseasons;
                                                                    -
                                                                    530  }
                                                                    -
                                                                    531 
                                                                    -
                                                                    537  void SetNseasons(size_t nseasons) {
                                                                    -
                                                                    538 
                                                                    -
                                                                    539  this->nseasons = nseasons;
                                                                    -
                                                                    540  }
                                                                    -
                                                                    541 
                                                                    -
                                                                    547  size_t GetNyears() const {
                                                                    -
                                                                    548 
                                                                    -
                                                                    549  return nyears;
                                                                    -
                                                                    550  }
                                                                    -
                                                                    551 
                                                                    -
                                                                    557  void SetNyears(size_t nyears) {
                                                                    -
                                                                    558 
                                                                    -
                                                                    559  this->nyears = nyears;
                                                                    -
                                                                    560  }
                                                                    -
                                                                    561 
                                                                    -
                                                                    567  std::vector<Type*>& GetParameters() {
                                                                    -
                                                                    568 
                                                                    -
                                                                    569  return parameters;
                                                                    -
                                                                    570  }
                                                                    -
                                                                    571 
                                                                    -
                                                                    577  std::vector<Type*>& GetFixedEffectsParameters() {
                                                                    -
                                                                    578 
                                                                    -
                                                                    579  return fixed_effects_parameters;
                                                                    -
                                                                    580  }
                                                                    -
                                                                    581 
                                                                    -
                                                                    587  std::vector<Type*>& GetRandomEffectsParameters() {
                                                                    -
                                                                    588  return random_effects_parameters;
                                                                    -
                                                                    589  }
                                                                    -
                                                                    590  };
                                                                    -
                                                                    591 
                                                                    -
                                                                    592  template <typename Type>
                                                                    -
                                                                    593  std::shared_ptr<Information<Type> > Information<Type>::fims_information =
                                                                    -
                                                                    594  nullptr; // singleton instance
                                                                    -
                                                                    595 
                                                                    -
                                                                    596 } // namespace fims_info
                                                                    -
                                                                    597 
                                                                    -
                                                                    598 #endif /* FIMS_COMMON_INFORMATION_HPP */
                                                                    -
                                                                    fims_info::Information
                                                                    Stores FIMS model information and creates model. Contains all objects and data pre-model construction...
                                                                    Definition: information.hpp:34
                                                                    -
                                                                    fims_info::Information::populations
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > > populations
                                                                    Definition: information.hpp:102
                                                                    -
                                                                    fims_info::Information::random_effects_parameters
                                                                    std::vector< Type * > random_effects_parameters
                                                                    Definition: information.hpp:44
                                                                    -
                                                                    fims_info::Information::nages
                                                                    size_t nages
                                                                    Definition: information.hpp:38
                                                                    -
                                                                    fims_info::Information::recruitment_models_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > >::iterator recruitment_models_iterator
                                                                    Definition: information.hpp:63
                                                                    -
                                                                    fims_info::Information::setup_priors
                                                                    void setup_priors()
                                                                    Definition: information.hpp:173
                                                                    -
                                                                    fims_info::Information::fleets
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > > fleets
                                                                    Definition: information.hpp:92
                                                                    -
                                                                    fims_info::Information::growth_models
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::GrowthBase< Type > > > growth_models
                                                                    Definition: information.hpp:75
                                                                    -
                                                                    fims_info::Information::selectivity_models_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::SelectivityBase< Type > > >::iterator selectivity_models_iterator
                                                                    Definition: information.hpp:71
                                                                    -
                                                                    fims_info::Information::RegisterParameter
                                                                    void RegisterParameter(Type &p)
                                                                    Definition: information.hpp:148
                                                                    -
                                                                    fims_info::Information::density_components_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_distributions::DensityComponentBase< Type > > >::iterator density_components_iterator
                                                                    Definition: information.hpp:117
                                                                    -
                                                                    fims_info::Information::density_components
                                                                    std::map< uint32_t, std::shared_ptr< fims_distributions::DensityComponentBase< Type > > > density_components
                                                                    Definition: information.hpp:112
                                                                    -
                                                                    fims_info::Information::RegisterRandomEffect
                                                                    void RegisterRandomEffect(Type &re)
                                                                    Definition: information.hpp:157
                                                                    -
                                                                    fims_info::Information::SetNyears
                                                                    void SetNyears(size_t nyears)
                                                                    Set the Nyears object.
                                                                    Definition: information.hpp:557
                                                                    -
                                                                    fims_info::Information::GetNages
                                                                    size_t GetNages() const
                                                                    Get the Nages object.
                                                                    Definition: information.hpp:507
                                                                    -
                                                                    fims_info::Information::fleet_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >::iterator fleet_iterator
                                                                    Definition: information.hpp:97
                                                                    -
                                                                    fims_info::Information::variable_map
                                                                    std::unordered_map< uint32_t, fims::Vector< Type > * > variable_map
                                                                    Definition: information.hpp:121
                                                                    -
                                                                    fims_info::Information::population_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > >::iterator population_iterator
                                                                    Definition: information.hpp:106
                                                                    -
                                                                    fims_info::Information::variable_map_iterator
                                                                    std::unordered_map< uint32_t, fims::Vector< Type > * >::iterator variable_map_iterator
                                                                    Definition: information.hpp:124
                                                                    -
                                                                    fims_info::Information::nseasons
                                                                    size_t nseasons
                                                                    Definition: information.hpp:37
                                                                    -
                                                                    fims_info::Information::data_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_data_object::DataObject< Type > > >::iterator data_iterator
                                                                    Definition: information.hpp:55
                                                                    -
                                                                    fims_info::Information::selectivity_models
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::SelectivityBase< Type > > > selectivity_models
                                                                    Definition: information.hpp:67
                                                                    -
                                                                    fims_info::Information::CreateModel
                                                                    bool CreateModel()
                                                                    Definition: information.hpp:256
                                                                    -
                                                                    fims_info::Information::GetNseasons
                                                                    size_t GetNseasons() const
                                                                    Get the Nseasons object.
                                                                    Definition: information.hpp:527
                                                                    -
                                                                    fims_info::Information::setup_random_effects
                                                                    void setup_random_effects()
                                                                    Definition: information.hpp:197
                                                                    -
                                                                    fims_info::Information::GetFixedEffectsParameters
                                                                    std::vector< Type * > & GetFixedEffectsParameters()
                                                                    Get the Fixed Effects Parameters object.
                                                                    Definition: information.hpp:577
                                                                    -
                                                                    fims_info::Information::maturity_models_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::MaturityBase< Type > > >::iterator maturity_models_iterator
                                                                    Definition: information.hpp:87
                                                                    -
                                                                    fims_info::Information::setup_data
                                                                    void setup_data()
                                                                    Definition: information.hpp:222
                                                                    -
                                                                    fims_info::Information::parameters
                                                                    std::vector< Type * > parameters
                                                                    Definition: information.hpp:42
                                                                    -
                                                                    fims_info::Information::nyears
                                                                    size_t nyears
                                                                    Definition: information.hpp:36
                                                                    -
                                                                    fims_info::Information::parameter_names
                                                                    std::vector< std::string > parameter_names
                                                                    Definition: information.hpp:48
                                                                    -
                                                                    fims_info::Information::maturity_models
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::MaturityBase< Type > > > maturity_models
                                                                    Definition: information.hpp:83
                                                                    -
                                                                    fims_info::Information::GetParameters
                                                                    std::vector< Type * > & GetParameters()
                                                                    Get the Parameters object.
                                                                    Definition: information.hpp:567
                                                                    -
                                                                    fims_info::Information::GetRandomEffectsParameters
                                                                    std::vector< Type * > & GetRandomEffectsParameters()
                                                                    Get the Random Effects Parameters object.
                                                                    Definition: information.hpp:587
                                                                    -
                                                                    fims_info::Information::GetNyears
                                                                    size_t GetNyears() const
                                                                    Get the Nyears object.
                                                                    Definition: information.hpp:547
                                                                    -
                                                                    fims_info::Information::RegisterParameterName
                                                                    void RegisterParameterName(std::string p_name)
                                                                    Definition: information.hpp:166
                                                                    -
                                                                    fims_info::Information::growth_models_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::GrowthBase< Type > > >::iterator growth_models_iterator
                                                                    Definition: information.hpp:79
                                                                    -
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:135
                                                                    -
                                                                    fims_info::Information::fims_information
                                                                    static std::shared_ptr< Information< Type > > fims_information
                                                                    Definition: information.hpp:41
                                                                    -
                                                                    fims_info::Information::recruitment_models
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > > recruitment_models
                                                                    Definition: information.hpp:59
                                                                    -
                                                                    fims_info::Information::fixed_effects_parameters
                                                                    std::vector< Type * > fixed_effects_parameters
                                                                    Definition: information.hpp:46
                                                                    -
                                                                    fims_info::Information::SetNseasons
                                                                    void SetNseasons(size_t nseasons)
                                                                    Set the Nseasons object.
                                                                    Definition: information.hpp:537
                                                                    -
                                                                    fims_info::Information::SetNages
                                                                    void SetNages(size_t nages)
                                                                    Set the Nages object.
                                                                    Definition: information.hpp:517
                                                                    -
                                                                    fims_info::Information::data_objects
                                                                    std::map< uint32_t, std::shared_ptr< fims_data_object::DataObject< Type > > > data_objects
                                                                    Definition: information.hpp:52
                                                                    -
                                                                    def.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    FIMS_INFO_LOG
                                                                    #define FIMS_INFO_LOG(MESSAGE)
                                                                    Definition: def.hpp:557
                                                                    -
                                                                    FIMS_ERROR_LOG
                                                                    #define FIMS_ERROR_LOG(MESSAGE)
                                                                    Definition: def.hpp:561
                                                                    -
                                                                    fims_vector.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    model_object.hpp
                                                                    TODO: provide a brief description.
                                                                    +
                                                                    498  void SetNages(size_t nages) { this->nages = nages; }
                                                                    +
                                                                    499 
                                                                    +
                                                                    505  size_t GetNseasons() const { return nseasons; }
                                                                    +
                                                                    506 
                                                                    +
                                                                    512  void SetNseasons(size_t nseasons) { this->nseasons = nseasons; }
                                                                    +
                                                                    513 
                                                                    +
                                                                    519  size_t GetNyears() const { return nyears; }
                                                                    +
                                                                    520 
                                                                    +
                                                                    526  void SetNyears(size_t nyears) { this->nyears = nyears; }
                                                                    +
                                                                    527 
                                                                    +
                                                                    533  std::vector<Type*>& GetParameters() { return parameters; }
                                                                    +
                                                                    534 
                                                                    +
                                                                    540  std::vector<Type*>& GetFixedEffectsParameters() {
                                                                    +
                                                                    541  return fixed_effects_parameters;
                                                                    +
                                                                    542  }
                                                                    +
                                                                    543 
                                                                    +
                                                                    549  std::vector<Type*>& GetRandomEffectsParameters() {
                                                                    +
                                                                    550  return random_effects_parameters;
                                                                    +
                                                                    551  }
                                                                    +
                                                                    552 };
                                                                    +
                                                                    553 
                                                                    +
                                                                    554 template <typename Type>
                                                                    +
                                                                    555 std::shared_ptr<Information<Type> > Information<Type>::fims_information =
                                                                    +
                                                                    556  nullptr; // singleton instance
                                                                    +
                                                                    557 
                                                                    +
                                                                    558 } // namespace fims_info
                                                                    +
                                                                    559 
                                                                    +
                                                                    560 #endif /* FIMS_COMMON_INFORMATION_HPP */
                                                                    +
                                                                    fims_info::Information
                                                                    Stores FIMS model information and creates model. Contains all objects and data pre-model construction...
                                                                    Definition: information.hpp:33
                                                                    +
                                                                    fims_info::Information::populations
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > > populations
                                                                    Definition: information.hpp:99
                                                                    +
                                                                    fims_info::Information::random_effects_parameters
                                                                    std::vector< Type * > random_effects_parameters
                                                                    Definition: information.hpp:43
                                                                    +
                                                                    fims_info::Information::nages
                                                                    size_t nages
                                                                    Definition: information.hpp:37
                                                                    +
                                                                    fims_info::Information::recruitment_models_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > >::iterator recruitment_models_iterator
                                                                    Definition: information.hpp:60
                                                                    +
                                                                    fims_info::Information::fleets
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > > fleets
                                                                    Definition: information.hpp:89
                                                                    +
                                                                    fims_info::Information::growth_models
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::GrowthBase< Type > > > growth_models
                                                                    Definition: information.hpp:72
                                                                    +
                                                                    fims_info::Information::selectivity_models_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::SelectivityBase< Type > > >::iterator selectivity_models_iterator
                                                                    Definition: information.hpp:68
                                                                    +
                                                                    fims_info::Information::distribution_models
                                                                    std::map< uint32_t, std::shared_ptr< fims_distributions::DistributionsBase< Type > > > distribution_models
                                                                    Definition: information.hpp:109
                                                                    +
                                                                    fims_info::Information::RegisterParameter
                                                                    void RegisterParameter(Type &p)
                                                                    Definition: information.hpp:139
                                                                    +
                                                                    fims_info::Information::RegisterRandomEffect
                                                                    void RegisterRandomEffect(Type &re)
                                                                    Definition: information.hpp:148
                                                                    +
                                                                    fims_info::Information::SetNyears
                                                                    void SetNyears(size_t nyears)
                                                                    Set the Nyears object.
                                                                    Definition: information.hpp:526
                                                                    +
                                                                    fims_info::Information::GetNages
                                                                    size_t GetNages() const
                                                                    Get the Nages object.
                                                                    Definition: information.hpp:491
                                                                    +
                                                                    fims_info::Information::fleet_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >::iterator fleet_iterator
                                                                    Definition: information.hpp:94
                                                                    +
                                                                    fims_info::Information::population_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > >::iterator population_iterator
                                                                    Definition: information.hpp:103
                                                                    +
                                                                    fims_info::Information::nseasons
                                                                    size_t nseasons
                                                                    Definition: information.hpp:36
                                                                    +
                                                                    fims_info::Information::data_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_data_object::DataObject< Type > > >::iterator data_iterator
                                                                    Definition: information.hpp:52
                                                                    +
                                                                    fims_info::Information::selectivity_models
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::SelectivityBase< Type > > > selectivity_models
                                                                    Definition: information.hpp:64
                                                                    +
                                                                    fims_info::Information::CreateModel
                                                                    bool CreateModel()
                                                                    Definition: information.hpp:162
                                                                    +
                                                                    fims_info::Information::GetNseasons
                                                                    size_t GetNseasons() const
                                                                    Get the Nseasons object.
                                                                    Definition: information.hpp:505
                                                                    +
                                                                    fims_info::Information::distribution_models_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_distributions::DistributionsBase< Type > > >::iterator distribution_models_iterator
                                                                    Definition: information.hpp:114
                                                                    +
                                                                    fims_info::Information::GetFixedEffectsParameters
                                                                    std::vector< Type * > & GetFixedEffectsParameters()
                                                                    Get the Fixed Effects Parameters object.
                                                                    Definition: information.hpp:540
                                                                    +
                                                                    fims_info::Information::maturity_models_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::MaturityBase< Type > > >::iterator maturity_models_iterator
                                                                    Definition: information.hpp:84
                                                                    +
                                                                    fims_info::Information::parameters
                                                                    std::vector< Type * > parameters
                                                                    Definition: information.hpp:41
                                                                    +
                                                                    fims_info::Information::nyears
                                                                    size_t nyears
                                                                    Definition: information.hpp:35
                                                                    +
                                                                    fims_info::Information::maturity_models
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::MaturityBase< Type > > > maturity_models
                                                                    Definition: information.hpp:80
                                                                    +
                                                                    fims_info::Information::GetParameters
                                                                    std::vector< Type * > & GetParameters()
                                                                    Get the Parameters object.
                                                                    Definition: information.hpp:533
                                                                    +
                                                                    fims_info::Information::GetRandomEffectsParameters
                                                                    std::vector< Type * > & GetRandomEffectsParameters()
                                                                    Get the Random Effects Parameters object.
                                                                    Definition: information.hpp:549
                                                                    +
                                                                    fims_info::Information::GetNyears
                                                                    size_t GetNyears() const
                                                                    Get the Nyears object.
                                                                    Definition: information.hpp:519
                                                                    +
                                                                    fims_info::Information::growth_models_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::GrowthBase< Type > > >::iterator growth_models_iterator
                                                                    Definition: information.hpp:76
                                                                    +
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:126
                                                                    +
                                                                    fims_info::Information::fims_information
                                                                    static std::shared_ptr< Information< Type > > fims_information
                                                                    Definition: information.hpp:40
                                                                    +
                                                                    fims_info::Information::recruitment_models
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > > recruitment_models
                                                                    Definition: information.hpp:56
                                                                    +
                                                                    fims_info::Information::fixed_effects_parameters
                                                                    std::vector< Type * > fixed_effects_parameters
                                                                    Definition: information.hpp:45
                                                                    +
                                                                    fims_info::Information::SetNseasons
                                                                    void SetNseasons(size_t nseasons)
                                                                    Set the Nseasons object.
                                                                    Definition: information.hpp:512
                                                                    +
                                                                    fims_info::Information::SetNages
                                                                    void SetNages(size_t nages)
                                                                    Set the Nages object.
                                                                    Definition: information.hpp:498
                                                                    +
                                                                    fims_info::Information::data_objects
                                                                    std::map< uint32_t, std::shared_ptr< fims_data_object::DataObject< Type > > > data_objects
                                                                    Definition: information.hpp:49
                                                                    + +
                                                                    ERROR_LOG
                                                                    std::ofstream ERROR_LOG("logs/error.log")
                                                                    +
                                                                    DATA_LOG
                                                                    std::ofstream DATA_LOG("logs/data.log")
                                                                    +
                                                                    INFO_LOG
                                                                    std::ofstream INFO_LOG("logs/info.log")
                                                                    diff --git a/docs/init_8hpp_source.html b/docs/init_8hpp_source.html index 04683fd..74a90e4 100644 --- a/docs/init_8hpp_source.html +++ b/docs/init_8hpp_source.html @@ -76,58 +76,51 @@
                                                                    init.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    8 #ifndef INTERFACE_INIT_HPP
                                                                    -
                                                                    9 #define INTERFACE_INIT_HPP
                                                                    -
                                                                    10 #include <R_ext/Rdynload.h>
                                                                    -
                                                                    11 #include <stdlib.h>
                                                                    -
                                                                    12 
                                                                    -
                                                                    18 #ifndef TMB_CALLDEFS
                                                                    -
                                                                    19 #define TMB_CALLDEFS \
                                                                    -
                                                                    20  {"MakeADFunObject", (DL_FUNC)&MakeADFunObject, 4}, \
                                                                    -
                                                                    21  {"InfoADFunObject", (DL_FUNC)&InfoADFunObject, 1}, \
                                                                    -
                                                                    22  {"EvalADFunObject", (DL_FUNC)&EvalADFunObject, 3}, \
                                                                    -
                                                                    23  {"MakeDoubleFunObject", (DL_FUNC)&MakeDoubleFunObject, 3}, \
                                                                    -
                                                                    24  {"EvalDoubleFunObject", (DL_FUNC)&EvalDoubleFunObject, 3}, \
                                                                    -
                                                                    25  {"getParameterOrder", (DL_FUNC)&getParameterOrder, 3}, \
                                                                    -
                                                                    26  {"MakeADGradObject", (DL_FUNC)&MakeADGradObject, 3}, \
                                                                    -
                                                                    27  {"MakeADHessObject2", (DL_FUNC)&MakeADHessObject2, 4}, \
                                                                    -
                                                                    28  {"usingAtomics", (DL_FUNC)&usingAtomics, 0}, { \
                                                                    -
                                                                    29  "TMBconfig", (DL_FUNC)&TMBconfig, 2 \
                                                                    -
                                                                    30  }
                                                                    -
                                                                    31 #endif
                                                                    -
                                                                    32 
                                                                    -
                                                                    37 #define CALLDEF(name, n) \
                                                                    -
                                                                    38  { #name, (DL_FUNC)&name, n }
                                                                    -
                                                                    39 
                                                                    -
                                                                    40 extern "C" {
                                                                    -
                                                                    41 
                                                                    -
                                                                    49 SEXP compois_calc_var(SEXP mean, SEXP nu);
                                                                    -
                                                                    55 SEXP omp_check();
                                                                    -
                                                                    61 SEXP omp_num_threads(SEXP);
                                                                    -
                                                                    67 SEXP _rcpp_module_boot_fims();
                                                                    -
                                                                    68 
                                                                    -
                                                                    74 static const R_CallMethodDef CallEntries[] = {
                                                                    -
                                                                    75  TMB_CALLDEFS,
                                                                    -
                                                                    76  {"_rcpp_module_boot_fims", (DL_FUNC)&_rcpp_module_boot_fims, 0},
                                                                    -
                                                                    77  {NULL, NULL, 0}};
                                                                    -
                                                                    78 
                                                                    -
                                                                    85 void R_init_FIMS(DllInfo *dll) {
                                                                    -
                                                                    86  R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
                                                                    -
                                                                    87  R_useDynamicSymbols(dll, FALSE);
                                                                    -
                                                                    88 #ifdef TMB_CCALLABLES
                                                                    -
                                                                    89  TMB_CCALLABLES("FIMS");
                                                                    -
                                                                    90 #endif
                                                                    -
                                                                    91 }
                                                                    -
                                                                    92 }
                                                                    -
                                                                    93 
                                                                    -
                                                                    94 #endif
                                                                    -
                                                                    TMB_CALLDEFS
                                                                    #define TMB_CALLDEFS
                                                                    Definition: init.hpp:19
                                                                    -
                                                                    compois_calc_var
                                                                    SEXP compois_calc_var(SEXP mean, SEXP nu)
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    _rcpp_module_boot_fims
                                                                    SEXP _rcpp_module_boot_fims()
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    omp_check
                                                                    SEXP omp_check()
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    omp_num_threads
                                                                    SEXP omp_num_threads(SEXP)
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    R_init_FIMS
                                                                    void R_init_FIMS(DllInfo *dll)
                                                                    Definition: init.hpp:85
                                                                    +
                                                                    1 #ifndef INTERFACE_INIT_HPP
                                                                    +
                                                                    2 #define INTERFACE_INIT_HPP
                                                                    +
                                                                    3 #include <R_ext/Rdynload.h>
                                                                    +
                                                                    4 #include <stdlib.h>
                                                                    +
                                                                    5 
                                                                    +
                                                                    11 #ifndef TMB_CALLDEFS
                                                                    +
                                                                    12 #define TMB_CALLDEFS \
                                                                    +
                                                                    13  {"MakeADFunObject", (DL_FUNC)&MakeADFunObject, 4}, \
                                                                    +
                                                                    14  {"InfoADFunObject", (DL_FUNC)&InfoADFunObject, 1}, \
                                                                    +
                                                                    15  {"EvalADFunObject", (DL_FUNC)&EvalADFunObject, 3}, \
                                                                    +
                                                                    16  {"MakeDoubleFunObject", (DL_FUNC)&MakeDoubleFunObject, 3}, \
                                                                    +
                                                                    17  {"EvalDoubleFunObject", (DL_FUNC)&EvalDoubleFunObject, 3}, \
                                                                    +
                                                                    18  {"getParameterOrder", (DL_FUNC)&getParameterOrder, 3}, \
                                                                    +
                                                                    19  {"MakeADGradObject", (DL_FUNC)&MakeADGradObject, 3}, \
                                                                    +
                                                                    20  {"MakeADHessObject2", (DL_FUNC)&MakeADHessObject2, 4}, \
                                                                    +
                                                                    21  {"usingAtomics", (DL_FUNC)&usingAtomics, 0}, { \
                                                                    +
                                                                    22  "TMBconfig", (DL_FUNC)&TMBconfig, 2 \
                                                                    +
                                                                    23  }
                                                                    +
                                                                    24 #endif
                                                                    +
                                                                    25 
                                                                    +
                                                                    26 #define CALLDEF(name, n) \
                                                                    +
                                                                    27  { #name, (DL_FUNC)&name, n }
                                                                    +
                                                                    28 
                                                                    +
                                                                    29 extern "C" {
                                                                    +
                                                                    30 
                                                                    +
                                                                    31 SEXP compois_calc_var(SEXP mean, SEXP nu);
                                                                    +
                                                                    32 SEXP omp_check();
                                                                    +
                                                                    33 SEXP omp_num_threads(SEXP);
                                                                    +
                                                                    34 SEXP _rcpp_module_boot_fims();
                                                                    +
                                                                    35 
                                                                    +
                                                                    41 static const R_CallMethodDef CallEntries[] = {
                                                                    +
                                                                    42  TMB_CALLDEFS,
                                                                    +
                                                                    43  {"_rcpp_module_boot_fims", (DL_FUNC)&_rcpp_module_boot_fims, 0},
                                                                    +
                                                                    44  {NULL, NULL, 0}};
                                                                    +
                                                                    45 
                                                                    +
                                                                    52 void R_init_FIMS(DllInfo *dll) {
                                                                    +
                                                                    53  R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
                                                                    +
                                                                    54  R_useDynamicSymbols(dll, FALSE);
                                                                    +
                                                                    55 #ifdef TMB_CCALLABLES
                                                                    +
                                                                    56  TMB_CCALLABLES("FIMS");
                                                                    +
                                                                    57 #endif
                                                                    +
                                                                    58 }
                                                                    +
                                                                    59 }
                                                                    +
                                                                    60 
                                                                    +
                                                                    61 #endif
                                                                    diff --git a/docs/interface_8hpp_source.html b/docs/interface_8hpp_source.html index 3723f16..9ed76f4 100644 --- a/docs/interface_8hpp_source.html +++ b/docs/interface_8hpp_source.html @@ -76,63 +76,63 @@
                                                                    interface.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    9 #ifndef FIMS_INTERFACE_HPP
                                                                    -
                                                                    10 #define FIMS_INTERFACE_HPP
                                                                    -
                                                                    11 /*
                                                                    -
                                                                    12  * Interface file. Uses pre-processing macros
                                                                    -
                                                                    13  * to interface with multiple modeling platforms.
                                                                    -
                                                                    14  */
                                                                    -
                                                                    15 
                                                                    -
                                                                    16 // traits for interfacing with TMB
                                                                    -
                                                                    17 
                                                                    -
                                                                    18 #ifdef TMB_MODEL
                                                                    -
                                                                    19 // use isnan macro in math.h instead of TMB's isnan for fixing the r-cmd-check
                                                                    -
                                                                    20 // issue
                                                                    -
                                                                    21 #include <math.h>
                                                                    -
                                                                    22 
                                                                    -
                                                                    23 #include <TMB.hpp>
                                                                    -
                                                                    24 
                                                                    -
                                                                    25 // define REPORT, ADREPORT, and SIMULATE
                                                                    -
                                                                    26 #define FIMS_REPORT_F(name, F) \
                                                                    -
                                                                    27  if (isDouble<Type>::value && F->current_parallel_region < 0) { \
                                                                    -
                                                                    28  Rf_defineVar(Rf_install(#name), PROTECT(asSEXP(name)), F->report); \
                                                                    -
                                                                    29  UNPROTECT(1); \
                                                                    -
                                                                    30  }
                                                                    -
                                                                    31 #define ADREPORT_F(name, F) F->reportvector.push(name, #name);
                                                                    -
                                                                    32 
                                                                    -
                                                                    33 template <typename Type>
                                                                    -
                                                                    34 vector<Type> ADREPORTvector(vector<vector<Type> > x) {
                                                                    -
                                                                    35  int outer_dim = x.size();
                                                                    -
                                                                    36  int dim = 0;
                                                                    -
                                                                    37  for (int i = 0; i < outer_dim; i++) {
                                                                    -
                                                                    38  dim += x(i).size();
                                                                    -
                                                                    39  }
                                                                    -
                                                                    40  vector<Type> res(dim);
                                                                    -
                                                                    41  int idx = 0;
                                                                    -
                                                                    42  for (int i = 0; i < outer_dim; i++) {
                                                                    -
                                                                    43  int inner_dim = x(i).size();
                                                                    -
                                                                    44  for (int j = 0; j < inner_dim; j++) {
                                                                    -
                                                                    45  res(idx) = x(i)(j);
                                                                    -
                                                                    46  idx += 1;
                                                                    -
                                                                    47  }
                                                                    -
                                                                    48  }
                                                                    -
                                                                    49  return res;
                                                                    -
                                                                    50 }
                                                                    -
                                                                    51 
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: interface.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    5  * Fisheries Integrated Modeling System project.
                                                                    +
                                                                    6  * Refer to the LICENSE file for reuse information.
                                                                    +
                                                                    7  *
                                                                    +
                                                                    8  */
                                                                    +
                                                                    9 
                                                                    +
                                                                    10 #ifndef FIMS_INTERFACE_HPP
                                                                    +
                                                                    11 #define FIMS_INTERFACE_HPP
                                                                    +
                                                                    12 /*
                                                                    +
                                                                    13  * Interface file. Uses pre-processing macros
                                                                    +
                                                                    14  * to interface with multiple modeling platforms.
                                                                    +
                                                                    15  */
                                                                    +
                                                                    16 
                                                                    +
                                                                    17 // traits for interfacing with TMB
                                                                    +
                                                                    18 
                                                                    +
                                                                    19 #ifdef TMB_MODEL
                                                                    +
                                                                    20 // use isnan macro in math.h instead of TMB's isnan for fixing the r-cmd-check
                                                                    +
                                                                    21 // issue
                                                                    +
                                                                    22 #include <math.h>
                                                                    +
                                                                    23 
                                                                    +
                                                                    24 #include <TMB.hpp>
                                                                    +
                                                                    25 
                                                                    +
                                                                    26 // define REPORT, ADREPORT, and SIMULATE
                                                                    +
                                                                    27 #define REPORT_F(name, F) \
                                                                    +
                                                                    28  if (isDouble<Type>::value && F->current_parallel_region < 0) { \
                                                                    +
                                                                    29  Rf_defineVar(Rf_install(#name), PROTECT(asSEXP(name)), F->report); \
                                                                    +
                                                                    30  UNPROTECT(1); \
                                                                    +
                                                                    31  }
                                                                    +
                                                                    32 #define ADREPORT_F(name, F) F->reportvector.push(name, #name);
                                                                    +
                                                                    33 
                                                                    +
                                                                    34 template <typename Type>
                                                                    +
                                                                    35 vector<Type> ADREPORTvector(vector<vector<Type> > x) {
                                                                    +
                                                                    36  int outer_dim = x.size();
                                                                    +
                                                                    37  int dim = 0;
                                                                    +
                                                                    38  for (int i = 0; i < outer_dim; i++) {
                                                                    +
                                                                    39  dim += x(i).size();
                                                                    +
                                                                    40  }
                                                                    +
                                                                    41  vector<Type> res(dim);
                                                                    +
                                                                    42  int idx = 0;
                                                                    +
                                                                    43  for (int i = 0; i < outer_dim; i++) {
                                                                    +
                                                                    44  int inner_dim = x(i).size();
                                                                    +
                                                                    45  for (int j = 0; j < inner_dim; j++) {
                                                                    +
                                                                    46  res(idx) = x(i)(j);
                                                                    +
                                                                    47  idx += 1;
                                                                    +
                                                                    48  }
                                                                    +
                                                                    49  }
                                                                    +
                                                                    50  return res;
                                                                    +
                                                                    51 }
                                                                    52 
                                                                    -
                                                                    53 
                                                                    -
                                                                    54 #define FIMS_SIMULATE_F(F) if (isDouble<Type>::value && F->do_simulate)
                                                                    -
                                                                    55 
                                                                    -
                                                                    56 #endif /* TMB_MODEL */
                                                                    -
                                                                    57 
                                                                    -
                                                                    58 #ifndef TMB_MODEL
                                                                    -
                                                                    63  #define FIMS_SIMULATE_F(F)
                                                                    -
                                                                    68  #define FIMS_REPORT_F(name, F)
                                                                    -
                                                                    73  #define ADREPORT_F(name, F)
                                                                    -
                                                                    74 #endif
                                                                    -
                                                                    75 
                                                                    -
                                                                    76 #endif /* FIMS_INTERFACE_HPP */
                                                                    +
                                                                    53 #define SIMULATE_F(F) if (isDouble<Type>::value && F->do_simulate)
                                                                    +
                                                                    54 
                                                                    +
                                                                    55 #endif /* TMB_MODEL */
                                                                    +
                                                                    56 
                                                                    +
                                                                    57 #endif /* FIMS_INTERFACE_HPP */
                                                                    diff --git a/docs/maturity_2functors_2logistic_8hpp_source.html b/docs/maturity_2functors_2logistic_8hpp_source.html index 16add54..73655bb 100644 --- a/docs/maturity_2functors_2logistic_8hpp_source.html +++ b/docs/maturity_2functors_2logistic_8hpp_source.html @@ -76,47 +76,42 @@
                                                                    logistic.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    10 #ifndef POPULATION_DYNAMICS_MATURITY_LOGISTIC_HPP
                                                                    -
                                                                    11 #define POPULATION_DYNAMICS_MATURITY_LOGISTIC_HPP
                                                                    -
                                                                    12 
                                                                    -
                                                                    13 //#include "../../../interface/interface.hpp"
                                                                    -
                                                                    14 #include "../../../common/fims_math.hpp"
                                                                    -
                                                                    15 #include "../../../common/fims_vector.hpp"
                                                                    -
                                                                    16 #include "maturity_base.hpp"
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    3  * Fisheries Integrated Modeling System project.
                                                                    +
                                                                    4  * Refer to the LICENSE file for reuse information.
                                                                    +
                                                                    5  *
                                                                    +
                                                                    6  * The purpose of this file is to define the LogisticMaturity class, which
                                                                    +
                                                                    7  * inherits from the MaturityBase class
                                                                    +
                                                                    8  */
                                                                    +
                                                                    9 #ifndef POPULATION_DYNAMICS_MATURITY_LOGISTIC_HPP
                                                                    +
                                                                    10 #define POPULATION_DYNAMICS_MATURITY_LOGISTIC_HPP
                                                                    +
                                                                    11 
                                                                    +
                                                                    12 //#include "../../../interface/interface.hpp"
                                                                    +
                                                                    13 #include "../../../common/fims_math.hpp"
                                                                    +
                                                                    14 #include "maturity_base.hpp"
                                                                    +
                                                                    15 
                                                                    +
                                                                    16 namespace fims_popdy {
                                                                    17 
                                                                    -
                                                                    18 namespace fims_popdy {
                                                                    -
                                                                    19 
                                                                    -
                                                                    24 template <typename Type>
                                                                    -
                                                                    25 struct LogisticMaturity : public MaturityBase<Type> {
                                                                    -
                                                                    26  fims::Vector<Type> inflection_point;
                                                                    -
                                                                    28  fims::Vector<Type> slope;
                                                                    -
                                                                    31  LogisticMaturity() : MaturityBase<Type>()
                                                                    -
                                                                    32  {
                                                                    -
                                                                    33  }
                                                                    -
                                                                    34 
                                                                    -
                                                                    45  virtual const Type evaluate(const Type& x)
                                                                    -
                                                                    46  {
                                                                    -
                                                                    47  return fims_math::logistic<Type>(inflection_point[0], slope[0], x);
                                                                    -
                                                                    48  }
                                                                    -
                                                                    49 
                                                                    -
                                                                    60  virtual const Type evaluate(const Type& x, size_t pos)
                                                                    -
                                                                    61  {
                                                                    -
                                                                    62  return fims_math::logistic<Type>(inflection_point.get_force_scalar(pos), slope.get_force_scalar(pos), x);
                                                                    -
                                                                    63  }
                                                                    -
                                                                    64 };
                                                                    -
                                                                    65 
                                                                    -
                                                                    66 } // namespace fims_popdy
                                                                    -
                                                                    67 
                                                                    -
                                                                    68 #endif /* POPULATION_DYNAMICS_MATURITY_LOGISTIC_HPP */
                                                                    -
                                                                    fims::Vector
                                                                    Definition: fims_vector.hpp:25
                                                                    -
                                                                    maturity_base.hpp
                                                                    Declares the MaturityBase class which is the base class for all maturity functors.
                                                                    -
                                                                    fims_popdy::LogisticMaturity
                                                                    LogisticMaturity class that returns the logistic function value from fims_math.
                                                                    Definition: logistic.hpp:25
                                                                    -
                                                                    fims_popdy::LogisticMaturity::slope
                                                                    fims::Vector< Type > slope
                                                                    Definition: logistic.hpp:28
                                                                    -
                                                                    fims_popdy::LogisticMaturity::inflection_point
                                                                    fims::Vector< Type > inflection_point
                                                                    Definition: logistic.hpp:26
                                                                    -
                                                                    fims_popdy::LogisticMaturity::evaluate
                                                                    virtual const Type evaluate(const Type &x)
                                                                    Method of the logistic maturity class that implements the logistic function from FIMS math.
                                                                    Definition: logistic.hpp:45
                                                                    -
                                                                    fims_popdy::LogisticMaturity::evaluate
                                                                    virtual const Type evaluate(const Type &x, size_t pos)
                                                                    Method of the logistic maturity class that implements the logistic function from FIMS math.
                                                                    Definition: logistic.hpp:60
                                                                    -
                                                                    fims_popdy::MaturityBase
                                                                    Base class for all maturity functors.
                                                                    Definition: maturity_base.hpp:24
                                                                    +
                                                                    22 template <typename Type>
                                                                    +
                                                                    23 struct LogisticMaturity : public MaturityBase<Type> {
                                                                    +
                                                                    24  Type inflection_point;
                                                                    +
                                                                    26  Type slope;
                                                                    +
                                                                    29  LogisticMaturity() : MaturityBase<Type>() {}
                                                                    +
                                                                    30 
                                                                    +
                                                                    41  virtual const Type evaluate(const Type& x) {
                                                                    +
                                                                    42  return fims_math::logistic<Type>(inflection_point, slope, x);
                                                                    +
                                                                    43  }
                                                                    +
                                                                    44 };
                                                                    +
                                                                    45 
                                                                    +
                                                                    46 } // namespace fims_popdy
                                                                    +
                                                                    47 
                                                                    +
                                                                    48 #endif /* POPULATION_DYNAMICS_MATURITY_LOGISTIC_HPP */
                                                                    +
                                                                    fims_popdy::LogisticMaturity
                                                                    LogisticMaturity class that returns the logistic function value from fims_math.
                                                                    Definition: logistic.hpp:23
                                                                    +
                                                                    fims_popdy::LogisticMaturity::slope
                                                                    Type slope
                                                                    Definition: logistic.hpp:26
                                                                    +
                                                                    fims_popdy::LogisticMaturity::inflection_point
                                                                    Type inflection_point
                                                                    Definition: logistic.hpp:24
                                                                    +
                                                                    fims_popdy::LogisticMaturity::evaluate
                                                                    virtual const Type evaluate(const Type &x)
                                                                    Method of the logistic maturity class that implements the logistic function from FIMS math.
                                                                    Definition: logistic.hpp:41
                                                                    +
                                                                    fims_popdy::MaturityBase
                                                                    Base class for all maturity functors.
                                                                    Definition: maturity_base.hpp:27
                                                                    diff --git a/docs/maturity_8hpp_source.html b/docs/maturity_8hpp_source.html index 34ff744..d2136c7 100644 --- a/docs/maturity_8hpp_source.html +++ b/docs/maturity_8hpp_source.html @@ -76,15 +76,26 @@
                                                                    maturity.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    12 #ifndef FIMS_POPULATION_DYNAMICS_MATURITY_HPP
                                                                    -
                                                                    13 #define FIMS_POPULATION_DYNAMICS_MATURITY_HPP
                                                                    -
                                                                    14 
                                                                    -
                                                                    15 #include "functors/logistic.hpp"
                                                                    -
                                                                    16 #include "functors/maturity_base.hpp"
                                                                    -
                                                                    17 
                                                                    -
                                                                    18 #endif /* FIMS_POPULATION_DYNAMICS_MATURITY_HPP */
                                                                    -
                                                                    maturity_base.hpp
                                                                    Declares the MaturityBase class which is the base class for all maturity functors.
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  *
                                                                    +
                                                                    3  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    4  * Fisheries Integrated Modeling System project. See LICENSE in the
                                                                    +
                                                                    5  * source folder for reuse information.
                                                                    +
                                                                    6  *
                                                                    +
                                                                    7  * Maturity module file
                                                                    +
                                                                    8  * The purpose of this file is to include any .hpp files within the
                                                                    +
                                                                    9  * subfolders so that only this file needs to included in the model.hpp file.
                                                                    +
                                                                    10  *
                                                                    +
                                                                    11  * DEFINE guards for module_type module outline to define the
                                                                    +
                                                                    12  * module_type hpp file if not already defined.
                                                                    +
                                                                    13  */
                                                                    +
                                                                    14 #ifndef FIMS_POPULATION_DYNAMICS_MATURITY_HPP
                                                                    +
                                                                    15 #define FIMS_POPULATION_DYNAMICS_MATURITY_HPP
                                                                    +
                                                                    16 
                                                                    +
                                                                    17 #include "functors/logistic.hpp"
                                                                    +
                                                                    18 #include "functors/maturity_base.hpp"
                                                                    +
                                                                    19 
                                                                    +
                                                                    20 #endif /* FIMS_POPULATION_DYNAMICS_MATURITY_HPP */
                                                                    diff --git a/docs/maturity__base_8hpp_source.html b/docs/maturity__base_8hpp_source.html index b8056d1..f027aef 100644 --- a/docs/maturity__base_8hpp_source.html +++ b/docs/maturity__base_8hpp_source.html @@ -76,44 +76,53 @@
                                                                    maturity_base.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    11 #ifndef POPULATION_DYNAMICS_MATURITY_BASE_HPP
                                                                    -
                                                                    12 #define POPULATION_DYNAMICS_MATURITY_BASE_HPP
                                                                    -
                                                                    13 
                                                                    -
                                                                    14 #include "../../../common/model_object.hpp"
                                                                    -
                                                                    15 
                                                                    -
                                                                    16 namespace fims_popdy {
                                                                    -
                                                                    17 
                                                                    -
                                                                    23 template <typename Type>
                                                                    -
                                                                    24 struct MaturityBase : public fims_model_object::FIMSObject<Type> {
                                                                    -
                                                                    25  // id_g is the ID of the instance of the MaturityBase class.
                                                                    -
                                                                    26  // this is like a memory tracker.
                                                                    -
                                                                    27  // Assigning each one its own ID is a way to keep track of
                                                                    -
                                                                    28  // all the instances of the MaturityBase class.
                                                                    -
                                                                    29  static uint32_t id_g;
                                                                    -
                                                                    33  MaturityBase()
                                                                    -
                                                                    34  {
                                                                    -
                                                                    35  // increment id of the singleton maturity class
                                                                    -
                                                                    36  this->id = MaturityBase::id_g++;
                                                                    -
                                                                    37  }
                                                                    -
                                                                    38 
                                                                    -
                                                                    44  virtual const Type evaluate(const Type& x) = 0;
                                                                    -
                                                                    51  virtual const Type evaluate(const Type& x, size_t pos) = 0;
                                                                    -
                                                                    52 };
                                                                    -
                                                                    53 
                                                                    -
                                                                    54 // default id of the singleton maturity class
                                                                    -
                                                                    55 template <typename Type>
                                                                    -
                                                                    56 uint32_t MaturityBase<Type>::id_g = 0;
                                                                    -
                                                                    57 
                                                                    -
                                                                    58 } // namespace fims_popdy
                                                                    -
                                                                    59 
                                                                    -
                                                                    60 #endif /* POPULATION_DYNAMICS_MATURITY_BASE_HPP */
                                                                    -
                                                                    fims_model_object::FIMSObject
                                                                    FIMSObject struct that defines member types and returns the unique id.
                                                                    Definition: model_object.hpp:24
                                                                    -
                                                                    fims_popdy::MaturityBase
                                                                    Base class for all maturity functors.
                                                                    Definition: maturity_base.hpp:24
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  *
                                                                    +
                                                                    3  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    4  * Fisheries Integrated Modeling System project. See LICENSE in the
                                                                    +
                                                                    5  * source folder for reuse information.
                                                                    +
                                                                    6  *
                                                                    +
                                                                    7  * maturity_base.hpp
                                                                    +
                                                                    8  * The purpose of this file is to declare the MaturityBase class
                                                                    +
                                                                    9  * which is the base class for all maturity functors.
                                                                    +
                                                                    10  *
                                                                    +
                                                                    11  * DEFINE guards for maturity module outline to define the
                                                                    +
                                                                    12  * maturity hpp file if not already defined.
                                                                    +
                                                                    13  */
                                                                    +
                                                                    14 #ifndef POPULATION_DYNAMICS_MATURITY_BASE_HPP
                                                                    +
                                                                    15 #define POPULATION_DYNAMICS_MATURITY_BASE_HPP
                                                                    +
                                                                    16 
                                                                    +
                                                                    17 #include "../../../common/model_object.hpp"
                                                                    +
                                                                    18 
                                                                    +
                                                                    19 namespace fims_popdy {
                                                                    +
                                                                    20 
                                                                    +
                                                                    26 template <typename Type>
                                                                    +
                                                                    27 struct MaturityBase : public fims_model_object::FIMSObject<Type> {
                                                                    +
                                                                    28  // id_g is the ID of the instance of the MaturityBase class.
                                                                    +
                                                                    29  // this is like a memory tracker.
                                                                    +
                                                                    30  // Assigning each one its own ID is a way to keep track of
                                                                    +
                                                                    31  // all the instances of the MaturityBase class.
                                                                    +
                                                                    32  static uint32_t id_g;
                                                                    +
                                                                    36  MaturityBase() {
                                                                    +
                                                                    37  // increment id of the singleton maturity class
                                                                    +
                                                                    38  this->id = MaturityBase::id_g++;
                                                                    +
                                                                    39  }
                                                                    +
                                                                    40 
                                                                    +
                                                                    46  virtual const Type evaluate(const Type& x) = 0;
                                                                    +
                                                                    47 };
                                                                    +
                                                                    48 
                                                                    +
                                                                    49 // default id of the singleton maturity class
                                                                    +
                                                                    50 template <typename Type>
                                                                    +
                                                                    51 uint32_t MaturityBase<Type>::id_g = 0;
                                                                    +
                                                                    52 
                                                                    +
                                                                    53 } // namespace fims_popdy
                                                                    +
                                                                    54 
                                                                    +
                                                                    55 #endif /* POPULATION_DYNAMICS_MATURITY_BASE_HPP */
                                                                    +
                                                                    fims_model_object::FIMSObject
                                                                    FIMSObject struct that defines member types and returns the unique id.
                                                                    Definition: model_object.hpp:25
                                                                    +
                                                                    fims_popdy::MaturityBase
                                                                    Base class for all maturity functors.
                                                                    Definition: maturity_base.hpp:27
                                                                    fims_popdy::MaturityBase::evaluate
                                                                    virtual const Type evaluate(const Type &x)=0
                                                                    Calculates the maturity.
                                                                    -
                                                                    fims_popdy::MaturityBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: maturity_base.hpp:29
                                                                    -
                                                                    fims_popdy::MaturityBase::evaluate
                                                                    virtual const Type evaluate(const Type &x, size_t pos)=0
                                                                    Calculates the selectivity.
                                                                    -
                                                                    fims_popdy::MaturityBase::MaturityBase
                                                                    MaturityBase()
                                                                    Constructor.
                                                                    Definition: maturity_base.hpp:33
                                                                    +
                                                                    fims_popdy::MaturityBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: maturity_base.hpp:32
                                                                    +
                                                                    fims_popdy::MaturityBase::MaturityBase
                                                                    MaturityBase()
                                                                    Constructor.
                                                                    Definition: maturity_base.hpp:36
                                                                    diff --git a/docs/menudata.js b/docs/menudata.js index 389f0cc..0a9972d 100644 --- a/docs/menudata.js +++ b/docs/menudata.js @@ -48,7 +48,6 @@ var menudata={children:[ {text:"q",url:"functions_q.html#index_q"}, {text:"r",url:"functions_r.html#index_r"}, {text:"s",url:"functions_s.html#index_s"}, -{text:"t",url:"functions_t.html#index_t"}, {text:"u",url:"functions_u.html#index_u"}, {text:"v",url:"functions_v.html#index_v"}, {text:"w",url:"functions_w.html#index_w"}, @@ -57,80 +56,53 @@ var menudata={children:[ {text:"~",url:"functions_~.html#index__7E"}]}, {text:"Functions",url:"functions_func.html",children:[ {text:"a",url:"functions_func.html#index_a"}, -{text:"b",url:"functions_func_b.html#index_b"}, -{text:"c",url:"functions_func_c.html#index_c"}, -{text:"d",url:"functions_func_d.html#index_d"}, -{text:"e",url:"functions_func_e.html#index_e"}, -{text:"f",url:"functions_func_f.html#index_f"}, -{text:"g",url:"functions_func_g.html#index_g"}, -{text:"i",url:"functions_func_i.html#index_i"}, -{text:"j",url:"functions_func_j.html#index_j"}, -{text:"l",url:"functions_func_l.html#index_l"}, -{text:"m",url:"functions_func_m.html#index_m"}, -{text:"n",url:"functions_func_n.html#index_n"}, -{text:"o",url:"functions_func_o.html#index_o"}, -{text:"p",url:"functions_func_p.html#index_p"}, -{text:"r",url:"functions_func_r.html#index_r"}, -{text:"s",url:"functions_func_s.html#index_s"}, -{text:"t",url:"functions_func_t.html#index_t"}, -{text:"v",url:"functions_func_v.html#index_v"}, -{text:"w",url:"functions_func_w.html#index_w"}, -{text:"~",url:"functions_func_~.html#index__7E"}]}, +{text:"b",url:"functions_func.html#index_b"}, +{text:"c",url:"functions_func.html#index_c"}, +{text:"d",url:"functions_func.html#index_d"}, +{text:"e",url:"functions_func.html#index_e"}, +{text:"f",url:"functions_func.html#index_f"}, +{text:"g",url:"functions_func.html#index_g"}, +{text:"i",url:"functions_func.html#index_i"}, +{text:"j",url:"functions_func.html#index_j"}, +{text:"m",url:"functions_func.html#index_m"}, +{text:"o",url:"functions_func.html#index_o"}, +{text:"p",url:"functions_func.html#index_p"}, +{text:"r",url:"functions_func.html#index_r"}, +{text:"s",url:"functions_func.html#index_s"}, +{text:"v",url:"functions_func.html#index_v"}, +{text:"w",url:"functions_func.html#index_w"}, +{text:"~",url:"functions_func.html#index__7E"}]}, {text:"Variables",url:"functions_vars.html",children:[ {text:"a",url:"functions_vars.html#index_a"}, -{text:"b",url:"functions_vars_b.html#index_b"}, -{text:"c",url:"functions_vars_c.html#index_c"}, -{text:"d",url:"functions_vars_d.html#index_d"}, -{text:"e",url:"functions_vars_e.html#index_e"}, -{text:"f",url:"functions_vars_f.html#index_f"}, -{text:"g",url:"functions_vars_g.html#index_g"}, -{text:"i",url:"functions_vars_i.html#index_i"}, -{text:"j",url:"functions_vars_j.html#index_j"}, -{text:"k",url:"functions_vars_k.html#index_k"}, -{text:"l",url:"functions_vars_l.html#index_l"}, -{text:"m",url:"functions_vars_m.html#index_m"}, -{text:"n",url:"functions_vars_n.html#index_n"}, -{text:"o",url:"functions_vars_o.html#index_o"}, -{text:"p",url:"functions_vars_p.html#index_p"}, -{text:"q",url:"functions_vars_q.html#index_q"}, -{text:"r",url:"functions_vars_r.html#index_r"}, -{text:"s",url:"functions_vars_s.html#index_s"}, -{text:"t",url:"functions_vars_t.html#index_t"}, -{text:"u",url:"functions_vars_u.html#index_u"}, -{text:"v",url:"functions_vars_v.html#index_v"}, -{text:"w",url:"functions_vars_w.html#index_w"}, -{text:"x",url:"functions_vars_x.html#index_x"}, -{text:"y",url:"functions_vars_y.html#index_y"}]}, +{text:"b",url:"functions_vars.html#index_b"}, +{text:"c",url:"functions_vars.html#index_c"}, +{text:"d",url:"functions_vars.html#index_d"}, +{text:"e",url:"functions_vars.html#index_e"}, +{text:"f",url:"functions_vars.html#index_f"}, +{text:"g",url:"functions_vars.html#index_g"}, +{text:"i",url:"functions_vars.html#index_i"}, +{text:"j",url:"functions_vars.html#index_j"}, +{text:"k",url:"functions_vars.html#index_k"}, +{text:"l",url:"functions_vars.html#index_l"}, +{text:"m",url:"functions_vars.html#index_m"}, +{text:"n",url:"functions_vars.html#index_n"}, +{text:"o",url:"functions_vars.html#index_o"}, +{text:"p",url:"functions_vars.html#index_p"}, +{text:"q",url:"functions_vars.html#index_q"}, +{text:"r",url:"functions_vars.html#index_r"}, +{text:"s",url:"functions_vars.html#index_s"}, +{text:"u",url:"functions_vars.html#index_u"}, +{text:"v",url:"functions_vars.html#index_v"}, +{text:"w",url:"functions_vars.html#index_w"}, +{text:"x",url:"functions_vars.html#index_x"}, +{text:"y",url:"functions_vars.html#index_y"}]}, {text:"Typedefs",url:"functions_type.html"}, {text:"Related Functions",url:"functions_rela.html"}]}]}, {text:"Files",url:"files.html",children:[ {text:"File List",url:"files.html"}, {text:"File Members",url:"globals.html",children:[ -{text:"All",url:"globals.html",children:[ -{text:"_",url:"globals.html#index__5F"}, -{text:"a",url:"globals.html#index_a"}, -{text:"c",url:"globals.html#index_c"}, -{text:"e",url:"globals.html#index_e"}, -{text:"f",url:"globals.html#index_f"}, -{text:"g",url:"globals.html#index_g"}, -{text:"i",url:"globals.html#index_i"}, -{text:"l",url:"globals.html#index_l"}, -{text:"o",url:"globals.html#index_o"}, -{text:"r",url:"globals.html#index_r"}, -{text:"s",url:"globals.html#index_s"}, -{text:"t",url:"globals.html#index_t"}, -{text:"w",url:"globals.html#index_w"}]}, -{text:"Functions",url:"globals_func.html",children:[ -{text:"_",url:"globals_func.html#index__5F"}, -{text:"c",url:"globals_func.html#index_c"}, -{text:"e",url:"globals_func.html#index_e"}, -{text:"f",url:"globals_func.html#index_f"}, -{text:"g",url:"globals_func.html#index_g"}, -{text:"i",url:"globals_func.html#index_i"}, -{text:"l",url:"globals_func.html#index_l"}, -{text:"o",url:"globals_func.html#index_o"}, -{text:"r",url:"globals_func.html#index_r"}, -{text:"s",url:"globals_func.html#index_s"}, -{text:"w",url:"globals_func.html#index_w"}]}, -{text:"Variables",url:"globals_vars.html"}, -{text:"Macros",url:"globals_defs.html"}]}]}]} +{text:"All",url:"globals.html"}, +{text:"Functions",url:"globals_func.html"}, +{text:"Typedefs",url:"globals_type.html"}, +{text:"Enumerations",url:"globals_enum.html"}, +{text:"Enumerator",url:"globals_eval.html"}]}]}]} diff --git a/docs/model_8hpp_source.html b/docs/model_8hpp_source.html index a83bc46..a9301f3 100644 --- a/docs/model_8hpp_source.html +++ b/docs/model_8hpp_source.html @@ -76,289 +76,230 @@
                                                                    model.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    8 #ifndef FIMS_COMMON_MODEL_HPP
                                                                    -
                                                                    9 #define FIMS_COMMON_MODEL_HPP
                                                                    -
                                                                    10 
                                                                    -
                                                                    11 #include <future>
                                                                    -
                                                                    12 #include <memory>
                                                                    -
                                                                    13 
                                                                    -
                                                                    14 #include "information.hpp"
                                                                    -
                                                                    15 
                                                                    -
                                                                    16 namespace fims_model {
                                                                    -
                                                                    17 
                                                                    -
                                                                    21  template <typename Type>
                                                                    -
                                                                    22  class Model { // may need singleton
                                                                    -
                                                                    23  public:
                                                                    -
                                                                    24  static std::shared_ptr<Model<Type> >
                                                                    -
                                                                    25  fims_model;
                                                                    -
                                                                    26  std::shared_ptr<fims_info::Information<Type> >
                                                                    -
                                                                    27  fims_information;
                                                                    -
                                                                    30 #ifdef TMB_MODEL
                                                                    -
                                                                    31  ::objective_function<Type> *of;
                                                                    -
                                                                    32 #endif
                                                                    -
                                                                    33 
                                                                    -
                                                                    34  // constructor
                                                                    -
                                                                    35 
                                                                    -
                                                                    36  virtual ~Model() {
                                                                    -
                                                                    37  }
                                                                    -
                                                                    38 
                                                                    -
                                                                    44  static std::shared_ptr<Model<Type> > GetInstance() {
                                                                    -
                                                                    45  if (Model<Type>::fims_model == nullptr) {
                                                                    -
                                                                    46  Model<Type>::fims_model = std::make_shared<fims_model::Model<Type> >();
                                                                    -
                                                                    47  Model<Type>::fims_model->fims_information =
                                                                    -
                                                                    48  fims_info::Information<Type>::GetInstance();
                                                                    -
                                                                    49  }
                                                                    -
                                                                    50  return Model<Type>::fims_model;
                                                                    -
                                                                    51  }
                                                                    -
                                                                    52 
                                                                    -
                                                                    56  const Type Evaluate() {
                                                                    -
                                                                    57  // jnll = negative-log-likelihood (the objective function)
                                                                    -
                                                                    58  Type jnll = 0.0;
                                                                    -
                                                                    59 
                                                                    -
                                                                    60 
                                                                    -
                                                                    61  int n_fleets = fims_information->fleets.size();
                                                                    -
                                                                    62  int n_pops = fims_information->populations.size();
                                                                    -
                                                                    63 
                                                                    -
                                                                    64  // Create vector lists to store output for reporting
                                                                    -
                                                                    65 #ifdef TMB_MODEL
                                                                    -
                                                                    66  // vector< vector<Type> > creates a nested vector structure where
                                                                    -
                                                                    67  // each vector can be a different dimension. Does not work with ADREPORT
                                                                    -
                                                                    68  // fleets
                                                                    -
                                                                    69  vector<vector<Type> > exp_index(n_fleets);
                                                                    -
                                                                    70  vector<vector<Type> > exp_catch(n_fleets);
                                                                    -
                                                                    71  vector<vector<Type> > cnaa(n_fleets);
                                                                    -
                                                                    72  vector<vector<Type> > cwaa(n_fleets);
                                                                    -
                                                                    73  vector<vector<Type> > cnal(n_fleets);
                                                                    -
                                                                    74  vector<vector<Type> > pcnaa(n_fleets);
                                                                    -
                                                                    75  vector<vector<Type> > pcnal(n_fleets);
                                                                    -
                                                                    76  vector<vector<Type> > F_mort(n_fleets);
                                                                    -
                                                                    77  vector<vector<Type> > q(n_fleets);
                                                                    -
                                                                    78  // populations
                                                                    -
                                                                    79  vector<vector<Type> > naa(n_pops);
                                                                    -
                                                                    80  vector<vector<Type> > ssb(n_pops);
                                                                    -
                                                                    81  vector<vector<Type> > biomass(n_pops);
                                                                    -
                                                                    82  vector<vector<Type> > log_recruit_dev(n_pops);
                                                                    -
                                                                    83  vector<vector<Type> > recruitment(n_pops);
                                                                    -
                                                                    84  vector<vector<Type> > M(n_pops);
                                                                    -
                                                                    85  vector<Type> nll_components(this->fims_information->density_components.size());
                                                                    -
                                                                    86 #endif
                                                                    -
                                                                    87  // Loop over densities and evaluate joint negative log densities for priors
                                                                    -
                                                                    88  typename fims_info::Information<Type>::density_components_iterator d_it;
                                                                    -
                                                                    89  nll_components.fill(0);
                                                                    -
                                                                    90  int nll_components_idx = 0;
                                                                    -
                                                                    91  size_t n_priors = 0;
                                                                    -
                                                                    92 
                                                                    -
                                                                    93  for (d_it = this->fims_information->density_components.begin();
                                                                    -
                                                                    94  d_it != this->fims_information->density_components.end(); ++d_it) {
                                                                    -
                                                                    95  std::shared_ptr<fims_distributions::DensityComponentBase<Type> > d = (*d_it).second;
                                                                    -
                                                                    96 #ifdef TMB_MODEL
                                                                    -
                                                                    97  d->of = this->of;
                                                                    -
                                                                    98 #endif
                                                                    -
                                                                    99  if (d->input_type == "prior") {
                                                                    -
                                                                    100  nll_components[nll_components_idx] = -d->evaluate();
                                                                    -
                                                                    101  jnll += nll_components[nll_components_idx];
                                                                    -
                                                                    102  n_priors += 1;
                                                                    -
                                                                    103  nll_components_idx += 1;
                                                                    -
                                                                    104  }
                                                                    -
                                                                    105  }
                                                                    -
                                                                    106 
                                                                    -
                                                                    107 
                                                                    -
                                                                    108 
                                                                    -
                                                                    109  // Loop over populations and evaluate recruitment component
                                                                    -
                                                                    110 
                                                                    -
                                                                    111  typename fims_info::Information<Type>::population_iterator p_it;
                                                                    -
                                                                    112 
                                                                    -
                                                                    113 
                                                                    -
                                                                    114  for (p_it = this->fims_information->populations.begin();
                                                                    -
                                                                    115  p_it != this->fims_information->populations.end(); ++p_it) {
                                                                    -
                                                                    116  //(*p_it).second points to the Population module
                                                                    -
                                                                    117  std::shared_ptr<fims_popdy::Population<Type> > p = (*p_it).second;
                                                                    -
                                                                    118 
                                                                    -
                                                                    119  // Prepare recruitment
                                                                    -
                                                                    120  p->recruitment->Prepare();
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: model.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  * Author: Matthew Supernaw, Andrea Havron
                                                                    +
                                                                    5  * National Oceanic and Atmospheric Administration
                                                                    +
                                                                    6  * National Marine Fisheries Service
                                                                    +
                                                                    7  * Email: matthew.supernaw@noaa.gov, andrea.havron@noaa.gov
                                                                    +
                                                                    8  *
                                                                    +
                                                                    9  * Created on September 30, 2021, 1:08 PM
                                                                    +
                                                                    10  *
                                                                    +
                                                                    11  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    12  * Fisheries Integrated Modeling System project. See LICENSE in the
                                                                    +
                                                                    13  * source folder for reuse information.
                                                                    +
                                                                    14  *
                                                                    +
                                                                    15  */
                                                                    +
                                                                    16 #ifndef FIMS_COMMON_MODEL_HPP
                                                                    +
                                                                    17 #define FIMS_COMMON_MODEL_HPP
                                                                    +
                                                                    18 
                                                                    +
                                                                    19 #include <future>
                                                                    +
                                                                    20 #include <memory>
                                                                    +
                                                                    21 
                                                                    +
                                                                    22 #include "information.hpp"
                                                                    +
                                                                    23 
                                                                    +
                                                                    24 namespace fims_model {
                                                                    +
                                                                    25 
                                                                    +
                                                                    29 template <typename Type>
                                                                    +
                                                                    30 class Model { // may need singleton
                                                                    +
                                                                    31  public:
                                                                    +
                                                                    32  static std::shared_ptr<Model<Type> >
                                                                    +
                                                                    33  fims_model;
                                                                    +
                                                                    34  std::shared_ptr<fims_info::Information<Type> >
                                                                    +
                                                                    35  fims_information;
                                                                    +
                                                                    38 #ifdef TMB_MODEL
                                                                    +
                                                                    39  ::objective_function<Type> *of;
                                                                    +
                                                                    40 #endif
                                                                    +
                                                                    41 
                                                                    +
                                                                    42  // constructor
                                                                    +
                                                                    43  virtual ~Model() {}
                                                                    +
                                                                    44 
                                                                    +
                                                                    50  static std::shared_ptr<Model<Type> > GetInstance() {
                                                                    +
                                                                    51  if (Model<Type>::fims_model == nullptr) {
                                                                    +
                                                                    52  Model<Type>::fims_model = std::make_shared<fims_model::Model<Type> >();
                                                                    +
                                                                    53  Model<Type>::fims_model->fims_information =
                                                                    +
                                                                    54  fims_info::Information<Type>::GetInstance();
                                                                    +
                                                                    55  }
                                                                    +
                                                                    56  return Model<Type>::fims_model;
                                                                    +
                                                                    57  }
                                                                    +
                                                                    58 
                                                                    +
                                                                    62  const Type Evaluate() {
                                                                    +
                                                                    63  // jnll = negative-log-likelihood (the objective function)
                                                                    +
                                                                    64  Type jnll = 0.0;
                                                                    +
                                                                    65  Type rec_nll = 0.0; // recrutiment nll
                                                                    +
                                                                    66  Type age_comp_nll = 0.0; // age composition nll
                                                                    +
                                                                    67  Type index_nll = 0.0; // survey and fishery cacth nll
                                                                    +
                                                                    68 
                                                                    +
                                                                    69  int n_fleets = fims_information->fleets.size();
                                                                    +
                                                                    70  int n_pops = fims_information->populations.size();
                                                                    +
                                                                    71 
                                                                    +
                                                                    72 // Create vector lists to store output for reporting
                                                                    +
                                                                    73 #ifdef TMB_MODEL
                                                                    +
                                                                    74  // vector< vector<Type> > creates a nested vector structure where
                                                                    +
                                                                    75  // each vector can be a different dimension. Does not work with ADREPORT
                                                                    +
                                                                    76  // fleets
                                                                    +
                                                                    77  vector<vector<Type> > exp_index(n_fleets);
                                                                    +
                                                                    78  vector<vector<Type> > exp_catch(n_fleets);
                                                                    +
                                                                    79  vector<vector<Type> > cnaa(n_fleets);
                                                                    +
                                                                    80  vector<vector<Type> > cwaa(n_fleets);
                                                                    +
                                                                    81  vector<vector<Type> > F_mort(n_fleets);
                                                                    +
                                                                    82  // populations
                                                                    +
                                                                    83  vector<vector<Type> > naa(n_pops);
                                                                    +
                                                                    84  vector<vector<Type> > ssb(n_pops);
                                                                    +
                                                                    85  vector<vector<Type> > biomass(n_pops);
                                                                    +
                                                                    86  vector<vector<Type> > log_recruit_dev(n_pops);
                                                                    +
                                                                    87  vector<vector<Type> > recruitment(n_pops);
                                                                    +
                                                                    88  vector<vector<Type> > M(n_pops);
                                                                    +
                                                                    89 
                                                                    +
                                                                    90 #endif
                                                                    +
                                                                    91 
                                                                    +
                                                                    92  // Loop over populations, evaluate, and sum up the recruitment likelihood
                                                                    +
                                                                    93  // component
                                                                    +
                                                                    94 
                                                                    +
                                                                    95  typename fims_info::Information<Type>::population_iterator it;
                                                                    +
                                                                    96  MODEL_LOG << "Evaluating expected values and summing recruitment nlls for "
                                                                    +
                                                                    97  << this->fims_information->populations.size() << " populations."
                                                                    +
                                                                    98  << std::endl;
                                                                    +
                                                                    99 
                                                                    +
                                                                    100  for (it = this->fims_information->populations.begin();
                                                                    +
                                                                    101  it != this->fims_information->populations.end(); ++it) {
                                                                    +
                                                                    102  //(*it).second points to the Population module
                                                                    +
                                                                    103  MODEL_LOG << "Setting up pointer to population " << (*it).second->id
                                                                    +
                                                                    104  << "." << std::endl;
                                                                    +
                                                                    105  // Prepare recruitment
                                                                    +
                                                                    106  (*it).second->recruitment->Prepare();
                                                                    +
                                                                    107  MODEL_LOG << "Recruitment for population successfully prepared"
                                                                    +
                                                                    108  << std::endl;
                                                                    +
                                                                    109 // link to TMB objective function
                                                                    +
                                                                    110 #ifdef TMB_MODEL
                                                                    +
                                                                    111  (*it).second->of = this->of;
                                                                    +
                                                                    112 #endif
                                                                    +
                                                                    113  // Evaluate population
                                                                    +
                                                                    114  (*it).second->Evaluate();
                                                                    +
                                                                    115  // Recrtuiment negative log-likelihood
                                                                    +
                                                                    116  rec_nll += (*it).second->recruitment->evaluate_nll();
                                                                    +
                                                                    117  MODEL_LOG << "Recruitment negative log-likelihood is: " << rec_nll
                                                                    +
                                                                    118  << std::endl;
                                                                    +
                                                                    119  }
                                                                    +
                                                                    120  MODEL_LOG << "All populations successfully evaluated." << std::endl;
                                                                    121 
                                                                    -
                                                                    122  }
                                                                    +
                                                                    122  // Loop over fleets/surveys, and sum up age comp and index nlls
                                                                    123 
                                                                    -
                                                                    124  // Loop over densities and evaluate joint negative log-likelihoods for random effects
                                                                    -
                                                                    125  this->fims_information->setup_random_effects();
                                                                    -
                                                                    126  size_t n_random_effects = 0;
                                                                    -
                                                                    127  for (d_it = this->fims_information->density_components.begin();
                                                                    -
                                                                    128  d_it != this->fims_information->density_components.end(); ++d_it) {
                                                                    -
                                                                    129  std::shared_ptr<fims_distributions::DensityComponentBase<Type> > d = (*d_it).second;
                                                                    -
                                                                    130 #ifdef TMB_MODEL
                                                                    -
                                                                    131  d->of = this->of;
                                                                    -
                                                                    132 #endif
                                                                    -
                                                                    133  if (d->input_type == "random_effects") {
                                                                    -
                                                                    134  nll_components[nll_components_idx] = -d->evaluate();
                                                                    -
                                                                    135  jnll += nll_components[nll_components_idx];
                                                                    -
                                                                    136  n_random_effects += 1;
                                                                    -
                                                                    137  nll_components_idx += 1;
                                                                    -
                                                                    138  }
                                                                    -
                                                                    139  }
                                                                    -
                                                                    140 
                                                                    -
                                                                    141 
                                                                    -
                                                                    142  // Loop over and evaluate populations
                                                                    -
                                                                    143  for (p_it = this->fims_information->populations.begin();
                                                                    -
                                                                    144  p_it != this->fims_information->populations.end(); ++p_it) {
                                                                    -
                                                                    145  //(*p_it).second points to the Population module
                                                                    -
                                                                    146  std::shared_ptr<fims_popdy::Population<Type> > p = (*p_it).second;
                                                                    -
                                                                    147  // link to TMB objective function
                                                                    -
                                                                    148 #ifdef TMB_MODEL
                                                                    -
                                                                    149  p->of = this->of;
                                                                    -
                                                                    150 #endif
                                                                    -
                                                                    151  // Evaluate population
                                                                    -
                                                                    152  p->Evaluate();
                                                                    -
                                                                    153  }
                                                                    -
                                                                    154 
                                                                    -
                                                                    155  typename fims_info::Information<Type>::fleet_iterator f_it;
                                                                    -
                                                                    156  // Loop over fleets/surveys, and evaluate age comp and index expected values
                                                                    -
                                                                    157  for (f_it = this->fims_information->fleets.begin();
                                                                    -
                                                                    158  f_it != this->fims_information->fleets.end(); ++f_it) {
                                                                    -
                                                                    159  //(*f_it).second points to each individual Fleet module
                                                                    -
                                                                    160  std::shared_ptr<fims_popdy::Fleet<Type> > f = (*f_it).second;
                                                                    -
                                                                    161 #ifdef TMB_MODEL
                                                                    -
                                                                    162  f->of = this->of;
                                                                    -
                                                                    163 #endif
                                                                    -
                                                                    164 
                                                                    -
                                                                    165  f->evaluate_age_comp();
                                                                    -
                                                                    166  if (f->nlengths > 0) {
                                                                    -
                                                                    167  f->evaluate_length_comp();
                                                                    -
                                                                    168  }
                                                                    -
                                                                    169  f->evaluate_index();
                                                                    -
                                                                    170  }
                                                                    -
                                                                    171  this->fims_information->setup_data();
                                                                    -
                                                                    172  // Loop over and evaluate data joint negative log-likelihoods
                                                                    -
                                                                    173  int n_data = 0;
                                                                    -
                                                                    174  for (d_it = this->fims_information->density_components.begin();
                                                                    -
                                                                    175  d_it != this->fims_information->density_components.end(); ++d_it) {
                                                                    -
                                                                    176  std::shared_ptr<fims_distributions::DensityComponentBase<Type> > d = (*d_it).second;
                                                                    -
                                                                    177 #ifdef TMB_MODEL
                                                                    -
                                                                    178  d->of = this->of;
                                                                    -
                                                                    179  //d->keep = this->keep;
                                                                    -
                                                                    180 #endif
                                                                    -
                                                                    181  if (d->input_type == "data") {
                                                                    -
                                                                    182  nll_components[nll_components_idx] = -d->evaluate();
                                                                    -
                                                                    183  jnll += nll_components[nll_components_idx];
                                                                    -
                                                                    184  n_data += 1;
                                                                    -
                                                                    185  nll_components_idx += 1;
                                                                    -
                                                                    186  }
                                                                    -
                                                                    187  }
                                                                    -
                                                                    188 
                                                                    -
                                                                    189  // initiate population index for structuring report out objects
                                                                    -
                                                                    190  int pop_idx = 0;
                                                                    -
                                                                    191  for (p_it = this->fims_information->populations.begin();
                                                                    -
                                                                    192  p_it != this->fims_information->populations.end(); ++p_it) {
                                                                    -
                                                                    193  std::shared_ptr<fims_popdy::Population<Type> > p = (*p_it).second;
                                                                    -
                                                                    194 #ifdef TMB_MODEL
                                                                    -
                                                                    195  naa(pop_idx) = vector<Type>(p->numbers_at_age);
                                                                    -
                                                                    196  ssb(pop_idx) = vector<Type>(p->spawning_biomass);
                                                                    -
                                                                    197  log_recruit_dev(pop_idx) =
                                                                    -
                                                                    198  vector<Type>(p->recruitment->log_recruit_devs);
                                                                    -
                                                                    199  recruitment(pop_idx) = vector<Type>(p->expected_recruitment);
                                                                    -
                                                                    200  biomass(pop_idx) = vector<Type>(p->biomass);
                                                                    -
                                                                    201  M(pop_idx) = vector<Type>(p->M);
                                                                    -
                                                                    202 #endif
                                                                    -
                                                                    203  pop_idx += 1;
                                                                    -
                                                                    204  }
                                                                    -
                                                                    205 
                                                                    -
                                                                    206  // initiate fleet index for structuring report out objects
                                                                    -
                                                                    207  int fleet_idx = 0;
                                                                    -
                                                                    208  for (f_it = this->fims_information->fleets.begin();
                                                                    -
                                                                    209  f_it != this->fims_information->fleets.end(); ++f_it) {
                                                                    -
                                                                    210  std::shared_ptr<fims_popdy::Fleet<Type> > f = (*f_it).second;
                                                                    -
                                                                    211 #ifdef TMB_MODEL
                                                                    -
                                                                    212  exp_index(fleet_idx) = f->expected_index;
                                                                    -
                                                                    213  exp_catch(fleet_idx) = f->expected_catch;
                                                                    -
                                                                    214  F_mort(fleet_idx) = f->Fmort;
                                                                    -
                                                                    215  q(fleet_idx) = f->q;
                                                                    -
                                                                    216  cnaa(fleet_idx) = f->catch_numbers_at_age;
                                                                    -
                                                                    217  cnal(fleet_idx) = f->catch_numbers_at_length;
                                                                    -
                                                                    218  pcnaa(fleet_idx) = f->proportion_catch_numbers_at_age;
                                                                    -
                                                                    219  pcnal(fleet_idx) = f->proportion_catch_numbers_at_length;
                                                                    -
                                                                    220  cwaa(fleet_idx) = f->catch_weight_at_age;
                                                                    -
                                                                    221 #endif
                                                                    -
                                                                    222  fleet_idx += 1;
                                                                    -
                                                                    223  }
                                                                    -
                                                                    224 
                                                                    -
                                                                    225  // jnll = rec_nll + age_comp_nll + index_nll;
                                                                    -
                                                                    226 
                                                                    -
                                                                    227  // Reporting
                                                                    -
                                                                    228 #ifdef TMB_MODEL
                                                                    -
                                                                    229  //FIMS_REPORT_F(rec_nll, of);
                                                                    -
                                                                    230  //FIMS_REPORT_F(age_comp_nll, of);
                                                                    -
                                                                    231  //FIMS_REPORT_F(index_nll, of);
                                                                    -
                                                                    232  FIMS_REPORT_F(jnll, of);
                                                                    -
                                                                    233  FIMS_REPORT_F(naa, of);
                                                                    -
                                                                    234  FIMS_REPORT_F(ssb, of);
                                                                    -
                                                                    235  FIMS_REPORT_F(log_recruit_dev, of);
                                                                    -
                                                                    236  FIMS_REPORT_F(recruitment, of);
                                                                    -
                                                                    237  FIMS_REPORT_F(biomass, of);
                                                                    -
                                                                    238  FIMS_REPORT_F(M, of);
                                                                    -
                                                                    239  FIMS_REPORT_F(exp_index, of);
                                                                    -
                                                                    240  FIMS_REPORT_F(exp_catch, of);
                                                                    -
                                                                    241  FIMS_REPORT_F(F_mort, of);
                                                                    -
                                                                    242  FIMS_REPORT_F(q, of);
                                                                    -
                                                                    243  FIMS_REPORT_F(cnaa, of);
                                                                    -
                                                                    244  FIMS_REPORT_F(cnal, of);
                                                                    -
                                                                    245  FIMS_REPORT_F(pcnaa, of);
                                                                    -
                                                                    246  FIMS_REPORT_F(pcnal, of);
                                                                    -
                                                                    247  FIMS_REPORT_F(cwaa, of);
                                                                    -
                                                                    248  FIMS_REPORT_F(nll_components, of);
                                                                    -
                                                                    249 
                                                                    -
                                                                    250  /*ADREPORT using ADREPORTvector defined in
                                                                    -
                                                                    251  * inst/include/interface/interface.hpp:
                                                                    -
                                                                    252  * function collapses the nested vector into a single vector
                                                                    -
                                                                    253  */
                                                                    -
                                                                    254  vector<Type> NAA = ADREPORTvector(naa);
                                                                    -
                                                                    255  vector<Type> Biomass = ADREPORTvector(biomass);
                                                                    -
                                                                    256  vector<Type> SSB = ADREPORTvector(ssb);
                                                                    -
                                                                    257  vector<Type> LogRecDev = ADREPORTvector(log_recruit_dev);
                                                                    -
                                                                    258  vector<Type> FMort = ADREPORTvector(F_mort);
                                                                    -
                                                                    259  vector<Type> Q = ADREPORTvector(q);
                                                                    -
                                                                    260  vector<Type> ExpectedIndex = ADREPORTvector(exp_index);
                                                                    -
                                                                    261  vector<Type> CNAA = ADREPORTvector(cnaa);
                                                                    -
                                                                    262  vector<Type> CNAL = ADREPORTvector(cnal);
                                                                    -
                                                                    263  vector<Type> PCNAA = ADREPORTvector(pcnaa);
                                                                    -
                                                                    264  vector<Type> PCNAL = ADREPORTvector(pcnal);
                                                                    -
                                                                    265 
                                                                    -
                                                                    266  ADREPORT_F(NAA, of);
                                                                    -
                                                                    267  ADREPORT_F(Biomass, of);
                                                                    -
                                                                    268  ADREPORT_F(SSB, of);
                                                                    -
                                                                    269  ADREPORT_F(LogRecDev, of);
                                                                    -
                                                                    270  ADREPORT_F(FMort, of);
                                                                    -
                                                                    271  ADREPORT_F(Q, of);
                                                                    -
                                                                    272  ADREPORT_F(ExpectedIndex, of);
                                                                    -
                                                                    273  ADREPORT_F(CNAA, of);
                                                                    -
                                                                    274  ADREPORT_F(CNAL, of);
                                                                    -
                                                                    275  ADREPORT_F(PCNAA, of);
                                                                    -
                                                                    276  ADREPORT_F(PCNAL, of);
                                                                    -
                                                                    277 #endif
                                                                    -
                                                                    278 
                                                                    -
                                                                    279  return jnll;
                                                                    -
                                                                    280  }
                                                                    -
                                                                    281  };
                                                                    -
                                                                    282 
                                                                    -
                                                                    283  // Create singleton instance of Model class
                                                                    -
                                                                    284  template <typename Type>
                                                                    -
                                                                    285  std::shared_ptr<Model<Type> > Model<Type>::fims_model =
                                                                    -
                                                                    286  nullptr; // singleton instance
                                                                    -
                                                                    287 } // namespace fims_model
                                                                    -
                                                                    288 
                                                                    -
                                                                    289 #endif /* FIMS_COMMON_MODEL_HPP */
                                                                    -
                                                                    fims_info::Information::density_components_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_distributions::DensityComponentBase< Type > > >::iterator density_components_iterator
                                                                    Definition: information.hpp:117
                                                                    -
                                                                    fims_info::Information::fleet_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >::iterator fleet_iterator
                                                                    Definition: information.hpp:97
                                                                    -
                                                                    fims_info::Information::population_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > >::iterator population_iterator
                                                                    Definition: information.hpp:106
                                                                    -
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:135
                                                                    -
                                                                    fims_info::Information::fims_information
                                                                    static std::shared_ptr< Information< Type > > fims_information
                                                                    Definition: information.hpp:41
                                                                    -
                                                                    fims_model::Model
                                                                    Model class. FIMS objective function.
                                                                    Definition: model.hpp:22
                                                                    -
                                                                    fims_model::Model::fims_model
                                                                    static std::shared_ptr< Model< Type > > fims_model
                                                                    Definition: model.hpp:25
                                                                    -
                                                                    fims_model::Model::Evaluate
                                                                    const Type Evaluate()
                                                                    Evaluate. Calculates the joint negative log-likelihood function.
                                                                    Definition: model.hpp:56
                                                                    -
                                                                    fims_model::Model::fims_information
                                                                    std::shared_ptr< fims_info::Information< Type > > fims_information
                                                                    Definition: model.hpp:27
                                                                    -
                                                                    fims_model::Model::GetInstance
                                                                    static std::shared_ptr< Model< Type > > GetInstance()
                                                                    Definition: model.hpp:44
                                                                    -
                                                                    information.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    ADREPORT_F
                                                                    #define ADREPORT_F(name, F)
                                                                    TODO: provide a brief description.
                                                                    Definition: interface.hpp:73
                                                                    -
                                                                    FIMS_REPORT_F
                                                                    #define FIMS_REPORT_F(name, F)
                                                                    TODO: provide a brief description.
                                                                    Definition: interface.hpp:68
                                                                    +
                                                                    124  typename fims_info::Information<Type>::fleet_iterator jt;
                                                                    +
                                                                    125  MODEL_LOG << "Evaluating expected values and summing nlls for "
                                                                    +
                                                                    126  << this->fims_information->fleets.size() << " fleets."
                                                                    +
                                                                    127  << std::endl;
                                                                    +
                                                                    128 
                                                                    +
                                                                    129  for (jt = this->fims_information->fleets.begin();
                                                                    +
                                                                    130  jt != this->fims_information->fleets.end(); ++jt) {
                                                                    +
                                                                    131  //(*jt).second points to each individual Fleet module
                                                                    +
                                                                    132 #ifdef TMB_MODEL
                                                                    +
                                                                    133  (*jt).second->of = this->of;
                                                                    +
                                                                    134 #endif
                                                                    +
                                                                    135  MODEL_LOG << "Setting up pointer to fleet " << (*jt).second->id << "."
                                                                    +
                                                                    136  << std::endl;
                                                                    +
                                                                    137  age_comp_nll += (*jt).second->evaluate_age_comp_nll();
                                                                    +
                                                                    138  MODEL_LOG << "Sum of survey and age comp negative log-likelihood is: "
                                                                    +
                                                                    139  << age_comp_nll << std::endl;
                                                                    +
                                                                    140  index_nll += (*jt).second->evaluate_index_nll();
                                                                    +
                                                                    141  }
                                                                    +
                                                                    142  MODEL_LOG << "All fleets successfully evaluated." << std::endl;
                                                                    +
                                                                    143  // Loop over populations and fleets/surveys and fill in reporting
                                                                    +
                                                                    144 
                                                                    +
                                                                    145  // initiate population index for structuring report out objects
                                                                    +
                                                                    146  int pop_idx = 0;
                                                                    +
                                                                    147  for (it = this->fims_information->populations.begin();
                                                                    +
                                                                    148  it != this->fims_information->populations.end(); ++it) {
                                                                    +
                                                                    149 #ifdef TMB_MODEL
                                                                    +
                                                                    150  naa(pop_idx) = vector<Type>((*it).second->numbers_at_age);
                                                                    +
                                                                    151  ssb(pop_idx) = vector<Type>((*it).second->spawning_biomass);
                                                                    +
                                                                    152  log_recruit_dev(pop_idx) =
                                                                    +
                                                                    153  vector<Type>((*it).second->recruitment->log_recruit_devs);
                                                                    +
                                                                    154  recruitment(pop_idx) = vector<Type>((*it).second->expected_recruitment);
                                                                    +
                                                                    155  biomass(pop_idx) = vector<Type>((*it).second->biomass);
                                                                    +
                                                                    156  M(pop_idx) = vector<Type>((*it).second->M);
                                                                    +
                                                                    157 #endif
                                                                    +
                                                                    158  pop_idx += 1;
                                                                    +
                                                                    159  }
                                                                    +
                                                                    160 
                                                                    +
                                                                    161  // initiate fleet index for structuring report out objects
                                                                    +
                                                                    162  int fleet_idx = 0;
                                                                    +
                                                                    163  for (jt = this->fims_information->fleets.begin();
                                                                    +
                                                                    164  jt != this->fims_information->fleets.end(); ++jt) {
                                                                    +
                                                                    165 #ifdef TMB_MODEL
                                                                    +
                                                                    166  exp_index(fleet_idx) = (*jt).second->expected_index;
                                                                    +
                                                                    167  exp_catch(fleet_idx) = (*jt).second->expected_catch;
                                                                    +
                                                                    168  F_mort(fleet_idx) = (*jt).second->Fmort;
                                                                    +
                                                                    169  cnaa(fleet_idx) = (*jt).second->catch_numbers_at_age;
                                                                    +
                                                                    170  cwaa(fleet_idx) = (*jt).second->catch_weight_at_age;
                                                                    +
                                                                    171 #endif
                                                                    +
                                                                    172  fleet_idx += 1;
                                                                    +
                                                                    173  }
                                                                    +
                                                                    174 
                                                                    +
                                                                    175  jnll = rec_nll + age_comp_nll + index_nll;
                                                                    +
                                                                    176 
                                                                    +
                                                                    177 // Reporting
                                                                    +
                                                                    178 #ifdef TMB_MODEL
                                                                    +
                                                                    179  REPORT_F(rec_nll, of);
                                                                    +
                                                                    180  REPORT_F(age_comp_nll, of);
                                                                    +
                                                                    181  REPORT_F(index_nll, of);
                                                                    +
                                                                    182  REPORT_F(jnll, of);
                                                                    +
                                                                    183  REPORT_F(naa, of);
                                                                    +
                                                                    184  REPORT_F(ssb, of);
                                                                    +
                                                                    185  REPORT_F(log_recruit_dev, of);
                                                                    +
                                                                    186  REPORT_F(recruitment, of);
                                                                    +
                                                                    187  REPORT_F(biomass, of);
                                                                    +
                                                                    188  REPORT_F(M, of);
                                                                    +
                                                                    189  REPORT_F(exp_index, of);
                                                                    +
                                                                    190  REPORT_F(exp_catch, of);
                                                                    +
                                                                    191  REPORT_F(F_mort, of);
                                                                    +
                                                                    192  REPORT_F(cnaa, of);
                                                                    +
                                                                    193  REPORT_F(cwaa, of);
                                                                    +
                                                                    194 
                                                                    +
                                                                    195  /*ADREPORT using ADREPORTvector defined in
                                                                    +
                                                                    196  * inst/include/interface/interface.hpp:
                                                                    +
                                                                    197  * function collapses the nested vector into a single vector
                                                                    +
                                                                    198  */
                                                                    +
                                                                    199  vector<Type> NAA = ADREPORTvector(naa);
                                                                    +
                                                                    200  vector<Type> Biomass = ADREPORTvector(biomass);
                                                                    +
                                                                    201  vector<Type> SSB = ADREPORTvector(ssb);
                                                                    +
                                                                    202  vector<Type> LogRecDev = ADREPORTvector(log_recruit_dev);
                                                                    +
                                                                    203  vector<Type> FMort = ADREPORTvector(F_mort);
                                                                    +
                                                                    204  vector<Type> ExpectedIndex = ADREPORTvector(exp_index);
                                                                    +
                                                                    205  vector<Type> CNAA = ADREPORTvector(cnaa);
                                                                    +
                                                                    206 
                                                                    +
                                                                    207  ADREPORT_F(NAA, of);
                                                                    +
                                                                    208  ADREPORT_F(Biomass, of);
                                                                    +
                                                                    209  ADREPORT_F(SSB, of);
                                                                    +
                                                                    210  ADREPORT_F(LogRecDev, of);
                                                                    +
                                                                    211  ADREPORT_F(FMort, of);
                                                                    +
                                                                    212  ADREPORT_F(ExpectedIndex, of);
                                                                    +
                                                                    213  ADREPORT_F(CNAA, of);
                                                                    +
                                                                    214 #endif
                                                                    +
                                                                    215 
                                                                    +
                                                                    216  return jnll;
                                                                    +
                                                                    217  }
                                                                    +
                                                                    218 };
                                                                    +
                                                                    219 
                                                                    +
                                                                    220 // Create singleton instance of Model class
                                                                    +
                                                                    221 template <typename Type>
                                                                    +
                                                                    222 std::shared_ptr<Model<Type> > Model<Type>::fims_model =
                                                                    +
                                                                    223  nullptr; // singleton instance
                                                                    +
                                                                    224 } // namespace fims_model
                                                                    +
                                                                    225 
                                                                    +
                                                                    226 #endif /* FIMS_COMMON_MODEL_HPP */
                                                                    +
                                                                    fims_info::Information::fleet_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >::iterator fleet_iterator
                                                                    Definition: information.hpp:94
                                                                    +
                                                                    fims_info::Information::population_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > >::iterator population_iterator
                                                                    Definition: information.hpp:103
                                                                    +
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:126
                                                                    +
                                                                    fims_info::Information::fims_information
                                                                    static std::shared_ptr< Information< Type > > fims_information
                                                                    Definition: information.hpp:40
                                                                    +
                                                                    fims_model::Model
                                                                    Model class. FIMS objective function.
                                                                    Definition: model.hpp:30
                                                                    +
                                                                    fims_model::Model::fims_model
                                                                    static std::shared_ptr< Model< Type > > fims_model
                                                                    Definition: model.hpp:33
                                                                    +
                                                                    fims_model::Model::Evaluate
                                                                    const Type Evaluate()
                                                                    Evaluate. Calculates the joint negative log-likelihood function.
                                                                    Definition: model.hpp:62
                                                                    +
                                                                    fims_model::Model::fims_information
                                                                    std::shared_ptr< fims_info::Information< Type > > fims_information
                                                                    Definition: model.hpp:35
                                                                    +
                                                                    fims_model::Model::GetInstance
                                                                    static std::shared_ptr< Model< Type > > GetInstance()
                                                                    Definition: model.hpp:50
                                                                    +
                                                                    MODEL_LOG
                                                                    std::ofstream MODEL_LOG("logs/model.log")
                                                                    +
                                                                    diff --git a/docs/model__object_8hpp_source.html b/docs/model__object_8hpp_source.html index 679e6f4..0b4ee2d 100644 --- a/docs/model__object_8hpp_source.html +++ b/docs/model__object_8hpp_source.html @@ -76,54 +76,48 @@
                                                                    model_object.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    9 #ifndef FIMS_COMMON_MODEL_OBJECT_HPP
                                                                    -
                                                                    10 #define FIMS_COMMON_MODEL_OBJECT_HPP
                                                                    -
                                                                    11 
                                                                    -
                                                                    12 #include <stdint.h>
                                                                    -
                                                                    13 
                                                                    -
                                                                    14 #include <vector>
                                                                    -
                                                                    15 
                                                                    -
                                                                    16 #include "def.hpp"
                                                                    -
                                                                    17 
                                                                    -
                                                                    18 namespace fims_model_object {
                                                                    -
                                                                    19 
                                                                    -
                                                                    23  template <typename Type>
                                                                    -
                                                                    24  struct FIMSObject {
                                                                    -
                                                                    25  uint32_t id;
                                                                    -
                                                                    26  std::vector<Type*> parameters;
                                                                    -
                                                                    27  std::vector<Type*>
                                                                    -
                                                                    28  random_effects_parameters;
                                                                    -
                                                                    29  std::vector<Type*>
                                                                    -
                                                                    30  fixed_effects_parameters;
                                                                    -
                                                                    32  virtual ~FIMSObject() {
                                                                    -
                                                                    33  }
                                                                    -
                                                                    34 
                                                                    -
                                                                    38  uint32_t GetId() const {
                                                                    -
                                                                    39  return id;
                                                                    -
                                                                    40  }
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: model_object.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    5  * Fisheries Integrated Modeling System project. See LICENSE in the
                                                                    +
                                                                    6  * source folder for reuse information.
                                                                    +
                                                                    7  *
                                                                    +
                                                                    8  */
                                                                    +
                                                                    9 
                                                                    +
                                                                    10 #ifndef FIMS_COMMON_MODEL_OBJECT_HPP
                                                                    +
                                                                    11 #define FIMS_COMMON_MODEL_OBJECT_HPP
                                                                    +
                                                                    12 
                                                                    +
                                                                    13 #include <stdint.h>
                                                                    +
                                                                    14 
                                                                    +
                                                                    15 #include <vector>
                                                                    +
                                                                    16 
                                                                    +
                                                                    17 #include "def.hpp"
                                                                    +
                                                                    18 
                                                                    +
                                                                    19 namespace fims_model_object {
                                                                    +
                                                                    20 
                                                                    +
                                                                    24 template <typename Type>
                                                                    +
                                                                    25 struct FIMSObject {
                                                                    +
                                                                    26  uint32_t id;
                                                                    +
                                                                    27  std::vector<Type*> parameters;
                                                                    +
                                                                    28  std::vector<Type*>
                                                                    +
                                                                    29  random_effects_parameters;
                                                                    +
                                                                    30  std::vector<Type*>
                                                                    +
                                                                    31  fixed_effects_parameters;
                                                                    +
                                                                    33  virtual ~FIMSObject() {}
                                                                    +
                                                                    37  uint32_t GetId() const { return id; }
                                                                    +
                                                                    38 };
                                                                    +
                                                                    39 
                                                                    +
                                                                    40 } // namespace fims_model_object
                                                                    41 
                                                                    -
                                                                    50  inline bool CheckDimensions(size_t actual, size_t expected) {
                                                                    -
                                                                    51  if (actual != expected) {
                                                                    -
                                                                    52  return false;
                                                                    -
                                                                    53  }
                                                                    -
                                                                    54 
                                                                    -
                                                                    55  return true;
                                                                    -
                                                                    56  }
                                                                    -
                                                                    57 
                                                                    -
                                                                    58  };
                                                                    -
                                                                    59 
                                                                    -
                                                                    60 } // namespace fims_model_object
                                                                    -
                                                                    61 
                                                                    -
                                                                    62 #endif /* FIMS_COMMON_MODEL_OBJECT_HPP */
                                                                    -
                                                                    def.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    fims_model_object::FIMSObject
                                                                    FIMSObject struct that defines member types and returns the unique id.
                                                                    Definition: model_object.hpp:24
                                                                    -
                                                                    fims_model_object::FIMSObject::id
                                                                    uint32_t id
                                                                    Definition: model_object.hpp:25
                                                                    -
                                                                    fims_model_object::FIMSObject::GetId
                                                                    uint32_t GetId() const
                                                                    Getter that returns the unique id for parameters in the model.
                                                                    Definition: model_object.hpp:38
                                                                    -
                                                                    fims_model_object::FIMSObject::CheckDimensions
                                                                    bool CheckDimensions(size_t actual, size_t expected)
                                                                    Check the dimensions of an object.
                                                                    Definition: model_object.hpp:50
                                                                    -
                                                                    fims_model_object::FIMSObject::random_effects_parameters
                                                                    std::vector< Type * > random_effects_parameters
                                                                    Definition: model_object.hpp:28
                                                                    -
                                                                    fims_model_object::FIMSObject::parameters
                                                                    std::vector< Type * > parameters
                                                                    Definition: model_object.hpp:26
                                                                    -
                                                                    fims_model_object::FIMSObject::fixed_effects_parameters
                                                                    std::vector< Type * > fixed_effects_parameters
                                                                    Definition: model_object.hpp:30
                                                                    +
                                                                    42 #endif /* FIMS_COMMON_MODEL_OBJECT_HPP */
                                                                    + +
                                                                    fims_model_object::FIMSObject
                                                                    FIMSObject struct that defines member types and returns the unique id.
                                                                    Definition: model_object.hpp:25
                                                                    +
                                                                    fims_model_object::FIMSObject::id
                                                                    uint32_t id
                                                                    Definition: model_object.hpp:26
                                                                    +
                                                                    fims_model_object::FIMSObject::GetId
                                                                    uint32_t GetId() const
                                                                    Getter that returns the unique id for parameters in the model.
                                                                    Definition: model_object.hpp:37
                                                                    +
                                                                    fims_model_object::FIMSObject::random_effects_parameters
                                                                    std::vector< Type * > random_effects_parameters
                                                                    Definition: model_object.hpp:29
                                                                    +
                                                                    fims_model_object::FIMSObject::parameters
                                                                    std::vector< Type * > parameters
                                                                    Definition: model_object.hpp:27
                                                                    +
                                                                    fims_model_object::FIMSObject::fixed_effects_parameters
                                                                    std::vector< Type * > fixed_effects_parameters
                                                                    Definition: model_object.hpp:31
                                                                    diff --git a/docs/population_8hpp_source.html b/docs/population_8hpp_source.html index 6dce8b2..8e46ada 100644 --- a/docs/population_8hpp_source.html +++ b/docs/population_8hpp_source.html @@ -76,535 +76,638 @@
                                                                    population.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    8 #ifndef FIMS_POPULATION_DYNAMICS_POPULATION_HPP
                                                                    -
                                                                    9 #define FIMS_POPULATION_DYNAMICS_POPULATION_HPP
                                                                    -
                                                                    10 
                                                                    -
                                                                    11 #include "../../common/model_object.hpp"
                                                                    -
                                                                    12 #include "../fleet/fleet.hpp"
                                                                    -
                                                                    13 #include "../growth/growth.hpp"
                                                                    -
                                                                    14 #include "../recruitment/recruitment.hpp"
                                                                    -
                                                                    15 //#include "subpopulation.hpp"
                                                                    -
                                                                    16 #include "../../interface/interface.hpp"
                                                                    -
                                                                    17 #include "../maturity/maturity.hpp"
                                                                    -
                                                                    18 
                                                                    -
                                                                    19 namespace fims_popdy {
                                                                    -
                                                                    20  /*TODO:
                                                                    -
                                                                    21  Review, add functions to evaluate, push vectors back to fleet (or point to
                                                                    -
                                                                    22  fleet directly?)
                                                                    -
                                                                    23  */
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: population.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    5  * Fisheries Integrated Modeling System project. See LICENSE in the
                                                                    +
                                                                    6  * source folder for reuse information.
                                                                    +
                                                                    7  *
                                                                    +
                                                                    8  * Population module file
                                                                    +
                                                                    9  * The purpose of this file is to define the Population class and its fields
                                                                    +
                                                                    10  * and methods.
                                                                    +
                                                                    11  *
                                                                    +
                                                                    12  *
                                                                    +
                                                                    13  */
                                                                    +
                                                                    14 #ifndef FIMS_POPULATION_DYNAMICS_POPULATION_HPP
                                                                    +
                                                                    15 #define FIMS_POPULATION_DYNAMICS_POPULATION_HPP
                                                                    +
                                                                    16 
                                                                    +
                                                                    17 #include "../../common/model_object.hpp"
                                                                    +
                                                                    18 #include "../fleet/fleet.hpp"
                                                                    +
                                                                    19 #include "../growth/growth.hpp"
                                                                    +
                                                                    20 #include "../recruitment/recruitment.hpp"
                                                                    +
                                                                    21 //#include "subpopulation.hpp"
                                                                    +
                                                                    22 #include "../../interface/interface.hpp"
                                                                    +
                                                                    23 #include "../maturity/maturity.hpp"
                                                                    24 
                                                                    -
                                                                    29  template <typename Type>
                                                                    -
                                                                    30  struct Population : public fims_model_object::FIMSObject<Type> {
                                                                    -
                                                                    31  static uint32_t id_g;
                                                                    -
                                                                    32  size_t nyears;
                                                                    -
                                                                    33  size_t nseasons;
                                                                    -
                                                                    34  size_t nages;
                                                                    -
                                                                    35  size_t nfleets;
                                                                    -
                                                                    37  // parameters are estimated; after initialize in create_model, push_back to
                                                                    -
                                                                    38  // parameter list - in information.hpp (same for initial F in fleet)
                                                                    -
                                                                    39  fims::Vector<Type>
                                                                    -
                                                                    40  log_init_naa;
                                                                    -
                                                                    41  fims::Vector<Type> log_M;
                                                                    -
                                                                    42  fims::Vector<Type>
                                                                    -
                                                                    43  proportion_female;
                                                                    -
                                                                    45  // Transformed values
                                                                    -
                                                                    46  fims::Vector<Type> M;
                                                                    -
                                                                    48  fims::Vector<double> ages;
                                                                    -
                                                                    49  fims::Vector<double> years;
                                                                    -
                                                                    50  fims::Vector<Type> mortality_F;
                                                                    -
                                                                    52  fims::Vector<Type>
                                                                    -
                                                                    53  mortality_Z;
                                                                    -
                                                                    55  // derived quantities
                                                                    -
                                                                    56  fims::Vector<Type>
                                                                    -
                                                                    57  weight_at_age;
                                                                    -
                                                                    58  // fecundity removed because we don't need it yet
                                                                    -
                                                                    59  fims::Vector<Type> numbers_at_age;
                                                                    -
                                                                    61  fims::Vector<Type>
                                                                    -
                                                                    62  unfished_numbers_at_age;
                                                                    -
                                                                    64  fims::Vector<Type>
                                                                    -
                                                                    65  biomass;
                                                                    -
                                                                    66  fims::Vector<Type> spawning_biomass;
                                                                    -
                                                                    67  fims::Vector<Type> unfished_biomass;
                                                                    -
                                                                    69  fims::Vector<Type> unfished_spawning_biomass;
                                                                    -
                                                                    71  fims::Vector<Type> proportion_mature_at_age;
                                                                    -
                                                                    73  fims::Vector<Type> expected_numbers_at_age;
                                                                    -
                                                                    75  fims::Vector<Type> expected_catch;
                                                                    -
                                                                    76  fims::Vector<Type> expected_recruitment;
                                                                    -
                                                                    78  int recruitment_id = -999;
                                                                    -
                                                                    79  std::shared_ptr<fims_popdy::RecruitmentBase<Type>>
                                                                    -
                                                                    80  recruitment;
                                                                    -
                                                                    82  // growth
                                                                    -
                                                                    83  int growth_id = -999;
                                                                    -
                                                                    84  std::shared_ptr<fims_popdy::GrowthBase<Type>>
                                                                    -
                                                                    85  growth;
                                                                    -
                                                                    87  // maturity
                                                                    -
                                                                    88  int maturity_id = -999;
                                                                    -
                                                                    89  std::shared_ptr<fims_popdy::MaturityBase<Type>>
                                                                    -
                                                                    90  maturity;
                                                                    -
                                                                    92  // fleet
                                                                    -
                                                                    93  int fleet_id = -999;
                                                                    -
                                                                    94  std::vector<std::shared_ptr<fims_popdy::Fleet<Type>>>
                                                                    -
                                                                    95  fleets;
                                                                    -
                                                                    97  // Define objective function object to be able to REPORT and ADREPORT
                                                                    -
                                                                    98 
                                                                    -
                                                                    99 #ifdef TMB_MODEL
                                                                    -
                                                                    100  ::objective_function<Type>
                                                                    -
                                                                    101  *of; // :: references global namespace, defined in src/FIMS.cpp,
                                                                    -
                                                                    102  // available anywhere in the R package
                                                                    -
                                                                    103 #endif
                                                                    +
                                                                    25 namespace fims_popdy {
                                                                    +
                                                                    26 /*TODO:
                                                                    +
                                                                    27  Review, add functions to evaluate, push vectors back to fleet (or point to
                                                                    +
                                                                    28  fleet directly?)
                                                                    +
                                                                    29  */
                                                                    +
                                                                    30 
                                                                    +
                                                                    35 template <typename Type>
                                                                    +
                                                                    36 struct Population : public fims_model_object::FIMSObject<Type> {
                                                                    +
                                                                    37  static uint32_t id_g;
                                                                    +
                                                                    38  size_t nyears;
                                                                    +
                                                                    39  size_t nseasons;
                                                                    +
                                                                    40  size_t nages;
                                                                    +
                                                                    41  size_t nfleets;
                                                                    +
                                                                    43  // parameters are estimated; after initialize in create_model, push_back to
                                                                    +
                                                                    44  // parameter list - in information.hpp (same for initial F in fleet)
                                                                    +
                                                                    45  fims::Vector<Type>
                                                                    +
                                                                    46  log_init_naa;
                                                                    +
                                                                    47  fims::Vector<Type> log_M;
                                                                    +
                                                                    48  fims::Vector<Type>
                                                                    +
                                                                    49  proportion_female;
                                                                    +
                                                                    51  // Transformed values
                                                                    +
                                                                    52  fims::Vector<Type> M;
                                                                    +
                                                                    54  fims::Vector<double> ages;
                                                                    +
                                                                    55  fims::Vector<double> years;
                                                                    +
                                                                    56  fims::Vector<Type> mortality_F;
                                                                    +
                                                                    58  fims::Vector<Type>
                                                                    +
                                                                    59  mortality_Z;
                                                                    +
                                                                    61  // derived quantities
                                                                    +
                                                                    62  fims::Vector<Type>
                                                                    +
                                                                    63  weight_at_age;
                                                                    +
                                                                    64  // fecundity removed because we don't need it yet
                                                                    +
                                                                    65  fims::Vector<Type> numbers_at_age;
                                                                    +
                                                                    67  fims::Vector<Type>
                                                                    +
                                                                    68  unfished_numbers_at_age;
                                                                    +
                                                                    70  fims::Vector<Type>
                                                                    +
                                                                    71  biomass;
                                                                    +
                                                                    72  fims::Vector<Type> spawning_biomass;
                                                                    +
                                                                    73  fims::Vector<Type> unfished_biomass;
                                                                    +
                                                                    75  fims::Vector<Type> unfished_spawning_biomass;
                                                                    +
                                                                    77  fims::Vector<Type> proportion_mature_at_age;
                                                                    +
                                                                    79  fims::Vector<Type> expected_numbers_at_age;
                                                                    +
                                                                    81  fims::Vector<Type> expected_catch;
                                                                    +
                                                                    82  fims::Vector<Type> expected_recruitment;
                                                                    +
                                                                    84  int recruitment_id = -999;
                                                                    +
                                                                    85  std::shared_ptr<fims_popdy::RecruitmentBase<Type>>
                                                                    +
                                                                    86  recruitment;
                                                                    +
                                                                    88  // growth
                                                                    +
                                                                    89  int growth_id = -999;
                                                                    +
                                                                    90  std::shared_ptr<fims_popdy::GrowthBase<Type>>
                                                                    +
                                                                    91  growth;
                                                                    +
                                                                    93  // maturity
                                                                    +
                                                                    94  int maturity_id = -999;
                                                                    +
                                                                    95  std::shared_ptr<fims_popdy::MaturityBase<Type>>
                                                                    +
                                                                    96  maturity;
                                                                    +
                                                                    98  // fleet
                                                                    +
                                                                    99  int fleet_id = -999;
                                                                    +
                                                                    100  std::vector<std::shared_ptr<fims_popdy::Fleet<Type>>>
                                                                    +
                                                                    101  fleets;
                                                                    +
                                                                    103  // Define objective function object to be able to REPORT and ADREPORT
                                                                    104 
                                                                    -
                                                                    105  // this -> means you're referring to a class member (member of self)
                                                                    -
                                                                    106 
                                                                    -
                                                                    107  Population() {
                                                                    -
                                                                    108  this->id = Population::id_g++;
                                                                    -
                                                                    109  }
                                                                    +
                                                                    105 #ifdef TMB_MODEL
                                                                    +
                                                                    106  ::objective_function<Type>
                                                                    +
                                                                    107  *of; // :: references global namespace, defined in src/FIMS.cpp,
                                                                    +
                                                                    108  // available anywhere in the R package
                                                                    +
                                                                    109 #endif
                                                                    110 
                                                                    -
                                                                    118  void Initialize(int nyears, int nseasons, int nages) {
                                                                    -
                                                                    119  this->nyears = nyears;
                                                                    -
                                                                    120  this->nseasons = nseasons;
                                                                    -
                                                                    121  this->nages = nages;
                                                                    -
                                                                    122 
                                                                    -
                                                                    123  // size all the vectors to length of nages
                                                                    -
                                                                    124  nfleets = fleets.size();
                                                                    -
                                                                    125  expected_catch.resize(nyears * nfleets);
                                                                    -
                                                                    126  years.resize(nyears);
                                                                    -
                                                                    127  mortality_F.resize(nyears * nages);
                                                                    -
                                                                    128  mortality_Z.resize(nyears * nages);
                                                                    -
                                                                    129  proportion_mature_at_age.resize((nyears + 1) * nages);
                                                                    -
                                                                    130  proportion_female.resize(nages);
                                                                    -
                                                                    131  weight_at_age.resize(nages);
                                                                    -
                                                                    132  unfished_numbers_at_age.resize((nyears + 1) * nages);
                                                                    -
                                                                    133  biomass.resize((nyears + 1));
                                                                    -
                                                                    134  unfished_biomass.resize((nyears + 1));
                                                                    -
                                                                    135  unfished_spawning_biomass.resize((nyears + 1));
                                                                    -
                                                                    136  spawning_biomass.resize((nyears + 1));
                                                                    -
                                                                    137  expected_recruitment.resize((nyears + 1));
                                                                    -
                                                                    138  M.resize(nyears * nages);
                                                                    -
                                                                    139  ages.resize(nages);
                                                                    -
                                                                    140  log_init_naa.resize(nages);
                                                                    -
                                                                    141  log_M.resize(nyears * nages);
                                                                    -
                                                                    142  }
                                                                    -
                                                                    143 
                                                                    -
                                                                    149  void Prepare() {
                                                                    -
                                                                    150 
                                                                    -
                                                                    151  for (size_t fleet = 0; fleet < this->fleets.size(); fleet++) {
                                                                    -
                                                                    152  this->fleets[fleet]->Prepare();
                                                                    -
                                                                    153  }
                                                                    -
                                                                    154 
                                                                    -
                                                                    155  std::fill(biomass.begin(), biomass.end(), 0.0);
                                                                    -
                                                                    156  std::fill(unfished_spawning_biomass.begin(),
                                                                    -
                                                                    157  unfished_spawning_biomass.end(), 0.0);
                                                                    -
                                                                    158  std::fill(spawning_biomass.begin(), spawning_biomass.end(), 0.0);
                                                                    -
                                                                    159  std::fill(expected_catch.begin(), expected_catch.end(), 0.0);
                                                                    -
                                                                    160  std::fill(expected_recruitment.begin(), expected_recruitment.end(), 0.0);
                                                                    -
                                                                    161  std::fill(proportion_mature_at_age.begin(), proportion_mature_at_age.end(),
                                                                    -
                                                                    162  0.0);
                                                                    -
                                                                    163  std::fill(mortality_Z.begin(), mortality_Z.end(), 0.0);
                                                                    -
                                                                    164  std::fill(proportion_female.begin(), proportion_female.end(), 0.5);
                                                                    -
                                                                    165 
                                                                    -
                                                                    166  // Transformation Section
                                                                    -
                                                                    167  for (size_t age = 0; age < this->nages; age++) {
                                                                    -
                                                                    168  this->weight_at_age[age] = growth->evaluate(ages[age]);
                                                                    -
                                                                    169  for (size_t year = 0; year < this->nyears; year++) {
                                                                    -
                                                                    170  size_t i_age_year = age * this->nyears + year;
                                                                    -
                                                                    171  this->M[i_age_year] = fims_math::exp(this->log_M[i_age_year]);
                                                                    -
                                                                    172  // mortality_F is a fims::Vector and therefore needs to be filled
                                                                    -
                                                                    173  // within a loop
                                                                    -
                                                                    174  this->mortality_F[i_age_year] = 0.0;
                                                                    -
                                                                    175  }
                                                                    -
                                                                    176  }
                                                                    -
                                                                    177  }
                                                                    -
                                                                    178 
                                                                    -
                                                                    189  inline void CalculateInitialNumbersAA(
                                                                    -
                                                                    190  size_t i_age_year, size_t a) { // inline all function unless complicated
                                                                    -
                                                                    191  this->numbers_at_age[i_age_year] = fims_math::exp(this->log_init_naa[a]);
                                                                    -
                                                                    192  }
                                                                    -
                                                                    193 
                                                                    -
                                                                    201  void CalculateMortality(size_t i_age_year, size_t year, size_t age) {
                                                                    -
                                                                    202  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                    -
                                                                    203  if (this->fleets[fleet_]->is_survey == false) {
                                                                    -
                                                                    204  this->mortality_F[i_age_year] +=
                                                                    -
                                                                    205  this->fleets[fleet_]->Fmort[year] *
                                                                    -
                                                                    206  // evaluate is a member function of the selectivity class
                                                                    -
                                                                    207  this->fleets[fleet_]->selectivity->evaluate(ages[age]);
                                                                    -
                                                                    208 
                                                                    -
                                                                    209  }
                                                                    -
                                                                    210  }
                                                                    -
                                                                    211 
                                                                    -
                                                                    212  this->mortality_Z[i_age_year] =
                                                                    -
                                                                    213  this->M[i_age_year] + this->mortality_F[i_age_year];
                                                                    -
                                                                    214  }
                                                                    -
                                                                    215 
                                                                    -
                                                                    223  inline void CalculateNumbersAA(size_t i_age_year, size_t i_agem1_yearm1,
                                                                    -
                                                                    224  size_t age) {
                                                                    -
                                                                    225  // using Z from previous age/year
                                                                    -
                                                                    226  this->numbers_at_age[i_age_year] =
                                                                    -
                                                                    227  this->numbers_at_age[i_agem1_yearm1] *
                                                                    -
                                                                    228  (fims_math::exp(-this->mortality_Z[i_agem1_yearm1]));
                                                                    -
                                                                    229 
                                                                    -
                                                                    230  // Plus group calculation
                                                                    -
                                                                    231  if (age == (this->nages - 1)) {
                                                                    -
                                                                    232  this->numbers_at_age[i_age_year] =
                                                                    -
                                                                    233  this->numbers_at_age[i_age_year] +
                                                                    -
                                                                    234  this->numbers_at_age[i_agem1_yearm1 + 1] *
                                                                    -
                                                                    235  (fims_math::exp(-this->mortality_Z[i_agem1_yearm1 + 1]));
                                                                    -
                                                                    236  }
                                                                    -
                                                                    237  }
                                                                    -
                                                                    238 
                                                                    -
                                                                    246  inline void CalculateUnfishedNumbersAA(size_t i_age_year,
                                                                    -
                                                                    247  size_t i_agem1_yearm1, size_t age) {
                                                                    -
                                                                    248  // using M from previous age/year
                                                                    -
                                                                    249  this->unfished_numbers_at_age[i_age_year] =
                                                                    -
                                                                    250  this->unfished_numbers_at_age[i_agem1_yearm1] *
                                                                    -
                                                                    251 
                                                                    -
                                                                    252  (fims_math::exp(-this->M[i_agem1_yearm1]));
                                                                    -
                                                                    253 
                                                                    -
                                                                    254  // Plus group calculation
                                                                    -
                                                                    255  if (age == (this->nages - 1)) {
                                                                    -
                                                                    256  this->unfished_numbers_at_age[i_age_year] =
                                                                    -
                                                                    257  this->unfished_numbers_at_age[i_age_year] +
                                                                    -
                                                                    258  this->unfished_numbers_at_age[i_agem1_yearm1 + 1] *
                                                                    -
                                                                    259  (fims_math::exp(-this->M[i_agem1_yearm1 + 1]));
                                                                    -
                                                                    260  }
                                                                    -
                                                                    261  }
                                                                    -
                                                                    262 
                                                                    -
                                                                    270  void CalculateBiomass(size_t i_age_year, size_t year, size_t age) {
                                                                    -
                                                                    271  this->biomass[year] +=
                                                                    -
                                                                    272  this->numbers_at_age[i_age_year] * this->weight_at_age[age];
                                                                    -
                                                                    273  }
                                                                    -
                                                                    274 
                                                                    -
                                                                    283  void CalculateUnfishedBiomass(size_t i_age_year, size_t year, size_t age) {
                                                                    -
                                                                    284  this->unfished_biomass[year] +=
                                                                    -
                                                                    285  this->unfished_numbers_at_age[i_age_year] * this->weight_at_age[age];
                                                                    -
                                                                    286  }
                                                                    -
                                                                    287 
                                                                    -
                                                                    295  void CalculateSpawningBiomass(size_t i_age_year, size_t year, size_t age) {
                                                                    -
                                                                    296  this->spawning_biomass[year] +=
                                                                    -
                                                                    297  this->proportion_female[age] * this->numbers_at_age[i_age_year] *
                                                                    -
                                                                    298  this->proportion_mature_at_age[i_age_year] * this->weight_at_age[age];
                                                                    -
                                                                    299  }
                                                                    -
                                                                    300 
                                                                    -
                                                                    309  void CalculateUnfishedSpawningBiomass(size_t i_age_year, size_t year,
                                                                    -
                                                                    310  size_t age) {
                                                                    -
                                                                    311  this->unfished_spawning_biomass[year] +=
                                                                    -
                                                                    312  this->proportion_female[age] *
                                                                    -
                                                                    313  this->unfished_numbers_at_age[i_age_year] *
                                                                    -
                                                                    314  this->proportion_mature_at_age[i_age_year] * this->weight_at_age[age];
                                                                    -
                                                                    315  }
                                                                    -
                                                                    316 
                                                                    -
                                                                    322  Type CalculateSBPR0() {
                                                                    -
                                                                    323  std::vector<Type> numbers_spr(this->nages, 1.0);
                                                                    -
                                                                    324  Type phi_0 = 0.0;
                                                                    -
                                                                    325  phi_0 += numbers_spr[0] * this->proportion_female[0] *
                                                                    -
                                                                    326  this->proportion_mature_at_age[0] *
                                                                    -
                                                                    327  this->growth->evaluate(ages[0]);
                                                                    -
                                                                    328  for (size_t a = 1; a < (this->nages - 1); a++) {
                                                                    -
                                                                    329  numbers_spr[a] = numbers_spr[a - 1] * fims_math::exp(-this->M[a]);
                                                                    -
                                                                    330  phi_0 += numbers_spr[a] * this->proportion_female[a] *
                                                                    -
                                                                    331  this->proportion_mature_at_age[a] *
                                                                    -
                                                                    332  this->growth->evaluate(ages[a]);
                                                                    -
                                                                    333  }
                                                                    -
                                                                    334 
                                                                    -
                                                                    335  numbers_spr[this->nages - 1] =
                                                                    -
                                                                    336  (numbers_spr[nages - 2] * fims_math::exp(-this->M[nages - 2])) /
                                                                    -
                                                                    337  (1 - fims_math::exp(-this->M[this->nages - 1]));
                                                                    -
                                                                    338  phi_0 += numbers_spr[this->nages - 1] *
                                                                    -
                                                                    339  this->proportion_female[this->nages - 1] *
                                                                    -
                                                                    340  this->proportion_mature_at_age[this->nages - 1] *
                                                                    -
                                                                    341  this->growth->evaluate(ages[this->nages - 1]);
                                                                    -
                                                                    342  return phi_0;
                                                                    -
                                                                    343  }
                                                                    -
                                                                    344 
                                                                    -
                                                                    352  void CalculateRecruitment(size_t i_age_year, size_t year, size_t i_dev) {
                                                                    -
                                                                    353  Type phi0 = CalculateSBPR0();
                                                                    -
                                                                    354 
                                                                    -
                                                                    355  if (i_dev == this->nyears) {
                                                                    -
                                                                    356  this->numbers_at_age[i_age_year] =
                                                                    -
                                                                    357  this->recruitment->evaluate(this->spawning_biomass[year - 1], phi0);
                                                                    -
                                                                    358  /*the final year of the time series has no data to inform recruitment
                                                                    -
                                                                    359  devs, so this value is set to the mean recruitment.*/
                                                                    -
                                                                    360  } else {
                                                                    -
                                                                    361  this->numbers_at_age[i_age_year] =
                                                                    -
                                                                    362  this->recruitment->evaluate(this->spawning_biomass[year - 1], phi0) *
                                                                    -
                                                                    363  /*the log_recruit_dev vector does not include a value for year == 0
                                                                    -
                                                                    364  and is of length nyears - 1 where the first position of the vector
                                                                    -
                                                                    365  corresponds to the second year of the time series.*/
                                                                    -
                                                                    366  fims_math::exp(this->recruitment->log_recruit_devs[i_dev - 1]);
                                                                    -
                                                                    367  this->expected_recruitment[year] = this->numbers_at_age[i_age_year];
                                                                    -
                                                                    368  }
                                                                    -
                                                                    369 
                                                                    -
                                                                    370  }
                                                                    -
                                                                    371 
                                                                    -
                                                                    378  void CalculateCatch(size_t year, size_t age) {
                                                                    -
                                                                    379  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                    -
                                                                    380  if (this->fleets[fleet_]->is_survey == false) {
                                                                    -
                                                                    381  size_t index_yf = year * this->nfleets +
                                                                    -
                                                                    382  fleet_; // index by fleet and years to dimension fold
                                                                    -
                                                                    383  size_t i_age_year = year * this->nages + age;
                                                                    -
                                                                    384 
                                                                    -
                                                                    385  this->expected_catch[index_yf] +=
                                                                    -
                                                                    386  this->fleets[fleet_]->catch_weight_at_age[i_age_year];
                                                                    -
                                                                    387 
                                                                    -
                                                                    388  fleets[fleet_]->expected_catch[year] +=
                                                                    -
                                                                    389  this->fleets[fleet_]->catch_weight_at_age[i_age_year];
                                                                    -
                                                                    390  }
                                                                    -
                                                                    391  }
                                                                    -
                                                                    392  }
                                                                    -
                                                                    393 
                                                                    -
                                                                    401  void CalculateIndex(size_t i_age_year, size_t year, size_t age) {
                                                                    -
                                                                    402  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                    -
                                                                    403  Type index_;
                                                                    -
                                                                    404  // I = qN (N is total numbers), I is an index in numbers
                                                                    -
                                                                    405  if (this->fleets[fleet_]->is_survey == false) {
                                                                    -
                                                                    406  index_ = this->fleets[fleet_]->catch_numbers_at_age[i_age_year] *
                                                                    -
                                                                    407  this->weight_at_age[age];
                                                                    -
                                                                    408  } else {
                                                                    -
                                                                    409  index_ = this->fleets[fleet_]->q.get_force_scalar(year) *
                                                                    -
                                                                    410  this->fleets[fleet_]->selectivity->evaluate(ages[age]) *
                                                                    -
                                                                    411  this->numbers_at_age[i_age_year] *
                                                                    -
                                                                    412  this->weight_at_age[age]; // this->weight_at_age[age];
                                                                    -
                                                                    413  }
                                                                    -
                                                                    414  fleets[fleet_]->expected_index[year] += index_;
                                                                    -
                                                                    415  }
                                                                    -
                                                                    416  }
                                                                    -
                                                                    417 
                                                                    -
                                                                    427  void CalculateCatchNumbersAA(size_t i_age_year, size_t year, size_t age) {
                                                                    -
                                                                    428  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                    -
                                                                    429  // make an intermediate value in order to set multiple members (of
                                                                    -
                                                                    430  // current and fleet objects) to that value.
                                                                    -
                                                                    431  Type catch_; // catch_ is used to avoid using the c++ keyword catch
                                                                    -
                                                                    432  // Baranov Catch Equation
                                                                    -
                                                                    433  if (this->fleets[fleet_]->is_survey == false) {
                                                                    -
                                                                    434  catch_ = (this->fleets[fleet_]->Fmort[year] *
                                                                    -
                                                                    435  this->fleets[fleet_]->selectivity->evaluate(ages[age])) /
                                                                    -
                                                                    436  this->mortality_Z[i_age_year] *
                                                                    -
                                                                    437  this->numbers_at_age[i_age_year] *
                                                                    -
                                                                    438  (1 - fims_math::exp(-(this->mortality_Z[i_age_year])));
                                                                    -
                                                                    439  } else {
                                                                    -
                                                                    440  catch_ = (this->fleets[fleet_]->selectivity->evaluate(ages[age])) *
                                                                    -
                                                                    441  this->numbers_at_age[i_age_year];
                                                                    -
                                                                    442  }
                                                                    -
                                                                    443 
                                                                    -
                                                                    444  // this->catch_numbers_at_age[i_age_yearf] += catch_;
                                                                    -
                                                                    445  // catch_numbers_at_age for the fleet module has different
                                                                    -
                                                                    446  // dimensions (year/age, not year/fleet/age)
                                                                    -
                                                                    447  this->fleets[fleet_]->catch_numbers_at_age[i_age_year] += catch_;
                                                                    -
                                                                    448  }
                                                                    -
                                                                    449  }
                                                                    -
                                                                    450 
                                                                    -
                                                                    458  void CalculateCatchWeightAA(size_t year, size_t age) {
                                                                    -
                                                                    459  int i_age_year = year * this->nages + age;
                                                                    -
                                                                    460  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                    -
                                                                    461 
                                                                    -
                                                                    462  this->fleets[fleet_]->catch_weight_at_age[i_age_year] =
                                                                    -
                                                                    463  this->fleets[fleet_]->catch_numbers_at_age[i_age_year] *
                                                                    -
                                                                    464  this->weight_at_age[age];
                                                                    -
                                                                    465 
                                                                    -
                                                                    466  }
                                                                    -
                                                                    467  }
                                                                    -
                                                                    468 
                                                                    -
                                                                    476  void CalculateMaturityAA(size_t i_age_year, size_t age) {
                                                                    -
                                                                    477  // this->maturity is pointing to the maturity module, which has
                                                                    -
                                                                    478  // an evaluate function. -> can be nested.
                                                                    -
                                                                    479 
                                                                    -
                                                                    480  this->proportion_mature_at_age[i_age_year] =
                                                                    -
                                                                    481  this->maturity->evaluate(ages[age]);
                                                                    -
                                                                    482 
                                                                    -
                                                                    483  }
                                                                    -
                                                                    484 
                                                                    -
                                                                    489  void Evaluate() {
                                                                    -
                                                                    490  /*
                                                                    -
                                                                    491  Sets derived vectors to zero
                                                                    -
                                                                    492  Performs parameters transformations
                                                                    -
                                                                    493  Sets recruitment deviations to mean 0.
                                                                    -
                                                                    494  */
                                                                    -
                                                                    495  Prepare();
                                                                    -
                                                                    496  /*
                                                                    -
                                                                    497  start at year=0, age=0;
                                                                    -
                                                                    498  here year 0 is the estimated initial stock structure and age 0 are recruits
                                                                    -
                                                                    499  loops start at zero with if statements inside to specify unique code for
                                                                    -
                                                                    500  initial structure and recruitment 0 loops. Could also have started loops at
                                                                    -
                                                                    501  1 with initial structure and recruitment setup outside the loops.
                                                                    -
                                                                    502 
                                                                    -
                                                                    503  year loop is extended to <= nyears because SSB is calculted as the start of
                                                                    -
                                                                    504  the year value and by extending one extra year we get estimates of the
                                                                    -
                                                                    505  population structure at the end of the final year. An alternative approach
                                                                    -
                                                                    506  would be to keep initial numbers at age in it's own vector and each year to
                                                                    -
                                                                    507  include the population structure at the end of the year. This is likely a
                                                                    -
                                                                    508  null point given that we are planning to modify to an event/stanza based
                                                                    -
                                                                    509  structure in later milestones which will elimitate this confusion by
                                                                    -
                                                                    510  explicity referencing the exact date (or period of averaging) at which any
                                                                    -
                                                                    511  calculation or output is being made.
                                                                    -
                                                                    512  */
                                                                    -
                                                                    513  for (size_t y = 0; y <= this->nyears; y++) {
                                                                    -
                                                                    514  for (size_t a = 0; a < this->nages; a++) {
                                                                    -
                                                                    515  /*
                                                                    -
                                                                    516  index naming defines the dimensional folding structure
                                                                    -
                                                                    517  i.e. i_age_year is referencing folding over years and ages.
                                                                    -
                                                                    518  */
                                                                    -
                                                                    519  size_t i_age_year = y * this->nages + a;
                                                                    -
                                                                    520  /*
                                                                    -
                                                                    521  Mortality rates are not estimated in the final year which is
                                                                    -
                                                                    522  used to show expected stock structure at the end of the model period.
                                                                    -
                                                                    523  This is because biomass in year i represents biomass at the start of
                                                                    -
                                                                    524  the year.
                                                                    -
                                                                    525  Should we add complexity to track more values such as start,
                                                                    -
                                                                    526  mid, and end biomass in all years where, start biomass=end biomass of
                                                                    -
                                                                    527  the previous year? Referenced above, this is probably not worth
                                                                    -
                                                                    528  exploring as later milestone changes will eliminate this confusion.
                                                                    -
                                                                    529  */
                                                                    -
                                                                    530  if (y < this->nyears) {
                                                                    -
                                                                    531  /*
                                                                    -
                                                                    532  First thing we need is total mortality aggregated across all fleets
                                                                    -
                                                                    533  to inform the subsequent catch and change in numbers at age
                                                                    -
                                                                    534  calculations. This is only calculated for years < nyears as these are
                                                                    -
                                                                    535  the model estimated years with data. The year loop extends to
                                                                    -
                                                                    536  y=nyears so that population numbers at age and SSB can be calculated
                                                                    -
                                                                    537  at the end of the last year of the model
                                                                    -
                                                                    538  */
                                                                    -
                                                                    539  CalculateMortality(i_age_year, y, a);
                                                                    -
                                                                    540  }
                                                                    -
                                                                    541  CalculateMaturityAA(i_age_year, a);
                                                                    -
                                                                    542  /* if statements needed because some quantities are only needed
                                                                    -
                                                                    543  for the first year and/or age, so these steps are included here.
                                                                    -
                                                                    544  */
                                                                    -
                                                                    545  if (y == 0) {
                                                                    -
                                                                    546  // Initial numbers at age is a user input or estimated parameter
                                                                    -
                                                                    547  // vector.
                                                                    -
                                                                    548  CalculateInitialNumbersAA(i_age_year, a);
                                                                    -
                                                                    549 
                                                                    -
                                                                    550  if (a == 0) {
                                                                    -
                                                                    551  // this->numbers_at_age[i_age_year] = this->recruitment->rzero;
                                                                    -
                                                                    552  this->unfished_numbers_at_age[i_age_year] =
                                                                    -
                                                                    553  fims_math::exp(this->recruitment->log_rzero[0]);
                                                                    -
                                                                    554  } else {
                                                                    -
                                                                    555  CalculateUnfishedNumbersAA(i_age_year, a - 1, a);
                                                                    -
                                                                    556  }
                                                                    -
                                                                    557 
                                                                    -
                                                                    558  /*
                                                                    -
                                                                    559  Fished and unfished biomass vectors are summing biomass at
                                                                    -
                                                                    560  age across ages.
                                                                    -
                                                                    561  */
                                                                    -
                                                                    562 
                                                                    -
                                                                    563  CalculateBiomass(i_age_year, y, a);
                                                                    -
                                                                    564 
                                                                    -
                                                                    565  CalculateUnfishedBiomass(i_age_year, y, a);
                                                                    -
                                                                    566 
                                                                    -
                                                                    567  /*
                                                                    -
                                                                    568  Fished and unfished spawning biomass vectors are summing biomass at
                                                                    -
                                                                    569  age across ages to allow calculation of recruitment in the next year.
                                                                    -
                                                                    570  */
                                                                    -
                                                                    571 
                                                                    -
                                                                    572  CalculateSpawningBiomass(i_age_year, y, a);
                                                                    -
                                                                    573 
                                                                    -
                                                                    574  CalculateUnfishedSpawningBiomass(i_age_year, y, a);
                                                                    -
                                                                    575 
                                                                    -
                                                                    576  /*
                                                                    -
                                                                    577  Expected recruitment in year 0 is numbers at age 0 in year 0.
                                                                    -
                                                                    578  */
                                                                    -
                                                                    579 
                                                                    -
                                                                    580  this->expected_recruitment[i_age_year] =
                                                                    -
                                                                    581  this->numbers_at_age[i_age_year];
                                                                    -
                                                                    582 
                                                                    -
                                                                    583  } else {
                                                                    -
                                                                    584  if (a == 0) {
                                                                    -
                                                                    585  // Set the nrecruits for age a=0 year y (use pointers instead of
                                                                    -
                                                                    586  // functional returns) assuming fecundity = 1 and 50:50 sex ratio
                                                                    -
                                                                    587  CalculateRecruitment(i_age_year, y, y);
                                                                    -
                                                                    588  this->unfished_numbers_at_age[i_age_year] =
                                                                    -
                                                                    589  fims_math::exp(this->recruitment->log_rzero[0]);
                                                                    -
                                                                    590 
                                                                    -
                                                                    591  } else {
                                                                    -
                                                                    592  size_t i_agem1_yearm1 = (y - 1) * nages + (a - 1);
                                                                    -
                                                                    593  CalculateNumbersAA(i_age_year, i_agem1_yearm1, a);
                                                                    -
                                                                    594  CalculateUnfishedNumbersAA(i_age_year, i_agem1_yearm1, a);
                                                                    -
                                                                    595  }
                                                                    -
                                                                    596  CalculateBiomass(i_age_year, y, a);
                                                                    -
                                                                    597  CalculateSpawningBiomass(i_age_year, y, a);
                                                                    -
                                                                    598 
                                                                    -
                                                                    599  CalculateUnfishedBiomass(i_age_year, y, a);
                                                                    -
                                                                    600  CalculateUnfishedSpawningBiomass(i_age_year, y, a);
                                                                    -
                                                                    601  }
                                                                    -
                                                                    602 
                                                                    -
                                                                    603  /*
                                                                    -
                                                                    604  Here composition, total catch, and index values are calculated for all
                                                                    -
                                                                    605  years with reference data. They are not calculated for y=nyears as there
                                                                    -
                                                                    606  is this is just to get final population structure at the end of the
                                                                    -
                                                                    607  terminal year.
                                                                    -
                                                                    608  */
                                                                    -
                                                                    609  if (y < this->nyears) {
                                                                    -
                                                                    610  CalculateCatchNumbersAA(i_age_year, y, a);
                                                                    -
                                                                    611 
                                                                    -
                                                                    612  CalculateCatchWeightAA(y, a);
                                                                    -
                                                                    613  CalculateCatch(y, a);
                                                                    -
                                                                    614  CalculateIndex(i_age_year, y, a);
                                                                    -
                                                                    615  }
                                                                    -
                                                                    616  }
                                                                    -
                                                                    617  }
                                                                    -
                                                                    618 
                                                                    -
                                                                    619  }
                                                                    -
                                                                    620  };
                                                                    -
                                                                    621  template <class Type>
                                                                    -
                                                                    622  uint32_t Population<Type>::id_g = 0;
                                                                    -
                                                                    623 
                                                                    -
                                                                    624 } // namespace fims_popdy
                                                                    -
                                                                    625 
                                                                    -
                                                                    626 #endif /* FIMS_POPULATION_DYNAMICS_POPULATION_HPP */
                                                                    -
                                                                    fims::Vector
                                                                    Definition: fims_vector.hpp:25
                                                                    -
                                                                    fims::Vector::resize
                                                                    void resize(size_t s)
                                                                    Changes the number of elements stored.
                                                                    Definition: fims_vector.hpp:431
                                                                    -
                                                                    fims_model_object::FIMSObject
                                                                    FIMSObject struct that defines member types and returns the unique id.
                                                                    Definition: model_object.hpp:24
                                                                    -
                                                                    fims_popdy::Population
                                                                    Population class. Contains subpopulations that are divided into generic partitions (eg....
                                                                    Definition: population.hpp:30
                                                                    -
                                                                    fims_popdy::Population::spawning_biomass
                                                                    fims::Vector< Type > spawning_biomass
                                                                    Definition: population.hpp:66
                                                                    -
                                                                    fims_popdy::Population::nseasons
                                                                    size_t nseasons
                                                                    Definition: population.hpp:33
                                                                    -
                                                                    fims_popdy::Population::mortality_F
                                                                    fims::Vector< Type > mortality_F
                                                                    Definition: population.hpp:50
                                                                    -
                                                                    fims_popdy::Population::ages
                                                                    fims::Vector< double > ages
                                                                    Definition: population.hpp:48
                                                                    -
                                                                    fims_popdy::Population::growth_id
                                                                    int growth_id
                                                                    Definition: population.hpp:83
                                                                    -
                                                                    fims_popdy::Population::nyears
                                                                    size_t nyears
                                                                    Definition: population.hpp:32
                                                                    -
                                                                    fims_popdy::Population::nfleets
                                                                    size_t nfleets
                                                                    Definition: population.hpp:35
                                                                    -
                                                                    fims_popdy::Population::CalculateUnfishedSpawningBiomass
                                                                    void CalculateUnfishedSpawningBiomass(size_t i_age_year, size_t year, size_t age)
                                                                    Adds to existing yearly unfished spawning biomass estimates the biomass for a specified year and age.
                                                                    Definition: population.hpp:309
                                                                    -
                                                                    fims_popdy::Population::CalculateNumbersAA
                                                                    void CalculateNumbersAA(size_t i_age_year, size_t i_agem1_yearm1, size_t age)
                                                                    Calculates numbers at age at year and age specific indices.
                                                                    Definition: population.hpp:223
                                                                    -
                                                                    fims_popdy::Population::CalculateSpawningBiomass
                                                                    void CalculateSpawningBiomass(size_t i_age_year, size_t year, size_t age)
                                                                    Calculates spawning biomass.
                                                                    Definition: population.hpp:295
                                                                    -
                                                                    fims_popdy::Population::proportion_mature_at_age
                                                                    fims::Vector< Type > proportion_mature_at_age
                                                                    Definition: population.hpp:71
                                                                    -
                                                                    fims_popdy::Population::Evaluate
                                                                    void Evaluate()
                                                                    Executes the population loop.
                                                                    Definition: population.hpp:489
                                                                    -
                                                                    fims_popdy::Population::log_M
                                                                    fims::Vector< Type > log_M
                                                                    Definition: population.hpp:41
                                                                    -
                                                                    fims_popdy::Population::numbers_at_age
                                                                    fims::Vector< Type > numbers_at_age
                                                                    Definition: population.hpp:59
                                                                    -
                                                                    fims_popdy::Population::CalculateMaturityAA
                                                                    void CalculateMaturityAA(size_t i_age_year, size_t age)
                                                                    Calculates expected proportion of individuals mature at a selected ageage.
                                                                    Definition: population.hpp:476
                                                                    -
                                                                    fims_popdy::Population::maturity
                                                                    std::shared_ptr< fims_popdy::MaturityBase< Type > > maturity
                                                                    Definition: population.hpp:90
                                                                    -
                                                                    fims_popdy::Population::fleets
                                                                    std::vector< std::shared_ptr< fims_popdy::Fleet< Type > > > fleets
                                                                    Definition: population.hpp:95
                                                                    -
                                                                    fims_popdy::Population::CalculateRecruitment
                                                                    void CalculateRecruitment(size_t i_age_year, size_t year, size_t i_dev)
                                                                    Calculates expected recruitment for a given year.
                                                                    Definition: population.hpp:352
                                                                    -
                                                                    fims_popdy::Population::Initialize
                                                                    void Initialize(int nyears, int nseasons, int nages)
                                                                    Initialize values. Called once at the start of model run.
                                                                    Definition: population.hpp:118
                                                                    -
                                                                    fims_popdy::Population::expected_catch
                                                                    fims::Vector< Type > expected_catch
                                                                    Definition: population.hpp:75
                                                                    -
                                                                    fims_popdy::Population::CalculateBiomass
                                                                    void CalculateBiomass(size_t i_age_year, size_t year, size_t age)
                                                                    Calculates biomass.
                                                                    Definition: population.hpp:270
                                                                    -
                                                                    fims_popdy::Population::unfished_numbers_at_age
                                                                    fims::Vector< Type > unfished_numbers_at_age
                                                                    Definition: population.hpp:62
                                                                    -
                                                                    fims_popdy::Population::fleet_id
                                                                    int fleet_id
                                                                    Definition: population.hpp:93
                                                                    -
                                                                    fims_popdy::Population::expected_numbers_at_age
                                                                    fims::Vector< Type > expected_numbers_at_age
                                                                    Definition: population.hpp:73
                                                                    -
                                                                    fims_popdy::Population::recruitment_id
                                                                    int recruitment_id
                                                                    recruitment
                                                                    Definition: population.hpp:78
                                                                    -
                                                                    fims_popdy::Population::recruitment
                                                                    std::shared_ptr< fims_popdy::RecruitmentBase< Type > > recruitment
                                                                    Definition: population.hpp:80
                                                                    -
                                                                    fims_popdy::Population::CalculateUnfishedBiomass
                                                                    void CalculateUnfishedBiomass(size_t i_age_year, size_t year, size_t age)
                                                                    Adds to existing yearly unfished biomass estimates the biomass for a specified year and age.
                                                                    Definition: population.hpp:283
                                                                    -
                                                                    fims_popdy::Population::biomass
                                                                    fims::Vector< Type > biomass
                                                                    Definition: population.hpp:65
                                                                    -
                                                                    fims_popdy::Population::weight_at_age
                                                                    fims::Vector< Type > weight_at_age
                                                                    Definition: population.hpp:57
                                                                    -
                                                                    fims_popdy::Population::id_g
                                                                    static uint32_t id_g
                                                                    Definition: population.hpp:31
                                                                    -
                                                                    fims_popdy::Population::maturity_id
                                                                    int maturity_id
                                                                    Definition: population.hpp:88
                                                                    -
                                                                    fims_popdy::Population::expected_recruitment
                                                                    fims::Vector< Type > expected_recruitment
                                                                    Definition: population.hpp:76
                                                                    -
                                                                    fims_popdy::Population::unfished_spawning_biomass
                                                                    fims::Vector< Type > unfished_spawning_biomass
                                                                    Definition: population.hpp:69
                                                                    -
                                                                    fims_popdy::Population::nages
                                                                    size_t nages
                                                                    Definition: population.hpp:34
                                                                    -
                                                                    fims_popdy::Population::CalculateCatchWeightAA
                                                                    void CalculateCatchWeightAA(size_t year, size_t age)
                                                                    Calculates expected catch weight at age for each fleet for a given year and age.
                                                                    Definition: population.hpp:458
                                                                    -
                                                                    fims_popdy::Population::mortality_Z
                                                                    fims::Vector< Type > mortality_Z
                                                                    Definition: population.hpp:53
                                                                    -
                                                                    fims_popdy::Population::CalculateUnfishedNumbersAA
                                                                    void CalculateUnfishedNumbersAA(size_t i_age_year, size_t i_agem1_yearm1, size_t age)
                                                                    Calculates unfished numbers at age at year and age specific indices.
                                                                    Definition: population.hpp:246
                                                                    -
                                                                    fims_popdy::Population::unfished_biomass
                                                                    fims::Vector< Type > unfished_biomass
                                                                    Definition: population.hpp:67
                                                                    -
                                                                    fims_popdy::Population::CalculateCatchNumbersAA
                                                                    void CalculateCatchNumbersAA(size_t i_age_year, size_t year, size_t age)
                                                                    Calculates catch in numbers at age for each fleet for a given year and age, then adds the value to th...
                                                                    Definition: population.hpp:427
                                                                    -
                                                                    fims_popdy::Population::M
                                                                    fims::Vector< Type > M
                                                                    Definition: population.hpp:46
                                                                    -
                                                                    fims_popdy::Population::CalculateIndex
                                                                    void CalculateIndex(size_t i_age_year, size_t year, size_t age)
                                                                    Adds to the expected population indices by fleet.
                                                                    Definition: population.hpp:401
                                                                    -
                                                                    fims_popdy::Population::proportion_female
                                                                    fims::Vector< Type > proportion_female
                                                                    Definition: population.hpp:43
                                                                    -
                                                                    fims_popdy::Population::CalculateMortality
                                                                    void CalculateMortality(size_t i_age_year, size_t year, size_t age)
                                                                    Calculates total mortality at an index, year, and age.
                                                                    Definition: population.hpp:201
                                                                    -
                                                                    fims_popdy::Population::CalculateCatch
                                                                    void CalculateCatch(size_t year, size_t age)
                                                                    Adds to exiting expected total catch by fleet in weight.
                                                                    Definition: population.hpp:378
                                                                    -
                                                                    fims_popdy::Population::CalculateInitialNumbersAA
                                                                    void CalculateInitialNumbersAA(size_t i_age_year, size_t a)
                                                                    Calculates initial numbers at age for index and age.
                                                                    Definition: population.hpp:189
                                                                    -
                                                                    fims_popdy::Population::CalculateSBPR0
                                                                    Type CalculateSBPR0()
                                                                    Calculates equilibrium spawning biomass per recruit.
                                                                    Definition: population.hpp:322
                                                                    -
                                                                    fims_popdy::Population::years
                                                                    fims::Vector< double > years
                                                                    Definition: population.hpp:49
                                                                    -
                                                                    fims_popdy::Population::log_init_naa
                                                                    fims::Vector< Type > log_init_naa
                                                                    Definition: population.hpp:40
                                                                    -
                                                                    fims_popdy::Population::growth
                                                                    std::shared_ptr< fims_popdy::GrowthBase< Type > > growth
                                                                    Definition: population.hpp:85
                                                                    -
                                                                    fims_popdy::Population::Prepare
                                                                    void Prepare()
                                                                    Prepare to run the population loop. Called at each model iteration, and used to zero out derived quan...
                                                                    Definition: population.hpp:149
                                                                    +
                                                                    111  // this -> means you're referring to a class member (member of self)
                                                                    +
                                                                    112 
                                                                    +
                                                                    113  Population() { this->id = Population::id_g++; }
                                                                    +
                                                                    114 
                                                                    +
                                                                    122  void Initialize(int nyears, int nseasons, int nages) {
                                                                    +
                                                                    123  this->nyears = nyears;
                                                                    +
                                                                    124  this->nseasons = nseasons;
                                                                    +
                                                                    125  this->nages = nages;
                                                                    +
                                                                    126 
                                                                    +
                                                                    127  // size all the vectors to length of nages
                                                                    +
                                                                    128  nfleets = fleets.size();
                                                                    +
                                                                    129  expected_catch.resize(nyears * nfleets);
                                                                    +
                                                                    130  years.resize(nyears);
                                                                    +
                                                                    131  mortality_F.resize(nyears * nages);
                                                                    +
                                                                    132  mortality_Z.resize(nyears * nages);
                                                                    +
                                                                    133  proportion_mature_at_age.resize((nyears + 1) * nages);
                                                                    +
                                                                    134  proportion_female.resize(nages);
                                                                    +
                                                                    135  weight_at_age.resize(nages);
                                                                    +
                                                                    136  unfished_numbers_at_age.resize((nyears + 1) * nages);
                                                                    +
                                                                    137  numbers_at_age.resize((nyears + 1) * nages);
                                                                    +
                                                                    138  biomass.resize((nyears + 1));
                                                                    +
                                                                    139  unfished_biomass.resize((nyears + 1));
                                                                    +
                                                                    140  unfished_spawning_biomass.resize((nyears + 1));
                                                                    +
                                                                    141  spawning_biomass.resize((nyears + 1));
                                                                    +
                                                                    142  expected_recruitment.resize((nyears + 1));
                                                                    +
                                                                    143  M.resize(nyears * nages);
                                                                    +
                                                                    144  ages.resize(nages);
                                                                    +
                                                                    145  log_init_naa.resize(nages);
                                                                    +
                                                                    146  log_M.resize(nyears * nages);
                                                                    +
                                                                    147  }
                                                                    +
                                                                    148 
                                                                    +
                                                                    154  void Prepare() {
                                                                    +
                                                                    155  POPULATION_LOG << " population prepare " << this->nages << std::endl;
                                                                    +
                                                                    156  POPULATION_LOG << "nfleets: " << this->nfleets << std::endl;
                                                                    +
                                                                    157  POPULATION_LOG << "nseasons: " << this->nseasons << std::endl;
                                                                    +
                                                                    158  POPULATION_LOG << "nyears: " << this->nyears << std::endl;
                                                                    +
                                                                    159 
                                                                    +
                                                                    160  for (size_t fleet = 0; fleet < this->nfleets; fleet++) {
                                                                    +
                                                                    161  this->fleets[fleet]->Prepare();
                                                                    +
                                                                    162  }
                                                                    +
                                                                    163 
                                                                    +
                                                                    164  std::fill(biomass.begin(), biomass.end(), 0.0);
                                                                    +
                                                                    165  std::fill(unfished_spawning_biomass.begin(),
                                                                    +
                                                                    166  unfished_spawning_biomass.end(), 0.0);
                                                                    +
                                                                    167  std::fill(spawning_biomass.begin(), spawning_biomass.end(), 0.0);
                                                                    +
                                                                    168  std::fill(expected_catch.begin(), expected_catch.end(), 0.0);
                                                                    +
                                                                    169  std::fill(expected_recruitment.begin(), expected_recruitment.end(), 0.0);
                                                                    +
                                                                    170  std::fill(proportion_mature_at_age.begin(), proportion_mature_at_age.end(),
                                                                    +
                                                                    171  0.0);
                                                                    +
                                                                    172  std::fill(mortality_Z.begin(), mortality_Z.end(), 0.0);
                                                                    +
                                                                    173  std::fill(proportion_female.begin(), proportion_female.end(), 0.5);
                                                                    +
                                                                    174 
                                                                    +
                                                                    175  // Transformation Section
                                                                    +
                                                                    176  for (size_t age = 0; age < this->nages; age++) {
                                                                    +
                                                                    177  this->weight_at_age[age] = growth->evaluate(ages[age]);
                                                                    +
                                                                    178  for (size_t year = 0; year < this->nyears; year++) {
                                                                    +
                                                                    179  size_t i_age_year = age * this->nyears + year;
                                                                    +
                                                                    180  this->M[i_age_year] = fims_math::exp(this->log_M[i_age_year]);
                                                                    +
                                                                    181  // mortality_F is a fims::Vector and therefore needs to be filled
                                                                    +
                                                                    182  // within a loop
                                                                    +
                                                                    183  this->mortality_F[i_age_year] = 0.0;
                                                                    +
                                                                    184  }
                                                                    +
                                                                    185  }
                                                                    +
                                                                    186  }
                                                                    +
                                                                    187 
                                                                    +
                                                                    198  inline void CalculateInitialNumbersAA(
                                                                    +
                                                                    199  size_t i_age_year, size_t a) { // inline all function unless complicated
                                                                    +
                                                                    200  this->numbers_at_age[i_age_year] = fims_math::exp(this->log_init_naa[a]);
                                                                    +
                                                                    201  }
                                                                    +
                                                                    202 
                                                                    +
                                                                    210  void CalculateMortality(size_t i_age_year, size_t year, size_t age) {
                                                                    +
                                                                    211  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                    +
                                                                    212  if (this->fleets[fleet_]->is_survey == false) {
                                                                    +
                                                                    213  this->mortality_F[i_age_year] +=
                                                                    +
                                                                    214  this->fleets[fleet_]->Fmort[year] *
                                                                    +
                                                                    215  // evaluate is a member function of the selectivity class
                                                                    +
                                                                    216  this->fleets[fleet_]->selectivity->evaluate(ages[age]);
                                                                    +
                                                                    217  POPULATION_LOG << " selectivity at age " << ages[age] << " for fleet "
                                                                    +
                                                                    218  << fleet_ << " is "
                                                                    +
                                                                    219  << this->fleets[fleet_]->selectivity->evaluate(ages[age])
                                                                    +
                                                                    220  << " apical fishing mortality F for the fleet in year "
                                                                    +
                                                                    221  << year << " is " << this->fleets[fleet_]->Fmort[year]
                                                                    +
                                                                    222  << std::endl;
                                                                    +
                                                                    223  }
                                                                    +
                                                                    224  }
                                                                    +
                                                                    225  POPULATION_LOG << "M in calculate mortality is " << this->M[i_age_year]
                                                                    +
                                                                    226  << std::endl;
                                                                    +
                                                                    227  this->mortality_Z[i_age_year] =
                                                                    +
                                                                    228  this->M[i_age_year] + this->mortality_F[i_age_year];
                                                                    +
                                                                    229  }
                                                                    +
                                                                    230 
                                                                    +
                                                                    238  inline void CalculateNumbersAA(size_t i_age_year, size_t i_agem1_yearm1,
                                                                    +
                                                                    239  size_t age) {
                                                                    +
                                                                    240  // using Z from previous age/year
                                                                    +
                                                                    241  this->numbers_at_age[i_age_year] =
                                                                    +
                                                                    242  this->numbers_at_age[i_agem1_yearm1] *
                                                                    +
                                                                    243 
                                                                    +
                                                                    244  (fims_math::exp(-this->mortality_Z[i_agem1_yearm1]));
                                                                    +
                                                                    245  POPULATION_LOG << " z at i_agem1_yearm1 = " << i_agem1_yearm1 << " is "
                                                                    +
                                                                    246  << this->mortality_Z[i_agem1_yearm1] << std::endl;
                                                                    +
                                                                    247  // Plus group calculation
                                                                    +
                                                                    248  if (age == (this->nages - 1)) {
                                                                    +
                                                                    249  this->numbers_at_age[i_age_year] =
                                                                    +
                                                                    250  this->numbers_at_age[i_age_year] +
                                                                    +
                                                                    251  this->numbers_at_age[i_agem1_yearm1 + 1] *
                                                                    +
                                                                    252  (fims_math::exp(-this->mortality_Z[i_agem1_yearm1 + 1]));
                                                                    +
                                                                    253  }
                                                                    +
                                                                    254  }
                                                                    +
                                                                    255 
                                                                    +
                                                                    263  inline void CalculateUnfishedNumbersAA(size_t i_age_year,
                                                                    +
                                                                    264  size_t i_agem1_yearm1, size_t age) {
                                                                    +
                                                                    265  // using M from previous age/year
                                                                    +
                                                                    266  this->unfished_numbers_at_age[i_age_year] =
                                                                    +
                                                                    267  this->unfished_numbers_at_age[i_agem1_yearm1] *
                                                                    +
                                                                    268 
                                                                    +
                                                                    269  (fims_math::exp(-this->M[i_agem1_yearm1]));
                                                                    +
                                                                    270  POPULATION_LOG << "survival rate at index " << i_agem1_yearm1 << " is "
                                                                    +
                                                                    271  << fims_math::exp(-(this->M[i_agem1_yearm1])) << std::endl;
                                                                    +
                                                                    272 
                                                                    +
                                                                    273  // Plus group calculation
                                                                    +
                                                                    274  if (age == (this->nages - 1)) {
                                                                    +
                                                                    275  this->unfished_numbers_at_age[i_age_year] =
                                                                    +
                                                                    276  this->unfished_numbers_at_age[i_age_year] +
                                                                    +
                                                                    277  this->unfished_numbers_at_age[i_agem1_yearm1 + 1] *
                                                                    +
                                                                    278  (fims_math::exp(-this->M[i_agem1_yearm1 + 1]));
                                                                    +
                                                                    279  }
                                                                    +
                                                                    280  }
                                                                    +
                                                                    281 
                                                                    +
                                                                    289  void CalculateBiomass(size_t i_age_year, size_t year, size_t age) {
                                                                    +
                                                                    290  this->biomass[year] +=
                                                                    +
                                                                    291  this->numbers_at_age[i_age_year] * this->weight_at_age[age];
                                                                    +
                                                                    292  POPULATION_LOG << " age " << ages[age] << std::endl;
                                                                    +
                                                                    293  POPULATION_LOG << "growth evaluate: " << this->weight_at_age[age]
                                                                    +
                                                                    294  << " biomass inputs----- +++\n";
                                                                    +
                                                                    295  }
                                                                    +
                                                                    296 
                                                                    +
                                                                    305  void CalculateUnfishedBiomass(size_t i_age_year, size_t year, size_t age) {
                                                                    +
                                                                    306  this->unfished_biomass[year] +=
                                                                    +
                                                                    307  this->unfished_numbers_at_age[i_age_year] * this->weight_at_age[age];
                                                                    +
                                                                    308  }
                                                                    +
                                                                    309 
                                                                    +
                                                                    317  void CalculateSpawningBiomass(size_t i_age_year, size_t year, size_t age) {
                                                                    +
                                                                    318  this->spawning_biomass[year] +=
                                                                    +
                                                                    319  this->proportion_female[age] * this->numbers_at_age[i_age_year] *
                                                                    +
                                                                    320  this->proportion_mature_at_age[i_age_year] * this->weight_at_age[age];
                                                                    +
                                                                    321  POPULATION_LOG << " proportion female " << this->proportion_female[age]
                                                                    +
                                                                    322  << " "
                                                                    +
                                                                    323  << " mature age " << age << " is "
                                                                    +
                                                                    324  << this->proportion_mature_at_age[i_age_year] << " "
                                                                    +
                                                                    325  << " numbers at age " << this->numbers_at_age[i_age_year]
                                                                    +
                                                                    326  << " "
                                                                    +
                                                                    327  << " growth " << this->weight_at_age[age] << " "
                                                                    +
                                                                    328  << " spawning biomass " << this->spawning_biomass[year]
                                                                    +
                                                                    329  << " "
                                                                    +
                                                                    330  << " spawning biomass inputs----- +++\n";
                                                                    +
                                                                    331  }
                                                                    +
                                                                    332 
                                                                    +
                                                                    341  void CalculateUnfishedSpawningBiomass(size_t i_age_year, size_t year,
                                                                    +
                                                                    342  size_t age) {
                                                                    +
                                                                    343  this->unfished_spawning_biomass[year] +=
                                                                    +
                                                                    344  this->proportion_female[age] *
                                                                    +
                                                                    345  this->unfished_numbers_at_age[i_age_year] *
                                                                    +
                                                                    346  this->proportion_mature_at_age[i_age_year] * this->weight_at_age[age];
                                                                    +
                                                                    347  }
                                                                    +
                                                                    348 
                                                                    +
                                                                    354  Type CalculateSBPR0() {
                                                                    +
                                                                    355  std::vector<Type> numbers_spr(this->nages, 1.0);
                                                                    +
                                                                    356  Type phi_0 = 0.0;
                                                                    +
                                                                    357  phi_0 += numbers_spr[0] * this->proportion_female[0] *
                                                                    +
                                                                    358  this->proportion_mature_at_age[0] *
                                                                    +
                                                                    359  this->growth->evaluate(ages[0]);
                                                                    +
                                                                    360  for (size_t a = 1; a < (this->nages - 1); a++) {
                                                                    +
                                                                    361  numbers_spr[a] = numbers_spr[a - 1] * fims_math::exp(-this->M[a]);
                                                                    +
                                                                    362  phi_0 += numbers_spr[a] * this->proportion_female[a] *
                                                                    +
                                                                    363  this->proportion_mature_at_age[a] *
                                                                    +
                                                                    364  this->growth->evaluate(ages[a]);
                                                                    +
                                                                    365  }
                                                                    +
                                                                    366 
                                                                    +
                                                                    367  numbers_spr[this->nages - 1] =
                                                                    +
                                                                    368  (numbers_spr[nages - 2] * fims_math::exp(-this->M[nages - 2])) /
                                                                    +
                                                                    369  (1 - fims_math::exp(-this->M[this->nages - 1]));
                                                                    +
                                                                    370  phi_0 += numbers_spr[this->nages - 1] *
                                                                    +
                                                                    371  this->proportion_female[this->nages - 1] *
                                                                    +
                                                                    372  this->proportion_mature_at_age[this->nages - 1] *
                                                                    +
                                                                    373  this->growth->evaluate(ages[this->nages - 1]);
                                                                    +
                                                                    374  return phi_0;
                                                                    +
                                                                    375  }
                                                                    +
                                                                    376 
                                                                    +
                                                                    384  void CalculateRecruitment(size_t i_age_year, size_t year, size_t i_dev) {
                                                                    +
                                                                    385  POPULATION_LOG << "recruitment 1" << std::endl;
                                                                    +
                                                                    386  Type phi0 = CalculateSBPR0();
                                                                    +
                                                                    387  POPULATION_LOG << "recruitment 2" << std::endl;
                                                                    +
                                                                    388  POPULATION_LOG << "phi0 = " << phi0 << std::endl;
                                                                    +
                                                                    389  POPULATION_LOG << "spawning_biomass[year - 1] = "
                                                                    +
                                                                    390  << this->spawning_biomass[year - 1] << std::endl;
                                                                    +
                                                                    391  POPULATION_LOG << "log recruit devs = "
                                                                    +
                                                                    392  << this->recruitment->log_recruit_devs[i_dev - 1]
                                                                    +
                                                                    393  << std::endl;
                                                                    +
                                                                    394  POPULATION_LOG << "rec eval = "
                                                                    +
                                                                    395  << this->recruitment->evaluate(
                                                                    +
                                                                    396  this->spawning_biomass[year - 1], phi0)
                                                                    +
                                                                    397  << std::endl;
                                                                    +
                                                                    398  if (i_dev == this->nyears) {
                                                                    +
                                                                    399  this->numbers_at_age[i_age_year] =
                                                                    +
                                                                    400  this->recruitment->evaluate(this->spawning_biomass[year - 1], phi0);
                                                                    +
                                                                    401  /*the final year of the time series has no data to inform recruitment
                                                                    +
                                                                    402  devs, so this value is set to the mean recruitment.*/
                                                                    +
                                                                    403  } else {
                                                                    +
                                                                    404  this->numbers_at_age[i_age_year] =
                                                                    +
                                                                    405  this->recruitment->evaluate(this->spawning_biomass[year - 1], phi0) *
                                                                    +
                                                                    406  /*the log_recruit_dev vector does not include a value for year == 0
                                                                    +
                                                                    407  and is of length nyears - 1 where the first position of the vector
                                                                    +
                                                                    408  corresponds to the second year of the time series.*/
                                                                    +
                                                                    409  fims_math::exp(this->recruitment->log_recruit_devs[i_dev - 1]);
                                                                    +
                                                                    410  this->expected_recruitment[year] = this->numbers_at_age[i_age_year];
                                                                    +
                                                                    411  }
                                                                    +
                                                                    412  POPULATION_LOG << " numbers at age at index i_age_year " << i_age_year
                                                                    +
                                                                    413  << " is " << this->numbers_at_age[i_age_year] << std::endl;
                                                                    +
                                                                    414  }
                                                                    +
                                                                    415 
                                                                    +
                                                                    422  void CalculateCatch(size_t year, size_t age) {
                                                                    +
                                                                    423  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                    +
                                                                    424  if (this->fleets[fleet_]->is_survey == false) {
                                                                    +
                                                                    425  size_t index_yf = year * this->nfleets +
                                                                    +
                                                                    426  fleet_; // index by fleet and years to dimension fold
                                                                    +
                                                                    427  size_t i_age_year = year * this->nages + age;
                                                                    +
                                                                    428 
                                                                    +
                                                                    429  POPULATION_LOG << " fleet " << fleet_ << " year " << year << " age "
                                                                    +
                                                                    430  << age << std::endl;
                                                                    +
                                                                    431  this->expected_catch[index_yf] +=
                                                                    +
                                                                    432  this->fleets[fleet_]->catch_weight_at_age[i_age_year];
                                                                    +
                                                                    433 
                                                                    +
                                                                    434  POPULATION_LOG << "expected catch: " << this->expected_catch[index_yf]
                                                                    +
                                                                    435  << std::endl;
                                                                    +
                                                                    436  POPULATION_LOG << "----------------------------------------------"
                                                                    +
                                                                    437  << std::endl;
                                                                    +
                                                                    438 
                                                                    +
                                                                    439  fleets[fleet_]->expected_catch[year] +=
                                                                    +
                                                                    440  this->fleets[fleet_]->catch_weight_at_age[i_age_year];
                                                                    +
                                                                    441  }
                                                                    +
                                                                    442  }
                                                                    +
                                                                    443  }
                                                                    +
                                                                    444 
                                                                    +
                                                                    452  void CalculateIndex(size_t i_age_year, size_t year, size_t age) {
                                                                    +
                                                                    453  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                    +
                                                                    454  Type index_;
                                                                    +
                                                                    455  // I = qN (N is total numbers), I is an index in numbers
                                                                    +
                                                                    456  if (this->fleets[fleet_]->is_survey == false) {
                                                                    +
                                                                    457  index_ = this->fleets[fleet_]->catch_numbers_at_age[i_age_year] *
                                                                    +
                                                                    458  this->weight_at_age[age];
                                                                    +
                                                                    459  } else {
                                                                    +
                                                                    460  POPULATION_LOG << "fleet " << fleet_ << " is a survey" << std::endl;
                                                                    +
                                                                    461  index_ = this->fleets[fleet_]->q *
                                                                    +
                                                                    462  this->fleets[fleet_]->selectivity->evaluate(ages[age]) *
                                                                    +
                                                                    463  this->numbers_at_age[i_age_year] *
                                                                    +
                                                                    464  this->weight_at_age[age]; // this->weight_at_age[age];
                                                                    +
                                                                    465  }
                                                                    +
                                                                    466  fleets[fleet_]->expected_index[year] += index_;
                                                                    +
                                                                    467  POPULATION_LOG << " expected index in year " << year << " is "
                                                                    +
                                                                    468  << fleets[fleet_]->expected_index[year] << std::endl;
                                                                    +
                                                                    469  }
                                                                    +
                                                                    470  }
                                                                    +
                                                                    471 
                                                                    +
                                                                    481  void CalculateCatchNumbersAA(size_t i_age_year, size_t year, size_t age) {
                                                                    +
                                                                    482  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                    +
                                                                    483  // make an intermediate value in order to set multiple members (of
                                                                    +
                                                                    484  // current and fleet objects) to that value.
                                                                    +
                                                                    485  Type catch_; // catch_ is used to avoid using the c++ keyword catch
                                                                    +
                                                                    486  // Baranov Catch Equation
                                                                    +
                                                                    487  if (this->fleets[fleet_]->is_survey == false) {
                                                                    +
                                                                    488  catch_ = (this->fleets[fleet_]->Fmort[year] *
                                                                    +
                                                                    489  this->fleets[fleet_]->selectivity->evaluate(ages[age])) /
                                                                    +
                                                                    490  this->mortality_Z[i_age_year] *
                                                                    +
                                                                    491  this->numbers_at_age[i_age_year] *
                                                                    +
                                                                    492  (1 - fims_math::exp(-(this->mortality_Z[i_age_year])));
                                                                    +
                                                                    493  } else {
                                                                    +
                                                                    494  catch_ = (this->fleets[fleet_]->selectivity->evaluate(ages[age])) *
                                                                    +
                                                                    495  this->numbers_at_age[i_age_year];
                                                                    +
                                                                    496  }
                                                                    +
                                                                    497  POPULATION_LOG << " F " << fleet_ << " "
                                                                    +
                                                                    498  << this->fleets[fleet_]->Fmort[year] << std::endl;
                                                                    +
                                                                    499  POPULATION_LOG << " selectivity "
                                                                    +
                                                                    500  << this->fleets[fleet_]->selectivity->evaluate(ages[age])
                                                                    +
                                                                    501  << std::endl;
                                                                    +
                                                                    502  POPULATION_LOG << " catch " << catch_ << std::endl;
                                                                    +
                                                                    503  // this->catch_numbers_at_age[i_age_yearf] += catch_;
                                                                    +
                                                                    504  // catch_numbers_at_age for the fleet module has different
                                                                    +
                                                                    505  // dimensions (year/age, not year/fleet/age)
                                                                    +
                                                                    506  this->fleets[fleet_]->catch_numbers_at_age[i_age_year] += catch_;
                                                                    +
                                                                    507  }
                                                                    +
                                                                    508  }
                                                                    +
                                                                    509 
                                                                    +
                                                                    517  void CalculateCatchWeightAA(size_t year, size_t age) {
                                                                    +
                                                                    518  int i_age_year = year * this->nages + age;
                                                                    +
                                                                    519  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                    +
                                                                    520  POPULATION_LOG << " fleet " << fleet_ << std::endl;
                                                                    +
                                                                    521  POPULATION_LOG << " catchnaa "
                                                                    +
                                                                    522  << this->fleets[fleet_]->catch_numbers_at_age[year]
                                                                    +
                                                                    523  << std::endl;
                                                                    +
                                                                    524  POPULATION_LOG << " weight " << this->weight_at_age[age] << std::endl;
                                                                    +
                                                                    525  this->fleets[fleet_]->catch_weight_at_age[i_age_year] =
                                                                    +
                                                                    526  this->fleets[fleet_]->catch_numbers_at_age[i_age_year] *
                                                                    +
                                                                    527  this->weight_at_age[age];
                                                                    +
                                                                    528  POPULATION_LOG << " catch_waa "
                                                                    +
                                                                    529  << this->fleets[fleet_]->catch_weight_at_age[i_age_year]
                                                                    +
                                                                    530  << std::endl;
                                                                    +
                                                                    531  }
                                                                    +
                                                                    532  }
                                                                    +
                                                                    533 
                                                                    +
                                                                    541  void CalculateMaturityAA(size_t i_age_year, size_t age) {
                                                                    +
                                                                    542  // this->maturity is pointing to the maturity module, which has
                                                                    +
                                                                    543  // an evaluate function. -> can be nested.
                                                                    +
                                                                    544  POPULATION_LOG << " age " << age << std::endl;
                                                                    +
                                                                    545  POPULATION_LOG << " ages size " << this->ages.size() << std::endl;
                                                                    +
                                                                    546  POPULATION_LOG << " i_age_year " << i_age_year << std::endl;
                                                                    +
                                                                    547  POPULATION_LOG << "p mature" << this->proportion_mature_at_age[i_age_year]
                                                                    +
                                                                    548  << std::endl;
                                                                    +
                                                                    549  POPULATION_LOG << this->ages[age] << std::endl;
                                                                    +
                                                                    550  this->proportion_mature_at_age[i_age_year] =
                                                                    +
                                                                    551  this->maturity->evaluate(ages[age]);
                                                                    +
                                                                    552 
                                                                    +
                                                                    553  POPULATION_LOG << "p mature set to "
                                                                    +
                                                                    554  << this->proportion_mature_at_age[i_age_year] << std::endl;
                                                                    +
                                                                    555  }
                                                                    +
                                                                    556 
                                                                    +
                                                                    561  void Evaluate() {
                                                                    +
                                                                    562  /*
                                                                    +
                                                                    563  Sets derived vectors to zero
                                                                    +
                                                                    564  Performs parameters transformations
                                                                    +
                                                                    565  Sets recruitment deviations to mean 0.
                                                                    +
                                                                    566  */
                                                                    +
                                                                    567  Prepare();
                                                                    +
                                                                    568  /*
                                                                    +
                                                                    569  start at year=0, age=0;
                                                                    +
                                                                    570  here year 0 is the estimated initial stock structure and age 0 are recruits
                                                                    +
                                                                    571  loops start at zero with if statements inside to specify unique code for
                                                                    +
                                                                    572  initial structure and recruitment 0 loops. Could also have started loops at
                                                                    +
                                                                    573  1 with initial structure and recruitment setup outside the loops.
                                                                    +
                                                                    574 
                                                                    +
                                                                    575  year loop is extended to <= nyears because SSB is calculted as the start of
                                                                    +
                                                                    576  the year value and by extending one extra year we get estimates of the
                                                                    +
                                                                    577  population structure at the end of the final year. An alternative approach
                                                                    +
                                                                    578  would be to keep initial numbers at age in it's own vector and each year to
                                                                    +
                                                                    579  include the population structure at the end of the year. This is likely a
                                                                    +
                                                                    580  null point given that we are planning to modify to an event/stanza based
                                                                    +
                                                                    581  structure in later milestones which will elimitate this confusion by
                                                                    +
                                                                    582  explicity referencing the exact date (or period of averaging) at which any
                                                                    +
                                                                    583  calculation or output is being made.
                                                                    +
                                                                    584  */
                                                                    +
                                                                    585  for (size_t y = 0; y <= this->nyears; y++) {
                                                                    +
                                                                    586  for (size_t a = 0; a < this->nages; a++) {
                                                                    +
                                                                    587  /*
                                                                    +
                                                                    588  index naming defines the dimensional folding structure
                                                                    +
                                                                    589  i.e. i_age_year is referencing folding over years and ages.
                                                                    +
                                                                    590  */
                                                                    +
                                                                    591  size_t i_age_year = y * this->nages + a;
                                                                    +
                                                                    592  /*
                                                                    +
                                                                    593  Mortality rates are not estimated in the final year which is
                                                                    +
                                                                    594  used to show expected stock structure at the end of the model period.
                                                                    +
                                                                    595  This is because biomass in year i represents biomass at the start of
                                                                    +
                                                                    596  the year.
                                                                    +
                                                                    597  Should we add complexity to track more values such as start,
                                                                    +
                                                                    598  mid, and end biomass in all years where, start biomass=end biomass of
                                                                    +
                                                                    599  the previous year? Referenced above, this is probably not worth
                                                                    +
                                                                    600  exploring as later milestone changes will eliminate this confusion.
                                                                    +
                                                                    601  */
                                                                    +
                                                                    602  if (y < this->nyears) {
                                                                    +
                                                                    603  /*
                                                                    +
                                                                    604  First thing we need is total mortality aggregated across all fleets
                                                                    +
                                                                    605  to inform the subsequent catch and change in numbers at age
                                                                    +
                                                                    606  calculations. This is only calculated for years < nyears as these are
                                                                    +
                                                                    607  the model estimated years with data. The year loop extends to
                                                                    +
                                                                    608  y=nyears so that population numbers at age and SSB can be calculated
                                                                    +
                                                                    609  at the end of the last year of the model
                                                                    +
                                                                    610  */
                                                                    +
                                                                    611  CalculateMortality(i_age_year, y, a);
                                                                    +
                                                                    612  }
                                                                    +
                                                                    613  CalculateMaturityAA(i_age_year, a);
                                                                    +
                                                                    614  /* if statements needed because some quantities are only needed
                                                                    +
                                                                    615  for the first year and/or age, so these steps are included here.
                                                                    +
                                                                    616  */
                                                                    +
                                                                    617  if (y == 0) {
                                                                    +
                                                                    618  // Initial numbers at age is a user input or estimated parameter
                                                                    +
                                                                    619  // vector.
                                                                    +
                                                                    620  CalculateInitialNumbersAA(i_age_year, a);
                                                                    +
                                                                    621 
                                                                    +
                                                                    622  if (a == 0) {
                                                                    +
                                                                    623  // this->numbers_at_age[i_age_year] = this->recruitment->rzero;
                                                                    +
                                                                    624  this->unfished_numbers_at_age[i_age_year] =
                                                                    +
                                                                    625  fims_math::exp(this->recruitment->log_rzero);
                                                                    +
                                                                    626  } else {
                                                                    +
                                                                    627  CalculateUnfishedNumbersAA(i_age_year, a - 1, a);
                                                                    +
                                                                    628  }
                                                                    +
                                                                    629 
                                                                    +
                                                                    630  /*
                                                                    +
                                                                    631  Fished and unfished biomass vectors are summing biomass at
                                                                    +
                                                                    632  age across ages.
                                                                    +
                                                                    633  */
                                                                    +
                                                                    634 
                                                                    +
                                                                    635  CalculateBiomass(i_age_year, y, a);
                                                                    +
                                                                    636 
                                                                    +
                                                                    637  CalculateUnfishedBiomass(i_age_year, y, a);
                                                                    +
                                                                    638 
                                                                    +
                                                                    639  /*
                                                                    +
                                                                    640  Fished and unfished spawning biomass vectors are summing biomass at
                                                                    +
                                                                    641  age across ages to allow calculation of recruitment in the next year.
                                                                    +
                                                                    642  */
                                                                    +
                                                                    643 
                                                                    +
                                                                    644  CalculateSpawningBiomass(i_age_year, y, a);
                                                                    +
                                                                    645 
                                                                    +
                                                                    646  CalculateUnfishedSpawningBiomass(i_age_year, y, a);
                                                                    +
                                                                    647 
                                                                    +
                                                                    648  /*
                                                                    +
                                                                    649  Expected recruitment in year 0 is numbers at age 0 in year 0.
                                                                    +
                                                                    650  */
                                                                    +
                                                                    651 
                                                                    +
                                                                    652  this->expected_recruitment[i_age_year] =
                                                                    +
                                                                    653  this->numbers_at_age[i_age_year];
                                                                    +
                                                                    654 
                                                                    +
                                                                    655  } else {
                                                                    +
                                                                    656  if (a == 0) {
                                                                    +
                                                                    657  // Set the nrecruits for age a=0 year y (use pointers instead of
                                                                    +
                                                                    658  // functional returns) assuming fecundity = 1 and 50:50 sex ratio
                                                                    +
                                                                    659  POPULATION_LOG << "Recruitment: " << std::endl;
                                                                    +
                                                                    660  CalculateRecruitment(i_age_year, y, y);
                                                                    +
                                                                    661  this->unfished_numbers_at_age[i_age_year] =
                                                                    +
                                                                    662  fims_math::exp(this->recruitment->log_rzero);
                                                                    +
                                                                    663 
                                                                    +
                                                                    664  } else {
                                                                    +
                                                                    665  size_t i_agem1_yearm1 = (y - 1) * nages + (a - 1);
                                                                    +
                                                                    666  CalculateNumbersAA(i_age_year, i_agem1_yearm1, a);
                                                                    +
                                                                    667  CalculateUnfishedNumbersAA(i_age_year, i_agem1_yearm1, a);
                                                                    +
                                                                    668  }
                                                                    +
                                                                    669  CalculateBiomass(i_age_year, y, a);
                                                                    +
                                                                    670  CalculateSpawningBiomass(i_age_year, y, a);
                                                                    +
                                                                    671 
                                                                    +
                                                                    672  POPULATION_LOG << "index age year: " << i_age_year << std::endl;
                                                                    +
                                                                    673  CalculateUnfishedBiomass(i_age_year, y, a);
                                                                    +
                                                                    674  CalculateUnfishedSpawningBiomass(i_age_year, y, a);
                                                                    +
                                                                    675  }
                                                                    +
                                                                    676 
                                                                    +
                                                                    677  /*
                                                                    +
                                                                    678  Here composition, total catch, and index values are calculated for all
                                                                    +
                                                                    679  years with reference data. They are not calculated for y=nyears as there
                                                                    +
                                                                    680  is this is just to get final population structure at the end of the
                                                                    +
                                                                    681  terminal year.
                                                                    +
                                                                    682  */
                                                                    +
                                                                    683  if (y < this->nyears) {
                                                                    +
                                                                    684  POPULATION_LOG << i_age_year << std::endl;
                                                                    +
                                                                    685  CalculateCatchNumbersAA(i_age_year, y, a);
                                                                    +
                                                                    686 
                                                                    +
                                                                    687  CalculateCatchWeightAA(y, a);
                                                                    +
                                                                    688  POPULATION_LOG << "year " << y << " and age " << a << std::endl;
                                                                    +
                                                                    689  CalculateCatch(y, a);
                                                                    +
                                                                    690  CalculateIndex(i_age_year, y, a);
                                                                    +
                                                                    691  }
                                                                    +
                                                                    692  }
                                                                    +
                                                                    693  }
                                                                    +
                                                                    694 
                                                                    +
                                                                    695  POPULATION_LOG << "NAA\n";
                                                                    +
                                                                    696  for (size_t i = 0; i < nyears; i++) {
                                                                    +
                                                                    697  for (size_t j = 0; j < nages; j++) {
                                                                    +
                                                                    698  POPULATION_LOG << numbers_at_age[i * nages + j] << "\t";
                                                                    +
                                                                    699  }
                                                                    +
                                                                    700  POPULATION_LOG << "\n";
                                                                    +
                                                                    701  }
                                                                    +
                                                                    702 
                                                                    +
                                                                    703  POPULATION_LOG << "CAA\n";
                                                                    +
                                                                    704  for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
                                                                    +
                                                                    705  for (size_t i = 0; i < nyears; i++) {
                                                                    +
                                                                    706  for (size_t j = 0; j < nages; j++) {
                                                                    +
                                                                    707  POPULATION_LOG << "Fleet " << fleet_ + 1 << "\n";
                                                                    +
                                                                    708  POPULATION_LOG << fleets[fleet_]->catch_numbers_at_age[i * nages + j]
                                                                    +
                                                                    709  << "\t";
                                                                    +
                                                                    710  }
                                                                    +
                                                                    711  POPULATION_LOG << "\n";
                                                                    +
                                                                    712  }
                                                                    +
                                                                    713  }
                                                                    +
                                                                    714  }
                                                                    +
                                                                    715 };
                                                                    +
                                                                    716 template <class Type>
                                                                    +
                                                                    717 uint32_t Population<Type>::id_g = 0;
                                                                    +
                                                                    718 
                                                                    +
                                                                    719 } // namespace fims_popdy
                                                                    +
                                                                    720 
                                                                    +
                                                                    721 #endif /* FIMS_POPULATION_DYNAMICS_POPULATION_HPP */
                                                                    +
                                                                    fims::Vector
                                                                    Definition: fims_vector.hpp:18
                                                                    +
                                                                    fims::Vector::resize
                                                                    void resize(size_t s)
                                                                    Changes the number of elements stored.
                                                                    Definition: fims_vector.hpp:310
                                                                    +
                                                                    fims::Vector::size
                                                                    size_type size() const
                                                                    Returns the number of elements.
                                                                    Definition: fims_vector.hpp:208
                                                                    +
                                                                    POPULATION_LOG
                                                                    std::ofstream POPULATION_LOG("logs/population.log")
                                                                    +
                                                                    fims_model_object::FIMSObject
                                                                    FIMSObject struct that defines member types and returns the unique id.
                                                                    Definition: model_object.hpp:25
                                                                    +
                                                                    fims_popdy::Population
                                                                    Population class. Contains subpopulations that are divided into generic partitions (eg....
                                                                    Definition: population.hpp:36
                                                                    +
                                                                    fims_popdy::Population::spawning_biomass
                                                                    fims::Vector< Type > spawning_biomass
                                                                    Definition: population.hpp:72
                                                                    +
                                                                    fims_popdy::Population::nseasons
                                                                    size_t nseasons
                                                                    Definition: population.hpp:39
                                                                    +
                                                                    fims_popdy::Population::mortality_F
                                                                    fims::Vector< Type > mortality_F
                                                                    Definition: population.hpp:56
                                                                    +
                                                                    fims_popdy::Population::ages
                                                                    fims::Vector< double > ages
                                                                    Definition: population.hpp:54
                                                                    +
                                                                    fims_popdy::Population::growth_id
                                                                    int growth_id
                                                                    Definition: population.hpp:89
                                                                    +
                                                                    fims_popdy::Population::nyears
                                                                    size_t nyears
                                                                    Definition: population.hpp:38
                                                                    +
                                                                    fims_popdy::Population::nfleets
                                                                    size_t nfleets
                                                                    Definition: population.hpp:41
                                                                    +
                                                                    fims_popdy::Population::CalculateUnfishedSpawningBiomass
                                                                    void CalculateUnfishedSpawningBiomass(size_t i_age_year, size_t year, size_t age)
                                                                    Adds to existing yearly unfished spawning biomass estimates the biomass for a specified year and age.
                                                                    Definition: population.hpp:341
                                                                    +
                                                                    fims_popdy::Population::CalculateNumbersAA
                                                                    void CalculateNumbersAA(size_t i_age_year, size_t i_agem1_yearm1, size_t age)
                                                                    Calculates numbers at age at year and age specific indices.
                                                                    Definition: population.hpp:238
                                                                    +
                                                                    fims_popdy::Population::CalculateSpawningBiomass
                                                                    void CalculateSpawningBiomass(size_t i_age_year, size_t year, size_t age)
                                                                    Calculates spawning biomass.
                                                                    Definition: population.hpp:317
                                                                    +
                                                                    fims_popdy::Population::proportion_mature_at_age
                                                                    fims::Vector< Type > proportion_mature_at_age
                                                                    Definition: population.hpp:77
                                                                    +
                                                                    fims_popdy::Population::Evaluate
                                                                    void Evaluate()
                                                                    Executes the population loop.
                                                                    Definition: population.hpp:561
                                                                    +
                                                                    fims_popdy::Population::log_M
                                                                    fims::Vector< Type > log_M
                                                                    Definition: population.hpp:47
                                                                    +
                                                                    fims_popdy::Population::numbers_at_age
                                                                    fims::Vector< Type > numbers_at_age
                                                                    Definition: population.hpp:65
                                                                    +
                                                                    fims_popdy::Population::CalculateMaturityAA
                                                                    void CalculateMaturityAA(size_t i_age_year, size_t age)
                                                                    Calculates expected proportion of individuals mature at a selected ageage.
                                                                    Definition: population.hpp:541
                                                                    +
                                                                    fims_popdy::Population::maturity
                                                                    std::shared_ptr< fims_popdy::MaturityBase< Type > > maturity
                                                                    Definition: population.hpp:96
                                                                    +
                                                                    fims_popdy::Population::fleets
                                                                    std::vector< std::shared_ptr< fims_popdy::Fleet< Type > > > fleets
                                                                    Definition: population.hpp:101
                                                                    +
                                                                    fims_popdy::Population::CalculateRecruitment
                                                                    void CalculateRecruitment(size_t i_age_year, size_t year, size_t i_dev)
                                                                    Calculates expected recruitment for a given year.
                                                                    Definition: population.hpp:384
                                                                    +
                                                                    fims_popdy::Population::Initialize
                                                                    void Initialize(int nyears, int nseasons, int nages)
                                                                    Initialize values. Called once at the start of model run.
                                                                    Definition: population.hpp:122
                                                                    +
                                                                    fims_popdy::Population::expected_catch
                                                                    fims::Vector< Type > expected_catch
                                                                    Definition: population.hpp:81
                                                                    +
                                                                    fims_popdy::Population::CalculateBiomass
                                                                    void CalculateBiomass(size_t i_age_year, size_t year, size_t age)
                                                                    Calculates biomass.
                                                                    Definition: population.hpp:289
                                                                    +
                                                                    fims_popdy::Population::unfished_numbers_at_age
                                                                    fims::Vector< Type > unfished_numbers_at_age
                                                                    Definition: population.hpp:68
                                                                    +
                                                                    fims_popdy::Population::fleet_id
                                                                    int fleet_id
                                                                    Definition: population.hpp:99
                                                                    +
                                                                    fims_popdy::Population::expected_numbers_at_age
                                                                    fims::Vector< Type > expected_numbers_at_age
                                                                    Definition: population.hpp:79
                                                                    +
                                                                    fims_popdy::Population::recruitment_id
                                                                    int recruitment_id
                                                                    recruitment
                                                                    Definition: population.hpp:84
                                                                    +
                                                                    fims_popdy::Population::recruitment
                                                                    std::shared_ptr< fims_popdy::RecruitmentBase< Type > > recruitment
                                                                    Definition: population.hpp:86
                                                                    +
                                                                    fims_popdy::Population::CalculateUnfishedBiomass
                                                                    void CalculateUnfishedBiomass(size_t i_age_year, size_t year, size_t age)
                                                                    Adds to existing yearly unfished biomass estimates the biomass for a specified year and age.
                                                                    Definition: population.hpp:305
                                                                    +
                                                                    fims_popdy::Population::biomass
                                                                    fims::Vector< Type > biomass
                                                                    Definition: population.hpp:71
                                                                    +
                                                                    fims_popdy::Population::weight_at_age
                                                                    fims::Vector< Type > weight_at_age
                                                                    Definition: population.hpp:63
                                                                    +
                                                                    fims_popdy::Population::id_g
                                                                    static uint32_t id_g
                                                                    Definition: population.hpp:37
                                                                    +
                                                                    fims_popdy::Population::maturity_id
                                                                    int maturity_id
                                                                    Definition: population.hpp:94
                                                                    +
                                                                    fims_popdy::Population::expected_recruitment
                                                                    fims::Vector< Type > expected_recruitment
                                                                    Definition: population.hpp:82
                                                                    +
                                                                    fims_popdy::Population::unfished_spawning_biomass
                                                                    fims::Vector< Type > unfished_spawning_biomass
                                                                    Definition: population.hpp:75
                                                                    +
                                                                    fims_popdy::Population::nages
                                                                    size_t nages
                                                                    Definition: population.hpp:40
                                                                    +
                                                                    fims_popdy::Population::CalculateCatchWeightAA
                                                                    void CalculateCatchWeightAA(size_t year, size_t age)
                                                                    Calculates expected catch weight at age for each fleet for a given year and age.
                                                                    Definition: population.hpp:517
                                                                    +
                                                                    fims_popdy::Population::mortality_Z
                                                                    fims::Vector< Type > mortality_Z
                                                                    Definition: population.hpp:59
                                                                    +
                                                                    fims_popdy::Population::CalculateUnfishedNumbersAA
                                                                    void CalculateUnfishedNumbersAA(size_t i_age_year, size_t i_agem1_yearm1, size_t age)
                                                                    Calculates unfished numbers at age at year and age specific indices.
                                                                    Definition: population.hpp:263
                                                                    +
                                                                    fims_popdy::Population::unfished_biomass
                                                                    fims::Vector< Type > unfished_biomass
                                                                    Definition: population.hpp:73
                                                                    +
                                                                    fims_popdy::Population::CalculateCatchNumbersAA
                                                                    void CalculateCatchNumbersAA(size_t i_age_year, size_t year, size_t age)
                                                                    Calculates catch in numbers at age for each fleet for a given year and age, then adds the value to th...
                                                                    Definition: population.hpp:481
                                                                    +
                                                                    fims_popdy::Population::M
                                                                    fims::Vector< Type > M
                                                                    Definition: population.hpp:52
                                                                    +
                                                                    fims_popdy::Population::CalculateIndex
                                                                    void CalculateIndex(size_t i_age_year, size_t year, size_t age)
                                                                    Adds to the expected population indices by fleet.
                                                                    Definition: population.hpp:452
                                                                    +
                                                                    fims_popdy::Population::proportion_female
                                                                    fims::Vector< Type > proportion_female
                                                                    Definition: population.hpp:49
                                                                    +
                                                                    fims_popdy::Population::CalculateMortality
                                                                    void CalculateMortality(size_t i_age_year, size_t year, size_t age)
                                                                    Calculates total mortality at an index, year, and age.
                                                                    Definition: population.hpp:210
                                                                    +
                                                                    fims_popdy::Population::CalculateCatch
                                                                    void CalculateCatch(size_t year, size_t age)
                                                                    Adds to exiting expected total catch by fleet in weight.
                                                                    Definition: population.hpp:422
                                                                    +
                                                                    fims_popdy::Population::CalculateInitialNumbersAA
                                                                    void CalculateInitialNumbersAA(size_t i_age_year, size_t a)
                                                                    Calculates initial numbers at age for index and age.
                                                                    Definition: population.hpp:198
                                                                    +
                                                                    fims_popdy::Population::CalculateSBPR0
                                                                    Type CalculateSBPR0()
                                                                    Calculates equilibrium spawning biomass per recruit.
                                                                    Definition: population.hpp:354
                                                                    +
                                                                    fims_popdy::Population::years
                                                                    fims::Vector< double > years
                                                                    Definition: population.hpp:55
                                                                    +
                                                                    fims_popdy::Population::log_init_naa
                                                                    fims::Vector< Type > log_init_naa
                                                                    Definition: population.hpp:46
                                                                    +
                                                                    fims_popdy::Population::growth
                                                                    std::shared_ptr< fims_popdy::GrowthBase< Type > > growth
                                                                    Definition: population.hpp:91
                                                                    +
                                                                    fims_popdy::Population::Prepare
                                                                    void Prepare()
                                                                    Prepare to run the population loop. Called at each model iteration, and used to zero out derived quan...
                                                                    Definition: population.hpp:154
                                                                    diff --git a/docs/rcpp__data_8hpp_source.html b/docs/rcpp__data_8hpp_source.html index 7507b8e..e8b6af5 100644 --- a/docs/rcpp__data_8hpp_source.html +++ b/docs/rcpp__data_8hpp_source.html @@ -76,12 +76,18 @@
                                                                    rcpp_data.hpp
                                                                    -
                                                                    1 
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: rcpp_fleet.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    5  * Fisheries Integrated Modeling System project. See LICENSE file
                                                                    +
                                                                    6  * for reuse information.
                                                                    +
                                                                    7  */
                                                                    8 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_DATA_HPP
                                                                    9 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_DATA_HPP
                                                                    10 
                                                                    11 #include "../../../common/information.hpp"
                                                                    -
                                                                    12 #include "rcpp_interface_base.hpp"
                                                                    +
                                                                    12 #include "rcpp_interface_base.hpp"
                                                                    13 
                                                                    20 class DataInterfaceBase : public FIMSRcppInterfaceBase {
                                                                    21  public:
                                                                    @@ -121,186 +127,90 @@
                                                                    78  virtual ~AgeCompDataInterface() {}
                                                                    79 
                                                                    82  virtual uint32_t get_id() { return this->id; }
                                                                    -
                                                                    83 
                                                                    -
                                                                    87  virtual std::string to_json() {
                                                                    -
                                                                    88  std::stringstream ss;
                                                                    -
                                                                    89 
                                                                    -
                                                                    90  ss << "\"module\" : {\n";
                                                                    -
                                                                    91  ss << " \"name\": \"data\",\n";
                                                                    -
                                                                    92  ss << " \"type\" : \"AgeComp\",\n";
                                                                    -
                                                                    93  ss << " \"id\":" << this->id << ",\n";
                                                                    -
                                                                    94  ss << " \"rank\": " << 2 << ",\n";
                                                                    -
                                                                    95  ss << " \"dimensions\": [" << this->ymax << "," << this->amax << "],\n";
                                                                    -
                                                                    96  ss << " \"values\": [";
                                                                    -
                                                                    97  for (size_t i = 0; i < age_comp_data.size() - 1; i++) {
                                                                    -
                                                                    98  ss << age_comp_data[i] << ", ";
                                                                    -
                                                                    99  }
                                                                    -
                                                                    100  ss << age_comp_data[age_comp_data.size() - 1] << "]\n";
                                                                    -
                                                                    101  ss << "}";
                                                                    -
                                                                    102  return ss.str();
                                                                    -
                                                                    103  }
                                                                    -
                                                                    104 
                                                                    -
                                                                    105 
                                                                    -
                                                                    106 #ifdef TMB_MODEL
                                                                    +
                                                                    83 
                                                                    +
                                                                    84 #ifdef TMB_MODEL
                                                                    +
                                                                    85 
                                                                    +
                                                                    86  template <typename Type>
                                                                    +
                                                                    87  bool add_to_fims_tmb_internal() {
                                                                    +
                                                                    88  std::shared_ptr<fims_data_object::DataObject<Type>> age_comp_data =
                                                                    +
                                                                    89  std::make_shared<fims_data_object::DataObject<Type>>(this->ymax,
                                                                    +
                                                                    90  this->amax);
                                                                    +
                                                                    91 
                                                                    +
                                                                    92  age_comp_data->id = this->id;
                                                                    +
                                                                    93  for (int y = 0; y < ymax; y++) {
                                                                    +
                                                                    94  for (int a = 0; a < amax; a++) {
                                                                    +
                                                                    95  int i_age_year = y * amax + a;
                                                                    +
                                                                    96  age_comp_data->at(y, a) = this->age_comp_data[i_age_year];
                                                                    +
                                                                    97  }
                                                                    +
                                                                    98  }
                                                                    +
                                                                    99 
                                                                    +
                                                                    100  std::shared_ptr<fims_info::Information<Type>> info =
                                                                    +
                                                                    101  fims_info::Information<Type>::GetInstance();
                                                                    +
                                                                    102 
                                                                    +
                                                                    103  info->data_objects[this->id] = age_comp_data;
                                                                    +
                                                                    104 
                                                                    +
                                                                    105  return true;
                                                                    +
                                                                    106  }
                                                                    107 
                                                                    -
                                                                    108  template <typename Type>
                                                                    -
                                                                    109  bool add_to_fims_tmb_internal() {
                                                                    -
                                                                    110  std::shared_ptr<fims_data_object::DataObject<Type>> age_comp_data =
                                                                    -
                                                                    111  std::make_shared<fims_data_object::DataObject<Type>>(this->ymax,
                                                                    -
                                                                    112  this->amax);
                                                                    -
                                                                    113 
                                                                    -
                                                                    114  age_comp_data->id = this->id;
                                                                    -
                                                                    115  for (int y = 0; y < ymax; y++) {
                                                                    -
                                                                    116  for (int a = 0; a < amax; a++) {
                                                                    -
                                                                    117  int i_age_year = y * amax + a;
                                                                    -
                                                                    118  age_comp_data->at(y, a) = this->age_comp_data[i_age_year];
                                                                    -
                                                                    119  }
                                                                    -
                                                                    120  }
                                                                    -
                                                                    121 
                                                                    -
                                                                    122  std::shared_ptr<fims_info::Information<Type>> info =
                                                                    -
                                                                    123  fims_info::Information<Type>::GetInstance();
                                                                    -
                                                                    124 
                                                                    -
                                                                    125  info->data_objects[this->id] = age_comp_data;
                                                                    -
                                                                    126 
                                                                    -
                                                                    127  return true;
                                                                    -
                                                                    128  }
                                                                    -
                                                                    129 
                                                                    -
                                                                    133  virtual bool add_to_fims_tmb() {
                                                                    -
                                                                    134  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    -
                                                                    135  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    -
                                                                    136  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    -
                                                                    137  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    -
                                                                    138 
                                                                    -
                                                                    139  return true;
                                                                    -
                                                                    140  }
                                                                    -
                                                                    141 
                                                                    -
                                                                    142 #endif
                                                                    -
                                                                    143 };
                                                                    -
                                                                    144 
                                                                    -
                                                                    150 class LengthCompDataInterface : public DataInterfaceBase {
                                                                    -
                                                                    151  public:
                                                                    -
                                                                    152  int lmax;
                                                                    -
                                                                    153  int ymax;
                                                                    -
                                                                    154  Rcpp::NumericVector length_comp_data;
                                                                    -
                                                                    158  LengthCompDataInterface(int ymax = 0, int lmax = 0) : DataInterfaceBase() {
                                                                    -
                                                                    159  this->lmax = lmax;
                                                                    -
                                                                    160  this->ymax = ymax;
                                                                    -
                                                                    161  }
                                                                    -
                                                                    165  virtual ~LengthCompDataInterface() {}
                                                                    -
                                                                    168  virtual uint32_t get_id() { return this->id; }
                                                                    -
                                                                    169 
                                                                    -
                                                                    173  virtual std::string to_json() {
                                                                    -
                                                                    174  std::stringstream ss;
                                                                    -
                                                                    175 
                                                                    -
                                                                    176  ss << "\"module\" : {\n";
                                                                    -
                                                                    177  ss << " \"name\": \"data\",\n";
                                                                    -
                                                                    178  ss << " \"type\" : \"LengthComp\",\n";
                                                                    -
                                                                    179  ss << " \"id\":" << this->id << ",\n";
                                                                    -
                                                                    180  ss << " \"rank\": " << 2 << ",\n";
                                                                    -
                                                                    181  ss << " \"dimensions\": [" << this->ymax << "," << this->lmax << "],\n";
                                                                    -
                                                                    182  ss << " \"values\": [";
                                                                    -
                                                                    183  for (size_t i = 0; i < length_comp_data.size() - 1; i++) {
                                                                    -
                                                                    184  ss << length_comp_data[i] << ", ";
                                                                    -
                                                                    185  }
                                                                    -
                                                                    186  ss << length_comp_data[length_comp_data.size() - 1] << "]\n";
                                                                    -
                                                                    187  ss << "}";
                                                                    -
                                                                    188  return ss.str();
                                                                    -
                                                                    189  }
                                                                    -
                                                                    190 
                                                                    -
                                                                    191 #ifdef TMB_MODEL
                                                                    -
                                                                    192  template <typename Type>
                                                                    -
                                                                    193  bool add_to_fims_tmb_internal() {
                                                                    -
                                                                    194  std::shared_ptr<fims_data_object::DataObject<Type>> length_comp_data =
                                                                    -
                                                                    195  std::make_shared<fims_data_object::DataObject<Type>>(this->ymax,
                                                                    -
                                                                    196  this->lmax);
                                                                    -
                                                                    197  length_comp_data->id = this->id;
                                                                    -
                                                                    198  for (int y = 0; y < ymax; y++) {
                                                                    -
                                                                    199  for (int l = 0; l < lmax; l++) {
                                                                    -
                                                                    200  int i_length_year = y * lmax + l;
                                                                    -
                                                                    201  length_comp_data->at(y, l) = this->length_comp_data[i_length_year];
                                                                    -
                                                                    202  }
                                                                    -
                                                                    203  }
                                                                    -
                                                                    204  std::shared_ptr<fims_info::Information<Type>> info =
                                                                    -
                                                                    205  fims_info::Information<Type>::GetInstance();
                                                                    -
                                                                    206  info->data_objects[this->id] = length_comp_data;
                                                                    -
                                                                    207  return true;
                                                                    -
                                                                    208  }
                                                                    -
                                                                    212  virtual bool add_to_fims_tmb() {
                                                                    -
                                                                    213  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    -
                                                                    214  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    -
                                                                    215  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    -
                                                                    216  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    -
                                                                    217  return true;
                                                                    -
                                                                    218  }
                                                                    -
                                                                    219 #endif
                                                                    -
                                                                    220 };
                                                                    -
                                                                    221 
                                                                    -
                                                                    227 class IndexDataInterface : public DataInterfaceBase {
                                                                    -
                                                                    228  public:
                                                                    -
                                                                    229  int ymax;
                                                                    -
                                                                    230  Rcpp::NumericVector index_data;
                                                                    -
                                                                    235  IndexDataInterface(int ymax = 0) : DataInterfaceBase() { this->ymax = ymax; }
                                                                    -
                                                                    236 
                                                                    -
                                                                    240  virtual ~IndexDataInterface() {}
                                                                    -
                                                                    241 
                                                                    -
                                                                    244  virtual uint32_t get_id() { return this->id; }
                                                                    -
                                                                    245 
                                                                    -
                                                                    249  virtual std::string to_json() {
                                                                    -
                                                                    250  std::stringstream ss;
                                                                    -
                                                                    251 
                                                                    -
                                                                    252  ss << "\"module\" : {\n";
                                                                    -
                                                                    253  ss << " \"name\": \"data\",\n";
                                                                    -
                                                                    254  ss << " \"type\": \"Index\",\n";
                                                                    -
                                                                    255  ss << " \"id\": " << this->id << ",\n";
                                                                    -
                                                                    256  ss << " \"rank\": " << 1 << ",\n";
                                                                    -
                                                                    257  ss << " \"dimensions\": [" << this->ymax << "],\n";
                                                                    -
                                                                    258  ss << " \"values\": [";
                                                                    -
                                                                    259  for (size_t i = 0; i < index_data.size() - 1; i++) {
                                                                    -
                                                                    260  ss << index_data[i] << ", ";
                                                                    -
                                                                    261  }
                                                                    -
                                                                    262  ss << index_data[index_data.size() - 1] << "]\n";
                                                                    -
                                                                    263  ss << "}";
                                                                    -
                                                                    264  return ss.str();
                                                                    -
                                                                    265  }
                                                                    -
                                                                    266 
                                                                    -
                                                                    267 #ifdef TMB_MODEL
                                                                    -
                                                                    268 
                                                                    -
                                                                    269  template <typename Type>
                                                                    -
                                                                    270  bool add_to_fims_tmb_internal() {
                                                                    -
                                                                    271  std::shared_ptr<fims_data_object::DataObject<Type>> data =
                                                                    -
                                                                    272  std::make_shared<fims_data_object::DataObject<Type>>(this->ymax);
                                                                    -
                                                                    273 
                                                                    -
                                                                    274  data->id = this->id;
                                                                    -
                                                                    275 
                                                                    -
                                                                    276  for (int y = 0; y < ymax; y++) {
                                                                    -
                                                                    277  data->at(y) = this->index_data[y];
                                                                    -
                                                                    278  }
                                                                    -
                                                                    279 
                                                                    -
                                                                    280  std::shared_ptr<fims_info::Information<Type>> info =
                                                                    -
                                                                    281  fims_info::Information<Type>::GetInstance();
                                                                    -
                                                                    282 
                                                                    -
                                                                    283  info->data_objects[this->id] = data;
                                                                    -
                                                                    284  return true;
                                                                    -
                                                                    285  }
                                                                    -
                                                                    286 
                                                                    -
                                                                    290  virtual bool add_to_fims_tmb() {
                                                                    -
                                                                    291  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    -
                                                                    292  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    -
                                                                    293  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    -
                                                                    294  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    -
                                                                    295 
                                                                    -
                                                                    296  return true;
                                                                    -
                                                                    297  }
                                                                    -
                                                                    298 
                                                                    -
                                                                    299 #endif
                                                                    -
                                                                    300 };
                                                                    -
                                                                    301 
                                                                    -
                                                                    302 #endif
                                                                    +
                                                                    111  virtual bool add_to_fims_tmb() {
                                                                    +
                                                                    112  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    +
                                                                    113  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    +
                                                                    114  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    +
                                                                    115  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    +
                                                                    116 
                                                                    +
                                                                    117  return true;
                                                                    +
                                                                    118  }
                                                                    +
                                                                    119 
                                                                    +
                                                                    120 #endif
                                                                    +
                                                                    121 };
                                                                    +
                                                                    122 
                                                                    +
                                                                    128 class IndexDataInterface : public DataInterfaceBase {
                                                                    +
                                                                    129  public:
                                                                    +
                                                                    130  int ymax;
                                                                    +
                                                                    131  Rcpp::NumericVector index_data;
                                                                    +
                                                                    136  IndexDataInterface(int ymax = 0) : DataInterfaceBase() { this->ymax = ymax; }
                                                                    +
                                                                    137 
                                                                    +
                                                                    141  virtual ~IndexDataInterface() {}
                                                                    +
                                                                    142 
                                                                    +
                                                                    145  virtual uint32_t get_id() { return this->id; }
                                                                    +
                                                                    146 
                                                                    +
                                                                    147 #ifdef TMB_MODEL
                                                                    +
                                                                    148 
                                                                    +
                                                                    149  template <typename Type>
                                                                    +
                                                                    150  bool add_to_fims_tmb_internal() {
                                                                    +
                                                                    151  std::shared_ptr<fims_data_object::DataObject<Type>> data =
                                                                    +
                                                                    152  std::make_shared<fims_data_object::DataObject<Type>>(this->ymax);
                                                                    +
                                                                    153 
                                                                    +
                                                                    154  data->id = this->id;
                                                                    +
                                                                    155 
                                                                    +
                                                                    156  for (int y = 0; y < ymax; y++) {
                                                                    +
                                                                    157  data->at(y) = this->index_data[y];
                                                                    +
                                                                    158  }
                                                                    +
                                                                    159 
                                                                    +
                                                                    160  std::shared_ptr<fims_info::Information<Type>> info =
                                                                    +
                                                                    161  fims_info::Information<Type>::GetInstance();
                                                                    +
                                                                    162 
                                                                    +
                                                                    163  info->data_objects[this->id] = data;
                                                                    +
                                                                    164  return true;
                                                                    +
                                                                    165  }
                                                                    +
                                                                    166 
                                                                    +
                                                                    170  virtual bool add_to_fims_tmb() {
                                                                    +
                                                                    171  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    +
                                                                    172  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    +
                                                                    173  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    +
                                                                    174  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    +
                                                                    175 
                                                                    +
                                                                    176  return true;
                                                                    +
                                                                    177  }
                                                                    +
                                                                    178 
                                                                    +
                                                                    179 #endif
                                                                    +
                                                                    180 };
                                                                    +
                                                                    181 
                                                                    +
                                                                    182 #endif
                                                                    AgeCompDataInterface
                                                                    Rcpp interface for age comp data as an S4 object. To instantiate from R: acomp <- new(AgeComp)
                                                                    Definition: rcpp_data.hpp:61
                                                                    AgeCompDataInterface::ymax
                                                                    int ymax
                                                                    Definition: rcpp_data.hpp:64
                                                                    AgeCompDataInterface::age_comp_data
                                                                    Rcpp::NumericVector age_comp_data
                                                                    Definition: rcpp_data.hpp:65
                                                                    AgeCompDataInterface::~AgeCompDataInterface
                                                                    virtual ~AgeCompDataInterface()
                                                                    destructor
                                                                    Definition: rcpp_data.hpp:78
                                                                    -
                                                                    AgeCompDataInterface::to_json
                                                                    virtual std::string to_json()
                                                                    Convert the data to json representation for the output.
                                                                    Definition: rcpp_data.hpp:87
                                                                    AgeCompDataInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_data.hpp:82
                                                                    AgeCompDataInterface::amax
                                                                    int amax
                                                                    Definition: rcpp_data.hpp:63
                                                                    AgeCompDataInterface::AgeCompDataInterface
                                                                    AgeCompDataInterface(int ymax=0, int amax=0)
                                                                    constructor
                                                                    Definition: rcpp_data.hpp:70
                                                                    @@ -313,25 +223,15 @@
                                                                    DataInterfaceBase::id
                                                                    uint32_t id
                                                                    Definition: rcpp_data.hpp:24
                                                                    DataInterfaceBase::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_data.hpp:46
                                                                    DataInterfaceBase::observed_data
                                                                    Rcpp::NumericVector observed_data
                                                                    Definition: rcpp_data.hpp:22
                                                                    -
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:336
                                                                    -
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:342
                                                                    -
                                                                    IndexDataInterface
                                                                    Rcpp interface for data as an S4 object. To instantiate from R: fleet <- new(Index)
                                                                    Definition: rcpp_data.hpp:227
                                                                    -
                                                                    IndexDataInterface::to_json
                                                                    virtual std::string to_json()
                                                                    Convert the data to json representation for the output.
                                                                    Definition: rcpp_data.hpp:249
                                                                    -
                                                                    IndexDataInterface::ymax
                                                                    int ymax
                                                                    Definition: rcpp_data.hpp:229
                                                                    -
                                                                    IndexDataInterface::IndexDataInterface
                                                                    IndexDataInterface(int ymax=0)
                                                                    constructor
                                                                    Definition: rcpp_data.hpp:235
                                                                    -
                                                                    IndexDataInterface::index_data
                                                                    Rcpp::NumericVector index_data
                                                                    Definition: rcpp_data.hpp:230
                                                                    -
                                                                    IndexDataInterface::~IndexDataInterface
                                                                    virtual ~IndexDataInterface()
                                                                    destructor
                                                                    Definition: rcpp_data.hpp:240
                                                                    -
                                                                    IndexDataInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_data.hpp:244
                                                                    -
                                                                    LengthCompDataInterface
                                                                    Rcpp interface for length comp data as an S4 object. To instantiate from R: lcomp <- new(LengthComp)
                                                                    Definition: rcpp_data.hpp:150
                                                                    -
                                                                    LengthCompDataInterface::length_comp_data
                                                                    Rcpp::NumericVector length_comp_data
                                                                    Definition: rcpp_data.hpp:154
                                                                    -
                                                                    LengthCompDataInterface::lmax
                                                                    int lmax
                                                                    Definition: rcpp_data.hpp:152
                                                                    -
                                                                    LengthCompDataInterface::~LengthCompDataInterface
                                                                    virtual ~LengthCompDataInterface()
                                                                    destructor
                                                                    Definition: rcpp_data.hpp:165
                                                                    -
                                                                    LengthCompDataInterface::LengthCompDataInterface
                                                                    LengthCompDataInterface(int ymax=0, int lmax=0)
                                                                    constructor
                                                                    Definition: rcpp_data.hpp:158
                                                                    -
                                                                    LengthCompDataInterface::to_json
                                                                    virtual std::string to_json()
                                                                    Convert the data to json representation for the output.
                                                                    Definition: rcpp_data.hpp:173
                                                                    -
                                                                    LengthCompDataInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_data.hpp:168
                                                                    -
                                                                    LengthCompDataInterface::ymax
                                                                    int ymax
                                                                    Definition: rcpp_data.hpp:153
                                                                    -
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:135
                                                                    -
                                                                    rcpp_interface_base.hpp
                                                                    TODO: provide a brief description.
                                                                    +
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:61
                                                                    +
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:64
                                                                    +
                                                                    IndexDataInterface
                                                                    Rcpp interface for data as an S4 object. To instantiate from R: fleet <- new(Index)
                                                                    Definition: rcpp_data.hpp:128
                                                                    +
                                                                    IndexDataInterface::ymax
                                                                    int ymax
                                                                    Definition: rcpp_data.hpp:130
                                                                    +
                                                                    IndexDataInterface::IndexDataInterface
                                                                    IndexDataInterface(int ymax=0)
                                                                    constructor
                                                                    Definition: rcpp_data.hpp:136
                                                                    +
                                                                    IndexDataInterface::index_data
                                                                    Rcpp::NumericVector index_data
                                                                    Definition: rcpp_data.hpp:131
                                                                    +
                                                                    IndexDataInterface::~IndexDataInterface
                                                                    virtual ~IndexDataInterface()
                                                                    destructor
                                                                    Definition: rcpp_data.hpp:141
                                                                    +
                                                                    IndexDataInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_data.hpp:145
                                                                    +
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:126
                                                                    diff --git a/docs/rcpp__fleet_8hpp_source.html b/docs/rcpp__fleet_8hpp_source.html index b803bdd..83f65db 100644 --- a/docs/rcpp__fleet_8hpp_source.html +++ b/docs/rcpp__fleet_8hpp_source.html @@ -76,13 +76,19 @@
                                                                    rcpp_fleet.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: rcpp_fleet.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    5  * Fisheries Integrated Modeling System project. See LICENSE file
                                                                    +
                                                                    6  * for reuse information.
                                                                    +
                                                                    7  */
                                                                    8 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_FLEET_HPP
                                                                    9 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_FLEET_HPP
                                                                    10 
                                                                    11 #include "../../../common/def.hpp"
                                                                    12 #include "../../../population_dynamics/fleet/fleet.hpp"
                                                                    -
                                                                    13 #include "rcpp_interface_base.hpp"
                                                                    +
                                                                    13 #include "rcpp_interface_base.hpp"
                                                                    14 
                                                                    21 class FleetInterfaceBase : public FIMSRcppInterfaceBase {
                                                                    22  public:
                                                                    @@ -107,399 +113,150 @@
                                                                    45 std::map<uint32_t, FleetInterfaceBase*> FleetInterfaceBase::live_objects;
                                                                    46 
                                                                    53 class FleetInterface : public FleetInterfaceBase {
                                                                    -
                                                                    54  int interface_observed_agecomp_data_id_m =
                                                                    -
                                                                    55  -999;
                                                                    -
                                                                    56  int interface_observed_lengthcomp_data_id_m =
                                                                    -
                                                                    57  -999;
                                                                    -
                                                                    58  int interface_observed_index_data_id_m =
                                                                    -
                                                                    59  -999;
                                                                    -
                                                                    60  int interface_selectivity_id_m = -999;
                                                                    -
                                                                    62 public:
                                                                    -
                                                                    63  std::string name = "NA";
                                                                    -
                                                                    64  bool is_survey = false;
                                                                    -
                                                                    65  int nages;
                                                                    -
                                                                    66  int nlengths = 0;
                                                                    -
                                                                    67  int nyears;
                                                                    -
                                                                    68  ParameterVector log_q;
                                                                    -
                                                                    69  ParameterVector
                                                                    -
                                                                    70  log_Fmort;
                                                                    -
                                                                    71  ParameterVector log_expected_index;
                                                                    -
                                                                    72  ParameterVector proportion_catch_numbers_at_age;
                                                                    -
                                                                    73  ParameterVector proportion_catch_numbers_at_length;
                                                                    -
                                                                    74  ParameterVector age_length_conversion_matrix;
                                                                    -
                                                                    75  bool estimate_q = false;
                                                                    -
                                                                    76  bool random_q = false;
                                                                    -
                                                                    79  Rcpp::NumericVector derived_cnaa;
                                                                    -
                                                                    80  Rcpp::NumericVector derived_cnal;
                                                                    -
                                                                    81  Rcpp::NumericVector derived_cwaa;
                                                                    -
                                                                    82  Rcpp::NumericVector derived_index;
                                                                    -
                                                                    83  Rcpp::NumericVector derived_age_composition;
                                                                    -
                                                                    84  Rcpp::NumericVector derived_length_composition;
                                                                    -
                                                                    86  FleetInterface() : FleetInterfaceBase() {}
                                                                    +
                                                                    54  int interface_agecomp_likelihood_id_m =
                                                                    +
                                                                    55  -999;
                                                                    +
                                                                    58  int interface_index_likelihood_id_m =
                                                                    +
                                                                    59  -999;
                                                                    +
                                                                    60  int interface_observed_agecomp_data_id_m =
                                                                    +
                                                                    61  -999;
                                                                    +
                                                                    62  int interface_observed_index_data_id_m =
                                                                    +
                                                                    63  -999;
                                                                    +
                                                                    64  int interface_selectivity_id_m = -999;
                                                                    +
                                                                    66  public:
                                                                    +
                                                                    67  bool is_survey = false;
                                                                    +
                                                                    68  int nages;
                                                                    +
                                                                    69  int nyears;
                                                                    +
                                                                    70  double log_q;
                                                                    +
                                                                    71  Rcpp::NumericVector
                                                                    +
                                                                    72  log_Fmort;
                                                                    +
                                                                    73  bool estimate_F = false;
                                                                    +
                                                                    74  bool estimate_q = false;
                                                                    +
                                                                    75  bool estimate_obs_error = false;
                                                                    +
                                                                    77  bool random_q = false;
                                                                    +
                                                                    78  bool random_F = false;
                                                                    +
                                                                    79  Rcpp::NumericVector log_obs_error;
                                                                    +
                                                                    81  FleetInterface() : FleetInterfaceBase() {}
                                                                    +
                                                                    82 
                                                                    +
                                                                    83  virtual ~FleetInterface() {}
                                                                    +
                                                                    84 
                                                                    +
                                                                    86  virtual uint32_t get_id() { return this->id; }
                                                                    87 
                                                                    -
                                                                    88  virtual ~FleetInterface() {}
                                                                    -
                                                                    89 
                                                                    -
                                                                    91  virtual uint32_t get_id() { return this->id; }
                                                                    -
                                                                    92 
                                                                    -
                                                                    99  void SetObservedAgeCompData(int observed_agecomp_data_id) {
                                                                    -
                                                                    100  interface_observed_agecomp_data_id_m = observed_agecomp_data_id;
                                                                    -
                                                                    101  }
                                                                    -
                                                                    102 
                                                                    -
                                                                    109  void SetObservedLengthCompData(int observed_lengthcomp_data_id) {
                                                                    -
                                                                    110  interface_observed_lengthcomp_data_id_m = observed_lengthcomp_data_id;
                                                                    -
                                                                    111  }
                                                                    -
                                                                    112 
                                                                    -
                                                                    117  int GetObservedAgeCompDataID() {
                                                                    -
                                                                    118  return interface_observed_agecomp_data_id_m;
                                                                    -
                                                                    119  }
                                                                    -
                                                                    120 
                                                                    -
                                                                    125  int GetObservedLengthCompDataID() {
                                                                    -
                                                                    126  return interface_observed_lengthcomp_data_id_m;
                                                                    -
                                                                    127  }
                                                                    -
                                                                    128 
                                                                    -
                                                                    134  void SetObservedIndexData(int observed_index_data_id) {
                                                                    -
                                                                    135  interface_observed_index_data_id_m = observed_index_data_id;
                                                                    -
                                                                    136  }
                                                                    -
                                                                    137 
                                                                    -
                                                                    142  int GetObservedIndexDataID() {
                                                                    -
                                                                    143  return interface_observed_index_data_id_m;
                                                                    -
                                                                    144  }
                                                                    -
                                                                    145 
                                                                    -
                                                                    151  void SetSelectivity(int selectivity_id) {
                                                                    -
                                                                    152  interface_selectivity_id_m = selectivity_id;
                                                                    -
                                                                    153  }
                                                                    -
                                                                    158  virtual void finalize() {
                                                                    -
                                                                    159 
                                                                    -
                                                                    160  if (this->finalized) {
                                                                    -
                                                                    161  //log warning that finalize has been called more than once.
                                                                    -
                                                                    162  FIMS_WARNING_LOG("Fleet " + fims::to_string(this->id) + " has been finalized already.");
                                                                    -
                                                                    163  }
                                                                    -
                                                                    164 
                                                                    -
                                                                    165  this->finalized = true; //indicate this has been called already
                                                                    -
                                                                    166 
                                                                    -
                                                                    167  std::shared_ptr<fims_info::Information<double> > info =
                                                                    -
                                                                    168  fims_info::Information<double>::GetInstance();
                                                                    -
                                                                    169 
                                                                    -
                                                                    170  fims_info::Information<double>::fleet_iterator it;
                                                                    +
                                                                    93  void SetAgeCompLikelihood(int agecomp_likelihood_id) {
                                                                    +
                                                                    94  interface_agecomp_likelihood_id_m = agecomp_likelihood_id;
                                                                    +
                                                                    95  }
                                                                    +
                                                                    96 
                                                                    +
                                                                    102  void SetIndexLikelihood(int index_likelihood_id) {
                                                                    +
                                                                    103  interface_index_likelihood_id_m = index_likelihood_id;
                                                                    +
                                                                    104  }
                                                                    +
                                                                    105 
                                                                    +
                                                                    112  void SetObservedAgeCompData(int observed_agecomp_data_id) {
                                                                    +
                                                                    113  interface_observed_agecomp_data_id_m = observed_agecomp_data_id;
                                                                    +
                                                                    114  }
                                                                    +
                                                                    115 
                                                                    +
                                                                    121  void SetObservedIndexData(int observed_index_data_id) {
                                                                    +
                                                                    122  interface_observed_index_data_id_m = observed_index_data_id;
                                                                    +
                                                                    123  }
                                                                    +
                                                                    124 
                                                                    +
                                                                    130  void SetSelectivity(int selectivity_id) {
                                                                    +
                                                                    131  interface_selectivity_id_m = selectivity_id;
                                                                    +
                                                                    132  }
                                                                    +
                                                                    133 
                                                                    +
                                                                    134 #ifdef TMB_MODEL
                                                                    +
                                                                    135  template <typename Type>
                                                                    +
                                                                    136  bool add_to_fims_tmb_internal() {
                                                                    +
                                                                    137  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    +
                                                                    138  fims_info::Information<Type>::GetInstance();
                                                                    +
                                                                    139 
                                                                    +
                                                                    140  std::shared_ptr<fims_popdy::Fleet<Type> > fleet =
                                                                    +
                                                                    141  std::make_shared<fims_popdy::Fleet<Type> >();
                                                                    +
                                                                    142 
                                                                    +
                                                                    143  // set relative info
                                                                    +
                                                                    144  fleet->id = this->id;
                                                                    +
                                                                    145  fleet->is_survey = this->is_survey;
                                                                    +
                                                                    146  fleet->nages = this->nages;
                                                                    +
                                                                    147  fleet->nyears = this->nyears;
                                                                    +
                                                                    148  fleet->fleet_agecomp_likelihood_id_m = interface_agecomp_likelihood_id_m;
                                                                    +
                                                                    149  fleet->fleet_index_likelihood_id_m = interface_index_likelihood_id_m;
                                                                    +
                                                                    150  fleet->fleet_observed_agecomp_data_id_m =
                                                                    +
                                                                    151  interface_observed_agecomp_data_id_m;
                                                                    +
                                                                    152  fleet->fleet_observed_index_data_id_m = interface_observed_index_data_id_m;
                                                                    +
                                                                    153  fleet->fleet_selectivity_id_m = interface_selectivity_id_m;
                                                                    +
                                                                    154 
                                                                    +
                                                                    155  fleet->log_obs_error.resize(this->log_obs_error.size());
                                                                    +
                                                                    156  for (int i = 0; i < log_obs_error.size(); i++) {
                                                                    +
                                                                    157  fleet->log_obs_error[i] = this->log_obs_error[i];
                                                                    +
                                                                    158  if (this->estimate_obs_error) {
                                                                    +
                                                                    159  info->RegisterParameter(fleet->log_obs_error[i]);
                                                                    +
                                                                    160  }
                                                                    +
                                                                    161  }
                                                                    +
                                                                    162 
                                                                    +
                                                                    163  fleet->log_q = this->log_q;
                                                                    +
                                                                    164  if (this->estimate_q) {
                                                                    +
                                                                    165  if (this->random_q) {
                                                                    +
                                                                    166  info->RegisterRandomEffect(fleet->log_q);
                                                                    +
                                                                    167  } else {
                                                                    +
                                                                    168  info->RegisterParameter(fleet->log_q);
                                                                    +
                                                                    169  }
                                                                    +
                                                                    170  }
                                                                    171 
                                                                    -
                                                                    172 
                                                                    -
                                                                    173  it = info->fleets.find(this->id);
                                                                    -
                                                                    174 
                                                                    -
                                                                    175  if (it == info->fleets.end()) {
                                                                    -
                                                                    176  FIMS_WARNING_LOG("Fleet " + fims::to_string(this->id) + " not found in Information.");
                                                                    -
                                                                    177  return;
                                                                    -
                                                                    178  } else {
                                                                    -
                                                                    179 
                                                                    -
                                                                    180  std::shared_ptr<fims_popdy::Fleet<double> > fleet =
                                                                    -
                                                                    181  std::dynamic_pointer_cast<fims_popdy::Fleet<double> >(it->second);
                                                                    -
                                                                    182 
                                                                    -
                                                                    183 
                                                                    -
                                                                    184  for (size_t i = 0; i < this->log_Fmort.size(); i++) {
                                                                    -
                                                                    185  if (this->log_Fmort[i].estimated_m) {
                                                                    -
                                                                    186  this->log_Fmort[i].final_value_m = fleet->log_Fmort[i];
                                                                    -
                                                                    187  } else {
                                                                    -
                                                                    188  this->log_Fmort[i].final_value_m = this->log_Fmort[i].initial_value_m;
                                                                    -
                                                                    189  }
                                                                    -
                                                                    190  }
                                                                    -
                                                                    191 
                                                                    -
                                                                    192  for (size_t i = 0; i < this->log_q.size(); i++) {
                                                                    -
                                                                    193  if (this->log_q[i].estimated_m) {
                                                                    -
                                                                    194  this->log_q[i].final_value_m = fleet->log_q[i];
                                                                    -
                                                                    195  } else {
                                                                    -
                                                                    196  this->log_q[i].final_value_m = this->log_q[i].initial_value_m;
                                                                    -
                                                                    197  }
                                                                    -
                                                                    198  }
                                                                    +
                                                                    172  fleet->log_Fmort.resize(this->log_Fmort.size());
                                                                    +
                                                                    173  for (int i = 0; i < log_Fmort.size(); i++) {
                                                                    +
                                                                    174  fleet->log_Fmort[i] = this->log_Fmort[i];
                                                                    +
                                                                    175 
                                                                    +
                                                                    176  if (this->estimate_F) {
                                                                    +
                                                                    177  if (this->random_F) {
                                                                    +
                                                                    178  info->RegisterRandomEffect(fleet->log_Fmort[i]);
                                                                    +
                                                                    179  } else {
                                                                    +
                                                                    180  info->RegisterParameter(fleet->log_Fmort[i]);
                                                                    +
                                                                    181  }
                                                                    +
                                                                    182  }
                                                                    +
                                                                    183  }
                                                                    +
                                                                    184  // add to Information
                                                                    +
                                                                    185  info->fleets[fleet->id] = fleet;
                                                                    +
                                                                    186 
                                                                    +
                                                                    187  return true;
                                                                    +
                                                                    188  }
                                                                    +
                                                                    189 
                                                                    +
                                                                    191  virtual bool add_to_fims_tmb() {
                                                                    +
                                                                    192  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    +
                                                                    193  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    +
                                                                    194  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    +
                                                                    195  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    +
                                                                    196 
                                                                    +
                                                                    197  return true;
                                                                    +
                                                                    198  }
                                                                    199 
                                                                    -
                                                                    200  this->derived_cnaa = Rcpp::NumericVector(fleet->catch_numbers_at_age.size());
                                                                    -
                                                                    201  for (size_t i = 0; i < this->derived_cnaa.size(); i++) {
                                                                    -
                                                                    202  this->derived_cnaa[i] = fleet->catch_numbers_at_age[i];
                                                                    -
                                                                    203  }
                                                                    -
                                                                    204 
                                                                    -
                                                                    205  this->derived_cnal = Rcpp::NumericVector(fleet->catch_numbers_at_length.size());
                                                                    -
                                                                    206  for (size_t i = 0; i < this->derived_cnal.size(); i++) {
                                                                    -
                                                                    207  this->derived_cnal[i] = fleet->catch_numbers_at_length[i];
                                                                    -
                                                                    208  }
                                                                    -
                                                                    209 
                                                                    -
                                                                    210  this->derived_cwaa = Rcpp::NumericVector(fleet->catch_weight_at_age.size());
                                                                    -
                                                                    211  for (size_t i = 0; i < this->derived_cwaa.size(); i++) {
                                                                    -
                                                                    212  this->derived_cwaa[i] = fleet->catch_weight_at_age[i];
                                                                    -
                                                                    213  }
                                                                    -
                                                                    214 
                                                                    -
                                                                    215  this->derived_age_composition = Rcpp::NumericVector(fleet->proportion_catch_numbers_at_age.size());
                                                                    -
                                                                    216  for (size_t i = 0; i < this->derived_age_composition.size(); i++) {
                                                                    -
                                                                    217  this->derived_age_composition[i] = fleet->proportion_catch_numbers_at_age[i];
                                                                    -
                                                                    218  }
                                                                    -
                                                                    219 
                                                                    -
                                                                    220  this->derived_length_composition = Rcpp::NumericVector(fleet->proportion_catch_numbers_at_length.size());
                                                                    -
                                                                    221  for (size_t i = 0; i < this->derived_length_composition.size(); i++) {
                                                                    -
                                                                    222  this->derived_length_composition[i] = fleet->proportion_catch_numbers_at_length[i];
                                                                    -
                                                                    223  }
                                                                    -
                                                                    224 
                                                                    -
                                                                    225  this->derived_index = Rcpp::NumericVector(fleet->expected_index.size());
                                                                    -
                                                                    226  for (size_t i = 0; i < this->derived_index.size(); i++) {
                                                                    -
                                                                    227  this->derived_index[i] = fleet->expected_index[i];
                                                                    -
                                                                    228  }
                                                                    -
                                                                    229 
                                                                    -
                                                                    230  }
                                                                    -
                                                                    231 
                                                                    -
                                                                    232  }
                                                                    -
                                                                    233 
                                                                    -
                                                                    237  virtual std::string to_json() {
                                                                    -
                                                                    238  std::stringstream ss;
                                                                    -
                                                                    239 
                                                                    -
                                                                    240  ss << "\"module\" : {\n";
                                                                    -
                                                                    241  ss << " \"name\" : \"Fleet\",\n";
                                                                    -
                                                                    242 
                                                                    -
                                                                    243  ss << " \"type\" : \"fleet\",\n";
                                                                    -
                                                                    244  ss << " \"tag\" : \"" << this->name << "\",\n";
                                                                    -
                                                                    245  ss << " \"id\": " << this->id << ",\n";
                                                                    -
                                                                    246 
                                                                    -
                                                                    247  ss << " \"parameter\": {\n";
                                                                    -
                                                                    248  ss << " \"name\": \"log_Fmort\",\n";
                                                                    -
                                                                    249  ss << " \"id\":" << this->log_Fmort.id_m << ",\n";
                                                                    -
                                                                    250  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    251  ss << " \"values\": " << this->log_Fmort << "\n},\n";
                                                                    -
                                                                    252 
                                                                    -
                                                                    253  ss << " \"parameter\": {\n";
                                                                    -
                                                                    254  ss << " \"name\": \"log_Fmort\",\n";
                                                                    -
                                                                    255  ss << " \"id\":" << this->log_q.id_m << ",\n";
                                                                    -
                                                                    256  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    257  ss << " \"values\": " << this->log_q << "\n},\n";
                                                                    -
                                                                    258 
                                                                    -
                                                                    259 
                                                                    -
                                                                    260  ss << " \"derived_quantity\": {\n";
                                                                    -
                                                                    261  ss << " \"name\": \"cnaa\",\n";
                                                                    -
                                                                    262  ss << " \"values\":[";
                                                                    -
                                                                    263  if (this->derived_cnaa.size() == 0) {
                                                                    -
                                                                    264  ss << "]\n";
                                                                    -
                                                                    265  } else {
                                                                    -
                                                                    266  for (size_t i = 0; i < this->derived_cnaa.size() - 1; i++) {
                                                                    -
                                                                    267  ss << this->derived_cnaa[i] << ", ";
                                                                    -
                                                                    268  }
                                                                    -
                                                                    269  ss << this->derived_cnaa[this->derived_cnaa.size() - 1] << "]\n";
                                                                    -
                                                                    270  }
                                                                    -
                                                                    271  ss << " },\n";
                                                                    -
                                                                    272 
                                                                    -
                                                                    273  ss << " \"derived_quantity\": {\n";
                                                                    -
                                                                    274  ss << " \"name\": \"cnal\",\n";
                                                                    -
                                                                    275  ss << " \"values\":[";
                                                                    -
                                                                    276  if (this->derived_cnal.size() == 0) {
                                                                    -
                                                                    277  ss << "]\n";
                                                                    -
                                                                    278  } else {
                                                                    -
                                                                    279  for (size_t i = 0; i < this->derived_cnal.size() - 1; i++) {
                                                                    -
                                                                    280  ss << this->derived_cnal[i] << ", ";
                                                                    -
                                                                    281  }
                                                                    -
                                                                    282  ss << this->derived_cnal[this->derived_cnal.size() - 1] << "]\n";
                                                                    -
                                                                    283  }
                                                                    -
                                                                    284  ss << " },\n";
                                                                    -
                                                                    285 
                                                                    -
                                                                    286  ss << " \"derived_quantity\": {\n";
                                                                    -
                                                                    287  ss << " \"name\": \"cwaa\",\n";
                                                                    -
                                                                    288  ss << " \"values\":[";
                                                                    -
                                                                    289  if (this->derived_cwaa.size() == 0) {
                                                                    -
                                                                    290  ss << "]\n";
                                                                    -
                                                                    291  } else {
                                                                    -
                                                                    292  for (size_t i = 0; i < this->derived_cwaa.size() - 1; i++) {
                                                                    -
                                                                    293  ss << this->derived_cwaa[i] << ", ";
                                                                    -
                                                                    294  }
                                                                    -
                                                                    295  ss << this->derived_cwaa[this->derived_cwaa.size() - 1] << "]\n";
                                                                    -
                                                                    296  }
                                                                    -
                                                                    297  ss << " },\n";
                                                                    -
                                                                    298 
                                                                    -
                                                                    299 
                                                                    -
                                                                    300  ss << " \"derived_quantity\": {\n";
                                                                    -
                                                                    301  ss << " \"name\": \"age_composition \",\n";
                                                                    -
                                                                    302  ss << " \"values\":[";
                                                                    -
                                                                    303  if (this->derived_age_composition.size() == 0) {
                                                                    -
                                                                    304  ss << "]\n";
                                                                    -
                                                                    305  } else {
                                                                    -
                                                                    306  for (size_t i = 0; i < this->derived_age_composition.size() - 1; i++) {
                                                                    -
                                                                    307  ss << this->derived_age_composition[i] << ", ";
                                                                    -
                                                                    308  }
                                                                    -
                                                                    309  ss << this->derived_age_composition[this->derived_age_composition.size() - 1] << "]\n";
                                                                    -
                                                                    310  }
                                                                    -
                                                                    311  ss << " },\n";
                                                                    -
                                                                    312 
                                                                    -
                                                                    313  ss << " \"derived_quantity\": {\n";
                                                                    -
                                                                    314  ss << " \"name\": \"length_composition \",\n";
                                                                    -
                                                                    315  ss << " \"values\":[";
                                                                    -
                                                                    316  if (this->derived_length_composition.size() == 0) {
                                                                    -
                                                                    317  ss << "]\n";
                                                                    -
                                                                    318  } else {
                                                                    -
                                                                    319  for (size_t i = 0; i < this->derived_length_composition.size() - 1; i++) {
                                                                    -
                                                                    320  ss << this->derived_length_composition[i] << ", ";
                                                                    -
                                                                    321  }
                                                                    -
                                                                    322  ss << this->derived_length_composition[this->derived_length_composition.size() - 1] << "]\n";
                                                                    -
                                                                    323  }
                                                                    -
                                                                    324  ss << " },\n";
                                                                    -
                                                                    325 
                                                                    -
                                                                    326  ss << " \"derived_quantity\": {\n";
                                                                    -
                                                                    327  ss << " \"name\": \"index \",\n";
                                                                    -
                                                                    328  ss << " \"values\":[";
                                                                    -
                                                                    329  if (this->derived_index.size() == 0) {
                                                                    -
                                                                    330  ss << "]\n";
                                                                    -
                                                                    331  } else {
                                                                    -
                                                                    332  for (size_t i = 0; i < this->derived_index.size() - 1; i++) {
                                                                    -
                                                                    333  ss << this->derived_index[i] << ", ";
                                                                    -
                                                                    334  }
                                                                    -
                                                                    335  ss << this->derived_index[this->derived_index.size() - 1] << "]\n";
                                                                    -
                                                                    336  }
                                                                    -
                                                                    337  ss << " },\n";
                                                                    -
                                                                    338 
                                                                    -
                                                                    339  return ss.str();
                                                                    -
                                                                    340 
                                                                    -
                                                                    341  }
                                                                    -
                                                                    342 
                                                                    -
                                                                    343 
                                                                    -
                                                                    344 
                                                                    -
                                                                    345 #ifdef TMB_MODEL
                                                                    -
                                                                    346 
                                                                    -
                                                                    347  template <typename Type>
                                                                    -
                                                                    348  bool add_to_fims_tmb_internal() {
                                                                    -
                                                                    349  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    -
                                                                    350  fims_info::Information<Type>::GetInstance();
                                                                    -
                                                                    351 
                                                                    -
                                                                    352  std::shared_ptr<fims_popdy::Fleet<Type> > fleet =
                                                                    -
                                                                    353  std::make_shared<fims_popdy::Fleet<Type> >();
                                                                    -
                                                                    354 
                                                                    -
                                                                    355  // set relative info
                                                                    -
                                                                    356  fleet->id = this->id;
                                                                    -
                                                                    357  fleet->is_survey = this->is_survey;
                                                                    -
                                                                    358  fleet->nages = this->nages;
                                                                    -
                                                                    359  fleet->nlengths = this->nlengths;
                                                                    -
                                                                    360  fleet->nyears = this->nyears;
                                                                    -
                                                                    361  fleet->fleet_observed_agecomp_data_id_m =
                                                                    -
                                                                    362  interface_observed_agecomp_data_id_m;
                                                                    -
                                                                    363  fleet->fleet_observed_lengthcomp_data_id_m =
                                                                    -
                                                                    364  interface_observed_lengthcomp_data_id_m;
                                                                    -
                                                                    365  fleet->fleet_observed_index_data_id_m = interface_observed_index_data_id_m;
                                                                    -
                                                                    366  fleet->fleet_selectivity_id_m = interface_selectivity_id_m;
                                                                    -
                                                                    367 
                                                                    -
                                                                    368  fleet->log_q.resize(this->log_q.size());
                                                                    -
                                                                    369  for (size_t i = 0; i < this->log_q.size(); i++) {
                                                                    -
                                                                    370  fleet->log_q[i] = this->log_q[i].initial_value_m;
                                                                    -
                                                                    371 
                                                                    -
                                                                    372  if (this->log_q[i].estimated_m) {
                                                                    -
                                                                    373  info->RegisterParameterName("log_q");
                                                                    -
                                                                    374  if (this->log_q[i].is_random_effect_m) {
                                                                    -
                                                                    375  info->RegisterRandomEffect(fleet->log_q[i]);
                                                                    -
                                                                    376  } else {
                                                                    -
                                                                    377  info->RegisterParameter(fleet->log_q[i]);
                                                                    -
                                                                    378  }
                                                                    -
                                                                    379  }
                                                                    -
                                                                    380  }
                                                                    -
                                                                    381 
                                                                    -
                                                                    382 
                                                                    -
                                                                    383  fleet->log_Fmort.resize(this->log_Fmort.size());
                                                                    -
                                                                    384  for (size_t i = 0; i < log_Fmort.size(); i++) {
                                                                    -
                                                                    385  fleet->log_Fmort[i] = this->log_Fmort[i].initial_value_m;
                                                                    -
                                                                    386 
                                                                    -
                                                                    387  if (this->log_Fmort[i].estimated_m) {
                                                                    -
                                                                    388  info->RegisterParameterName("log_Fmort");
                                                                    -
                                                                    389  if (this->log_Fmort[i].is_random_effect_m) {
                                                                    -
                                                                    390  info->RegisterRandomEffect(fleet->log_Fmort[i]);
                                                                    -
                                                                    391  } else {
                                                                    -
                                                                    392  info->RegisterParameter(fleet->log_Fmort[i]);
                                                                    -
                                                                    393  }
                                                                    -
                                                                    394  }
                                                                    -
                                                                    395  }
                                                                    -
                                                                    396  //add to variable_map
                                                                    -
                                                                    397  info->variable_map[this->log_Fmort.id_m] = &(fleet)->log_Fmort;
                                                                    -
                                                                    398 
                                                                    -
                                                                    399  //exp_catch
                                                                    -
                                                                    400  fleet->log_expected_index.resize(nyears); // assume index is for all ages.
                                                                    -
                                                                    401  info->variable_map[this->log_expected_index.id_m] = &(fleet)->log_expected_index;
                                                                    -
                                                                    402  fleet->proportion_catch_numbers_at_age.resize(nyears * nages);
                                                                    -
                                                                    403  info->variable_map[this->proportion_catch_numbers_at_age.id_m] = &(fleet)->proportion_catch_numbers_at_age;
                                                                    -
                                                                    404 
                                                                    -
                                                                    405  if(this->nlengths > 0){
                                                                    -
                                                                    406  fleet->proportion_catch_numbers_at_length.resize(nyears * nlengths);
                                                                    -
                                                                    407  fleet->age_length_conversion_matrix.resize(nages * nlengths);
                                                                    -
                                                                    408  for (size_t i = 0; i < fleet->age_length_conversion_matrix.size(); i++){
                                                                    -
                                                                    409  fleet->age_length_conversion_matrix[i] = this->age_length_conversion_matrix[i].initial_value_m;
                                                                    -
                                                                    410 
                                                                    -
                                                                    411  if (this->age_length_conversion_matrix[i].estimated_m) {
                                                                    -
                                                                    412  info->RegisterParameterName("age_length_conversion_matrix");
                                                                    -
                                                                    413  if (this->age_length_conversion_matrix[i].is_random_effect_m) {
                                                                    -
                                                                    414  info->RegisterRandomEffect(fleet->age_length_conversion_matrix[i]);
                                                                    -
                                                                    415  } else {
                                                                    -
                                                                    416  info->RegisterParameter(fleet->age_length_conversion_matrix[i]);
                                                                    -
                                                                    417  }
                                                                    -
                                                                    418  }
                                                                    -
                                                                    419  }
                                                                    -
                                                                    420  info->variable_map[this->age_length_conversion_matrix.id_m] = &(fleet)->age_length_conversion_matrix;
                                                                    -
                                                                    421  info->variable_map[this->proportion_catch_numbers_at_length.id_m] = &(fleet)->proportion_catch_numbers_at_length;
                                                                    -
                                                                    422  }
                                                                    -
                                                                    423 
                                                                    -
                                                                    424  // add to Information
                                                                    -
                                                                    425  info->fleets[fleet->id] = fleet;
                                                                    -
                                                                    426 
                                                                    -
                                                                    427  return true;
                                                                    -
                                                                    428  }
                                                                    -
                                                                    429 
                                                                    -
                                                                    431  virtual bool add_to_fims_tmb() {
                                                                    -
                                                                    432  FIMS_INFO_LOG("adding Fleet object to TMB");
                                                                    -
                                                                    433  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    -
                                                                    434  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    -
                                                                    435  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    -
                                                                    436  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    -
                                                                    437 
                                                                    -
                                                                    438  return true;
                                                                    -
                                                                    439  }
                                                                    -
                                                                    440 
                                                                    -
                                                                    441 #endif
                                                                    -
                                                                    442 };
                                                                    -
                                                                    443 
                                                                    -
                                                                    444 #endif
                                                                    -
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:336
                                                                    -
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:342
                                                                    -
                                                                    FIMSRcppInterfaceBase::finalized
                                                                    bool finalized
                                                                    Definition: rcpp_interface_base.hpp:339
                                                                    -
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:345
                                                                    +
                                                                    200 #endif
                                                                    +
                                                                    201 };
                                                                    +
                                                                    202 
                                                                    +
                                                                    203 #endif
                                                                    +
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:61
                                                                    +
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:64
                                                                    +
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:67
                                                                    FleetInterfaceBase
                                                                    Rcpp interface that serves as the parent class for Rcpp fleet interfaces. This type should be inherit...
                                                                    Definition: rcpp_fleet.hpp:21
                                                                    FleetInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_fleet.hpp:23
                                                                    FleetInterfaceBase::live_objects
                                                                    static std::map< uint32_t, FleetInterfaceBase * > live_objects
                                                                    Definition: rcpp_fleet.hpp:26
                                                                    FleetInterfaceBase::id
                                                                    uint32_t id
                                                                    Definition: rcpp_fleet.hpp:24
                                                                    FleetInterfaceBase::get_id
                                                                    virtual uint32_t get_id()=0
                                                                    get_id method for child fleet interface objects to inherit
                                                                    FleetInterface
                                                                    Rcpp interface for Fleet as an S4 object. To instantiate from R: fleet <- new(Fleet)
                                                                    Definition: rcpp_fleet.hpp:53
                                                                    -
                                                                    FleetInterface::nlengths
                                                                    int nlengths
                                                                    Definition: rcpp_fleet.hpp:66
                                                                    -
                                                                    FleetInterface::SetSelectivity
                                                                    void SetSelectivity(int selectivity_id)
                                                                    Set the unique id for the Selectivity object.
                                                                    Definition: rcpp_fleet.hpp:151
                                                                    -
                                                                    FleetInterface::estimate_q
                                                                    bool estimate_q
                                                                    Definition: rcpp_fleet.hpp:75
                                                                    -
                                                                    FleetInterface::log_expected_index
                                                                    ParameterVector log_expected_index
                                                                    Definition: rcpp_fleet.hpp:71
                                                                    -
                                                                    FleetInterface::random_q
                                                                    bool random_q
                                                                    Definition: rcpp_fleet.hpp:76
                                                                    -
                                                                    FleetInterface::proportion_catch_numbers_at_length
                                                                    ParameterVector proportion_catch_numbers_at_length
                                                                    Definition: rcpp_fleet.hpp:73
                                                                    -
                                                                    FleetInterface::derived_cwaa
                                                                    Rcpp::NumericVector derived_cwaa
                                                                    Definition: rcpp_fleet.hpp:81
                                                                    -
                                                                    FleetInterface::nages
                                                                    int nages
                                                                    Definition: rcpp_fleet.hpp:65
                                                                    -
                                                                    FleetInterface::derived_age_composition
                                                                    Rcpp::NumericVector derived_age_composition
                                                                    Definition: rcpp_fleet.hpp:83
                                                                    -
                                                                    FleetInterface::GetObservedIndexDataID
                                                                    int GetObservedIndexDataID()
                                                                    Return the unique id for the Observed Index Data object.
                                                                    Definition: rcpp_fleet.hpp:142
                                                                    -
                                                                    FleetInterface::proportion_catch_numbers_at_age
                                                                    ParameterVector proportion_catch_numbers_at_age
                                                                    Definition: rcpp_fleet.hpp:72
                                                                    -
                                                                    FleetInterface::finalize
                                                                    virtual void finalize()
                                                                    finalize function. Extracts derived quantities back to the Rcpp interface object from the Information...
                                                                    Definition: rcpp_fleet.hpp:158
                                                                    -
                                                                    FleetInterface::GetObservedAgeCompDataID
                                                                    int GetObservedAgeCompDataID()
                                                                    Return the unique id for the Observed Age Comp Data object.
                                                                    Definition: rcpp_fleet.hpp:117
                                                                    -
                                                                    FleetInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the fleet interface
                                                                    Definition: rcpp_fleet.hpp:91
                                                                    -
                                                                    FleetInterface::log_q
                                                                    ParameterVector log_q
                                                                    Definition: rcpp_fleet.hpp:68
                                                                    -
                                                                    FleetInterface::derived_index
                                                                    Rcpp::NumericVector derived_index
                                                                    Definition: rcpp_fleet.hpp:82
                                                                    -
                                                                    FleetInterface::name
                                                                    std::string name
                                                                    Definition: rcpp_fleet.hpp:63
                                                                    -
                                                                    FleetInterface::is_survey
                                                                    bool is_survey
                                                                    Definition: rcpp_fleet.hpp:64
                                                                    -
                                                                    FleetInterface::GetObservedLengthCompDataID
                                                                    int GetObservedLengthCompDataID()
                                                                    Return the unique id for the Observed Length Comp Data object.
                                                                    Definition: rcpp_fleet.hpp:125
                                                                    -
                                                                    FleetInterface::log_Fmort
                                                                    ParameterVector log_Fmort
                                                                    Definition: rcpp_fleet.hpp:70
                                                                    -
                                                                    FleetInterface::SetObservedIndexData
                                                                    void SetObservedIndexData(int observed_index_data_id)
                                                                    Set the unique id for the Observed Index Data object.
                                                                    Definition: rcpp_fleet.hpp:134
                                                                    -
                                                                    FleetInterface::derived_cnal
                                                                    Rcpp::NumericVector derived_cnal
                                                                    Definition: rcpp_fleet.hpp:80
                                                                    -
                                                                    FleetInterface::to_json
                                                                    virtual std::string to_json()
                                                                    Convert the data to json representation for the output.
                                                                    Definition: rcpp_fleet.hpp:237
                                                                    -
                                                                    FleetInterface::age_length_conversion_matrix
                                                                    ParameterVector age_length_conversion_matrix
                                                                    Definition: rcpp_fleet.hpp:74
                                                                    -
                                                                    FleetInterface::SetObservedLengthCompData
                                                                    void SetObservedLengthCompData(int observed_lengthcomp_data_id)
                                                                    Set the unique id for the Observed Length Comp Data object.
                                                                    Definition: rcpp_fleet.hpp:109
                                                                    -
                                                                    FleetInterface::SetObservedAgeCompData
                                                                    void SetObservedAgeCompData(int observed_agecomp_data_id)
                                                                    Set the unique id for the Observed Age Comp Data object.
                                                                    Definition: rcpp_fleet.hpp:99
                                                                    -
                                                                    FleetInterface::nyears
                                                                    int nyears
                                                                    Definition: rcpp_fleet.hpp:67
                                                                    -
                                                                    FleetInterface::derived_cnaa
                                                                    Rcpp::NumericVector derived_cnaa
                                                                    Definition: rcpp_fleet.hpp:79
                                                                    -
                                                                    FleetInterface::derived_length_composition
                                                                    Rcpp::NumericVector derived_length_composition
                                                                    Definition: rcpp_fleet.hpp:84
                                                                    -
                                                                    ParameterVector
                                                                    Rcpp representation of a Parameter vector interface between R and cpp.
                                                                    Definition: rcpp_interface_base.hpp:120
                                                                    -
                                                                    ParameterVector::resize
                                                                    void resize(size_t size)
                                                                    resize to length "size"
                                                                    Definition: rcpp_interface_base.hpp:242
                                                                    -
                                                                    ParameterVector::size
                                                                    size_t size()
                                                                    returns vector length
                                                                    Definition: rcpp_interface_base.hpp:234
                                                                    -
                                                                    ParameterVector::id_m
                                                                    uint32_t id_m
                                                                    Definition: rcpp_interface_base.hpp:124
                                                                    -
                                                                    fims_info::Information::fleets
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > > fleets
                                                                    Definition: information.hpp:92
                                                                    -
                                                                    fims_info::Information::fleet_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >::iterator fleet_iterator
                                                                    Definition: information.hpp:97
                                                                    -
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:135
                                                                    -
                                                                    FIMS_WARNING_LOG
                                                                    #define FIMS_WARNING_LOG(MESSAGE)
                                                                    Definition: def.hpp:559
                                                                    -
                                                                    FIMS_INFO_LOG
                                                                    #define FIMS_INFO_LOG(MESSAGE)
                                                                    Definition: def.hpp:557
                                                                    -
                                                                    rcpp_interface_base.hpp
                                                                    TODO: provide a brief description.
                                                                    +
                                                                    FleetInterface::random_F
                                                                    bool random_F
                                                                    Definition: rcpp_fleet.hpp:78
                                                                    +
                                                                    FleetInterface::SetSelectivity
                                                                    void SetSelectivity(int selectivity_id)
                                                                    Set the unique id for the Selectivity object.
                                                                    Definition: rcpp_fleet.hpp:130
                                                                    +
                                                                    FleetInterface::estimate_q
                                                                    bool estimate_q
                                                                    Definition: rcpp_fleet.hpp:74
                                                                    +
                                                                    FleetInterface::random_q
                                                                    bool random_q
                                                                    Definition: rcpp_fleet.hpp:77
                                                                    +
                                                                    FleetInterface::SetAgeCompLikelihood
                                                                    void SetAgeCompLikelihood(int agecomp_likelihood_id)
                                                                    Set the unique id for the Age Comp Likelihood object.
                                                                    Definition: rcpp_fleet.hpp:93
                                                                    +
                                                                    FleetInterface::nages
                                                                    int nages
                                                                    Definition: rcpp_fleet.hpp:68
                                                                    +
                                                                    FleetInterface::estimate_obs_error
                                                                    bool estimate_obs_error
                                                                    Definition: rcpp_fleet.hpp:75
                                                                    +
                                                                    FleetInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the fleet interface
                                                                    Definition: rcpp_fleet.hpp:86
                                                                    +
                                                                    FleetInterface::is_survey
                                                                    bool is_survey
                                                                    Definition: rcpp_fleet.hpp:67
                                                                    +
                                                                    FleetInterface::SetObservedIndexData
                                                                    void SetObservedIndexData(int observed_index_data_id)
                                                                    Set the unique id for the Observed Index Data object.
                                                                    Definition: rcpp_fleet.hpp:121
                                                                    +
                                                                    FleetInterface::log_Fmort
                                                                    Rcpp::NumericVector log_Fmort
                                                                    Definition: rcpp_fleet.hpp:72
                                                                    +
                                                                    FleetInterface::log_obs_error
                                                                    Rcpp::NumericVector log_obs_error
                                                                    Definition: rcpp_fleet.hpp:79
                                                                    +
                                                                    FleetInterface::SetIndexLikelihood
                                                                    void SetIndexLikelihood(int index_likelihood_id)
                                                                    Set the unique id for the Index Likelihood object.
                                                                    Definition: rcpp_fleet.hpp:102
                                                                    +
                                                                    FleetInterface::log_q
                                                                    double log_q
                                                                    Definition: rcpp_fleet.hpp:70
                                                                    +
                                                                    FleetInterface::estimate_F
                                                                    bool estimate_F
                                                                    Definition: rcpp_fleet.hpp:73
                                                                    +
                                                                    FleetInterface::SetObservedAgeCompData
                                                                    void SetObservedAgeCompData(int observed_agecomp_data_id)
                                                                    Set the unique id for the Observed Age Comp Data object.
                                                                    Definition: rcpp_fleet.hpp:112
                                                                    +
                                                                    FleetInterface::nyears
                                                                    int nyears
                                                                    Definition: rcpp_fleet.hpp:69
                                                                    +
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:126
                                                                    diff --git a/docs/rcpp__growth_8hpp_source.html b/docs/rcpp__growth_8hpp_source.html index e0a0499..8a9254e 100644 --- a/docs/rcpp__growth_8hpp_source.html +++ b/docs/rcpp__growth_8hpp_source.html @@ -76,12 +76,18 @@
                                                                    rcpp_growth.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: rcpp_growth.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    5  * Fisheries Integrated Modeling System project. See LICENSE file
                                                                    +
                                                                    6  * for reuse information.
                                                                    +
                                                                    7  */
                                                                    8 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_GROWTH_HPP
                                                                    9 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_GROWTH_HPP
                                                                    10 
                                                                    11 #include "../../../population_dynamics/growth/growth.hpp"
                                                                    -
                                                                    12 #include "rcpp_interface_base.hpp"
                                                                    +
                                                                    12 #include "rcpp_interface_base.hpp"
                                                                    13 
                                                                    24 class GrowthInterfaceBase : public FIMSRcppInterfaceBase {
                                                                    25  public:
                                                                    @@ -144,63 +150,38 @@
                                                                    108  EWAAGrowth.ewaa = this->ewaa;
                                                                    109  return EWAAGrowth.evaluate(age);
                                                                    110  }
                                                                    -
                                                                    111 
                                                                    -
                                                                    115  virtual std::string to_json() {
                                                                    -
                                                                    116  std::stringstream ss;
                                                                    -
                                                                    117  ss << "\"module\" : {\n";
                                                                    -
                                                                    118  ss << " \"name\": \"growth\",\n";
                                                                    -
                                                                    119  ss << " \"type\" : \"EWAA\",\n";
                                                                    -
                                                                    120  ss << " \"id\":" << this->id << ",\n";
                                                                    -
                                                                    121  ss << " \"rank\": " << 1 << ",\n";
                                                                    -
                                                                    122  ss << " \"dimensions\": [" << this->weights.size() << "],\n";
                                                                    -
                                                                    123 
                                                                    -
                                                                    124  ss << " \"ages\": [";
                                                                    -
                                                                    125  for (size_t i = 0; i < ages.size() - 1; i++) {
                                                                    -
                                                                    126  ss << ages[i] << ", ";
                                                                    -
                                                                    127  }
                                                                    -
                                                                    128  ss << ages[ages.size() - 1] << "],\n";
                                                                    +
                                                                    111 #ifdef TMB_MODEL
                                                                    +
                                                                    112 
                                                                    +
                                                                    113  template <typename Type>
                                                                    +
                                                                    114  bool add_to_fims_tmb_internal() {
                                                                    +
                                                                    115  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    +
                                                                    116  fims_info::Information<Type>::GetInstance();
                                                                    +
                                                                    117 
                                                                    +
                                                                    118  std::shared_ptr<fims_popdy::EWAAgrowth<Type> > ewaa_growth =
                                                                    +
                                                                    119  std::make_shared<fims_popdy::EWAAgrowth<Type> >();
                                                                    +
                                                                    120 
                                                                    +
                                                                    121  // set relative info
                                                                    +
                                                                    122  ewaa_growth->id = this->id;
                                                                    +
                                                                    123  ewaa_growth->ewaa = make_map(this->ages, this->weights); // this->ewaa;
                                                                    +
                                                                    124  // add to Information
                                                                    +
                                                                    125  info->growth_models[ewaa_growth->id] = ewaa_growth;
                                                                    +
                                                                    126 
                                                                    +
                                                                    127  return true;
                                                                    +
                                                                    128  }
                                                                    129 
                                                                    -
                                                                    130  ss << " \"values\": [";
                                                                    -
                                                                    131  for (size_t i = 0; i < weights.size() - 1; i++) {
                                                                    -
                                                                    132  ss << weights[i] << ", ";
                                                                    -
                                                                    133  }
                                                                    -
                                                                    134  ss << weights[weights.size() - 1] << "]\n";
                                                                    -
                                                                    135  ss << "}";
                                                                    -
                                                                    136  return ss.str();
                                                                    -
                                                                    137  }
                                                                    -
                                                                    138 
                                                                    -
                                                                    139 #ifdef TMB_MODEL
                                                                    -
                                                                    140 
                                                                    -
                                                                    141  template <typename Type>
                                                                    -
                                                                    142  bool add_to_fims_tmb_internal() {
                                                                    -
                                                                    143  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    -
                                                                    144  fims_info::Information<Type>::GetInstance();
                                                                    -
                                                                    145 
                                                                    -
                                                                    146  std::shared_ptr<fims_popdy::EWAAgrowth<Type> > ewaa_growth =
                                                                    -
                                                                    147  std::make_shared<fims_popdy::EWAAgrowth<Type> >();
                                                                    -
                                                                    148 
                                                                    -
                                                                    149  // set relative info
                                                                    -
                                                                    150  ewaa_growth->id = this->id;
                                                                    -
                                                                    151  ewaa_growth->ewaa = make_map(this->ages, this->weights); // this->ewaa;
                                                                    -
                                                                    152  // add to Information
                                                                    -
                                                                    153  info->growth_models[ewaa_growth->id] = ewaa_growth;
                                                                    -
                                                                    154 
                                                                    -
                                                                    155  return true;
                                                                    -
                                                                    156  }
                                                                    -
                                                                    157 
                                                                    -
                                                                    159  virtual bool add_to_fims_tmb() {
                                                                    -
                                                                    160  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    -
                                                                    161  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    -
                                                                    162  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    -
                                                                    163  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    -
                                                                    164 
                                                                    -
                                                                    165  return true;
                                                                    -
                                                                    166  }
                                                                    -
                                                                    167 
                                                                    -
                                                                    168 #endif
                                                                    -
                                                                    169 };
                                                                    -
                                                                    170 
                                                                    -
                                                                    171 #endif
                                                                    +
                                                                    131  virtual bool add_to_fims_tmb() {
                                                                    +
                                                                    132  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    +
                                                                    133  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    +
                                                                    134  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    +
                                                                    135  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    +
                                                                    136 
                                                                    +
                                                                    137  return true;
                                                                    +
                                                                    138  }
                                                                    +
                                                                    139 
                                                                    +
                                                                    140 #endif
                                                                    +
                                                                    141 };
                                                                    +
                                                                    142 
                                                                    +
                                                                    143 #endif
                                                                    EWAAGrowthInterface
                                                                    Rcpp interface for EWAAgrowth as an S4 object. To instantiate from R: ewaa <- new(EWAAgrowth)
                                                                    Definition: rcpp_growth.hpp:59
                                                                    EWAAGrowthInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the id of the GrowthInterfaceBase object
                                                                    Definition: rcpp_growth.hpp:73
                                                                    EWAAGrowthInterface::ewaa
                                                                    std::map< double, double > ewaa
                                                                    Definition: rcpp_growth.hpp:63
                                                                    @@ -208,22 +189,20 @@
                                                                    EWAAGrowthInterface::initialized
                                                                    bool initialized
                                                                    Definition: rcpp_growth.hpp:65
                                                                    EWAAGrowthInterface::weights
                                                                    std::vector< double > weights
                                                                    Definition: rcpp_growth.hpp:61
                                                                    EWAAGrowthInterface::make_map
                                                                    std::map< double, double > make_map(std::vector< double > ages, std::vector< double > weights)
                                                                    Create a map of input numeric vectors.
                                                                    Definition: rcpp_growth.hpp:82
                                                                    -
                                                                    EWAAGrowthInterface::to_json
                                                                    virtual std::string to_json()
                                                                    Convert the data to json representation for the output.
                                                                    Definition: rcpp_growth.hpp:115
                                                                    EWAAGrowthInterface::ages
                                                                    std::vector< double > ages
                                                                    Definition: rcpp_growth.hpp:62
                                                                    -
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:336
                                                                    -
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:342
                                                                    -
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:345
                                                                    +
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:61
                                                                    +
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:64
                                                                    +
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:67
                                                                    GrowthInterfaceBase
                                                                    Rcpp interface that serves as the parent class for Rcpp growth interfaces. This type should be inheri...
                                                                    Definition: rcpp_growth.hpp:24
                                                                    GrowthInterfaceBase::evaluate
                                                                    virtual double evaluate(double age)=0
                                                                    evaluate method for child growth interface objects to inherit
                                                                    GrowthInterfaceBase::live_objects
                                                                    static std::map< uint32_t, GrowthInterfaceBase * > live_objects
                                                                    Definition: rcpp_growth.hpp:29
                                                                    GrowthInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_growth.hpp:26
                                                                    GrowthInterfaceBase::id
                                                                    uint32_t id
                                                                    Definition: rcpp_growth.hpp:27
                                                                    GrowthInterfaceBase::get_id
                                                                    virtual uint32_t get_id()=0
                                                                    get_id method for child growth interface objects to inherit
                                                                    -
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:135
                                                                    -
                                                                    rcpp_interface_base.hpp
                                                                    TODO: provide a brief description.
                                                                    +
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:126
                                                                    fims_popdy::EWAAgrowth
                                                                    EWAAgrowth class that returns the EWAA function value.
                                                                    Definition: ewaa.hpp:23
                                                                    fims_popdy::EWAAgrowth::ewaa
                                                                    std::map< double, double > ewaa
                                                                    Definition: ewaa.hpp:29
                                                                    -
                                                                    fims_popdy::EWAAgrowth::evaluate
                                                                    virtual const Type evaluate(const double &a)
                                                                    Returns the weight at age a (in kg) from the input vector.
                                                                    Definition: ewaa.hpp:42
                                                                    +
                                                                    fims_popdy::EWAAgrowth::evaluate
                                                                    virtual const Type evaluate(const double &a)
                                                                    Returns the weight at age a (in kg) from the input vector.
                                                                    Definition: ewaa.hpp:41
                                                                    diff --git a/docs/rcpp__interface_8hpp_source.html b/docs/rcpp__interface_8hpp_source.html index ab03ec2..6a1b0f7 100644 --- a/docs/rcpp__interface_8hpp_source.html +++ b/docs/rcpp__interface_8hpp_source.html @@ -76,887 +76,541 @@
                                                                    rcpp_interface.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    8 #ifndef FIMS_INTERFACE_RCPP_INTERFACE_HPP
                                                                    -
                                                                    9 #define FIMS_INTERFACE_RCPP_INTERFACE_HPP
                                                                    -
                                                                    10 
                                                                    -
                                                                    11 #include "rcpp_objects/rcpp_data.hpp"
                                                                    -
                                                                    12 #include "rcpp_objects/rcpp_fleet.hpp"
                                                                    -
                                                                    13 #include "rcpp_objects/rcpp_growth.hpp"
                                                                    -
                                                                    14 #include "rcpp_objects/rcpp_maturity.hpp"
                                                                    -
                                                                    15 #include "rcpp_objects/rcpp_natural_mortality.hpp"
                                                                    -
                                                                    16 #include "../../common/model.hpp"
                                                                    -
                                                                    17 #include "rcpp_objects/rcpp_population.hpp"
                                                                    -
                                                                    18 #include "rcpp_objects/rcpp_recruitment.hpp"
                                                                    -
                                                                    19 #include "rcpp_objects/rcpp_selectivity.hpp"
                                                                    -
                                                                    20 #include "rcpp_objects/rcpp_distribution.hpp"
                                                                    -
                                                                    21 #include "../../utilities/fims_json.hpp"
                                                                    -
                                                                    22 
                                                                    -
                                                                    27 SEXP FIMS_objective_function;
                                                                    -
                                                                    32 SEXP FIMS_gradient_function;
                                                                    -
                                                                    37 double FIMS_function_value = 0;
                                                                    -
                                                                    42 Rcpp::NumericVector FIMS_function_parameters;
                                                                    -
                                                                    47 Rcpp::NumericVector FIMS_function_gradient;
                                                                    -
                                                                    52 double FIMS_mgc_value = 0;
                                                                    -
                                                                    57 bool FIMS_finalized = false;
                                                                    -
                                                                    58 
                                                                    -
                                                                    62 void init_logging() {
                                                                    -
                                                                    63  std::signal(SIGSEGV, &fims::WriteAtExit);
                                                                    -
                                                                    64  std::signal(SIGINT, &fims::WriteAtExit);
                                                                    -
                                                                    65  std::signal(SIGABRT, &fims::WriteAtExit);
                                                                    -
                                                                    66  std::signal(SIGFPE, &fims::WriteAtExit);
                                                                    -
                                                                    67  std::signal(SIGILL, &fims::WriteAtExit);
                                                                    -
                                                                    68  std::signal(SIGTERM, &fims::WriteAtExit);
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: rcpp_interface.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  *
                                                                    +
                                                                    5  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    6  * Fisheries Integrated Modeling System project. See LICENSE file for reuse
                                                                    +
                                                                    7  * information.
                                                                    +
                                                                    8  *
                                                                    +
                                                                    9  *
                                                                    +
                                                                    10  */
                                                                    +
                                                                    11 #ifndef FIMS_INTERFACE_RCPP_INTERFACE_HPP
                                                                    +
                                                                    12 #define FIMS_INTERFACE_RCPP_INTERFACE_HPP
                                                                    +
                                                                    13 
                                                                    +
                                                                    14 #include "rcpp_objects/rcpp_data.hpp"
                                                                    +
                                                                    15 #include "rcpp_objects/rcpp_fleet.hpp"
                                                                    +
                                                                    16 #include "rcpp_objects/rcpp_growth.hpp"
                                                                    +
                                                                    17 #include "rcpp_objects/rcpp_maturity.hpp"
                                                                    +
                                                                    18 #include "rcpp_objects/rcpp_natural_mortality.hpp"
                                                                    +
                                                                    19 //#include "rcpp_objects/rcpp_nll.hpp"
                                                                    +
                                                                    20 #include "../../common/model.hpp"
                                                                    +
                                                                    21 #include "rcpp_objects/rcpp_population.hpp"
                                                                    +
                                                                    22 #include "rcpp_objects/rcpp_recruitment.hpp"
                                                                    +
                                                                    23 #include "rcpp_objects/rcpp_selectivity.hpp"
                                                                    +
                                                                    24 #include "rcpp_objects/rcpp_tmb_distribution.hpp"
                                                                    +
                                                                    28 bool CreateTMBModel() {
                                                                    +
                                                                    29  for (size_t i = 0; i < FIMSRcppInterfaceBase::fims_interface_objects.size();
                                                                    +
                                                                    30  i++) {
                                                                    +
                                                                    31  FIMSRcppInterfaceBase::fims_interface_objects[i]->add_to_fims_tmb();
                                                                    +
                                                                    32  }
                                                                    +
                                                                    33 
                                                                    +
                                                                    34  // base model
                                                                    +
                                                                    35  std::shared_ptr<fims_info::Information<TMB_FIMS_REAL_TYPE>> d0 =
                                                                    +
                                                                    36  fims_info::Information<TMB_FIMS_REAL_TYPE>::GetInstance();
                                                                    +
                                                                    37  d0->CreateModel();
                                                                    +
                                                                    38 
                                                                    +
                                                                    39  // first-order derivative
                                                                    +
                                                                    40  std::shared_ptr<fims_info::Information<TMB_FIMS_FIRST_ORDER>> d1 =
                                                                    +
                                                                    41  fims_info::Information<TMB_FIMS_FIRST_ORDER>::GetInstance();
                                                                    +
                                                                    42  d1->CreateModel();
                                                                    +
                                                                    43 
                                                                    +
                                                                    44  // second-order derivative
                                                                    +
                                                                    45  std::shared_ptr<fims_info::Information<TMB_FIMS_SECOND_ORDER>> d2 =
                                                                    +
                                                                    46  fims_info::Information<TMB_FIMS_SECOND_ORDER>::GetInstance();
                                                                    +
                                                                    47  d2->CreateModel();
                                                                    +
                                                                    48 
                                                                    +
                                                                    49  // third-order derivative
                                                                    +
                                                                    50  std::shared_ptr<fims_info::Information<TMB_FIMS_THIRD_ORDER>> d3 =
                                                                    +
                                                                    51  fims_info::Information<TMB_FIMS_THIRD_ORDER>::GetInstance();
                                                                    +
                                                                    52  d3->CreateModel();
                                                                    +
                                                                    53 
                                                                    +
                                                                    54  return true;
                                                                    +
                                                                    55 }
                                                                    +
                                                                    56 
                                                                    +
                                                                    57 Rcpp::NumericVector get_fixed_parameters_vector() {
                                                                    +
                                                                    58  // base model
                                                                    +
                                                                    59  std::shared_ptr<fims_info::Information<TMB_FIMS_REAL_TYPE>> d0 =
                                                                    +
                                                                    60  fims_info::Information<TMB_FIMS_REAL_TYPE>::GetInstance();
                                                                    +
                                                                    61 
                                                                    +
                                                                    62  Rcpp::NumericVector p;
                                                                    +
                                                                    63 
                                                                    +
                                                                    64  for (size_t i = 0; i < d0->fixed_effects_parameters.size(); i++) {
                                                                    +
                                                                    65  p.push_back(*d0->fixed_effects_parameters[i]);
                                                                    +
                                                                    66  }
                                                                    +
                                                                    67 
                                                                    +
                                                                    68  return p;
                                                                    69 }
                                                                    70 
                                                                    -
                                                                    74 bool CreateTMBModel() {
                                                                    +
                                                                    71 Rcpp::NumericVector get_random_parameters_vector() {
                                                                    +
                                                                    72  // base model
                                                                    +
                                                                    73  std::shared_ptr<fims_info::Information<TMB_FIMS_REAL_TYPE>> d0 =
                                                                    +
                                                                    74  fims_info::Information<TMB_FIMS_REAL_TYPE>::GetInstance();
                                                                    75 
                                                                    -
                                                                    76  init_logging();
                                                                    +
                                                                    76  Rcpp::NumericVector p;
                                                                    77 
                                                                    -
                                                                    78  FIMS_INFO_LOG("adding FIMS objects to TMB");
                                                                    -
                                                                    79  for (size_t i = 0; i < FIMSRcppInterfaceBase::fims_interface_objects.size();
                                                                    -
                                                                    80  i++) {
                                                                    -
                                                                    81  FIMSRcppInterfaceBase::fims_interface_objects[i]->add_to_fims_tmb();
                                                                    -
                                                                    82  }
                                                                    -
                                                                    83 
                                                                    -
                                                                    84  // base model
                                                                    -
                                                                    85  std::shared_ptr<fims_info::Information < TMB_FIMS_REAL_TYPE>> d0 =
                                                                    -
                                                                    86  fims_info::Information<TMB_FIMS_REAL_TYPE>::GetInstance();
                                                                    -
                                                                    87  d0->CreateModel();
                                                                    -
                                                                    88 
                                                                    -
                                                                    89  // first-order derivative
                                                                    -
                                                                    90  std::shared_ptr<fims_info::Information < TMB_FIMS_FIRST_ORDER>> d1 =
                                                                    -
                                                                    91  fims_info::Information<TMB_FIMS_FIRST_ORDER>::GetInstance();
                                                                    -
                                                                    92  d1->CreateModel();
                                                                    -
                                                                    93 
                                                                    -
                                                                    94  // second-order derivative
                                                                    -
                                                                    95  std::shared_ptr<fims_info::Information < TMB_FIMS_SECOND_ORDER>> d2 =
                                                                    -
                                                                    96  fims_info::Information<TMB_FIMS_SECOND_ORDER>::GetInstance();
                                                                    -
                                                                    97  d2->CreateModel();
                                                                    -
                                                                    98 
                                                                    -
                                                                    99  // third-order derivative
                                                                    -
                                                                    100  std::shared_ptr<fims_info::Information < TMB_FIMS_THIRD_ORDER>> d3 =
                                                                    -
                                                                    101  fims_info::Information<TMB_FIMS_THIRD_ORDER>::GetInstance();
                                                                    -
                                                                    102  d3->CreateModel();
                                                                    -
                                                                    103 
                                                                    -
                                                                    104  return true;
                                                                    -
                                                                    105 }
                                                                    -
                                                                    106 
                                                                    -
                                                                    113 void SetFIMSFunctions(SEXP fn, SEXP gr) {
                                                                    -
                                                                    114  FIMS_objective_function = fn;
                                                                    -
                                                                    115  FIMS_gradient_function = gr;
                                                                    -
                                                                    116 }
                                                                    -
                                                                    117 
                                                                    -
                                                                    122 void finalize_objects(Rcpp::NumericVector p) {
                                                                    -
                                                                    123  FIMS_function_parameters = p;
                                                                    -
                                                                    124 
                                                                    -
                                                                    125 
                                                                    -
                                                                    126 
                                                                    -
                                                                    127  std::shared_ptr<fims_info::Information < double>> information =
                                                                    -
                                                                    128  fims_info::Information<double>::GetInstance();
                                                                    -
                                                                    129 
                                                                    -
                                                                    130  std::shared_ptr<fims_model::Model < double>> model =
                                                                    -
                                                                    131  fims_model::Model<double>::GetInstance();
                                                                    +
                                                                    78  for (size_t i = 0; i < d0->random_effects_parameters.size(); i++) {
                                                                    +
                                                                    79  p.push_back(*d0->random_effects_parameters[i]);
                                                                    +
                                                                    80  }
                                                                    +
                                                                    81 
                                                                    +
                                                                    82  return p;
                                                                    +
                                                                    83 }
                                                                    +
                                                                    84 
                                                                    +
                                                                    88 void clear_info_log() {
                                                                    +
                                                                    89  // First flush the output stream to make sure nothing
                                                                    +
                                                                    90  // is left in the stream memory bufffer.
                                                                    +
                                                                    91  INFO_LOG.flush();
                                                                    +
                                                                    92 
                                                                    +
                                                                    93  // Next an new stream is opened and closed to
                                                                    +
                                                                    94  // overwrite the file.
                                                                    +
                                                                    95  std::ofstream CLEAR_LOG("logs/info.log");
                                                                    +
                                                                    96  CLEAR_LOG.close();
                                                                    +
                                                                    97 
                                                                    +
                                                                    98  // Finally the stream output location is reset back to the start
                                                                    +
                                                                    99  // of the file.
                                                                    +
                                                                    100  INFO_LOG.seekp(0);
                                                                    +
                                                                    101 }
                                                                    +
                                                                    102 
                                                                    +
                                                                    106 void clear_fims_log() {
                                                                    +
                                                                    107  FIMS_LOG.flush();
                                                                    +
                                                                    108  std::ofstream CLEAR_LOG("logs/fims.log");
                                                                    +
                                                                    109  CLEAR_LOG.close();
                                                                    +
                                                                    110  FIMS_LOG.seekp(0);
                                                                    +
                                                                    111 }
                                                                    +
                                                                    112 
                                                                    +
                                                                    116 void clear_data_log() {
                                                                    +
                                                                    117  DATA_LOG.flush();
                                                                    +
                                                                    118  std::ofstream CLEAR_LOG("logs/data.log");
                                                                    +
                                                                    119  CLEAR_LOG.close();
                                                                    +
                                                                    120  DATA_LOG.seekp(0);
                                                                    +
                                                                    121 }
                                                                    +
                                                                    122 
                                                                    +
                                                                    126 void clear_error_log() {
                                                                    +
                                                                    127  ERROR_LOG.flush();
                                                                    +
                                                                    128  std::ofstream CLEAR_LOG("logs/error.log");
                                                                    +
                                                                    129  CLEAR_LOG.close();
                                                                    +
                                                                    130  ERROR_LOG.seekp(0);
                                                                    +
                                                                    131 }
                                                                    132 
                                                                    -
                                                                    133  for (size_t i = 0; i < information->fixed_effects_parameters.size(); i++) {
                                                                    -
                                                                    134  *information->fixed_effects_parameters[i] = p[i];
                                                                    -
                                                                    135  }
                                                                    -
                                                                    136 
                                                                    -
                                                                    137  model->Evaluate();
                                                                    -
                                                                    138 
                                                                    -
                                                                    139  Rcpp::Function f = Rcpp::as<Rcpp::Function>(FIMS_objective_function);
                                                                    -
                                                                    140  Rcpp::Function g = Rcpp::as<Rcpp::Function>(FIMS_gradient_function);
                                                                    -
                                                                    141  double ret = Rcpp::as<double>(f(p));
                                                                    -
                                                                    142  Rcpp::NumericVector grad = Rcpp::as<Rcpp::NumericVector>(g(p));
                                                                    -
                                                                    143 
                                                                    -
                                                                    144  FIMS_function_value = ret;
                                                                    -
                                                                    145  FIMS_function_gradient = grad;
                                                                    -
                                                                    146  std::cout << "Final value = " << FIMS_function_value << "\nGradient: \n";
                                                                    -
                                                                    147  double maxgc = -999;
                                                                    -
                                                                    148  for (size_t i = 0; i < FIMS_function_gradient.size(); i++) {
                                                                    -
                                                                    149  if (std::fabs(FIMS_function_gradient[i]) > maxgc) {
                                                                    -
                                                                    150  maxgc = std::fabs(FIMS_function_gradient[i]);
                                                                    -
                                                                    151  }
                                                                    -
                                                                    152  }
                                                                    -
                                                                    153  FIMS_mgc_value = maxgc;
                                                                    -
                                                                    154 
                                                                    -
                                                                    155  for (size_t i = 0; i < FIMSRcppInterfaceBase::fims_interface_objects.size();
                                                                    -
                                                                    156  i++) {
                                                                    -
                                                                    157  FIMSRcppInterfaceBase::fims_interface_objects[i]->finalize();
                                                                    -
                                                                    158  }
                                                                    -
                                                                    159 }
                                                                    -
                                                                    160 
                                                                    -
                                                                    174 void finalize_fims(Rcpp::Nullable< Rcpp::List> obj = R_NilValue,
                                                                    -
                                                                    175  Rcpp::Nullable< Rcpp::List> opt = R_NilValue) {
                                                                    -
                                                                    176 
                                                                    -
                                                                    177  bool has_obj = false;
                                                                    -
                                                                    178  bool has_opt = false;
                                                                    -
                                                                    179  bool is_single_argument = false;
                                                                    -
                                                                    180  bool valid_list = true;
                                                                    -
                                                                    181  Rcpp::NumericVector parameters;
                                                                    +
                                                                    136 void clear_model_log() {
                                                                    +
                                                                    137  MODEL_LOG.flush();
                                                                    +
                                                                    138  std::ofstream CLEAR_LOG("logs/model.log");
                                                                    +
                                                                    139  CLEAR_LOG.close();
                                                                    +
                                                                    140  MODEL_LOG.seekp(0);
                                                                    +
                                                                    141 }
                                                                    +
                                                                    142 
                                                                    +
                                                                    146 void clear_fleet_log() {
                                                                    +
                                                                    147  FLEET_LOG.flush();
                                                                    +
                                                                    148  std::ofstream CLEAR_LOG("logs/fleet.log");
                                                                    +
                                                                    149  CLEAR_LOG.close();
                                                                    +
                                                                    150  FLEET_LOG.seekp(0);
                                                                    +
                                                                    151 }
                                                                    +
                                                                    152 
                                                                    +
                                                                    156 void clear_population_log() {
                                                                    +
                                                                    157  POPULATION_LOG.flush();
                                                                    +
                                                                    158  std::ofstream CLEAR_LOG("logs/population.log");
                                                                    +
                                                                    159  CLEAR_LOG.close();
                                                                    +
                                                                    160  POPULATION_LOG.seekp(0);
                                                                    +
                                                                    161 }
                                                                    +
                                                                    162 
                                                                    +
                                                                    166 void clear_maturity_log() {
                                                                    +
                                                                    167  MATURITY_LOG.flush();
                                                                    +
                                                                    168  std::ofstream CLEAR_LOG("logs/maturity.log");
                                                                    +
                                                                    169  CLEAR_LOG.close();
                                                                    +
                                                                    170  MATURITY_LOG.seekp(0);
                                                                    +
                                                                    171 }
                                                                    +
                                                                    172 
                                                                    +
                                                                    176 void clear_recruitment_log() {
                                                                    +
                                                                    177  RECRUITMENT_LOG.flush();
                                                                    +
                                                                    178  std::ofstream CLEAR_LOG("logs/recruitment.log");
                                                                    +
                                                                    179  CLEAR_LOG.close();
                                                                    +
                                                                    180  RECRUITMENT_LOG.seekp(0);
                                                                    +
                                                                    181 }
                                                                    182 
                                                                    -
                                                                    183  //check and handle the first argument.
                                                                    -
                                                                    184  if (!Rf_isNull(obj.get())) {
                                                                    -
                                                                    185  Rcpp::List input_list = Rcpp::as<Rcpp::List>(obj);
                                                                    -
                                                                    186  if (input_list.containsElementNamed("obj")
                                                                    -
                                                                    187  && input_list.containsElementNamed("opt")) {
                                                                    -
                                                                    188  Rcpp::List obj_list = input_list["obj"];
                                                                    -
                                                                    189  Rcpp::List opt_list = input_list["opt"];
                                                                    -
                                                                    190 
                                                                    -
                                                                    191  if (obj_list.containsElementNamed("fn")) {
                                                                    -
                                                                    192  FIMS_objective_function = obj_list["fn"];
                                                                    -
                                                                    193  } else {
                                                                    -
                                                                    194  valid_list = false;
                                                                    -
                                                                    195  FIMS_ERROR_LOG("Invalid call, \"fn\" not found in argument list.");
                                                                    -
                                                                    196  }
                                                                    -
                                                                    197 
                                                                    -
                                                                    198  if (obj_list.containsElementNamed("gr")) {
                                                                    -
                                                                    199  FIMS_gradient_function = obj_list["gr"];
                                                                    -
                                                                    200  } else {
                                                                    -
                                                                    201  valid_list = false;
                                                                    -
                                                                    202  FIMS_ERROR_LOG("Invalid call, \"gr\" not found in argument list.");
                                                                    -
                                                                    203  }
                                                                    -
                                                                    204 
                                                                    -
                                                                    205  if (opt_list.containsElementNamed("par")) {
                                                                    -
                                                                    206  parameters = Rcpp::as<Rcpp::NumericVector>(opt_list["par"]);
                                                                    -
                                                                    207  } else {
                                                                    -
                                                                    208  valid_list = false;
                                                                    -
                                                                    209  FIMS_ERROR_LOG("Invalid call, \"par\" not found in argument list.");
                                                                    -
                                                                    210 
                                                                    -
                                                                    211  }
                                                                    +
                                                                    186 void clear_growth_log() {
                                                                    +
                                                                    187  GROWTH_LOG.flush();
                                                                    +
                                                                    188  std::ofstream CLEAR_LOG("logs/growth.log");
                                                                    +
                                                                    189  CLEAR_LOG.close();
                                                                    +
                                                                    190  GROWTH_LOG.seekp(0);
                                                                    +
                                                                    191 }
                                                                    +
                                                                    192 
                                                                    +
                                                                    196 void clear_selectivity_log() {
                                                                    +
                                                                    197  SELECTIVITY_LOG.flush();
                                                                    +
                                                                    198  std::ofstream CLEAR_LOG("logs/selectivity.log");
                                                                    +
                                                                    199  CLEAR_LOG.close();
                                                                    +
                                                                    200  SELECTIVITY_LOG.seekp(0);
                                                                    +
                                                                    201 }
                                                                    +
                                                                    202 
                                                                    +
                                                                    206 void clear_debug_log() {
                                                                    +
                                                                    207  DEBUG_LOG.flush();
                                                                    +
                                                                    208  std::ofstream CLEAR_LOG("logs/debug/debug.log");
                                                                    +
                                                                    209  CLEAR_LOG.close();
                                                                    +
                                                                    210  DEBUG_LOG.seekp(0);
                                                                    +
                                                                    211 }
                                                                    212 
                                                                    -
                                                                    213  //if we are here, a single argument was used. if it contains the
                                                                    -
                                                                    214  //expected elements, the list is valid and objects can be finalize.
                                                                    -
                                                                    215  if (valid_list) {
                                                                    -
                                                                    216  finalize_objects(parameters);
                                                                    -
                                                                    217  FIMS_finalized = true;
                                                                    -
                                                                    218  return;
                                                                    -
                                                                    219  } else {
                                                                    -
                                                                    220  return;
                                                                    -
                                                                    221  }
                                                                    -
                                                                    222 
                                                                    -
                                                                    223 
                                                                    -
                                                                    224  } else {//two arguments?
                                                                    -
                                                                    225  if (input_list.containsElementNamed("fn")) {
                                                                    -
                                                                    226  FIMS_objective_function = input_list["fn"];
                                                                    -
                                                                    227  } else {
                                                                    -
                                                                    228  valid_list = false;
                                                                    -
                                                                    229  FIMS_ERROR_LOG("Invalid call, \"fn\" not found in argument list.");
                                                                    -
                                                                    230  }
                                                                    -
                                                                    231 
                                                                    -
                                                                    232  if (input_list.containsElementNamed("gr")) {
                                                                    -
                                                                    233  FIMS_gradient_function = input_list["gr"];
                                                                    -
                                                                    234  } else {
                                                                    -
                                                                    235  valid_list = false;
                                                                    -
                                                                    236  FIMS_ERROR_LOG("Invalid call, \"gr\" not found in argument list.");
                                                                    -
                                                                    237  }
                                                                    -
                                                                    238  }
                                                                    -
                                                                    239  }
                                                                    -
                                                                    240 
                                                                    -
                                                                    241 
                                                                    -
                                                                    242  //check second argument.
                                                                    -
                                                                    243  if (!Rf_isNull(opt.get())) {
                                                                    +
                                                                    216 void clear_logs() {
                                                                    +
                                                                    217  clear_fims_log();
                                                                    +
                                                                    218  clear_info_log();
                                                                    +
                                                                    219  clear_data_log();
                                                                    +
                                                                    220  clear_error_log();
                                                                    +
                                                                    221  clear_model_log();
                                                                    +
                                                                    222  clear_fleet_log();
                                                                    +
                                                                    223  clear_population_log();
                                                                    +
                                                                    224  clear_recruitment_log();
                                                                    +
                                                                    225  clear_growth_log();
                                                                    +
                                                                    226  clear_maturity_log();
                                                                    +
                                                                    227  clear_selectivity_log();
                                                                    +
                                                                    228  clear_debug_log();
                                                                    +
                                                                    229 }
                                                                    +
                                                                    230 
                                                                    +
                                                                    231 template <typename Type>
                                                                    +
                                                                    232 void clear_internal() {
                                                                    +
                                                                    233  std::shared_ptr<fims_info::Information<Type>> d0 =
                                                                    +
                                                                    234  fims_info::Information<Type>::GetInstance();
                                                                    +
                                                                    235  d0->fixed_effects_parameters.clear();
                                                                    +
                                                                    236  d0->random_effects_parameters.clear();
                                                                    +
                                                                    237 }
                                                                    +
                                                                    241 void clear() {
                                                                    +
                                                                    242  // rcpp_interface_base.hpp
                                                                    +
                                                                    243  FIMSRcppInterfaceBase::fims_interface_objects.clear();
                                                                    244 
                                                                    -
                                                                    245  Rcpp::List input_list = Rcpp::as<Rcpp::List>(opt);
                                                                    -
                                                                    246 
                                                                    -
                                                                    247  if (input_list.containsElementNamed("par")) {
                                                                    -
                                                                    248  parameters = Rcpp::as<Rcpp::NumericVector>(input_list["par"]);
                                                                    -
                                                                    249  } else {
                                                                    -
                                                                    250  valid_list = false;
                                                                    -
                                                                    251  FIMS_ERROR_LOG("Invalid call, \"par\" not found in argument list.");
                                                                    -
                                                                    252 
                                                                    -
                                                                    253  }
                                                                    -
                                                                    254  } else {
                                                                    -
                                                                    255  valid_list = false;
                                                                    -
                                                                    256  }
                                                                    -
                                                                    257 
                                                                    -
                                                                    258  //if we're here, two arguments were given. If they contain the expected
                                                                    -
                                                                    259  //elements, the lists are valid and objects can be finalized.
                                                                    -
                                                                    260  if (valid_list) {
                                                                    -
                                                                    261  finalize_objects(parameters);
                                                                    -
                                                                    262  FIMS_finalized = true;
                                                                    -
                                                                    263  }
                                                                    -
                                                                    264 
                                                                    +
                                                                    245  // rcpp_data.hpp
                                                                    +
                                                                    246  DataInterfaceBase::id_g = 1;
                                                                    +
                                                                    247  DataInterfaceBase::live_objects.clear();
                                                                    +
                                                                    248 
                                                                    +
                                                                    249  AgeCompDataInterface::id_g = 1;
                                                                    +
                                                                    250  AgeCompDataInterface::live_objects.clear();
                                                                    +
                                                                    251 
                                                                    +
                                                                    252  IndexDataInterface::id_g = 1;
                                                                    +
                                                                    253  IndexDataInterface::live_objects.clear();
                                                                    +
                                                                    254 
                                                                    +
                                                                    255  // rcpp_fleets.hpp
                                                                    +
                                                                    256  FleetInterfaceBase::id_g = 1;
                                                                    +
                                                                    257  FleetInterfaceBase::live_objects.clear();
                                                                    +
                                                                    258 
                                                                    +
                                                                    259  FleetInterface::id_g = 1;
                                                                    +
                                                                    260  FleetInterface::live_objects.clear();
                                                                    +
                                                                    261 
                                                                    +
                                                                    262  // rcpp_growth.hpp
                                                                    +
                                                                    263  GrowthInterfaceBase::id_g = 1;
                                                                    +
                                                                    264  GrowthInterfaceBase::live_objects.clear();
                                                                    265 
                                                                    -
                                                                    266 }
                                                                    -
                                                                    267 
                                                                    -
                                                                    275 void finalize_fims_deprecated(SEXP tmb_obj = R_NilValue) {
                                                                    -
                                                                    276 
                                                                    -
                                                                    277  Rcpp::NumericVector parameters;
                                                                    -
                                                                    278  bool valid_list = true;
                                                                    +
                                                                    266  EWAAGrowthInterface::id_g = 1;
                                                                    +
                                                                    267  EWAAGrowthInterface::live_objects.clear();
                                                                    +
                                                                    268 
                                                                    +
                                                                    269  // rcpp_maturity.hpp
                                                                    +
                                                                    270  MaturityInterfaceBase::id_g = 1;
                                                                    +
                                                                    271  MaturityInterfaceBase::live_objects.clear();
                                                                    +
                                                                    272 
                                                                    +
                                                                    273  LogisticMaturityInterface::id_g = 1;
                                                                    +
                                                                    274  LogisticMaturityInterface::live_objects.clear();
                                                                    +
                                                                    275 
                                                                    +
                                                                    276  // rcpp_population.hpp
                                                                    +
                                                                    277  PopulationInterfaceBase::id_g = 1;
                                                                    +
                                                                    278  PopulationInterfaceBase::live_objects.clear();
                                                                    279 
                                                                    -
                                                                    280  if (!Rf_isNull(tmb_obj)) {
                                                                    -
                                                                    281 
                                                                    -
                                                                    282  Rcpp::List tmb_list = Rcpp::as<Rcpp::List>(tmb_obj);
                                                                    -
                                                                    283 
                                                                    -
                                                                    284  if (tmb_list.containsElementNamed("obj")) {
                                                                    -
                                                                    285  Rcpp::List tmb_obj_list = tmb_list["obj"];
                                                                    +
                                                                    280  PopulationInterface::id_g = 1;
                                                                    +
                                                                    281  PopulationInterface::live_objects.clear();
                                                                    +
                                                                    282 
                                                                    +
                                                                    283  // rcpp_recruitment.hpp
                                                                    +
                                                                    284  RecruitmentInterfaceBase::id_g = 1;
                                                                    +
                                                                    285  RecruitmentInterfaceBase::live_objects.clear();
                                                                    286 
                                                                    -
                                                                    287  if (tmb_obj_list.containsElementNamed("fn")) {
                                                                    -
                                                                    288  FIMS_objective_function = tmb_obj_list["fn"];
                                                                    -
                                                                    289  } else {
                                                                    -
                                                                    290  valid_list = false;
                                                                    -
                                                                    291  FIMS_ERROR_LOG("Invalid call, \"fn\" not found in argument list.");
                                                                    -
                                                                    292  }
                                                                    +
                                                                    287  BevertonHoltRecruitmentInterface::id_g = 1;
                                                                    +
                                                                    288  BevertonHoltRecruitmentInterface::live_objects.clear();
                                                                    +
                                                                    289 
                                                                    +
                                                                    290  // rcpp_selectivity.hpp
                                                                    +
                                                                    291  SelectivityInterfaceBase::id_g = 1;
                                                                    +
                                                                    292  SelectivityInterfaceBase::live_objects.clear();
                                                                    293 
                                                                    -
                                                                    294  if (tmb_obj_list.containsElementNamed("gr")) {
                                                                    -
                                                                    295  FIMS_gradient_function = tmb_obj_list["gr"];
                                                                    -
                                                                    296  } else {
                                                                    -
                                                                    297  valid_list = false;
                                                                    -
                                                                    298  FIMS_ERROR_LOG("Invalid call, \"gr\" not found in argument list.");
                                                                    -
                                                                    299  }
                                                                    -
                                                                    300  } else {
                                                                    -
                                                                    301  valid_list = false;
                                                                    -
                                                                    302  FIMS_ERROR_LOG("Invalid call, \"obj\" not found in argument list.");
                                                                    +
                                                                    294  LogisticSelectivityInterface::id_g = 1;
                                                                    +
                                                                    295  LogisticSelectivityInterface::live_objects.clear();
                                                                    +
                                                                    296 
                                                                    +
                                                                    297  DoubleLogisticSelectivityInterface::id_g = 1;
                                                                    +
                                                                    298  DoubleLogisticSelectivityInterface::live_objects.clear();
                                                                    +
                                                                    299 
                                                                    +
                                                                    300  // rcpp_tmb_distribution.hpp
                                                                    +
                                                                    301  DistributionsInterfaceBase::id_g = 1;
                                                                    +
                                                                    302  DistributionsInterfaceBase::live_objects.clear();
                                                                    303 
                                                                    -
                                                                    304  }
                                                                    -
                                                                    305 
                                                                    +
                                                                    304  DnormDistributionsInterface::id_g = 1;
                                                                    +
                                                                    305  DnormDistributionsInterface::live_objects.clear();
                                                                    306 
                                                                    -
                                                                    307  if (tmb_list.containsElementNamed("opt")) {
                                                                    -
                                                                    308  Rcpp::List tmb_opt_list = tmb_list["opt"];
                                                                    -
                                                                    309  if (tmb_opt_list.containsElementNamed("par")) {
                                                                    -
                                                                    310  parameters = Rcpp::as<Rcpp::NumericVector>(tmb_opt_list["par"]);
                                                                    -
                                                                    311  } else {
                                                                    -
                                                                    312  valid_list = false;
                                                                    -
                                                                    313  FIMS_ERROR_LOG("Invalid call, \"par\" not found in argument list.");
                                                                    -
                                                                    314 
                                                                    -
                                                                    315  }
                                                                    -
                                                                    316  } else {
                                                                    -
                                                                    317  valid_list = false;
                                                                    -
                                                                    318  FIMS_ERROR_LOG("Invalid call, \"opt\" not found in argument list.");
                                                                    -
                                                                    319 
                                                                    -
                                                                    320  }
                                                                    -
                                                                    321 
                                                                    -
                                                                    322  if (valid_list) {
                                                                    -
                                                                    323  Rcpp::Rcout << "finalizing objects:)";
                                                                    -
                                                                    324  finalize_objects(parameters);
                                                                    -
                                                                    325  } else {
                                                                    -
                                                                    326  Rcpp::Rcout << "Invalid list argument for Finalize(List).";
                                                                    -
                                                                    327  FIMS_ERROR_LOG("Unable to finalize objects.");
                                                                    -
                                                                    328 
                                                                    -
                                                                    329  }
                                                                    -
                                                                    330  }
                                                                    -
                                                                    331 }
                                                                    -
                                                                    332 
                                                                    -
                                                                    336 std::string get_output() {
                                                                    -
                                                                    337  std::string ret;
                                                                    -
                                                                    338  if (FIMS_finalized) {
                                                                    -
                                                                    339  auto now = std::chrono::system_clock::now();
                                                                    -
                                                                    340  std::time_t now_time = std::chrono::system_clock::to_time_t(now);
                                                                    -
                                                                    341  std::string ctime_no_newline = strtok(ctime(&now_time), "\n");
                                                                    -
                                                                    342  std::shared_ptr<fims_info::Information < double>> info =
                                                                    -
                                                                    343  fims_info::Information<double>::GetInstance();
                                                                    -
                                                                    344  std::stringstream ss;
                                                                    -
                                                                    345  ss << "{\n";
                                                                    -
                                                                    346  ss << "\"timestamp\": \"" << ctime_no_newline << "\",\n";
                                                                    -
                                                                    347  ss << "\"nyears\":" << info->nyears << ",\n";
                                                                    -
                                                                    348  ss << "\"nseasons\":" << info->nseasons << ",\n";
                                                                    -
                                                                    349  ss << "\"nages\":" << info->nages << ",\n";
                                                                    -
                                                                    350  ss << "\"finalized\":" << FIMS_finalized << ",\n";
                                                                    -
                                                                    351  ss << "\"objective_function_value\": " << FIMS_function_value << ",\n";
                                                                    -
                                                                    352  ss << "\"max_gradient_component\": " << FIMS_mgc_value << ",\n";
                                                                    -
                                                                    353  ss << "\"final_gradient\": [";
                                                                    -
                                                                    354  if (FIMS_function_gradient.size() > 0) {
                                                                    -
                                                                    355  for (size_t i = 0; i < FIMS_function_gradient.size() - 1; i++) {
                                                                    -
                                                                    356  ss << FIMS_function_gradient[i] << ", ";
                                                                    -
                                                                    357  }
                                                                    -
                                                                    358  ss << FIMS_function_gradient[FIMS_function_gradient.size() - 1] << "],\n";
                                                                    -
                                                                    359  } else {
                                                                    -
                                                                    360  ss << "],";
                                                                    -
                                                                    361  }
                                                                    -
                                                                    362  size_t length = FIMSRcppInterfaceBase::fims_interface_objects.size();
                                                                    -
                                                                    363  for (size_t i = 0; i < length - 1; i++) {
                                                                    -
                                                                    364  ss << FIMSRcppInterfaceBase::fims_interface_objects[i]->to_json() << ",\n";
                                                                    -
                                                                    365  }
                                                                    -
                                                                    366 
                                                                    -
                                                                    367  ss << FIMSRcppInterfaceBase::fims_interface_objects[length - 1]->to_json() << "\n}";
                                                                    -
                                                                    368 
                                                                    -
                                                                    369  ret = fims::JsonParser::PrettyFormatJSON(ss.str());
                                                                    -
                                                                    370  } else {
                                                                    -
                                                                    371  Rcpp::Rcout << "Invalid request to \"get_output\". Please call finalize first.";
                                                                    -
                                                                    372  }
                                                                    -
                                                                    373  return ret;
                                                                    -
                                                                    374 }
                                                                    -
                                                                    375 
                                                                    -
                                                                    381 Rcpp::NumericVector get_fixed_parameters_vector() {
                                                                    -
                                                                    382  // base model
                                                                    -
                                                                    383  std::shared_ptr<fims_info::Information < TMB_FIMS_REAL_TYPE>> d0 =
                                                                    -
                                                                    384  fims_info::Information<TMB_FIMS_REAL_TYPE>::GetInstance();
                                                                    +
                                                                    307  DlnormDistributionsInterface::id_g = 1;
                                                                    +
                                                                    308  DlnormDistributionsInterface::live_objects.clear();
                                                                    +
                                                                    309 
                                                                    +
                                                                    310  DmultinomDistributionsInterface::id_g = 1;
                                                                    +
                                                                    311  DmultinomDistributionsInterface::live_objects.clear();
                                                                    +
                                                                    312 
                                                                    +
                                                                    313  clear_internal<TMB_FIMS_REAL_TYPE>();
                                                                    +
                                                                    314  clear_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    +
                                                                    315  clear_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    +
                                                                    316  clear_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    +
                                                                    317 }
                                                                    +
                                                                    318 
                                                                    +
                                                                    319 RCPP_EXPOSED_CLASS(Parameter)
                                                                    +
                                                                    320 RCPP_MODULE(fims) {
                                                                    +
                                                                    321  Rcpp::function("CreateTMBModel", &CreateTMBModel);
                                                                    +
                                                                    322  Rcpp::function("get_fixed", &get_fixed_parameters_vector);
                                                                    +
                                                                    323  Rcpp::function("get_random", &get_random_parameters_vector);
                                                                    +
                                                                    324  Rcpp::function("clear", clear);
                                                                    +
                                                                    325  Rcpp::function("clear_logs", clear_logs);
                                                                    +
                                                                    326  Rcpp::function("clear_fims_log", clear_fims_log);
                                                                    +
                                                                    327  Rcpp::function("clear_info_log", clear_info_log);
                                                                    +
                                                                    328  Rcpp::function("clear_error_log", clear_error_log);
                                                                    +
                                                                    329  Rcpp::function("clear_data_log", clear_data_log);
                                                                    +
                                                                    330  Rcpp::function("clear_population_log", clear_population_log);
                                                                    +
                                                                    331  Rcpp::function("clear_model_log", clear_model_log);
                                                                    +
                                                                    332  Rcpp::function("clear_recruitment_log", clear_recruitment_log);
                                                                    +
                                                                    333  Rcpp::function("clear_fleet_log", clear_fleet_log);
                                                                    +
                                                                    334  Rcpp::function("clear_growth_log", clear_growth_log);
                                                                    +
                                                                    335  Rcpp::function("clear_maturity_log", clear_maturity_log);
                                                                    +
                                                                    336  Rcpp::function("clear_selectivity_log", clear_selectivity_log);
                                                                    +
                                                                    337  Rcpp::function("clear_debug_log", clear_debug_log);
                                                                    +
                                                                    338 
                                                                    +
                                                                    339  Rcpp::class_<Parameter>("Parameter")
                                                                    +
                                                                    340  .constructor()
                                                                    +
                                                                    341  .constructor<double>()
                                                                    +
                                                                    342  .constructor<Parameter>()
                                                                    +
                                                                    343  .field("value", &Parameter::value_m)
                                                                    +
                                                                    344  .field("min", &Parameter::min_m)
                                                                    +
                                                                    345  .field("max", &Parameter::max_m)
                                                                    +
                                                                    346  .field("is_random_effect", &Parameter::is_random_effect_m)
                                                                    +
                                                                    347  .field("estimated", &Parameter::estimated_m);
                                                                    +
                                                                    348 
                                                                    +
                                                                    349  Rcpp::class_<BevertonHoltRecruitmentInterface>("BevertonHoltRecruitment")
                                                                    +
                                                                    350  .constructor()
                                                                    +
                                                                    351  .field("logit_steep", &BevertonHoltRecruitmentInterface::logit_steep)
                                                                    +
                                                                    352  .field("log_rzero", &BevertonHoltRecruitmentInterface::log_rzero)
                                                                    +
                                                                    353  .field("log_devs", &BevertonHoltRecruitmentInterface::log_devs)
                                                                    +
                                                                    354  .field("estimate_log_devs",
                                                                    +
                                                                    355  &BevertonHoltRecruitmentInterface::estimate_log_devs)
                                                                    +
                                                                    356  .method("get_id", &BevertonHoltRecruitmentInterface::get_id)
                                                                    +
                                                                    357  .field("log_sigma_recruit",
                                                                    +
                                                                    358  &BevertonHoltRecruitmentInterface::log_sigma_recruit)
                                                                    +
                                                                    359  .method("evaluate", &BevertonHoltRecruitmentInterface::evaluate)
                                                                    +
                                                                    360  .method("evaluate_nll", &BevertonHoltRecruitmentInterface::evaluate_nll);
                                                                    +
                                                                    361 
                                                                    +
                                                                    362  Rcpp::class_<FleetInterface>("Fleet")
                                                                    +
                                                                    363  .constructor()
                                                                    +
                                                                    364  .field("is_survey", &FleetInterface::is_survey)
                                                                    +
                                                                    365  .field("log_q", &FleetInterface::log_q)
                                                                    +
                                                                    366  .field("log_Fmort", &FleetInterface::log_Fmort)
                                                                    +
                                                                    367  .field("nages", &FleetInterface::nages)
                                                                    +
                                                                    368  .field("nyears", &FleetInterface::nyears)
                                                                    +
                                                                    369  .field("estimate_F", &FleetInterface::estimate_F)
                                                                    +
                                                                    370  .field("estimate_q", &FleetInterface::estimate_q)
                                                                    +
                                                                    371  .field("estimate_obs_error", &FleetInterface::estimate_obs_error)
                                                                    +
                                                                    372  .field("random_q", &FleetInterface::random_q)
                                                                    +
                                                                    373  .field("random_F", &FleetInterface::random_F)
                                                                    +
                                                                    374  .field("log_obs_error", &FleetInterface::log_obs_error)
                                                                    +
                                                                    375  .method("SetAgeCompLikelihood", &FleetInterface::SetAgeCompLikelihood)
                                                                    +
                                                                    376  .method("SetIndexLikelihood", &FleetInterface::SetIndexLikelihood)
                                                                    +
                                                                    377  .method("SetObservedAgeCompData", &FleetInterface::SetObservedAgeCompData)
                                                                    +
                                                                    378  .method("SetObservedIndexData", &FleetInterface::SetObservedIndexData)
                                                                    +
                                                                    379  .method("SetSelectivity", &FleetInterface::SetSelectivity);
                                                                    +
                                                                    380 
                                                                    +
                                                                    381  Rcpp::class_<AgeCompDataInterface>("AgeComp")
                                                                    +
                                                                    382  .constructor<int, int>()
                                                                    +
                                                                    383  .field("age_comp_data", &AgeCompDataInterface::age_comp_data)
                                                                    +
                                                                    384  .method("get_id", &AgeCompDataInterface::get_id);
                                                                    385 
                                                                    -
                                                                    386  Rcpp::NumericVector p;
                                                                    -
                                                                    387 
                                                                    -
                                                                    388  for (size_t i = 0; i < d0->fixed_effects_parameters.size(); i++) {
                                                                    -
                                                                    389  p.push_back(*d0->fixed_effects_parameters[i]);
                                                                    -
                                                                    390  }
                                                                    -
                                                                    391 
                                                                    -
                                                                    392  return p;
                                                                    -
                                                                    393 }
                                                                    -
                                                                    394 
                                                                    -
                                                                    400 Rcpp::NumericVector get_random_parameters_vector() {
                                                                    -
                                                                    401  // base model
                                                                    -
                                                                    402  std::shared_ptr<fims_info::Information < TMB_FIMS_REAL_TYPE>> d0 =
                                                                    -
                                                                    403  fims_info::Information<TMB_FIMS_REAL_TYPE>::GetInstance();
                                                                    -
                                                                    404 
                                                                    -
                                                                    405  Rcpp::NumericVector p;
                                                                    -
                                                                    406 
                                                                    -
                                                                    407  for (size_t i = 0; i < d0->random_effects_parameters.size(); i++) {
                                                                    -
                                                                    408  p.push_back(*d0->random_effects_parameters[i]);
                                                                    -
                                                                    409  }
                                                                    +
                                                                    386  Rcpp::class_<IndexDataInterface>("Index")
                                                                    +
                                                                    387  .constructor<int>()
                                                                    +
                                                                    388  .field("index_data", &IndexDataInterface::index_data)
                                                                    +
                                                                    389  .method("get_id", &IndexDataInterface::get_id);
                                                                    +
                                                                    390 
                                                                    +
                                                                    391  Rcpp::class_<PopulationInterface>("Population")
                                                                    +
                                                                    392  .constructor()
                                                                    +
                                                                    393  .method("get_id", &PopulationInterface::get_id)
                                                                    +
                                                                    394  .field("nages", &PopulationInterface::nages)
                                                                    +
                                                                    395  .field("nfleets", &PopulationInterface::nfleets)
                                                                    +
                                                                    396  .field("nseasons", &PopulationInterface::nseasons)
                                                                    +
                                                                    397  .field("nyears", &PopulationInterface::nyears)
                                                                    +
                                                                    398  .field("log_M", &PopulationInterface::log_M)
                                                                    +
                                                                    399  .field("log_init_naa", &PopulationInterface::log_init_naa)
                                                                    +
                                                                    400  .field("proportion_female", &PopulationInterface::proportion_female)
                                                                    +
                                                                    401  .field("ages", &PopulationInterface::ages)
                                                                    +
                                                                    402  .field("estimate_M", &PopulationInterface::estimate_M)
                                                                    +
                                                                    403  .field("estimate_init_naa", &PopulationInterface::estimate_initNAA)
                                                                    +
                                                                    404  .field("estimate_prop_female", &PopulationInterface::estimate_prop_female)
                                                                    +
                                                                    405  .method("evaluate", &PopulationInterface::evaluate)
                                                                    +
                                                                    406  .method("SetMaturity", &PopulationInterface::SetMaturity)
                                                                    +
                                                                    407  .method("SetGrowth", &PopulationInterface::SetGrowth)
                                                                    +
                                                                    408  .method("SetRecruitment", &PopulationInterface::SetRecruitment)
                                                                    +
                                                                    409  .method("evaluate", &PopulationInterface::evaluate);
                                                                    410 
                                                                    -
                                                                    411  return p;
                                                                    -
                                                                    412 }
                                                                    -
                                                                    413 
                                                                    -
                                                                    420 Rcpp::List get_parameter_names(Rcpp::List pars) {
                                                                    -
                                                                    421  // base model
                                                                    -
                                                                    422  std::shared_ptr<fims_info::Information < TMB_FIMS_REAL_TYPE>> d0 =
                                                                    -
                                                                    423  fims_info::Information<TMB_FIMS_REAL_TYPE>::GetInstance();
                                                                    -
                                                                    424 
                                                                    -
                                                                    425  pars.attr("names") = d0->parameter_names;
                                                                    -
                                                                    426 
                                                                    -
                                                                    427 
                                                                    -
                                                                    428  return pars;
                                                                    -
                                                                    429 }
                                                                    -
                                                                    430 
                                                                    -
                                                                    436 template <typename Type>
                                                                    -
                                                                    437 void clear_internal() {
                                                                    -
                                                                    438  std::shared_ptr<fims_info::Information < Type>> d0 =
                                                                    -
                                                                    439  fims_info::Information<Type>::GetInstance();
                                                                    -
                                                                    440  d0->fixed_effects_parameters.clear();
                                                                    -
                                                                    441  d0->random_effects_parameters.clear();
                                                                    -
                                                                    442  d0->variable_map.clear();
                                                                    -
                                                                    443 }
                                                                    +
                                                                    411  Rcpp::class_<DnormDistributionsInterface>("TMBDnormDistribution")
                                                                    +
                                                                    412  .constructor()
                                                                    +
                                                                    413  .method("get_id", &DnormDistributionsInterface::get_id)
                                                                    +
                                                                    414  .method("evaluate", &DnormDistributionsInterface::evaluate)
                                                                    +
                                                                    415  .field("x", &DnormDistributionsInterface::x)
                                                                    +
                                                                    416  .field("mean", &DnormDistributionsInterface::mean)
                                                                    +
                                                                    417  .field("sd", &DnormDistributionsInterface::sd);
                                                                    +
                                                                    418 
                                                                    +
                                                                    419  Rcpp::class_<LogisticMaturityInterface>("LogisticMaturity")
                                                                    +
                                                                    420  .constructor()
                                                                    +
                                                                    421  .field("inflection_point", &LogisticMaturityInterface::inflection_point)
                                                                    +
                                                                    422  .field("slope", &LogisticMaturityInterface::slope)
                                                                    +
                                                                    423  .method("get_id", &LogisticMaturityInterface::get_id)
                                                                    +
                                                                    424  .method("evaluate", &LogisticMaturityInterface::evaluate);
                                                                    +
                                                                    425 
                                                                    +
                                                                    426  Rcpp::class_<LogisticSelectivityInterface>("LogisticSelectivity")
                                                                    +
                                                                    427  .constructor()
                                                                    +
                                                                    428  .field("inflection_point",
                                                                    +
                                                                    429  &LogisticSelectivityInterface::inflection_point)
                                                                    +
                                                                    430  .field("slope", &LogisticSelectivityInterface::slope)
                                                                    +
                                                                    431  .method("get_id", &LogisticSelectivityInterface::get_id)
                                                                    +
                                                                    432  .method("evaluate", &LogisticSelectivityInterface::evaluate);
                                                                    +
                                                                    433 
                                                                    +
                                                                    434  Rcpp::class_<DoubleLogisticSelectivityInterface>("DoubleLogisticSelectivity")
                                                                    +
                                                                    435  .constructor()
                                                                    +
                                                                    436  .field("inflection_point_asc",
                                                                    +
                                                                    437  &DoubleLogisticSelectivityInterface::inflection_point_asc)
                                                                    +
                                                                    438  .field("slope_asc", &DoubleLogisticSelectivityInterface::slope_asc)
                                                                    +
                                                                    439  .field("inflection_point_desc",
                                                                    +
                                                                    440  &DoubleLogisticSelectivityInterface::inflection_point_desc)
                                                                    +
                                                                    441  .field("slope_desc", &DoubleLogisticSelectivityInterface::slope_desc)
                                                                    +
                                                                    442  .method("get_id", &DoubleLogisticSelectivityInterface::get_id)
                                                                    +
                                                                    443  .method("evaluate", &DoubleLogisticSelectivityInterface::evaluate);
                                                                    444 
                                                                    -
                                                                    448 void clear() {
                                                                    -
                                                                    449  // rcpp_interface_base.hpp
                                                                    -
                                                                    450  FIMSRcppInterfaceBase::fims_interface_objects.clear();
                                                                    +
                                                                    445  Rcpp::class_<EWAAGrowthInterface>("EWAAgrowth")
                                                                    +
                                                                    446  .constructor()
                                                                    +
                                                                    447  .field("ages", &EWAAGrowthInterface::ages)
                                                                    +
                                                                    448  .field("weights", &EWAAGrowthInterface::weights)
                                                                    +
                                                                    449  .method("get_id", &EWAAGrowthInterface::get_id)
                                                                    +
                                                                    450  .method("evaluate", &EWAAGrowthInterface::evaluate);
                                                                    451 
                                                                    -
                                                                    452  //Parameter and ParameterVector
                                                                    -
                                                                    453  Parameter::id_g = 1;
                                                                    -
                                                                    454  ParameterVector::id_g = 1;
                                                                    -
                                                                    455  // rcpp_data.hpp
                                                                    -
                                                                    456  DataInterfaceBase::id_g = 1;
                                                                    -
                                                                    457  DataInterfaceBase::live_objects.clear();
                                                                    -
                                                                    458 
                                                                    -
                                                                    459  AgeCompDataInterface::id_g = 1;
                                                                    -
                                                                    460  AgeCompDataInterface::live_objects.clear();
                                                                    -
                                                                    461 
                                                                    -
                                                                    462  LengthCompDataInterface::id_g = 1;
                                                                    -
                                                                    463  LengthCompDataInterface::live_objects.clear();
                                                                    -
                                                                    464 
                                                                    -
                                                                    465  IndexDataInterface::id_g = 1;
                                                                    -
                                                                    466  IndexDataInterface::live_objects.clear();
                                                                    +
                                                                    452  Rcpp::class_<DlnormDistributionsInterface>("TMBDlnormDistribution")
                                                                    +
                                                                    453  .constructor()
                                                                    +
                                                                    454  .method("get_id", &DlnormDistributionsInterface::get_id)
                                                                    +
                                                                    455  .method("evaluate", &DlnormDistributionsInterface::evaluate)
                                                                    +
                                                                    456  .field("x", &DlnormDistributionsInterface::x)
                                                                    +
                                                                    457  .field("meanlog", &DlnormDistributionsInterface::meanlog)
                                                                    +
                                                                    458  .field("sdlog", &DlnormDistributionsInterface::sdlog);
                                                                    +
                                                                    459 
                                                                    +
                                                                    460  Rcpp::class_<DmultinomDistributionsInterface>("TMBDmultinomDistribution")
                                                                    +
                                                                    461  .constructor()
                                                                    +
                                                                    462  .method("evaluate", &DmultinomDistributionsInterface::evaluate)
                                                                    +
                                                                    463  .method("get_id", &DmultinomDistributionsInterface::get_id)
                                                                    +
                                                                    464  .field("x", &DmultinomDistributionsInterface::x)
                                                                    +
                                                                    465  .field("p", &DmultinomDistributionsInterface::p);
                                                                    +
                                                                    466 }
                                                                    467 
                                                                    -
                                                                    468  // rcpp_fleets.hpp
                                                                    -
                                                                    469  FleetInterfaceBase::id_g = 1;
                                                                    -
                                                                    470  FleetInterfaceBase::live_objects.clear();
                                                                    -
                                                                    471 
                                                                    -
                                                                    472  FleetInterface::id_g = 1;
                                                                    -
                                                                    473  FleetInterface::live_objects.clear();
                                                                    -
                                                                    474 
                                                                    -
                                                                    475  // rcpp_growth.hpp
                                                                    -
                                                                    476  GrowthInterfaceBase::id_g = 1;
                                                                    -
                                                                    477  GrowthInterfaceBase::live_objects.clear();
                                                                    -
                                                                    478 
                                                                    -
                                                                    479  EWAAGrowthInterface::id_g = 1;
                                                                    -
                                                                    480  EWAAGrowthInterface::live_objects.clear();
                                                                    -
                                                                    481 
                                                                    -
                                                                    482  // rcpp_maturity.hpp
                                                                    -
                                                                    483  MaturityInterfaceBase::id_g = 1;
                                                                    -
                                                                    484  MaturityInterfaceBase::live_objects.clear();
                                                                    -
                                                                    485 
                                                                    -
                                                                    486  LogisticMaturityInterface::id_g = 1;
                                                                    -
                                                                    487  LogisticMaturityInterface::live_objects.clear();
                                                                    -
                                                                    488 
                                                                    -
                                                                    489  // rcpp_population.hpp
                                                                    -
                                                                    490  PopulationInterfaceBase::id_g = 1;
                                                                    -
                                                                    491  PopulationInterfaceBase::live_objects.clear();
                                                                    -
                                                                    492 
                                                                    -
                                                                    493  PopulationInterface::id_g = 1;
                                                                    -
                                                                    494  PopulationInterface::live_objects.clear();
                                                                    -
                                                                    495 
                                                                    -
                                                                    496  // rcpp_recruitment.hpp
                                                                    -
                                                                    497  RecruitmentInterfaceBase::id_g = 1;
                                                                    -
                                                                    498  RecruitmentInterfaceBase::live_objects.clear();
                                                                    -
                                                                    499 
                                                                    -
                                                                    500  BevertonHoltRecruitmentInterface::id_g = 1;
                                                                    -
                                                                    501  BevertonHoltRecruitmentInterface::live_objects.clear();
                                                                    -
                                                                    502 
                                                                    -
                                                                    503  // rcpp_selectivity.hpp
                                                                    -
                                                                    504  SelectivityInterfaceBase::id_g = 1;
                                                                    -
                                                                    505  SelectivityInterfaceBase::live_objects.clear();
                                                                    -
                                                                    506 
                                                                    -
                                                                    507  LogisticSelectivityInterface::id_g = 1;
                                                                    -
                                                                    508  LogisticSelectivityInterface::live_objects.clear();
                                                                    -
                                                                    509 
                                                                    -
                                                                    510  DoubleLogisticSelectivityInterface::id_g = 1;
                                                                    -
                                                                    511  DoubleLogisticSelectivityInterface::live_objects.clear();
                                                                    -
                                                                    512 
                                                                    -
                                                                    513  // rcpp_distribution.hpp
                                                                    -
                                                                    514  DistributionsInterfaceBase::id_g = 1;
                                                                    -
                                                                    515  DistributionsInterfaceBase::live_objects.clear();
                                                                    -
                                                                    516 
                                                                    -
                                                                    517  DnormDistributionsInterface::id_g = 1;
                                                                    -
                                                                    518  DnormDistributionsInterface::live_objects.clear();
                                                                    -
                                                                    519 
                                                                    -
                                                                    520  DlnormDistributionsInterface::id_g = 1;
                                                                    -
                                                                    521  DlnormDistributionsInterface::live_objects.clear();
                                                                    -
                                                                    522 
                                                                    -
                                                                    523  DmultinomDistributionsInterface::id_g = 1;
                                                                    -
                                                                    524  DmultinomDistributionsInterface::live_objects.clear();
                                                                    -
                                                                    525 
                                                                    -
                                                                    526  clear_internal<TMB_FIMS_REAL_TYPE>();
                                                                    -
                                                                    527  clear_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    -
                                                                    528  clear_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    -
                                                                    529  clear_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    -
                                                                    530 
                                                                    -
                                                                    531  fims::FIMSLog::fims_log->clear();
                                                                    -
                                                                    532 
                                                                    -
                                                                    533  FIMS_finalized = false;
                                                                    -
                                                                    534 }
                                                                    -
                                                                    535 
                                                                    -
                                                                    539 std::string get_log() {
                                                                    -
                                                                    540  return fims::FIMSLog::fims_log->get_log();
                                                                    -
                                                                    541 }
                                                                    -
                                                                    542 
                                                                    -
                                                                    546 std::string get_log_errors() {
                                                                    -
                                                                    547  return fims::FIMSLog::fims_log->get_errors();
                                                                    -
                                                                    548 }
                                                                    -
                                                                    549 
                                                                    -
                                                                    553 std::string get_log_warnings() {
                                                                    -
                                                                    554  return fims::FIMSLog::fims_log->get_warnings();
                                                                    -
                                                                    555 }
                                                                    -
                                                                    556 
                                                                    -
                                                                    560 std::string get_log_info() {
                                                                    -
                                                                    561  return fims::FIMSLog::fims_log->get_info();
                                                                    -
                                                                    562 }
                                                                    -
                                                                    563 
                                                                    -
                                                                    567 std::string get_log_module(const std::string& module) {
                                                                    -
                                                                    568  return fims::FIMSLog::fims_log->get_module(module);
                                                                    -
                                                                    569 }
                                                                    -
                                                                    570 
                                                                    -
                                                                    574 void write_log(bool write) {
                                                                    -
                                                                    575  FIMS_INFO_LOG("Setting FIMS write log: " + fims::to_string(write));
                                                                    -
                                                                    576  fims::FIMSLog::fims_log->write_on_exit = write;
                                                                    -
                                                                    577 }
                                                                    -
                                                                    578 
                                                                    -
                                                                    582 void set_log_path(const std::string& path) {
                                                                    -
                                                                    583  FIMS_INFO_LOG("Setting FIMS log path: " + path);
                                                                    -
                                                                    584  fims::FIMSLog::fims_log->set_path(path);
                                                                    -
                                                                    585 }
                                                                    -
                                                                    586 
                                                                    -
                                                                    590 void set_log_throw_on_error(bool throw_on_error) {
                                                                    -
                                                                    591  fims::FIMSLog::fims_log->throw_on_error = throw_on_error;
                                                                    -
                                                                    592 }
                                                                    -
                                                                    593 
                                                                    -
                                                                    597 void log_info(std::string log_entry) {
                                                                    -
                                                                    598  fims::FIMSLog::fims_log->info_message(log_entry, -1, "R_env", "R_script_entry");
                                                                    -
                                                                    599 }
                                                                    -
                                                                    600 
                                                                    -
                                                                    604 void log_warning(std::string log_entry) {
                                                                    -
                                                                    605  fims::FIMSLog::fims_log->warning_message(log_entry, -1, "R_env", "R_script_entry");
                                                                    -
                                                                    606 }
                                                                    -
                                                                    607 
                                                                    -
                                                                    614 std::string escapeQuotes(const std::string& input) {
                                                                    -
                                                                    615  std::string result = input;
                                                                    -
                                                                    616  std::string search = "\"";
                                                                    -
                                                                    617  std::string replace = "\\\"";
                                                                    -
                                                                    618 
                                                                    -
                                                                    619  // Find each occurrence of `"` and replace it with `\"`
                                                                    -
                                                                    620  size_t pos = result.find(search);
                                                                    -
                                                                    621  while (pos != std::string::npos) {
                                                                    -
                                                                    622  result.replace(pos, search.size(), replace);
                                                                    -
                                                                    623  pos = result.find(search, pos + replace.size()); // Move past the replaced position
                                                                    -
                                                                    624  }
                                                                    -
                                                                    625  return result;
                                                                    -
                                                                    626 }
                                                                    -
                                                                    627 
                                                                    -
                                                                    631 void log_error(std::string log_entry) {
                                                                    -
                                                                    632 
                                                                    -
                                                                    633  std::stringstream ss;
                                                                    -
                                                                    634  ss << "capture.output(traceback(4))";
                                                                    -
                                                                    635  SEXP expression, result;
                                                                    -
                                                                    636  ParseStatus status;
                                                                    -
                                                                    637 
                                                                    -
                                                                    638  PROTECT(expression = R_ParseVector(Rf_mkString(ss.str().c_str()), 1, &status, R_NilValue));
                                                                    -
                                                                    639  if (status != PARSE_OK) {
                                                                    -
                                                                    640  std::cout << "Error parsing expression" << std::endl;
                                                                    -
                                                                    641  UNPROTECT(1);
                                                                    -
                                                                    642  }
                                                                    -
                                                                    643  Rcpp::Rcout << "before call.";
                                                                    -
                                                                    644  PROTECT(result = Rf_eval(VECTOR_ELT(expression, 0), R_GlobalEnv));
                                                                    -
                                                                    645  Rcpp::Rcout << "after call.";
                                                                    -
                                                                    646  UNPROTECT(2);
                                                                    -
                                                                    647  std::stringstream ss_ret;
                                                                    -
                                                                    648  ss_ret << "traceback: ";
                                                                    -
                                                                    649  for (int j = 0; j < LENGTH(result); j++) {
                                                                    -
                                                                    650  std::string str(CHAR(STRING_ELT(result, j)));
                                                                    -
                                                                    651  ss_ret << escapeQuotes(str) << "\\n";
                                                                    -
                                                                    652  }
                                                                    -
                                                                    653 
                                                                    -
                                                                    654  std::string ret = ss_ret.str(); //"find error";//Rcpp::as<std::string>(result);
                                                                    -
                                                                    655 
                                                                    -
                                                                    656 
                                                                    -
                                                                    657  // Rcpp::Environment base = Rcpp::Environment::global_env();
                                                                    -
                                                                    658  // Rcpp::Function f = base["traceback"];
                                                                    -
                                                                    659  // std::string ret = Rcpp::as<std::string>(f());
                                                                    -
                                                                    660  fims::FIMSLog::fims_log->error_message(log_entry, -1, "R_env", ret.c_str());
                                                                    -
                                                                    661 }
                                                                    -
                                                                    662 
                                                                    -
                                                                    663 RCPP_EXPOSED_CLASS(Parameter)
                                                                    -
                                                                    664 RCPP_EXPOSED_CLASS(ParameterVector)
                                                                    -
                                                                    665 
                                                                    -
                                                                    666 
                                                                    -
                                                                    670 RCPP_MODULE(fims) {
                                                                    -
                                                                    671  Rcpp::function("CreateTMBModel", &CreateTMBModel);
                                                                    -
                                                                    672  Rcpp::function("SetFIMSFunctions", &SetFIMSFunctions);
                                                                    -
                                                                    673  Rcpp::function("finalize", &finalize_fims);
                                                                    -
                                                                    674  Rcpp::function("get_output", &get_output);
                                                                    -
                                                                    675  Rcpp::function("get_fixed", &get_fixed_parameters_vector);
                                                                    -
                                                                    676  Rcpp::function("get_random", &get_random_parameters_vector);
                                                                    -
                                                                    677  Rcpp::function("get_parameter_names", &get_parameter_names);
                                                                    -
                                                                    678  Rcpp::function("clear", clear);
                                                                    -
                                                                    679  Rcpp::function("get_log", get_log);
                                                                    -
                                                                    680  Rcpp::function("get_log_errors", get_log_errors);
                                                                    -
                                                                    681  Rcpp::function("get_log_warnings", get_log_warnings);
                                                                    -
                                                                    682  Rcpp::function("get_log_info", get_log_info);
                                                                    -
                                                                    683  Rcpp::function("get_log_module", get_log_module);
                                                                    -
                                                                    684  Rcpp::function("write_log", write_log);
                                                                    -
                                                                    685  Rcpp::function("set_log_path", set_log_path);
                                                                    -
                                                                    686  Rcpp::function("init_logging", init_logging);
                                                                    -
                                                                    687  Rcpp::function("set_log_throw_on_error", set_log_throw_on_error);
                                                                    -
                                                                    688  Rcpp::function("log_info", log_info);
                                                                    -
                                                                    689  Rcpp::function("log_warning", log_warning);
                                                                    -
                                                                    690  Rcpp::function("log_error", log_error);
                                                                    -
                                                                    691  Rcpp::class_<Parameter>("Parameter", "FIMS Parameter Class")
                                                                    -
                                                                    692  .constructor()
                                                                    -
                                                                    693  .constructor<double>()
                                                                    -
                                                                    694  .constructor<Parameter>()
                                                                    -
                                                                    695  .field("value", &Parameter::initial_value_m, "numeric parameter value")
                                                                    -
                                                                    696  .field("value", &Parameter::final_value_m, "numeric estimated parameter value")
                                                                    -
                                                                    697  .field("min", &Parameter::min_m, "minimum parameter value")
                                                                    -
                                                                    698  .field("max", &Parameter::max_m, "maximum parameter value")
                                                                    -
                                                                    699  .field("id", &Parameter::id_m, "unique id for parameter class")
                                                                    -
                                                                    700  .field("is_random_effect", &Parameter::is_random_effect_m, "A boolean indicating whether or not parameter is a random effect; default value is FALSE.")
                                                                    -
                                                                    701  .field("estimated", &Parameter::estimated_m, "A boolean indicating whether or not parameter is estimated; default value is FALSE.");
                                                                    -
                                                                    702 
                                                                    -
                                                                    703  Rcpp::class_<ParameterVector>("ParameterVector")
                                                                    -
                                                                    704  .constructor()
                                                                    -
                                                                    705  .constructor<size_t>()
                                                                    -
                                                                    706  .constructor<Rcpp::NumericVector, size_t>()
                                                                    -
                                                                    707  .method("get", &ParameterVector::get)
                                                                    -
                                                                    708  .method("set", &ParameterVector::set)
                                                                    -
                                                                    709  .method("show", &ParameterVector::show)
                                                                    -
                                                                    710  // .field("data", &ParameterVector::storage_m, "list where each element is a Parameter class")
                                                                    -
                                                                    711  .method("at", &ParameterVector::at, "Returns a Parameter at the indicated position given the index argument.")
                                                                    -
                                                                    712  .method("size", &ParameterVector::size, "Returns the size of the Parameter Vector.")
                                                                    -
                                                                    713  .method("resize", &ParameterVector::resize, "Resizes the Parameter Vector given the provided length argument.")
                                                                    -
                                                                    714  .method("set_all_estimable", &ParameterVector::set_all_estimable, "Sets all Parameters within vector as estimable.")
                                                                    -
                                                                    715  .method("set_all_random", &ParameterVector::set_all_random, "Sets all Parameters within vector as random.")
                                                                    -
                                                                    716  .method("fill", &ParameterVector::fill, "Sets the value of all Parameters in the vector with the provided value.")
                                                                    -
                                                                    717  .method("get_id", &ParameterVector::get_id, "Get the ID of the interface base object.");
                                                                    -
                                                                    718 
                                                                    -
                                                                    719  Rcpp::class_<BevertonHoltRecruitmentInterface>("BevertonHoltRecruitment")
                                                                    -
                                                                    720  .constructor()
                                                                    -
                                                                    721  .field("logit_steep", &BevertonHoltRecruitmentInterface::logit_steep)
                                                                    -
                                                                    722  .field("log_rzero", &BevertonHoltRecruitmentInterface::log_rzero)
                                                                    -
                                                                    723  .field("log_devs", &BevertonHoltRecruitmentInterface::log_devs)
                                                                    -
                                                                    724  .field("estimate_log_devs",
                                                                    -
                                                                    725  &BevertonHoltRecruitmentInterface::estimate_log_devs)
                                                                    -
                                                                    726  .method("get_id", &BevertonHoltRecruitmentInterface::get_id)
                                                                    -
                                                                    727  .method("evaluate", &BevertonHoltRecruitmentInterface::evaluate);
                                                                    -
                                                                    728 
                                                                    -
                                                                    729  Rcpp::class_<FleetInterface>("Fleet")
                                                                    -
                                                                    730  .constructor()
                                                                    -
                                                                    731  .field("is_survey", &FleetInterface::is_survey)
                                                                    -
                                                                    732  .field("log_q", &FleetInterface::log_q)
                                                                    -
                                                                    733  .field("log_Fmort", &FleetInterface::log_Fmort)
                                                                    -
                                                                    734  .field("nages", &FleetInterface::nages)
                                                                    -
                                                                    735  .field("nyears", &FleetInterface::nyears)
                                                                    -
                                                                    736  .field("nlengths", &FleetInterface::nlengths)
                                                                    -
                                                                    737  .field("estimate_q", &FleetInterface::estimate_q)
                                                                    -
                                                                    738  .field("random_q", &FleetInterface::random_q)
                                                                    -
                                                                    739  .field("log_expected_index", &FleetInterface::log_expected_index)
                                                                    -
                                                                    740  .field("proportion_catch_numbers_at_age", &FleetInterface::proportion_catch_numbers_at_age)
                                                                    -
                                                                    741  .field("proportion_catch_numbers_at_length", &FleetInterface::proportion_catch_numbers_at_length)
                                                                    -
                                                                    742  .field("age_length_conversion_matrix", &FleetInterface::age_length_conversion_matrix)
                                                                    -
                                                                    743  .method("SetObservedAgeCompData", &FleetInterface::SetObservedAgeCompData)
                                                                    -
                                                                    744  .method("GetObservedAgeCompDataID", &FleetInterface::GetObservedAgeCompDataID)
                                                                    -
                                                                    745  .method("SetObservedLengthCompData", &FleetInterface::SetObservedLengthCompData)
                                                                    -
                                                                    746  .method("GetObservedLengthCompDataID", &FleetInterface::GetObservedLengthCompDataID)
                                                                    -
                                                                    747  .method("SetObservedIndexData", &FleetInterface::SetObservedIndexData)
                                                                    -
                                                                    748  .method("GetObservedIndexDataID", &FleetInterface::GetObservedIndexDataID)
                                                                    -
                                                                    749  .method("SetSelectivity", &FleetInterface::SetSelectivity);
                                                                    -
                                                                    750 
                                                                    -
                                                                    751  Rcpp::class_<AgeCompDataInterface>("AgeComp")
                                                                    -
                                                                    752  .constructor<int, int>()
                                                                    -
                                                                    753  .field("age_comp_data", &AgeCompDataInterface::age_comp_data)
                                                                    -
                                                                    754  .method("get_id", &AgeCompDataInterface::get_id);
                                                                    -
                                                                    755 
                                                                    -
                                                                    756  Rcpp::class_<LengthCompDataInterface>("LengthComp")
                                                                    -
                                                                    757  .constructor<int, int>()
                                                                    -
                                                                    758  .field("length_comp_data", &LengthCompDataInterface::length_comp_data)
                                                                    -
                                                                    759  .method("get_id", &LengthCompDataInterface::get_id);
                                                                    -
                                                                    760 
                                                                    -
                                                                    761  Rcpp::class_<IndexDataInterface>("Index")
                                                                    -
                                                                    762  .constructor<int>()
                                                                    -
                                                                    763  .field("index_data", &IndexDataInterface::index_data)
                                                                    -
                                                                    764  .method("get_id", &IndexDataInterface::get_id);
                                                                    -
                                                                    765 
                                                                    -
                                                                    766  Rcpp::class_<PopulationInterface>("Population")
                                                                    -
                                                                    767  .constructor()
                                                                    -
                                                                    768  .method("get_id", &PopulationInterface::get_id)
                                                                    -
                                                                    769  .field("nages", &PopulationInterface::nages)
                                                                    -
                                                                    770  .field("nfleets", &PopulationInterface::nfleets)
                                                                    -
                                                                    771  .field("nseasons", &PopulationInterface::nseasons)
                                                                    -
                                                                    772  .field("nyears", &PopulationInterface::nyears)
                                                                    -
                                                                    773  .field("nlengths", &PopulationInterface::nlengths)
                                                                    -
                                                                    774  .field("log_M", &PopulationInterface::log_M)
                                                                    -
                                                                    775  .field("log_init_naa", &PopulationInterface::log_init_naa)
                                                                    -
                                                                    776  .field("proportion_female", &PopulationInterface::proportion_female)
                                                                    -
                                                                    777  .field("ages", &PopulationInterface::ages)
                                                                    -
                                                                    778  .field("estimate_prop_female", &PopulationInterface::estimate_prop_female)
                                                                    -
                                                                    779  .method("evaluate", &PopulationInterface::evaluate)
                                                                    -
                                                                    780  .method("SetMaturity", &PopulationInterface::SetMaturity)
                                                                    -
                                                                    781  .method("SetGrowth", &PopulationInterface::SetGrowth)
                                                                    -
                                                                    782  .method("SetRecruitment", &PopulationInterface::SetRecruitment)
                                                                    -
                                                                    783  .method("evaluate", &PopulationInterface::evaluate);
                                                                    -
                                                                    784 
                                                                    -
                                                                    785  Rcpp::class_<LogisticMaturityInterface>("LogisticMaturity")
                                                                    -
                                                                    786  .constructor()
                                                                    -
                                                                    787  .field("inflection_point", &LogisticMaturityInterface::inflection_point)
                                                                    -
                                                                    788  .field("slope", &LogisticMaturityInterface::slope)
                                                                    -
                                                                    789  .method("get_id", &LogisticMaturityInterface::get_id)
                                                                    -
                                                                    790  .method("evaluate", &LogisticMaturityInterface::evaluate);
                                                                    -
                                                                    791 
                                                                    -
                                                                    792  Rcpp::class_<LogisticSelectivityInterface>("LogisticSelectivity")
                                                                    -
                                                                    793  .constructor()
                                                                    -
                                                                    794  .field("inflection_point",
                                                                    -
                                                                    795  &LogisticSelectivityInterface::inflection_point)
                                                                    -
                                                                    796  .field("slope", &LogisticSelectivityInterface::slope)
                                                                    -
                                                                    797  .method("get_id", &LogisticSelectivityInterface::get_id)
                                                                    -
                                                                    798  .method("evaluate", &LogisticSelectivityInterface::evaluate);
                                                                    -
                                                                    799 
                                                                    -
                                                                    800  Rcpp::class_<DoubleLogisticSelectivityInterface>("DoubleLogisticSelectivity")
                                                                    -
                                                                    801  .constructor()
                                                                    -
                                                                    802  .field("inflection_point_asc",
                                                                    -
                                                                    803  &DoubleLogisticSelectivityInterface::inflection_point_asc)
                                                                    -
                                                                    804  .field("slope_asc", &DoubleLogisticSelectivityInterface::slope_asc)
                                                                    -
                                                                    805  .field("inflection_point_desc",
                                                                    -
                                                                    806  &DoubleLogisticSelectivityInterface::inflection_point_desc)
                                                                    -
                                                                    807  .field("slope_desc", &DoubleLogisticSelectivityInterface::slope_desc)
                                                                    -
                                                                    808  .method("get_id", &DoubleLogisticSelectivityInterface::get_id)
                                                                    -
                                                                    809  .method("evaluate", &DoubleLogisticSelectivityInterface::evaluate);
                                                                    -
                                                                    810 
                                                                    -
                                                                    811  Rcpp::class_<EWAAGrowthInterface>("EWAAgrowth")
                                                                    -
                                                                    812  .constructor()
                                                                    -
                                                                    813  .field("ages", &EWAAGrowthInterface::ages)
                                                                    -
                                                                    814  .field("weights", &EWAAGrowthInterface::weights)
                                                                    -
                                                                    815  .method("get_id", &EWAAGrowthInterface::get_id)
                                                                    -
                                                                    816  .method("evaluate", &EWAAGrowthInterface::evaluate);
                                                                    -
                                                                    817 
                                                                    -
                                                                    818  Rcpp::class_<DnormDistributionsInterface>("DnormDistribution")
                                                                    -
                                                                    819  .constructor()
                                                                    -
                                                                    820  .method("get_id", &DnormDistributionsInterface::get_id, "Returns a unique ID for the Dnorm distribution class.")
                                                                    -
                                                                    821  .method("evaluate", &DnormDistributionsInterface::evaluate, "Evaluates the normal distribution given input data and parameter values.")
                                                                    -
                                                                    822  .method("set_observed_data", &DnormDistributionsInterface::set_observed_data, "Accepts a unique ID for a given Data Object class to link the data with the distribution.")
                                                                    -
                                                                    823  .method("set_distribution_links", &DnormDistributionsInterface::set_distribution_links, "Accepts a unique ID for a given parameter to link the parameter with the distribution.")
                                                                    -
                                                                    824  .field("x", &DnormDistributionsInterface::x, "Input for distribution when not observations, e.g., prior or random effect.")
                                                                    -
                                                                    825  .field("expected_values", &DnormDistributionsInterface::expected_values, "Mean of the distribution.")
                                                                    -
                                                                    826  .field("log_sd", &DnormDistributionsInterface::log_sd, "The natural log of the standard deviation.");
                                                                    -
                                                                    827 
                                                                    -
                                                                    828  Rcpp::class_<DlnormDistributionsInterface>("DlnormDistribution")
                                                                    -
                                                                    829  .constructor()
                                                                    -
                                                                    830  .method("get_id", &DlnormDistributionsInterface::get_id, "Returns a unique ID for the Dnorm distribution class.")
                                                                    -
                                                                    831  .method("evaluate", &DlnormDistributionsInterface::evaluate, "Evaluates the normal distribution given input data and parameter values.")
                                                                    -
                                                                    832  .method("set_observed_data", &DlnormDistributionsInterface::set_observed_data, "Accepts a unique ID for a given Data Object class to link the data with the distribution.")
                                                                    -
                                                                    833  .method("set_distribution_links", &DlnormDistributionsInterface::set_distribution_links, "Accepts a unique ID for a given parameter to link the parameter with the distribution.")
                                                                    -
                                                                    834  .field("x", &DlnormDistributionsInterface::x, "Input for distribution when not observations, e.g., prior or random effect.")
                                                                    -
                                                                    835  .field("expected_values", &DlnormDistributionsInterface::expected_values, "Mean of the distribution on the log scale.")
                                                                    -
                                                                    836  .field("log_sd", &DlnormDistributionsInterface::log_sd, "The natural log of the standard deviation of the distribution on the log scale.");
                                                                    -
                                                                    837 
                                                                    -
                                                                    838  Rcpp::class_<DmultinomDistributionsInterface>("DmultinomDistribution")
                                                                    -
                                                                    839  .constructor()
                                                                    -
                                                                    840  .method("get_id", &DmultinomDistributionsInterface::get_id, "Returns a unique ID for the Dnorm distribution class.")
                                                                    -
                                                                    841  .method("evaluate", &DmultinomDistributionsInterface::evaluate, "Evaluates the normal distribution given input data and parameter values.")
                                                                    -
                                                                    842  .method("set_observed_data", &DmultinomDistributionsInterface::set_observed_data, "Accepts a unique ID for a given Data Object class to link the data with the distribution.")
                                                                    -
                                                                    843  .method("set_distribution_links", &DmultinomDistributionsInterface::set_distribution_links, "Accepts a unique ID for a given parameter to link the parameter with the distribution.")
                                                                    -
                                                                    844  .field("x", &DmultinomDistributionsInterface::x, "Input for distribution when not observations, e.g., prior or random effect.")
                                                                    -
                                                                    845  .field("expected_values", &DmultinomDistributionsInterface::expected_values, "numeric non-negative vector of length K, specifying the probability for the K classes.")
                                                                    -
                                                                    846  .field("dims", &DmultinomDistributionsInterface::dims, "dimension of the multivariate input, e.g., c(num rows, num cols).");
                                                                    -
                                                                    847 }
                                                                    -
                                                                    848 
                                                                    -
                                                                    849 
                                                                    -
                                                                    850 
                                                                    -
                                                                    851 #endif /* RCPP_INTERFACE_HPP */
                                                                    +
                                                                    468 #endif /* RCPP_INTERFACE_HPP */
                                                                    AgeCompDataInterface::age_comp_data
                                                                    Rcpp::NumericVector age_comp_data
                                                                    Definition: rcpp_data.hpp:65
                                                                    AgeCompDataInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_data.hpp:82
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::log_devs
                                                                    ParameterVector log_devs
                                                                    Definition: rcpp_recruitment.hpp:68
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::logit_steep
                                                                    ParameterVector logit_steep
                                                                    Definition: rcpp_recruitment.hpp:66
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::evaluate
                                                                    virtual double evaluate(double spawners, double ssbzero)
                                                                    evaluate method for child recruitment interface objects to inherit
                                                                    Definition: rcpp_recruitment.hpp:81
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::log_rzero
                                                                    ParameterVector log_rzero
                                                                    Definition: rcpp_recruitment.hpp:67
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_recruitment.hpp:79
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::estimate_log_devs
                                                                    bool estimate_log_devs
                                                                    Definition: rcpp_recruitment.hpp:69
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::evaluate_nll
                                                                    virtual double evaluate_nll()
                                                                    evaluate recruitment nll
                                                                    Definition: rcpp_recruitment.hpp:101
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::logit_steep
                                                                    Parameter logit_steep
                                                                    Definition: rcpp_recruitment.hpp:73
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::evaluate
                                                                    virtual double evaluate(double spawners, double ssbzero)
                                                                    evaluate method for child recruitment interface objects to inherit
                                                                    Definition: rcpp_recruitment.hpp:86
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::log_devs
                                                                    Rcpp::NumericVector log_devs
                                                                    Definition: rcpp_recruitment.hpp:77
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_recruitment.hpp:84
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::log_sigma_recruit
                                                                    Parameter log_sigma_recruit
                                                                    Definition: rcpp_recruitment.hpp:76
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::log_rzero
                                                                    Parameter log_rzero
                                                                    Definition: rcpp_recruitment.hpp:74
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::estimate_log_devs
                                                                    bool estimate_log_devs
                                                                    Definition: rcpp_recruitment.hpp:78
                                                                    DataInterfaceBase::live_objects
                                                                    static std::map< uint32_t, DataInterfaceBase * > live_objects
                                                                    Definition: rcpp_data.hpp:27
                                                                    DataInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_data.hpp:23
                                                                    -
                                                                    DistributionsInterfaceBase::live_objects
                                                                    static std::map< uint32_t, DistributionsInterfaceBase * > live_objects
                                                                    Definition: rcpp_distribution.hpp:27
                                                                    -
                                                                    DistributionsInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_distribution.hpp:22
                                                                    -
                                                                    DlnormDistributionsInterface::set_distribution_links
                                                                    virtual bool set_distribution_links(std::string input_type, Rcpp::IntegerVector ids)
                                                                    set_distribution_links sets pointers for data observations, random effects, or priors
                                                                    Definition: rcpp_distribution.hpp:322
                                                                    -
                                                                    DlnormDistributionsInterface::expected_values
                                                                    ParameterVector expected_values
                                                                    Definition: rcpp_distribution.hpp:289
                                                                    -
                                                                    DlnormDistributionsInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the id of the Dlnorm distributions interface class object
                                                                    Definition: rcpp_distribution.hpp:302
                                                                    -
                                                                    DlnormDistributionsInterface::evaluate
                                                                    virtual double evaluate()
                                                                    Evaluate lognormal probability density function, default returns the log of the pdf.
                                                                    Definition: rcpp_distribution.hpp:339
                                                                    -
                                                                    DlnormDistributionsInterface::log_sd
                                                                    ParameterVector log_sd
                                                                    Definition: rcpp_distribution.hpp:291
                                                                    -
                                                                    DlnormDistributionsInterface::set_observed_data
                                                                    virtual bool set_observed_data(int observed_data_id)
                                                                    Set the unique id for the Observed Data object.
                                                                    Definition: rcpp_distribution.hpp:310
                                                                    -
                                                                    DlnormDistributionsInterface::x
                                                                    ParameterVector x
                                                                    Definition: rcpp_distribution.hpp:288
                                                                    -
                                                                    DmultinomDistributionsInterface::set_distribution_links
                                                                    virtual bool set_distribution_links(std::string input_type, Rcpp::IntegerVector ids)
                                                                    set_distribution_links sets pointers for data observations, random effects, or priors
                                                                    Definition: rcpp_distribution.hpp:523
                                                                    -
                                                                    DmultinomDistributionsInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get_id method for child distribution interface objects to inherit
                                                                    Definition: rcpp_distribution.hpp:503
                                                                    -
                                                                    DmultinomDistributionsInterface::x
                                                                    ParameterVector x
                                                                    Definition: rcpp_distribution.hpp:493
                                                                    -
                                                                    DmultinomDistributionsInterface::expected_values
                                                                    ParameterVector expected_values
                                                                    Definition: rcpp_distribution.hpp:494
                                                                    -
                                                                    DmultinomDistributionsInterface::evaluate
                                                                    virtual double evaluate()
                                                                    Evaluate multinom probability density function, default returns the log of the pdf.
                                                                    Definition: rcpp_distribution.hpp:540
                                                                    -
                                                                    DmultinomDistributionsInterface::set_observed_data
                                                                    virtual bool set_observed_data(int observed_data_id)
                                                                    Set the unique id for the Observed Data object.
                                                                    Definition: rcpp_distribution.hpp:511
                                                                    -
                                                                    DmultinomDistributionsInterface::dims
                                                                    Rcpp::NumericVector dims
                                                                    Definition: rcpp_distribution.hpp:496
                                                                    -
                                                                    DnormDistributionsInterface::x
                                                                    ParameterVector x
                                                                    Definition: rcpp_distribution.hpp:90
                                                                    -
                                                                    DnormDistributionsInterface::evaluate
                                                                    virtual double evaluate()
                                                                    Evaluate normal probability density function, default returns the log of the pdf.
                                                                    Definition: rcpp_distribution.hpp:135
                                                                    -
                                                                    DnormDistributionsInterface::expected_values
                                                                    ParameterVector expected_values
                                                                    Definition: rcpp_distribution.hpp:91
                                                                    -
                                                                    DnormDistributionsInterface::set_observed_data
                                                                    virtual bool set_observed_data(int observed_data_id)
                                                                    Set the unique id for the Observed Data object.
                                                                    Definition: rcpp_distribution.hpp:107
                                                                    -
                                                                    DnormDistributionsInterface::log_sd
                                                                    ParameterVector log_sd
                                                                    Definition: rcpp_distribution.hpp:92
                                                                    -
                                                                    DnormDistributionsInterface::set_distribution_links
                                                                    virtual bool set_distribution_links(std::string input_type, Rcpp::IntegerVector ids)
                                                                    set_distribution_links sets pointers for data observations, random effects, or priors
                                                                    Definition: rcpp_distribution.hpp:118
                                                                    -
                                                                    DnormDistributionsInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get_id method for child distribution interface objects to inherit
                                                                    Definition: rcpp_distribution.hpp:97
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::slope_desc
                                                                    ParameterVector slope_desc
                                                                    Definition: rcpp_selectivity.hpp:241
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::inflection_point_desc
                                                                    ParameterVector inflection_point_desc
                                                                    Definition: rcpp_selectivity.hpp:239
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::slope_asc
                                                                    ParameterVector slope_asc
                                                                    Definition: rcpp_selectivity.hpp:238
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::evaluate
                                                                    virtual double evaluate(double x)
                                                                    evaluate the double logistic selectivity function
                                                                    Definition: rcpp_selectivity.hpp:255
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::inflection_point_asc
                                                                    ParameterVector inflection_point_asc
                                                                    Definition: rcpp_selectivity.hpp:236
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the double logistic selectivity interface
                                                                    Definition: rcpp_selectivity.hpp:249
                                                                    +
                                                                    DistributionsInterfaceBase::live_objects
                                                                    static std::map< uint32_t, DistributionsInterfaceBase * > live_objects
                                                                    Definition: rcpp_tmb_distribution.hpp:26
                                                                    +
                                                                    DistributionsInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_tmb_distribution.hpp:23
                                                                    +
                                                                    DlnormDistributionsInterface::meanlog
                                                                    Parameter meanlog
                                                                    Definition: rcpp_tmb_distribution.hpp:137
                                                                    +
                                                                    DlnormDistributionsInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the id of the Dlnorm distributions interface class object
                                                                    Definition: rcpp_tmb_distribution.hpp:147
                                                                    +
                                                                    DlnormDistributionsInterface::sdlog
                                                                    Parameter sdlog
                                                                    Definition: rcpp_tmb_distribution.hpp:138
                                                                    +
                                                                    DlnormDistributionsInterface::evaluate
                                                                    virtual double evaluate(bool do_log)
                                                                    Evaluate lognormal probability density function, default returns the log of the pdf.
                                                                    Definition: rcpp_tmb_distribution.hpp:156
                                                                    +
                                                                    DlnormDistributionsInterface::x
                                                                    Parameter x
                                                                    Definition: rcpp_tmb_distribution.hpp:136
                                                                    +
                                                                    DmultinomDistributionsInterface::evaluate
                                                                    virtual double evaluate(bool do_log)
                                                                    Evaluate multinom probability density function, default returns the log of the pdf.
                                                                    Definition: rcpp_tmb_distribution.hpp:227
                                                                    +
                                                                    DmultinomDistributionsInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get_id method for child distribution interface objects to inherit
                                                                    Definition: rcpp_tmb_distribution.hpp:218
                                                                    +
                                                                    DmultinomDistributionsInterface::p
                                                                    Rcpp::NumericVector p
                                                                    Definition: rcpp_tmb_distribution.hpp:211
                                                                    +
                                                                    DmultinomDistributionsInterface::x
                                                                    Rcpp::IntegerVector x
                                                                    Definition: rcpp_tmb_distribution.hpp:210
                                                                    +
                                                                    DnormDistributionsInterface::evaluate
                                                                    virtual double evaluate(bool do_log)
                                                                    Evaluate normal probability density function, default returns the log of the pdf.
                                                                    Definition: rcpp_tmb_distribution.hpp:83
                                                                    +
                                                                    DnormDistributionsInterface::mean
                                                                    Parameter mean
                                                                    Definition: rcpp_tmb_distribution.hpp:67
                                                                    +
                                                                    DnormDistributionsInterface::x
                                                                    Parameter x
                                                                    Definition: rcpp_tmb_distribution.hpp:66
                                                                    +
                                                                    DnormDistributionsInterface::sd
                                                                    Parameter sd
                                                                    Definition: rcpp_tmb_distribution.hpp:68
                                                                    +
                                                                    DnormDistributionsInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get_id method for child distribution interface objects to inherit
                                                                    Definition: rcpp_tmb_distribution.hpp:72
                                                                    +
                                                                    DoubleLogisticSelectivityInterface::evaluate
                                                                    virtual double evaluate(double x)
                                                                    evaluate the double logistic selectivity function
                                                                    Definition: rcpp_selectivity.hpp:158
                                                                    +
                                                                    DoubleLogisticSelectivityInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the double logistic selectivity interface
                                                                    Definition: rcpp_selectivity.hpp:152
                                                                    +
                                                                    DoubleLogisticSelectivityInterface::slope_asc
                                                                    Parameter slope_asc
                                                                    Definition: rcpp_selectivity.hpp:142
                                                                    +
                                                                    DoubleLogisticSelectivityInterface::inflection_point_asc
                                                                    Parameter inflection_point_asc
                                                                    Definition: rcpp_selectivity.hpp:140
                                                                    +
                                                                    DoubleLogisticSelectivityInterface::slope_desc
                                                                    Parameter slope_desc
                                                                    Definition: rcpp_selectivity.hpp:145
                                                                    +
                                                                    DoubleLogisticSelectivityInterface::inflection_point_desc
                                                                    Parameter inflection_point_desc
                                                                    Definition: rcpp_selectivity.hpp:143
                                                                    EWAAGrowthInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the id of the GrowthInterfaceBase object
                                                                    Definition: rcpp_growth.hpp:73
                                                                    EWAAGrowthInterface::evaluate
                                                                    virtual double evaluate(double age)
                                                                    Rcpp interface to the EWAAgrowth evaluate method you can call from R using ewaagrowth....
                                                                    Definition: rcpp_growth.hpp:95
                                                                    EWAAGrowthInterface::weights
                                                                    std::vector< double > weights
                                                                    Definition: rcpp_growth.hpp:61
                                                                    EWAAGrowthInterface::ages
                                                                    std::vector< double > ages
                                                                    Definition: rcpp_growth.hpp:62
                                                                    -
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:342
                                                                    +
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:64
                                                                    FleetInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_fleet.hpp:23
                                                                    FleetInterfaceBase::live_objects
                                                                    static std::map< uint32_t, FleetInterfaceBase * > live_objects
                                                                    Definition: rcpp_fleet.hpp:26
                                                                    -
                                                                    FleetInterface::nlengths
                                                                    int nlengths
                                                                    Definition: rcpp_fleet.hpp:66
                                                                    -
                                                                    FleetInterface::SetSelectivity
                                                                    void SetSelectivity(int selectivity_id)
                                                                    Set the unique id for the Selectivity object.
                                                                    Definition: rcpp_fleet.hpp:151
                                                                    -
                                                                    FleetInterface::estimate_q
                                                                    bool estimate_q
                                                                    Definition: rcpp_fleet.hpp:75
                                                                    -
                                                                    FleetInterface::log_expected_index
                                                                    ParameterVector log_expected_index
                                                                    Definition: rcpp_fleet.hpp:71
                                                                    -
                                                                    FleetInterface::random_q
                                                                    bool random_q
                                                                    Definition: rcpp_fleet.hpp:76
                                                                    -
                                                                    FleetInterface::proportion_catch_numbers_at_length
                                                                    ParameterVector proportion_catch_numbers_at_length
                                                                    Definition: rcpp_fleet.hpp:73
                                                                    -
                                                                    FleetInterface::nages
                                                                    int nages
                                                                    Definition: rcpp_fleet.hpp:65
                                                                    -
                                                                    FleetInterface::GetObservedIndexDataID
                                                                    int GetObservedIndexDataID()
                                                                    Return the unique id for the Observed Index Data object.
                                                                    Definition: rcpp_fleet.hpp:142
                                                                    -
                                                                    FleetInterface::proportion_catch_numbers_at_age
                                                                    ParameterVector proportion_catch_numbers_at_age
                                                                    Definition: rcpp_fleet.hpp:72
                                                                    -
                                                                    FleetInterface::GetObservedAgeCompDataID
                                                                    int GetObservedAgeCompDataID()
                                                                    Return the unique id for the Observed Age Comp Data object.
                                                                    Definition: rcpp_fleet.hpp:117
                                                                    -
                                                                    FleetInterface::log_q
                                                                    ParameterVector log_q
                                                                    Definition: rcpp_fleet.hpp:68
                                                                    -
                                                                    FleetInterface::is_survey
                                                                    bool is_survey
                                                                    Definition: rcpp_fleet.hpp:64
                                                                    -
                                                                    FleetInterface::GetObservedLengthCompDataID
                                                                    int GetObservedLengthCompDataID()
                                                                    Return the unique id for the Observed Length Comp Data object.
                                                                    Definition: rcpp_fleet.hpp:125
                                                                    -
                                                                    FleetInterface::log_Fmort
                                                                    ParameterVector log_Fmort
                                                                    Definition: rcpp_fleet.hpp:70
                                                                    -
                                                                    FleetInterface::SetObservedIndexData
                                                                    void SetObservedIndexData(int observed_index_data_id)
                                                                    Set the unique id for the Observed Index Data object.
                                                                    Definition: rcpp_fleet.hpp:134
                                                                    -
                                                                    FleetInterface::age_length_conversion_matrix
                                                                    ParameterVector age_length_conversion_matrix
                                                                    Definition: rcpp_fleet.hpp:74
                                                                    -
                                                                    FleetInterface::SetObservedLengthCompData
                                                                    void SetObservedLengthCompData(int observed_lengthcomp_data_id)
                                                                    Set the unique id for the Observed Length Comp Data object.
                                                                    Definition: rcpp_fleet.hpp:109
                                                                    -
                                                                    FleetInterface::SetObservedAgeCompData
                                                                    void SetObservedAgeCompData(int observed_agecomp_data_id)
                                                                    Set the unique id for the Observed Age Comp Data object.
                                                                    Definition: rcpp_fleet.hpp:99
                                                                    -
                                                                    FleetInterface::nyears
                                                                    int nyears
                                                                    Definition: rcpp_fleet.hpp:67
                                                                    +
                                                                    FleetInterface::random_F
                                                                    bool random_F
                                                                    Definition: rcpp_fleet.hpp:78
                                                                    +
                                                                    FleetInterface::SetSelectivity
                                                                    void SetSelectivity(int selectivity_id)
                                                                    Set the unique id for the Selectivity object.
                                                                    Definition: rcpp_fleet.hpp:130
                                                                    +
                                                                    FleetInterface::estimate_q
                                                                    bool estimate_q
                                                                    Definition: rcpp_fleet.hpp:74
                                                                    +
                                                                    FleetInterface::random_q
                                                                    bool random_q
                                                                    Definition: rcpp_fleet.hpp:77
                                                                    +
                                                                    FleetInterface::SetAgeCompLikelihood
                                                                    void SetAgeCompLikelihood(int agecomp_likelihood_id)
                                                                    Set the unique id for the Age Comp Likelihood object.
                                                                    Definition: rcpp_fleet.hpp:93
                                                                    +
                                                                    FleetInterface::nages
                                                                    int nages
                                                                    Definition: rcpp_fleet.hpp:68
                                                                    +
                                                                    FleetInterface::estimate_obs_error
                                                                    bool estimate_obs_error
                                                                    Definition: rcpp_fleet.hpp:75
                                                                    +
                                                                    FleetInterface::is_survey
                                                                    bool is_survey
                                                                    Definition: rcpp_fleet.hpp:67
                                                                    +
                                                                    FleetInterface::SetObservedIndexData
                                                                    void SetObservedIndexData(int observed_index_data_id)
                                                                    Set the unique id for the Observed Index Data object.
                                                                    Definition: rcpp_fleet.hpp:121
                                                                    +
                                                                    FleetInterface::log_Fmort
                                                                    Rcpp::NumericVector log_Fmort
                                                                    Definition: rcpp_fleet.hpp:72
                                                                    +
                                                                    FleetInterface::log_obs_error
                                                                    Rcpp::NumericVector log_obs_error
                                                                    Definition: rcpp_fleet.hpp:79
                                                                    +
                                                                    FleetInterface::SetIndexLikelihood
                                                                    void SetIndexLikelihood(int index_likelihood_id)
                                                                    Set the unique id for the Index Likelihood object.
                                                                    Definition: rcpp_fleet.hpp:102
                                                                    +
                                                                    FleetInterface::log_q
                                                                    double log_q
                                                                    Definition: rcpp_fleet.hpp:70
                                                                    +
                                                                    FleetInterface::estimate_F
                                                                    bool estimate_F
                                                                    Definition: rcpp_fleet.hpp:73
                                                                    +
                                                                    FleetInterface::SetObservedAgeCompData
                                                                    void SetObservedAgeCompData(int observed_agecomp_data_id)
                                                                    Set the unique id for the Observed Age Comp Data object.
                                                                    Definition: rcpp_fleet.hpp:112
                                                                    +
                                                                    FleetInterface::nyears
                                                                    int nyears
                                                                    Definition: rcpp_fleet.hpp:69
                                                                    GrowthInterfaceBase::live_objects
                                                                    static std::map< uint32_t, GrowthInterfaceBase * > live_objects
                                                                    Definition: rcpp_growth.hpp:29
                                                                    GrowthInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_growth.hpp:26
                                                                    -
                                                                    IndexDataInterface::index_data
                                                                    Rcpp::NumericVector index_data
                                                                    Definition: rcpp_data.hpp:230
                                                                    -
                                                                    IndexDataInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_data.hpp:244
                                                                    -
                                                                    LengthCompDataInterface::length_comp_data
                                                                    Rcpp::NumericVector length_comp_data
                                                                    Definition: rcpp_data.hpp:154
                                                                    -
                                                                    LengthCompDataInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_data.hpp:168
                                                                    -
                                                                    LogisticMaturityInterface::slope
                                                                    ParameterVector slope
                                                                    Definition: rcpp_maturity.hpp:63
                                                                    -
                                                                    LogisticMaturityInterface::inflection_point
                                                                    ParameterVector inflection_point
                                                                    Definition: rcpp_maturity.hpp:62
                                                                    -
                                                                    LogisticMaturityInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the logistic maturity interface
                                                                    Definition: rcpp_maturity.hpp:71
                                                                    -
                                                                    LogisticMaturityInterface::evaluate
                                                                    virtual double evaluate(double x)
                                                                    evaluate the logistic maturity function
                                                                    Definition: rcpp_maturity.hpp:77
                                                                    -
                                                                    LogisticSelectivityInterface::inflection_point
                                                                    ParameterVector inflection_point
                                                                    Definition: rcpp_selectivity.hpp:63
                                                                    -
                                                                    LogisticSelectivityInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the logistic selectivity interface
                                                                    Definition: rcpp_selectivity.hpp:71
                                                                    -
                                                                    LogisticSelectivityInterface::slope
                                                                    ParameterVector slope
                                                                    Definition: rcpp_selectivity.hpp:64
                                                                    -
                                                                    LogisticSelectivityInterface::evaluate
                                                                    virtual double evaluate(double x)
                                                                    evaluate the logistic selectivity function
                                                                    Definition: rcpp_selectivity.hpp:77
                                                                    -
                                                                    MaturityInterfaceBase::live_objects
                                                                    static std::map< uint32_t, MaturityInterfaceBase * > live_objects
                                                                    Definition: rcpp_maturity.hpp:28
                                                                    -
                                                                    MaturityInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_maturity.hpp:24
                                                                    -
                                                                    ParameterVector
                                                                    Rcpp representation of a Parameter vector interface between R and cpp.
                                                                    Definition: rcpp_interface_base.hpp:120
                                                                    -
                                                                    ParameterVector::show
                                                                    void show()
                                                                    Printing methods for ParameterVector.
                                                                    Definition: rcpp_interface_base.hpp:305
                                                                    -
                                                                    ParameterVector::set_all_random
                                                                    void set_all_random(bool random)
                                                                    Sets all parameters within a vector as random.
                                                                    Definition: rcpp_interface_base.hpp:262
                                                                    -
                                                                    ParameterVector::resize
                                                                    void resize(size_t size)
                                                                    resize to length "size"
                                                                    Definition: rcpp_interface_base.hpp:242
                                                                    -
                                                                    ParameterVector::size
                                                                    size_t size()
                                                                    returns vector length
                                                                    Definition: rcpp_interface_base.hpp:234
                                                                    -
                                                                    ParameterVector::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_interface_base.hpp:122
                                                                    -
                                                                    ParameterVector::at
                                                                    SEXP at(R_xlen_t pos)
                                                                    Accessor. First index is one. For calling from R.
                                                                    Definition: rcpp_interface_base.hpp:201
                                                                    -
                                                                    ParameterVector::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_interface_base.hpp:188
                                                                    -
                                                                    ParameterVector::get
                                                                    Parameter & get(size_t pos)
                                                                    Internal accessor. First index is one. For calling from R.
                                                                    Definition: rcpp_interface_base.hpp:214
                                                                    -
                                                                    ParameterVector::fill
                                                                    void fill(double value)
                                                                    Assigns the given values to all elements in the vector.
                                                                    Definition: rcpp_interface_base.hpp:273
                                                                    -
                                                                    ParameterVector::set
                                                                    void set(size_t pos, const Parameter &p)
                                                                    Internal setter.
                                                                    Definition: rcpp_interface_base.hpp:227
                                                                    -
                                                                    ParameterVector::set_all_estimable
                                                                    void set_all_estimable(bool estimable)
                                                                    Sets all parameters within a vector as estimable.
                                                                    Definition: rcpp_interface_base.hpp:251
                                                                    +
                                                                    IndexDataInterface::index_data
                                                                    Rcpp::NumericVector index_data
                                                                    Definition: rcpp_data.hpp:131
                                                                    +
                                                                    IndexDataInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_data.hpp:145
                                                                    +
                                                                    LogisticMaturityInterface::inflection_point
                                                                    Parameter inflection_point
                                                                    Definition: rcpp_maturity.hpp:64
                                                                    +
                                                                    LogisticMaturityInterface::slope
                                                                    Parameter slope
                                                                    Definition: rcpp_maturity.hpp:65
                                                                    +
                                                                    LogisticMaturityInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the logistic maturity interface
                                                                    Definition: rcpp_maturity.hpp:72
                                                                    +
                                                                    LogisticMaturityInterface::evaluate
                                                                    virtual double evaluate(double x)
                                                                    evaluate the logistic maturity function
                                                                    Definition: rcpp_maturity.hpp:78
                                                                    +
                                                                    LogisticSelectivityInterface::slope
                                                                    Parameter slope
                                                                    Definition: rcpp_selectivity.hpp:65
                                                                    +
                                                                    LogisticSelectivityInterface::inflection_point
                                                                    Parameter inflection_point
                                                                    Definition: rcpp_selectivity.hpp:64
                                                                    +
                                                                    LogisticSelectivityInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the logistic selectivity interface
                                                                    Definition: rcpp_selectivity.hpp:72
                                                                    +
                                                                    LogisticSelectivityInterface::evaluate
                                                                    virtual double evaluate(double x)
                                                                    evaluate the logistic selectivity function
                                                                    Definition: rcpp_selectivity.hpp:78
                                                                    +
                                                                    MaturityInterfaceBase::live_objects
                                                                    static std::map< uint32_t, MaturityInterfaceBase * > live_objects
                                                                    Definition: rcpp_maturity.hpp:30
                                                                    +
                                                                    MaturityInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_maturity.hpp:26
                                                                    Parameter
                                                                    RcppInterface class that defines the interface between R and C++ for parameter types.
                                                                    Definition: rcpp_interface_base.hpp:26
                                                                    -
                                                                    Parameter::initial_value_m
                                                                    double initial_value_m
                                                                    Definition: rcpp_interface_base.hpp:30
                                                                    -
                                                                    Parameter::final_value_m
                                                                    double final_value_m
                                                                    Definition: rcpp_interface_base.hpp:31
                                                                    -
                                                                    Parameter::estimated_m
                                                                    bool estimated_m
                                                                    Definition: rcpp_interface_base.hpp:38
                                                                    -
                                                                    Parameter::id_m
                                                                    uint32_t id_m
                                                                    Definition: rcpp_interface_base.hpp:29
                                                                    -
                                                                    Parameter::is_random_effect_m
                                                                    bool is_random_effect_m
                                                                    Definition: rcpp_interface_base.hpp:36
                                                                    -
                                                                    Parameter::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_interface_base.hpp:28
                                                                    -
                                                                    Parameter::max_m
                                                                    double max_m
                                                                    Definition: rcpp_interface_base.hpp:34
                                                                    -
                                                                    Parameter::min_m
                                                                    double min_m
                                                                    Definition: rcpp_interface_base.hpp:32
                                                                    +
                                                                    Parameter::estimated_m
                                                                    bool estimated_m
                                                                    Definition: rcpp_interface_base.hpp:35
                                                                    +
                                                                    Parameter::value_m
                                                                    double value_m
                                                                    Definition: rcpp_interface_base.hpp:28
                                                                    +
                                                                    Parameter::is_random_effect_m
                                                                    bool is_random_effect_m
                                                                    Definition: rcpp_interface_base.hpp:33
                                                                    +
                                                                    Parameter::max_m
                                                                    double max_m
                                                                    Definition: rcpp_interface_base.hpp:31
                                                                    +
                                                                    Parameter::min_m
                                                                    double min_m
                                                                    Definition: rcpp_interface_base.hpp:29
                                                                    PopulationInterfaceBase::live_objects
                                                                    static std::map< uint32_t, PopulationInterfaceBase * > live_objects
                                                                    Definition: rcpp_population.hpp:28
                                                                    PopulationInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_population.hpp:24
                                                                    -
                                                                    PopulationInterface::SetMaturity
                                                                    void SetMaturity(uint32_t maturity_id)
                                                                    Set the unique id for the Maturity object.
                                                                    Definition: rcpp_population.hpp:95
                                                                    -
                                                                    PopulationInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get_id method for child classes to inherit
                                                                    Definition: rcpp_population.hpp:88
                                                                    +
                                                                    PopulationInterface::SetMaturity
                                                                    void SetMaturity(uint32_t maturity_id)
                                                                    Set the unique id for the Maturity object.
                                                                    Definition: rcpp_population.hpp:83
                                                                    +
                                                                    PopulationInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get_id method for child classes to inherit
                                                                    Definition: rcpp_population.hpp:76
                                                                    PopulationInterface::nyears
                                                                    uint32_t nyears
                                                                    Definition: rcpp_population.hpp:59
                                                                    -
                                                                    PopulationInterface::log_init_naa
                                                                    ParameterVector log_init_naa
                                                                    Definition: rcpp_population.hpp:65
                                                                    +
                                                                    PopulationInterface::log_init_naa
                                                                    Rcpp::NumericVector log_init_naa
                                                                    Definition: rcpp_population.hpp:64
                                                                    PopulationInterface::nages
                                                                    uint32_t nages
                                                                    Definition: rcpp_population.hpp:56
                                                                    PopulationInterface::estimate_prop_female
                                                                    bool estimate_prop_female
                                                                    Definition: rcpp_population.hpp:70
                                                                    PopulationInterface::nfleets
                                                                    uint32_t nfleets
                                                                    Definition: rcpp_population.hpp:57
                                                                    PopulationInterface::nseasons
                                                                    uint32_t nseasons
                                                                    Definition: rcpp_population.hpp:58
                                                                    -
                                                                    PopulationInterface::SetRecruitment
                                                                    void SetRecruitment(uint32_t recruitment_id)
                                                                    Set the unique id for the Maturity object.
                                                                    Definition: rcpp_population.hpp:109
                                                                    -
                                                                    PopulationInterface::evaluate
                                                                    virtual void evaluate()
                                                                    evaluate the population function
                                                                    Definition: rcpp_population.hpp:114
                                                                    -
                                                                    PopulationInterface::log_M
                                                                    ParameterVector log_M
                                                                    Definition: rcpp_population.hpp:64
                                                                    -
                                                                    PopulationInterface::proportion_female
                                                                    Rcpp::NumericVector proportion_female
                                                                    Definition: rcpp_population.hpp:68
                                                                    -
                                                                    PopulationInterface::ages
                                                                    Rcpp::NumericVector ages
                                                                    Definition: rcpp_population.hpp:67
                                                                    -
                                                                    PopulationInterface::SetGrowth
                                                                    void SetGrowth(uint32_t growth_id)
                                                                    Set the unique id for the growth object.
                                                                    Definition: rcpp_population.hpp:102
                                                                    -
                                                                    PopulationInterface::nlengths
                                                                    uint32_t nlengths
                                                                    Definition: rcpp_population.hpp:60
                                                                    -
                                                                    RecruitmentInterfaceBase::live_objects
                                                                    static std::map< uint32_t, RecruitmentInterfaceBase * > live_objects
                                                                    Definition: rcpp_recruitment.hpp:27
                                                                    -
                                                                    RecruitmentInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_recruitment.hpp:24
                                                                    -
                                                                    SelectivityInterfaceBase::live_objects
                                                                    static std::map< uint32_t, SelectivityInterfaceBase * > live_objects
                                                                    Definition: rcpp_selectivity.hpp:28
                                                                    -
                                                                    SelectivityInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_selectivity.hpp:24
                                                                    -
                                                                    fims::FIMSLog::fims_log
                                                                    static std::shared_ptr< FIMSLog > fims_log
                                                                    Definition: def.hpp:171
                                                                    -
                                                                    fims::JsonParser::PrettyFormatJSON
                                                                    static std::string PrettyFormatJSON(const std::string &json)
                                                                    Formats a JSON string.
                                                                    Definition: fims_json.hpp:145
                                                                    -
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:135
                                                                    -
                                                                    fims_model::Model::GetInstance
                                                                    static std::shared_ptr< Model< Type > > GetInstance()
                                                                    Definition: model.hpp:44
                                                                    -
                                                                    FIMS_INFO_LOG
                                                                    #define FIMS_INFO_LOG(MESSAGE)
                                                                    Definition: def.hpp:557
                                                                    -
                                                                    FIMS_ERROR_LOG
                                                                    #define FIMS_ERROR_LOG(MESSAGE)
                                                                    Definition: def.hpp:561
                                                                    -
                                                                    rcpp_distribution.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    rcpp_fleet.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    rcpp_growth.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    set_log_path
                                                                    void set_log_path(const std::string &path)
                                                                    Definition: rcpp_interface.hpp:582
                                                                    -
                                                                    get_output
                                                                    std::string get_output()
                                                                    Extracts derived quantities from model objects.
                                                                    Definition: rcpp_interface.hpp:336
                                                                    -
                                                                    get_log_warnings
                                                                    std::string get_log_warnings()
                                                                    Definition: rcpp_interface.hpp:553
                                                                    -
                                                                    escapeQuotes
                                                                    std::string escapeQuotes(const std::string &input)
                                                                    Escape quotations.
                                                                    Definition: rcpp_interface.hpp:614
                                                                    -
                                                                    get_log_module
                                                                    std::string get_log_module(const std::string &module)
                                                                    Definition: rcpp_interface.hpp:567
                                                                    -
                                                                    CreateTMBModel
                                                                    bool CreateTMBModel()
                                                                    Create the TMB model object and add interface objects to it.
                                                                    Definition: rcpp_interface.hpp:74
                                                                    -
                                                                    get_log_info
                                                                    std::string get_log_info()
                                                                    Definition: rcpp_interface.hpp:560
                                                                    -
                                                                    log_error
                                                                    void log_error(std::string log_entry)
                                                                    Definition: rcpp_interface.hpp:631
                                                                    -
                                                                    finalize_fims_deprecated
                                                                    void finalize_fims_deprecated(SEXP tmb_obj=R_NilValue)
                                                                    Finalizes a FIMS run.
                                                                    Definition: rcpp_interface.hpp:275
                                                                    -
                                                                    SetFIMSFunctions
                                                                    void SetFIMSFunctions(SEXP fn, SEXP gr)
                                                                    TODO: provide a brief description.
                                                                    Definition: rcpp_interface.hpp:113
                                                                    -
                                                                    FIMS_gradient_function
                                                                    SEXP FIMS_gradient_function
                                                                    TODO: provide a brief description.
                                                                    Definition: rcpp_interface.hpp:32
                                                                    -
                                                                    FIMS_finalized
                                                                    bool FIMS_finalized
                                                                    Sets FIMS_finalized to false as the default.
                                                                    Definition: rcpp_interface.hpp:57
                                                                    -
                                                                    FIMS_function_gradient
                                                                    Rcpp::NumericVector FIMS_function_gradient
                                                                    TODO: provide a brief description.
                                                                    Definition: rcpp_interface.hpp:47
                                                                    -
                                                                    FIMS_mgc_value
                                                                    double FIMS_mgc_value
                                                                    TODO: provide a brief description.
                                                                    Definition: rcpp_interface.hpp:52
                                                                    -
                                                                    FIMS_function_value
                                                                    double FIMS_function_value
                                                                    TODO: provide a brief description.
                                                                    Definition: rcpp_interface.hpp:37
                                                                    -
                                                                    get_log_errors
                                                                    std::string get_log_errors()
                                                                    Definition: rcpp_interface.hpp:546
                                                                    -
                                                                    log_warning
                                                                    void log_warning(std::string log_entry)
                                                                    Definition: rcpp_interface.hpp:604
                                                                    -
                                                                    FIMS_objective_function
                                                                    SEXP FIMS_objective_function
                                                                    TODO: provide a brief description.
                                                                    Definition: rcpp_interface.hpp:27
                                                                    -
                                                                    get_parameter_names
                                                                    Rcpp::List get_parameter_names(Rcpp::List pars)
                                                                    Get the parameter names object.
                                                                    Definition: rcpp_interface.hpp:420
                                                                    -
                                                                    set_log_throw_on_error
                                                                    void set_log_throw_on_error(bool throw_on_error)
                                                                    Definition: rcpp_interface.hpp:590
                                                                    -
                                                                    RCPP_MODULE
                                                                    RCPP_MODULE(fims)
                                                                    Construct a new rcpp module object.
                                                                    Definition: rcpp_interface.hpp:670
                                                                    -
                                                                    FIMS_function_parameters
                                                                    Rcpp::NumericVector FIMS_function_parameters
                                                                    TODO: provide a brief description.
                                                                    Definition: rcpp_interface.hpp:42
                                                                    -
                                                                    get_log
                                                                    std::string get_log()
                                                                    Definition: rcpp_interface.hpp:539
                                                                    -
                                                                    finalize_fims
                                                                    void finalize_fims(Rcpp::Nullable< Rcpp::List > obj=R_NilValue, Rcpp::Nullable< Rcpp::List > opt=R_NilValue)
                                                                    Finalizes a FIMS model by updating the parameter set. This function evaluates the objective function ...
                                                                    Definition: rcpp_interface.hpp:174
                                                                    -
                                                                    finalize_objects
                                                                    void finalize_objects(Rcpp::NumericVector p)
                                                                    Loops through the Rcpp Interface objects and extracts derived quantities.Updates parameter estimates ...
                                                                    Definition: rcpp_interface.hpp:122
                                                                    -
                                                                    clear_internal
                                                                    void clear_internal()
                                                                    Clears the internal objects.
                                                                    Definition: rcpp_interface.hpp:437
                                                                    -
                                                                    log_info
                                                                    void log_info(std::string log_entry)
                                                                    Definition: rcpp_interface.hpp:597
                                                                    -
                                                                    clear
                                                                    void clear()
                                                                    Definition: rcpp_interface.hpp:448
                                                                    -
                                                                    get_fixed_parameters_vector
                                                                    Rcpp::NumericVector get_fixed_parameters_vector()
                                                                    Get the fixed parameters vector object.
                                                                    Definition: rcpp_interface.hpp:381
                                                                    -
                                                                    get_random_parameters_vector
                                                                    Rcpp::NumericVector get_random_parameters_vector()
                                                                    Get the random parameters vector object.
                                                                    Definition: rcpp_interface.hpp:400
                                                                    -
                                                                    write_log
                                                                    void write_log(bool write)
                                                                    Definition: rcpp_interface.hpp:574
                                                                    -
                                                                    init_logging
                                                                    void init_logging()
                                                                    Definition: rcpp_interface.hpp:62
                                                                    -
                                                                    rcpp_maturity.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    rcpp_natural_mortality.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    rcpp_population.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    rcpp_recruitment.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    rcpp_selectivity.hpp
                                                                    TODO: provide a brief description.
                                                                    +
                                                                    PopulationInterface::SetRecruitment
                                                                    void SetRecruitment(uint32_t recruitment_id)
                                                                    Set the unique id for the Maturity object.
                                                                    Definition: rcpp_population.hpp:97
                                                                    +
                                                                    PopulationInterface::evaluate
                                                                    virtual void evaluate()
                                                                    evaluate the population function
                                                                    Definition: rcpp_population.hpp:102
                                                                    +
                                                                    PopulationInterface::proportion_female
                                                                    Rcpp::NumericVector proportion_female
                                                                    Definition: rcpp_population.hpp:66
                                                                    +
                                                                    PopulationInterface::estimate_initNAA
                                                                    bool estimate_initNAA
                                                                    Definition: rcpp_population.hpp:69
                                                                    +
                                                                    PopulationInterface::ages
                                                                    Rcpp::NumericVector ages
                                                                    Definition: rcpp_population.hpp:65
                                                                    +
                                                                    PopulationInterface::estimate_M
                                                                    bool estimate_M
                                                                    Definition: rcpp_population.hpp:68
                                                                    +
                                                                    PopulationInterface::SetGrowth
                                                                    void SetGrowth(uint32_t growth_id)
                                                                    Set the unique id for the growth object.
                                                                    Definition: rcpp_population.hpp:90
                                                                    +
                                                                    PopulationInterface::log_M
                                                                    Rcpp::NumericVector log_M
                                                                    Definition: rcpp_population.hpp:63
                                                                    +
                                                                    RecruitmentInterfaceBase::live_objects
                                                                    static std::map< uint32_t, RecruitmentInterfaceBase * > live_objects
                                                                    Definition: rcpp_recruitment.hpp:28
                                                                    +
                                                                    RecruitmentInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_recruitment.hpp:25
                                                                    +
                                                                    SelectivityInterfaceBase::live_objects
                                                                    static std::map< uint32_t, SelectivityInterfaceBase * > live_objects
                                                                    Definition: rcpp_selectivity.hpp:29
                                                                    +
                                                                    SelectivityInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_selectivity.hpp:25
                                                                    +
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:126
                                                                    +
                                                                    MODEL_LOG
                                                                    std::ofstream MODEL_LOG("logs/model.log")
                                                                    +
                                                                    GROWTH_LOG
                                                                    std::ofstream GROWTH_LOG("logs/growth.log")
                                                                    +
                                                                    ERROR_LOG
                                                                    std::ofstream ERROR_LOG("logs/error.log")
                                                                    +
                                                                    SELECTIVITY_LOG
                                                                    std::ofstream SELECTIVITY_LOG("logs/selectivity.log")
                                                                    +
                                                                    DATA_LOG
                                                                    std::ofstream DATA_LOG("logs/data.log")
                                                                    +
                                                                    FLEET_LOG
                                                                    std::ofstream FLEET_LOG("logs/fleet.log")
                                                                    +
                                                                    DEBUG_LOG
                                                                    std::ofstream DEBUG_LOG("logs/debug/debug.log")
                                                                    +
                                                                    MATURITY_LOG
                                                                    std::ofstream MATURITY_LOG("logs/maturity.log")
                                                                    +
                                                                    FIMS_LOG
                                                                    std::ofstream FIMS_LOG("logs/fims.log")
                                                                    +
                                                                    RECRUITMENT_LOG
                                                                    std::ofstream RECRUITMENT_LOG("logs/recruitment.log")
                                                                    +
                                                                    POPULATION_LOG
                                                                    std::ofstream POPULATION_LOG("logs/population.log")
                                                                    +
                                                                    INFO_LOG
                                                                    std::ofstream INFO_LOG("logs/info.log")
                                                                    diff --git a/docs/rcpp__interface__base_8hpp_source.html b/docs/rcpp__interface__base_8hpp_source.html index 66cbaa2..f73c522 100644 --- a/docs/rcpp__interface__base_8hpp_source.html +++ b/docs/rcpp__interface__base_8hpp_source.html @@ -76,11 +76,17 @@
                                                                    rcpp_interface_base.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    8 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_INTERFACE_BASE_HPP
                                                                    -
                                                                    9 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_INTERFACE_BASE_HPP
                                                                    -
                                                                    10 
                                                                    -
                                                                    11 #include <RcppCommon.h>
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: rcpp_interface_base.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    5  * Fisheries Integrated Modeling System project. See LICENSE file
                                                                    +
                                                                    6  * for reuse information.
                                                                    +
                                                                    7  *
                                                                    +
                                                                    8  */
                                                                    +
                                                                    9 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_INTERFACE_BASE_HPP
                                                                    +
                                                                    10 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_INTERFACE_BASE_HPP
                                                                    +
                                                                    11 
                                                                    12 #include <map>
                                                                    13 #include <vector>
                                                                    14 
                                                                    @@ -93,267 +99,48 @@
                                                                    21 
                                                                    26 class Parameter {
                                                                    27  public:
                                                                    -
                                                                    28  static uint32_t id_g;
                                                                    -
                                                                    29  uint32_t id_m;
                                                                    -
                                                                    30  double initial_value_m = 0.0;
                                                                    -
                                                                    31  double final_value_m = 0.0;
                                                                    -
                                                                    32  double min_m =
                                                                    -
                                                                    33  -std::numeric_limits<double>::infinity();
                                                                    -
                                                                    34  double max_m =
                                                                    -
                                                                    35  std::numeric_limits<double>::infinity();
                                                                    -
                                                                    36  bool is_random_effect_m = false;
                                                                    -
                                                                    38  bool estimated_m =
                                                                    -
                                                                    39  false;
                                                                    -
                                                                    41  bool random_m =
                                                                    -
                                                                    42  false;
                                                                    -
                                                                    48  Parameter(double value, double min, double max, bool estimated)
                                                                    -
                                                                    49  : id_m(Parameter::id_g++), initial_value_m(value), min_m(min), max_m(max), estimated_m(estimated) {}
                                                                    +
                                                                    28  double value_m;
                                                                    +
                                                                    29  double min_m =
                                                                    +
                                                                    30  std::numeric_limits<double>::min();
                                                                    +
                                                                    31  double max_m =
                                                                    +
                                                                    32  std::numeric_limits<double>::max();
                                                                    +
                                                                    33  bool is_random_effect_m = false;
                                                                    +
                                                                    35  bool estimated_m =
                                                                    +
                                                                    36  false;
                                                                    +
                                                                    42  Parameter(double value, double min, double max, bool estimated)
                                                                    +
                                                                    43  : value_m(value), min_m(min), max_m(max), estimated_m(estimated) {}
                                                                    +
                                                                    44 
                                                                    +
                                                                    49  Parameter(double value) { value_m = value; }
                                                                    50 
                                                                    -
                                                                    54  Parameter(const Parameter& other) :
                                                                    -
                                                                    55  id_m(other.id_m), initial_value_m(other.initial_value_m),
                                                                    -
                                                                    56  final_value_m(other.final_value_m),
                                                                    -
                                                                    57  min_m(other.min_m), max_m(other.max_m),
                                                                    -
                                                                    58  is_random_effect_m(other.is_random_effect_m),
                                                                    -
                                                                    59  estimated_m(other.estimated_m),
                                                                    -
                                                                    60  random_m(other.random_m) {
                                                                    -
                                                                    61  }
                                                                    -
                                                                    62 
                                                                    -
                                                                    66  Parameter& operator=(const Parameter& right) {
                                                                    -
                                                                    67  // Check for self-assignment!
                                                                    -
                                                                    68  if (this == &right) // Same object?
                                                                    -
                                                                    69  return *this; // Yes, so skip assignment, and just return *this.
                                                                    -
                                                                    70  this->id_m = right.id_m;
                                                                    -
                                                                    71  this->initial_value_m = right.initial_value_m;
                                                                    -
                                                                    72  this->estimated_m = right.estimated_m;
                                                                    -
                                                                    73  this->random_m = right.random_m;
                                                                    -
                                                                    74  this->min_m = right.min_m;
                                                                    -
                                                                    75  this->max_m = right.max_m;
                                                                    -
                                                                    76  this->is_random_effect_m = right.is_random_effect_m;
                                                                    -
                                                                    77  return *this;
                                                                    -
                                                                    78  }
                                                                    -
                                                                    79 
                                                                    -
                                                                    80 
                                                                    -
                                                                    81 
                                                                    -
                                                                    86  Parameter(double value) {
                                                                    -
                                                                    87  initial_value_m = value;
                                                                    -
                                                                    88  id_m = Parameter::id_g++;
                                                                    -
                                                                    89  }
                                                                    -
                                                                    90 
                                                                    -
                                                                    95  Parameter() {
                                                                    -
                                                                    96  initial_value_m = 0;
                                                                    -
                                                                    97  id_m = Parameter::id_g++;}
                                                                    -
                                                                    98 };
                                                                    -
                                                                    99 
                                                                    -
                                                                    100 uint32_t Parameter::id_g = 0;
                                                                    -
                                                                    101 
                                                                    -
                                                                    109 std::ostream& operator<<(std::ostream& out, const Parameter& p) {
                                                                    -
                                                                    110  out << "Parameter:{" << "id:" << p.id_m << ",\nvalue:" << p.initial_value_m
                                                                    -
                                                                    111  << ",\nestimated_value:" << p.final_value_m << ",\nmin:"
                                                                    -
                                                                    112  << p.min_m << ",\nmax:" << p.max_m << ",\nestimated:" << p.estimated_m << "\n}";
                                                                    -
                                                                    113  return out;
                                                                    -
                                                                    114 }
                                                                    -
                                                                    115 
                                                                    -
                                                                    120 class ParameterVector{
                                                                    -
                                                                    121 public:
                                                                    -
                                                                    122  static uint32_t id_g;
                                                                    -
                                                                    123  std::shared_ptr<std::vector<Parameter> > storage_m;
                                                                    -
                                                                    124  uint32_t id_m;
                                                                    -
                                                                    129  ParameterVector(){
                                                                    -
                                                                    130  this->id_m = ParameterVector::id_g++;
                                                                    -
                                                                    131  this->storage_m = std::make_shared<std::vector<Parameter> >();
                                                                    -
                                                                    132  // Parameter p;
                                                                    -
                                                                    133  this->storage_m->resize(1); //push_back(Rcpp::wrap(p));
                                                                    -
                                                                    134  }
                                                                    -
                                                                    135 
                                                                    -
                                                                    136 
                                                                    -
                                                                    140  ParameterVector(const ParameterVector& other) :
                                                                    -
                                                                    141  storage_m(other.storage_m), id_m(other.id_m) {
                                                                    -
                                                                    142  }
                                                                    -
                                                                    143 
                                                                    -
                                                                    147  ParameterVector(size_t size ){
                                                                    -
                                                                    148 
                                                                    -
                                                                    149  this->id_m = ParameterVector::id_g++;
                                                                    -
                                                                    150  this->storage_m = std::make_shared<std::vector<Parameter> >();
                                                                    -
                                                                    151  this->storage_m->resize(size);
                                                                    -
                                                                    152  for (size_t i = 0; i < size; i++) {
                                                                    -
                                                                    153  storage_m->at(i) = Parameter();
                                                                    -
                                                                    154  }
                                                                    -
                                                                    155  }
                                                                    -
                                                                    156 
                                                                    -
                                                                    162  ParameterVector(Rcpp::NumericVector x, size_t size){
                                                                    -
                                                                    163  this->id_m = ParameterVector::id_g++;
                                                                    -
                                                                    164  this->storage_m = std::make_shared<std::vector<Parameter> >();
                                                                    -
                                                                    165  this->resize(size);
                                                                    -
                                                                    166  for (size_t i = 0; i < size; i++) {
                                                                    -
                                                                    167  storage_m->at(i).initial_value_m = x[i];
                                                                    -
                                                                    168  }
                                                                    -
                                                                    169  }
                                                                    -
                                                                    170 
                                                                    -
                                                                    175  ParameterVector(const fims::Vector<double>& v) {
                                                                    -
                                                                    176  this->id_m = ParameterVector::id_g++;
                                                                    -
                                                                    177  this->storage_m = std::make_shared<std::vector<Parameter> >();
                                                                    -
                                                                    178  this->storage_m->resize(v.size());
                                                                    -
                                                                    179  for (size_t i = 0; i < v.size(); i++) {
                                                                    -
                                                                    180  storage_m->at(i).initial_value_m = v[i];
                                                                    -
                                                                    181  }
                                                                    -
                                                                    182 
                                                                    -
                                                                    183  }
                                                                    -
                                                                    184 
                                                                    -
                                                                    188  virtual uint32_t get_id() { return this->id_m; }
                                                                    -
                                                                    189 
                                                                    -
                                                                    194  inline Parameter& operator[](size_t pos) {
                                                                    -
                                                                    195  return this->storage_m->at(pos); }
                                                                    -
                                                                    196 
                                                                    -
                                                                    201  SEXP at(R_xlen_t pos){
                                                                    -
                                                                    202  if (pos == 0 || pos > this->storage_m->size()) {
                                                                    -
                                                                    203  Rcpp::Rcout << "ParameterVector: Index out of range.\n";
                                                                    -
                                                                    204  FIMS_ERROR_LOG(fims::to_string(pos) + "!<" + fims::to_string(this->size()));
                                                                    -
                                                                    205  return NULL;
                                                                    -
                                                                    206  }
                                                                    -
                                                                    207  return Rcpp::wrap(this->storage_m->at(pos - 1));
                                                                    -
                                                                    208  }
                                                                    -
                                                                    209 
                                                                    -
                                                                    214  Parameter& get(size_t pos) {
                                                                    -
                                                                    215  if (pos >= this->storage_m->size()) {
                                                                    -
                                                                    216  std::cout << "ParameterVector: Index out of range.\n";
                                                                    -
                                                                    217  throw std::invalid_argument("ParameterVector: Index out of range");
                                                                    -
                                                                    218  }
                                                                    -
                                                                    219  return (this->storage_m->at(pos));
                                                                    -
                                                                    220  }
                                                                    -
                                                                    221 
                                                                    -
                                                                    227  void set(size_t pos, const Parameter& p) {
                                                                    -
                                                                    228  this->storage_m->at(pos) = p;
                                                                    -
                                                                    229  }
                                                                    -
                                                                    230 
                                                                    -
                                                                    234  size_t size() {
                                                                    -
                                                                    235  return this->storage_m->size();
                                                                    -
                                                                    236  }
                                                                    -
                                                                    237 
                                                                    -
                                                                    242  void resize(size_t size) {
                                                                    -
                                                                    243  this->storage_m->resize(size);
                                                                    -
                                                                    244  }
                                                                    -
                                                                    245 
                                                                    -
                                                                    251  void set_all_estimable(bool estimable){
                                                                    -
                                                                    252  for (size_t i = 0; i < this->storage_m->size(); i++) {
                                                                    -
                                                                    253  storage_m->at(i).estimated_m = estimable;
                                                                    -
                                                                    254  }
                                                                    -
                                                                    255  }
                                                                    -
                                                                    256 
                                                                    -
                                                                    262  void set_all_random(bool random){
                                                                    -
                                                                    263  for (size_t i = 0; i < this->storage_m->size(); i++) {
                                                                    -
                                                                    264  storage_m->at(i).random_m = random;
                                                                    -
                                                                    265  }
                                                                    -
                                                                    266  }
                                                                    -
                                                                    267 
                                                                    -
                                                                    273  void fill(double value){
                                                                    -
                                                                    274  for (size_t i = 0; i < this->storage_m->size(); i++) {
                                                                    -
                                                                    275  storage_m->at(i).initial_value_m = value;
                                                                    -
                                                                    276  }
                                                                    -
                                                                    277  }
                                                                    -
                                                                    278 
                                                                    -
                                                                    284  void fill_min(double value){
                                                                    -
                                                                    285  for (size_t i = 0; i < this->storage_m->size(); i++) {
                                                                    -
                                                                    286  storage_m->at(i).min_m = value;
                                                                    -
                                                                    287  }
                                                                    -
                                                                    288  }
                                                                    -
                                                                    289 
                                                                    -
                                                                    295  void fill_max(double value){
                                                                    -
                                                                    296  for (size_t i = 0; i < this->storage_m->size(); i++) {
                                                                    -
                                                                    297  storage_m->at(i).max_m = value;
                                                                    -
                                                                    298  }
                                                                    -
                                                                    299  }
                                                                    -
                                                                    300 
                                                                    -
                                                                    305  void show() {
                                                                    -
                                                                    306  std::cout << this->storage_m->data() << "\n";
                                                                    -
                                                                    307 
                                                                    -
                                                                    308  for (size_t i = 0; i < this->storage_m->size(); i++) {
                                                                    -
                                                                    309  std::cout << storage_m->at(i) << " ";
                                                                    -
                                                                    310  }
                                                                    -
                                                                    311  }
                                                                    -
                                                                    312 
                                                                    -
                                                                    313 };
                                                                    -
                                                                    314 uint32_t ParameterVector::id_g = 0;
                                                                    -
                                                                    315 
                                                                    -
                                                                    323 std::ostream& operator<<(std::ostream& out, ParameterVector& v) {
                                                                    -
                                                                    324  out << "[";
                                                                    -
                                                                    325  size_t size = v.size();
                                                                    -
                                                                    326  for (size_t i = 0; i < size - 1; i++) {
                                                                    -
                                                                    327  out << v[i] << ", ";
                                                                    -
                                                                    328  }
                                                                    -
                                                                    329  out << v[size - 1] << "]";
                                                                    -
                                                                    330  return out;
                                                                    -
                                                                    331 }
                                                                    -
                                                                    332 
                                                                    -
                                                                    336 class FIMSRcppInterfaceBase {
                                                                    -
                                                                    337 public:
                                                                    -
                                                                    338 
                                                                    -
                                                                    339  bool finalized = false;
                                                                    -
                                                                    341  static std::vector<FIMSRcppInterfaceBase *>
                                                                    -
                                                                    342  fims_interface_objects;
                                                                    -
                                                                    345  virtual bool add_to_fims_tmb() {
                                                                    -
                                                                    346  std::cout << "fims_rcpp_interface_base::add_to_fims_tmb(): Not yet "
                                                                    -
                                                                    347  "implemented.\n";
                                                                    -
                                                                    348  return false;
                                                                    -
                                                                    349  }
                                                                    -
                                                                    354  virtual void finalize() {
                                                                    -
                                                                    355 
                                                                    -
                                                                    356  }
                                                                    -
                                                                    357 
                                                                    -
                                                                    361  virtual std::string to_json() {
                                                                    -
                                                                    362  return "";
                                                                    -
                                                                    363  }
                                                                    -
                                                                    364 };
                                                                    -
                                                                    365 std::vector<FIMSRcppInterfaceBase *>
                                                                    -
                                                                    366  FIMSRcppInterfaceBase::fims_interface_objects;
                                                                    -
                                                                    367 
                                                                    -
                                                                    368 #endif
                                                                    -
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:336
                                                                    -
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:342
                                                                    -
                                                                    FIMSRcppInterfaceBase::finalized
                                                                    bool finalized
                                                                    Definition: rcpp_interface_base.hpp:339
                                                                    -
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:345
                                                                    -
                                                                    FIMSRcppInterfaceBase::to_json
                                                                    virtual std::string to_json()
                                                                    Convert the data to json representation for the output.
                                                                    Definition: rcpp_interface_base.hpp:361
                                                                    -
                                                                    FIMSRcppInterfaceBase::finalize
                                                                    virtual void finalize()
                                                                    finalize function. Extracts derived quantities back to the Rcpp interface object from the Information...
                                                                    Definition: rcpp_interface_base.hpp:354
                                                                    -
                                                                    ParameterVector
                                                                    Rcpp representation of a Parameter vector interface between R and cpp.
                                                                    Definition: rcpp_interface_base.hpp:120
                                                                    -
                                                                    ParameterVector::ParameterVector
                                                                    ParameterVector(size_t size)
                                                                    vector constructor
                                                                    Definition: rcpp_interface_base.hpp:147
                                                                    -
                                                                    ParameterVector::show
                                                                    void show()
                                                                    Printing methods for ParameterVector.
                                                                    Definition: rcpp_interface_base.hpp:305
                                                                    -
                                                                    ParameterVector::set_all_random
                                                                    void set_all_random(bool random)
                                                                    Sets all parameters within a vector as random.
                                                                    Definition: rcpp_interface_base.hpp:262
                                                                    -
                                                                    ParameterVector::resize
                                                                    void resize(size_t size)
                                                                    resize to length "size"
                                                                    Definition: rcpp_interface_base.hpp:242
                                                                    -
                                                                    ParameterVector::size
                                                                    size_t size()
                                                                    returns vector length
                                                                    Definition: rcpp_interface_base.hpp:234
                                                                    -
                                                                    ParameterVector::ParameterVector
                                                                    ParameterVector(Rcpp::NumericVector x, size_t size)
                                                                    vector constructor
                                                                    Definition: rcpp_interface_base.hpp:162
                                                                    -
                                                                    ParameterVector::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_interface_base.hpp:122
                                                                    -
                                                                    ParameterVector::id_m
                                                                    uint32_t id_m
                                                                    Definition: rcpp_interface_base.hpp:124
                                                                    -
                                                                    ParameterVector::at
                                                                    SEXP at(R_xlen_t pos)
                                                                    Accessor. First index is one. For calling from R.
                                                                    Definition: rcpp_interface_base.hpp:201
                                                                    -
                                                                    ParameterVector::ParameterVector
                                                                    ParameterVector(const fims::Vector< double > &v)
                                                                    vector constructor
                                                                    Definition: rcpp_interface_base.hpp:175
                                                                    -
                                                                    ParameterVector::ParameterVector
                                                                    ParameterVector(const ParameterVector &other)
                                                                    vector constructor
                                                                    Definition: rcpp_interface_base.hpp:140
                                                                    -
                                                                    ParameterVector::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_interface_base.hpp:188
                                                                    -
                                                                    ParameterVector::fill_max
                                                                    void fill_max(double value)
                                                                    Assigns the given values to the maximum value of all elements in the vector.
                                                                    Definition: rcpp_interface_base.hpp:295
                                                                    -
                                                                    ParameterVector::get
                                                                    Parameter & get(size_t pos)
                                                                    Internal accessor. First index is one. For calling from R.
                                                                    Definition: rcpp_interface_base.hpp:214
                                                                    -
                                                                    ParameterVector::fill
                                                                    void fill(double value)
                                                                    Assigns the given values to all elements in the vector.
                                                                    Definition: rcpp_interface_base.hpp:273
                                                                    -
                                                                    ParameterVector::operator[]
                                                                    Parameter & operator[](size_t pos)
                                                                    Accessor. First index starts is zero.
                                                                    Definition: rcpp_interface_base.hpp:194
                                                                    -
                                                                    ParameterVector::set
                                                                    void set(size_t pos, const Parameter &p)
                                                                    Internal setter.
                                                                    Definition: rcpp_interface_base.hpp:227
                                                                    -
                                                                    ParameterVector::ParameterVector
                                                                    ParameterVector()
                                                                    default constructor
                                                                    Definition: rcpp_interface_base.hpp:129
                                                                    -
                                                                    ParameterVector::storage_m
                                                                    std::shared_ptr< std::vector< Parameter > > storage_m
                                                                    Definition: rcpp_interface_base.hpp:123
                                                                    -
                                                                    ParameterVector::fill_min
                                                                    void fill_min(double value)
                                                                    Assigns the given values to the minimum value of all elements in the vector.
                                                                    Definition: rcpp_interface_base.hpp:284
                                                                    -
                                                                    ParameterVector::set_all_estimable
                                                                    void set_all_estimable(bool estimable)
                                                                    Sets all parameters within a vector as estimable.
                                                                    Definition: rcpp_interface_base.hpp:251
                                                                    +
                                                                    55  Parameter() { value_m = 0; }
                                                                    +
                                                                    56 };
                                                                    +
                                                                    57 
                                                                    +
                                                                    61 class FIMSRcppInterfaceBase {
                                                                    +
                                                                    62  public:
                                                                    +
                                                                    64  static std::vector<FIMSRcppInterfaceBase *> fims_interface_objects;
                                                                    +
                                                                    65 
                                                                    +
                                                                    67  virtual bool add_to_fims_tmb() {
                                                                    +
                                                                    68  std::cout << "fims_rcpp_interface_base::add_to_fims_tmb(): Not yet "
                                                                    +
                                                                    69  "implemented.\n";
                                                                    +
                                                                    70  return false;
                                                                    +
                                                                    71  }
                                                                    +
                                                                    72 };
                                                                    +
                                                                    73 std::vector<FIMSRcppInterfaceBase *>
                                                                    +
                                                                    74  FIMSRcppInterfaceBase::fims_interface_objects;
                                                                    +
                                                                    75 
                                                                    +
                                                                    76 #endif
                                                                    +
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:61
                                                                    +
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:64
                                                                    +
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:67
                                                                    Parameter
                                                                    RcppInterface class that defines the interface between R and C++ for parameter types.
                                                                    Definition: rcpp_interface_base.hpp:26
                                                                    -
                                                                    Parameter::operator=
                                                                    Parameter & operator=(const Parameter &right)
                                                                    Constructor for initializing Parameter.
                                                                    Definition: rcpp_interface_base.hpp:66
                                                                    -
                                                                    Parameter::initial_value_m
                                                                    double initial_value_m
                                                                    Definition: rcpp_interface_base.hpp:30
                                                                    -
                                                                    Parameter::Parameter
                                                                    Parameter(double value)
                                                                    Constructor for initializing Parameter.
                                                                    Definition: rcpp_interface_base.hpp:86
                                                                    -
                                                                    Parameter::Parameter
                                                                    Parameter()
                                                                    Constructor for initializing Parameter.
                                                                    Definition: rcpp_interface_base.hpp:95
                                                                    -
                                                                    Parameter::final_value_m
                                                                    double final_value_m
                                                                    Definition: rcpp_interface_base.hpp:31
                                                                    -
                                                                    Parameter::Parameter
                                                                    Parameter(double value, double min, double max, bool estimated)
                                                                    Constructor for initializing Parameter.
                                                                    Definition: rcpp_interface_base.hpp:48
                                                                    -
                                                                    Parameter::estimated_m
                                                                    bool estimated_m
                                                                    Definition: rcpp_interface_base.hpp:38
                                                                    -
                                                                    Parameter::id_m
                                                                    uint32_t id_m
                                                                    Definition: rcpp_interface_base.hpp:29
                                                                    -
                                                                    Parameter::is_random_effect_m
                                                                    bool is_random_effect_m
                                                                    Definition: rcpp_interface_base.hpp:36
                                                                    -
                                                                    Parameter::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_interface_base.hpp:28
                                                                    -
                                                                    Parameter::max_m
                                                                    double max_m
                                                                    Definition: rcpp_interface_base.hpp:34
                                                                    -
                                                                    Parameter::Parameter
                                                                    Parameter(const Parameter &other)
                                                                    Constructor for initializing Parameter.
                                                                    Definition: rcpp_interface_base.hpp:54
                                                                    -
                                                                    Parameter::random_m
                                                                    bool random_m
                                                                    Definition: rcpp_interface_base.hpp:41
                                                                    -
                                                                    Parameter::min_m
                                                                    double min_m
                                                                    Definition: rcpp_interface_base.hpp:32
                                                                    - -
                                                                    fims::Vector::size
                                                                    size_type size() const
                                                                    Returns the number of elements.
                                                                    Definition: fims_vector.hpp:295
                                                                    -
                                                                    FIMS_ERROR_LOG
                                                                    #define FIMS_ERROR_LOG(MESSAGE)
                                                                    Definition: def.hpp:561
                                                                    -
                                                                    operator<<
                                                                    std::ostream & operator<<(std::ostream &out, const Parameter &p)
                                                                    TODO: provide a brief description.
                                                                    Definition: rcpp_interface_base.hpp:109
                                                                    +
                                                                    Parameter::Parameter
                                                                    Parameter(double value)
                                                                    Constructor for initializing Parameter.
                                                                    Definition: rcpp_interface_base.hpp:49
                                                                    +
                                                                    Parameter::Parameter
                                                                    Parameter()
                                                                    Constructor for initializing Parameter.
                                                                    Definition: rcpp_interface_base.hpp:55
                                                                    +
                                                                    Parameter::Parameter
                                                                    Parameter(double value, double min, double max, bool estimated)
                                                                    Constructor for initializing Parameter.
                                                                    Definition: rcpp_interface_base.hpp:42
                                                                    +
                                                                    Parameter::estimated_m
                                                                    bool estimated_m
                                                                    Definition: rcpp_interface_base.hpp:35
                                                                    +
                                                                    Parameter::value_m
                                                                    double value_m
                                                                    Definition: rcpp_interface_base.hpp:28
                                                                    +
                                                                    Parameter::is_random_effect_m
                                                                    bool is_random_effect_m
                                                                    Definition: rcpp_interface_base.hpp:33
                                                                    +
                                                                    Parameter::max_m
                                                                    double max_m
                                                                    Definition: rcpp_interface_base.hpp:31
                                                                    +
                                                                    Parameter::min_m
                                                                    double min_m
                                                                    Definition: rcpp_interface_base.hpp:29
                                                                    diff --git a/docs/rcpp__maturity_8hpp_source.html b/docs/rcpp__maturity_8hpp_source.html index 9189166..9f1bdd4 100644 --- a/docs/rcpp__maturity_8hpp_source.html +++ b/docs/rcpp__maturity_8hpp_source.html @@ -76,225 +76,135 @@
                                                                    rcpp_maturity.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    8 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_MATURITY_HPP
                                                                    -
                                                                    9 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_MATURITY_HPP
                                                                    -
                                                                    10 
                                                                    -
                                                                    11 #include "../../../population_dynamics/maturity/maturity.hpp"
                                                                    -
                                                                    12 #include "rcpp_interface_base.hpp"
                                                                    -
                                                                    13 
                                                                    -
                                                                    22 class MaturityInterfaceBase : public FIMSRcppInterfaceBase {
                                                                    -
                                                                    23  public:
                                                                    -
                                                                    24  static uint32_t id_g;
                                                                    -
                                                                    25  uint32_t id;
                                                                    -
                                                                    26  // live objects in C++ are objects that have been created and live in memory
                                                                    -
                                                                    27  static std::map<uint32_t, MaturityInterfaceBase*>
                                                                    -
                                                                    28  live_objects;
                                                                    -
                                                                    31  MaturityInterfaceBase() {
                                                                    -
                                                                    32  this->id = MaturityInterfaceBase::id_g++;
                                                                    -
                                                                    33  /* Create instance of map: key is id and value is pointer to
                                                                    -
                                                                    34  MaturityInterfaceBase */
                                                                    -
                                                                    35  MaturityInterfaceBase::live_objects[this->id] = this;
                                                                    -
                                                                    36  FIMSRcppInterfaceBase::fims_interface_objects.push_back(this);
                                                                    -
                                                                    37  }
                                                                    -
                                                                    38 
                                                                    -
                                                                    39  virtual ~MaturityInterfaceBase() {}
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: rcpp_maturity.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  *
                                                                    +
                                                                    5  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    6  * Fisheries Integrated Modeling System project. See LICENSE file
                                                                    +
                                                                    7  * for reuse information.
                                                                    +
                                                                    8  *
                                                                    +
                                                                    9  */
                                                                    +
                                                                    10 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_MATURITY_HPP
                                                                    +
                                                                    11 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_MATURITY_HPP
                                                                    +
                                                                    12 
                                                                    +
                                                                    13 #include "../../../population_dynamics/maturity/maturity.hpp"
                                                                    +
                                                                    14 #include "rcpp_interface_base.hpp"
                                                                    +
                                                                    15 
                                                                    +
                                                                    24 class MaturityInterfaceBase : public FIMSRcppInterfaceBase {
                                                                    +
                                                                    25  public:
                                                                    +
                                                                    26  static uint32_t id_g;
                                                                    +
                                                                    27  uint32_t id;
                                                                    +
                                                                    28  // live objects in C++ are objects that have been created and live in memory
                                                                    +
                                                                    29  static std::map<uint32_t, MaturityInterfaceBase*>
                                                                    +
                                                                    30  live_objects;
                                                                    +
                                                                    33  MaturityInterfaceBase() {
                                                                    +
                                                                    34  this->id = MaturityInterfaceBase::id_g++;
                                                                    +
                                                                    35  /* Create instance of map: key is id and value is pointer to
                                                                    +
                                                                    36  MaturityInterfaceBase */
                                                                    +
                                                                    37  MaturityInterfaceBase::live_objects[this->id] = this;
                                                                    +
                                                                    38  FIMSRcppInterfaceBase::fims_interface_objects.push_back(this);
                                                                    +
                                                                    39  }
                                                                    40 
                                                                    -
                                                                    43  virtual uint32_t get_id() = 0;
                                                                    -
                                                                    44 
                                                                    -
                                                                    49  virtual double evaluate(double x) = 0;
                                                                    -
                                                                    50 };
                                                                    -
                                                                    51 
                                                                    -
                                                                    52 uint32_t MaturityInterfaceBase::id_g = 1;
                                                                    -
                                                                    53 std::map<uint32_t, MaturityInterfaceBase*> MaturityInterfaceBase::live_objects;
                                                                    -
                                                                    54 
                                                                    -
                                                                    59 class LogisticMaturityInterface : public MaturityInterfaceBase {
                                                                    -
                                                                    60 public:
                                                                    -
                                                                    61  ParameterVector
                                                                    -
                                                                    62  inflection_point;
                                                                    -
                                                                    63  ParameterVector slope;
                                                                    -
                                                                    65  LogisticMaturityInterface() : MaturityInterfaceBase() {
                                                                    -
                                                                    66  }
                                                                    -
                                                                    67 
                                                                    -
                                                                    68  virtual ~LogisticMaturityInterface() {}
                                                                    -
                                                                    69 
                                                                    -
                                                                    71  virtual uint32_t get_id() { return this->id; }
                                                                    -
                                                                    72 
                                                                    -
                                                                    77  virtual double evaluate(double x) {
                                                                    -
                                                                    78  fims_popdy::LogisticMaturity<double> LogisticMat;
                                                                    -
                                                                    79  LogisticMat.inflection_point.resize(1);
                                                                    -
                                                                    80  LogisticMat.inflection_point[0] = this->inflection_point[0].initial_value_m;
                                                                    -
                                                                    81  LogisticMat.slope.resize(1);
                                                                    -
                                                                    82  LogisticMat.slope[0] = this->slope[0].initial_value_m;
                                                                    -
                                                                    83  return LogisticMat.evaluate(x);
                                                                    -
                                                                    84  }
                                                                    -
                                                                    89  virtual void finalize() {
                                                                    -
                                                                    90 
                                                                    -
                                                                    91  if (this->finalized) {
                                                                    -
                                                                    92  //log warning that finalize has been called more than once.
                                                                    -
                                                                    93  FIMS_WARNING_LOG("Logistic Maturity " + fims::to_string(this->id) + " has been finalized already.");
                                                                    -
                                                                    94  }
                                                                    -
                                                                    95 
                                                                    -
                                                                    96  this->finalized = true; //indicate this has been called already
                                                                    -
                                                                    97 
                                                                    -
                                                                    98 
                                                                    -
                                                                    99  std::shared_ptr<fims_info::Information<double> > info =
                                                                    -
                                                                    100  fims_info::Information<double>::GetInstance();
                                                                    -
                                                                    101 
                                                                    -
                                                                    102  fims_info::Information<double>::maturity_models_iterator it;
                                                                    -
                                                                    103 
                                                                    -
                                                                    104 
                                                                    -
                                                                    105  //search for maturity in Information
                                                                    -
                                                                    106  it = info->maturity_models.find(this->id);
                                                                    -
                                                                    107  //if not found, just return
                                                                    -
                                                                    108  if (it == info->maturity_models.end()) {
                                                                    -
                                                                    109  FIMS_WARNING_LOG("Logistic Maturity " + fims::to_string(this->id) + " not found in Information.");
                                                                    -
                                                                    110  return;
                                                                    -
                                                                    111  } else {
                                                                    -
                                                                    112  std::shared_ptr<fims_popdy::LogisticMaturity<double> > mat =
                                                                    -
                                                                    113  std::dynamic_pointer_cast<fims_popdy::LogisticMaturity<double> >(it->second);
                                                                    -
                                                                    114 
                                                                    -
                                                                    115  for (size_t i = 0; i < inflection_point.size(); i++) {
                                                                    -
                                                                    116  if (this->inflection_point[i].estimated_m) {
                                                                    -
                                                                    117  this->inflection_point[i].final_value_m = mat->inflection_point[i];
                                                                    -
                                                                    118  } else {
                                                                    -
                                                                    119  this->inflection_point[i].final_value_m = this->inflection_point[i].initial_value_m;
                                                                    -
                                                                    120  }
                                                                    -
                                                                    121 
                                                                    -
                                                                    122  }
                                                                    -
                                                                    123 
                                                                    -
                                                                    124  for (size_t i = 0; i < slope.size(); i++) {
                                                                    -
                                                                    125  if (this->slope[i].estimated_m) {
                                                                    -
                                                                    126  this->slope[i].final_value_m = mat->slope[i];
                                                                    -
                                                                    127  } else {
                                                                    -
                                                                    128  this->slope[i].final_value_m = this->slope[i].initial_value_m;
                                                                    -
                                                                    129  }
                                                                    +
                                                                    41  virtual ~MaturityInterfaceBase() {}
                                                                    +
                                                                    42 
                                                                    +
                                                                    45  virtual uint32_t get_id() = 0;
                                                                    +
                                                                    46 
                                                                    +
                                                                    51  virtual double evaluate(double x) = 0;
                                                                    +
                                                                    52 };
                                                                    +
                                                                    53 
                                                                    +
                                                                    54 uint32_t MaturityInterfaceBase::id_g = 1;
                                                                    +
                                                                    55 std::map<uint32_t, MaturityInterfaceBase*> MaturityInterfaceBase::live_objects;
                                                                    +
                                                                    56 
                                                                    +
                                                                    61 class LogisticMaturityInterface : public MaturityInterfaceBase {
                                                                    +
                                                                    62  public:
                                                                    +
                                                                    63  Parameter
                                                                    +
                                                                    64  inflection_point;
                                                                    +
                                                                    65  Parameter slope;
                                                                    +
                                                                    67  LogisticMaturityInterface() : MaturityInterfaceBase() {}
                                                                    +
                                                                    68 
                                                                    +
                                                                    69  virtual ~LogisticMaturityInterface() {}
                                                                    +
                                                                    70 
                                                                    +
                                                                    72  virtual uint32_t get_id() { return this->id; }
                                                                    +
                                                                    73 
                                                                    +
                                                                    78  virtual double evaluate(double x) {
                                                                    +
                                                                    79  fims_popdy::LogisticMaturity<double> LogisticMat;
                                                                    +
                                                                    80  LogisticMat.inflection_point = this->inflection_point.value_m;
                                                                    +
                                                                    81  LogisticMat.slope = this->slope.value_m;
                                                                    +
                                                                    82  return LogisticMat.evaluate(x);
                                                                    +
                                                                    83  }
                                                                    +
                                                                    84 
                                                                    +
                                                                    85 #ifdef TMB_MODEL
                                                                    +
                                                                    86 
                                                                    +
                                                                    87  template <typename Type>
                                                                    +
                                                                    88  bool add_to_fims_tmb_internal() {
                                                                    +
                                                                    89  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    +
                                                                    90  fims_info::Information<Type>::GetInstance();
                                                                    +
                                                                    91 
                                                                    +
                                                                    92  std::shared_ptr<fims_popdy::LogisticMaturity<Type> > maturity =
                                                                    +
                                                                    93  std::make_shared<fims_popdy::LogisticMaturity<Type> >();
                                                                    +
                                                                    94 
                                                                    +
                                                                    95  // set relative info
                                                                    +
                                                                    96  maturity->id = this->id;
                                                                    +
                                                                    97  maturity->inflection_point = this->inflection_point.value_m;
                                                                    +
                                                                    98  if (this->inflection_point.estimated_m) {
                                                                    +
                                                                    99  if (this->inflection_point.is_random_effect_m) {
                                                                    +
                                                                    100  info->RegisterRandomEffect(maturity->inflection_point);
                                                                    +
                                                                    101  } else {
                                                                    +
                                                                    102  info->RegisterParameter(maturity->inflection_point);
                                                                    +
                                                                    103  }
                                                                    +
                                                                    104  }
                                                                    +
                                                                    105  maturity->slope = this->slope.value_m;
                                                                    +
                                                                    106  if (this->slope.estimated_m) {
                                                                    +
                                                                    107  if (this->slope.is_random_effect_m) {
                                                                    +
                                                                    108  info->RegisterRandomEffect(maturity->slope);
                                                                    +
                                                                    109  } else {
                                                                    +
                                                                    110  info->RegisterParameter(maturity->slope);
                                                                    +
                                                                    111  }
                                                                    +
                                                                    112  }
                                                                    +
                                                                    113 
                                                                    +
                                                                    114  // add to Information
                                                                    +
                                                                    115  info->maturity_models[maturity->id] = maturity;
                                                                    +
                                                                    116 
                                                                    +
                                                                    117  return true;
                                                                    +
                                                                    118  }
                                                                    +
                                                                    119 
                                                                    +
                                                                    122  virtual bool add_to_fims_tmb() {
                                                                    +
                                                                    123  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    +
                                                                    124  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    +
                                                                    125  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    +
                                                                    126  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    +
                                                                    127 
                                                                    +
                                                                    128  return true;
                                                                    +
                                                                    129  }
                                                                    130 
                                                                    -
                                                                    131  }
                                                                    -
                                                                    132 
                                                                    +
                                                                    131 #endif
                                                                    +
                                                                    132 };
                                                                    133 
                                                                    -
                                                                    134  }
                                                                    -
                                                                    135  }
                                                                    -
                                                                    136 
                                                                    -
                                                                    140  virtual std::string to_json() {
                                                                    -
                                                                    141  std::stringstream ss;
                                                                    -
                                                                    142  ss << "\"module\" : {\n";
                                                                    -
                                                                    143  ss << " \"name\": \"maturity\",\n";
                                                                    -
                                                                    144  ss << " \"type\": \"logistic\",\n";
                                                                    -
                                                                    145  ss << " \"id\": " << this->id << ",\n";
                                                                    -
                                                                    146 
                                                                    -
                                                                    147  ss << " \"parameter\": {\n";
                                                                    -
                                                                    148  ss << " \"name\": \"inflection_point\",\n";
                                                                    -
                                                                    149  ss << " \"id\":" << this->inflection_point.id_m << ",\n";
                                                                    -
                                                                    150  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    151  ss << " \"values\":" << this->inflection_point << ",\n";
                                                                    -
                                                                    152 
                                                                    -
                                                                    153  ss << " \"parameter\": {\n";
                                                                    -
                                                                    154  ss << " \"name\": \"slope\",\n";
                                                                    -
                                                                    155  ss << " \"id\":" << this->slope.id_m << ",\n";
                                                                    -
                                                                    156  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    157  ss << " \"values\":" << this->slope << ",\n";
                                                                    -
                                                                    158 
                                                                    -
                                                                    159 
                                                                    -
                                                                    160  ss << "}";
                                                                    -
                                                                    161 
                                                                    -
                                                                    162  return ss.str();
                                                                    -
                                                                    163  }
                                                                    -
                                                                    164 
                                                                    -
                                                                    165 #ifdef TMB_MODEL
                                                                    -
                                                                    166 
                                                                    -
                                                                    167  template <typename Type>
                                                                    -
                                                                    168  bool add_to_fims_tmb_internal() {
                                                                    -
                                                                    169  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    -
                                                                    170  fims_info::Information<Type>::GetInstance();
                                                                    -
                                                                    171 
                                                                    -
                                                                    172  std::shared_ptr<fims_popdy::LogisticMaturity<Type> > maturity =
                                                                    -
                                                                    173  std::make_shared<fims_popdy::LogisticMaturity<Type> >();
                                                                    -
                                                                    174 
                                                                    -
                                                                    175  // set relative info
                                                                    -
                                                                    176  maturity->id = this->id;
                                                                    -
                                                                    177  std::stringstream ss;
                                                                    -
                                                                    178  maturity->inflection_point.resize(this->inflection_point.size());
                                                                    -
                                                                    179  for (size_t i = 0; i < this->inflection_point.size(); i++) {
                                                                    -
                                                                    180  maturity->inflection_point[i] = this->inflection_point[i].initial_value_m;
                                                                    -
                                                                    181  if (this->inflection_point[i].estimated_m) {
                                                                    -
                                                                    182  ss.str("");
                                                                    -
                                                                    183  ss << "maturity.inflection_point." << this->id << "." << i;
                                                                    -
                                                                    184  info->RegisterParameterName(ss.str());
                                                                    -
                                                                    185  if (this->inflection_point[i].is_random_effect_m) {
                                                                    -
                                                                    186  info->RegisterRandomEffect(maturity->inflection_point[i]);
                                                                    -
                                                                    187  } else {
                                                                    -
                                                                    188  info->RegisterParameter(maturity->inflection_point[i]);
                                                                    -
                                                                    189  }
                                                                    -
                                                                    190  }
                                                                    -
                                                                    191  }
                                                                    -
                                                                    192 
                                                                    -
                                                                    193  maturity->slope.resize(this->slope.size());
                                                                    -
                                                                    194  for (size_t i = 0; i < this->slope.size(); i++) {
                                                                    -
                                                                    195  maturity->slope[i] = this->slope[i].initial_value_m;
                                                                    -
                                                                    196  if (this->slope[i].estimated_m) {
                                                                    -
                                                                    197  ss.str("");
                                                                    -
                                                                    198  ss << "maturity.slope_" << this->id << "." << i;
                                                                    -
                                                                    199  info->RegisterParameterName(ss.str());
                                                                    -
                                                                    200  if (this->slope[i].is_random_effect_m) {
                                                                    -
                                                                    201  info->RegisterRandomEffect(maturity->slope[i]);
                                                                    -
                                                                    202  } else {
                                                                    -
                                                                    203  info->RegisterParameter(maturity->slope[i]);
                                                                    -
                                                                    204  }
                                                                    -
                                                                    205  }
                                                                    -
                                                                    206  }
                                                                    -
                                                                    207 
                                                                    -
                                                                    208  // add to Information
                                                                    -
                                                                    209  info->maturity_models[maturity->id] = maturity;
                                                                    -
                                                                    210 
                                                                    -
                                                                    211  return true;
                                                                    -
                                                                    212  }
                                                                    -
                                                                    213 
                                                                    -
                                                                    216  virtual bool add_to_fims_tmb() {
                                                                    -
                                                                    217  FIMS_INFO_LOG("adding Maturity object to TMB");
                                                                    -
                                                                    218  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    -
                                                                    219  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    -
                                                                    220  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    -
                                                                    221  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    -
                                                                    222 
                                                                    -
                                                                    223  return true;
                                                                    -
                                                                    224  }
                                                                    -
                                                                    225 
                                                                    -
                                                                    226 #endif
                                                                    -
                                                                    227 };
                                                                    -
                                                                    228 
                                                                    -
                                                                    229 #endif
                                                                    -
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:336
                                                                    -
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:342
                                                                    -
                                                                    FIMSRcppInterfaceBase::finalized
                                                                    bool finalized
                                                                    Definition: rcpp_interface_base.hpp:339
                                                                    -
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:345
                                                                    -
                                                                    LogisticMaturityInterface
                                                                    Rcpp interface for logistic maturity as an S4 object. To instantiate from R: logistic_maturity <- new...
                                                                    Definition: rcpp_maturity.hpp:59
                                                                    -
                                                                    LogisticMaturityInterface::slope
                                                                    ParameterVector slope
                                                                    Definition: rcpp_maturity.hpp:63
                                                                    -
                                                                    LogisticMaturityInterface::inflection_point
                                                                    ParameterVector inflection_point
                                                                    Definition: rcpp_maturity.hpp:62
                                                                    -
                                                                    LogisticMaturityInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the logistic maturity interface
                                                                    Definition: rcpp_maturity.hpp:71
                                                                    -
                                                                    LogisticMaturityInterface::finalize
                                                                    virtual void finalize()
                                                                    finalize function. Extracts derived quantities back to the Rcpp interface object from the Information...
                                                                    Definition: rcpp_maturity.hpp:89
                                                                    -
                                                                    LogisticMaturityInterface::to_json
                                                                    virtual std::string to_json()
                                                                    Convert the data to json representation for the output.
                                                                    Definition: rcpp_maturity.hpp:140
                                                                    -
                                                                    LogisticMaturityInterface::evaluate
                                                                    virtual double evaluate(double x)
                                                                    evaluate the logistic maturity function
                                                                    Definition: rcpp_maturity.hpp:77
                                                                    -
                                                                    MaturityInterfaceBase
                                                                    MaturityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible...
                                                                    Definition: rcpp_maturity.hpp:22
                                                                    +
                                                                    134 #endif
                                                                    +
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:61
                                                                    +
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:64
                                                                    +
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:67
                                                                    +
                                                                    LogisticMaturityInterface
                                                                    Rcpp interface for logistic maturity as an S4 object. To instantiate from R: logistic_maturity <- new...
                                                                    Definition: rcpp_maturity.hpp:61
                                                                    +
                                                                    LogisticMaturityInterface::inflection_point
                                                                    Parameter inflection_point
                                                                    Definition: rcpp_maturity.hpp:64
                                                                    +
                                                                    LogisticMaturityInterface::slope
                                                                    Parameter slope
                                                                    Definition: rcpp_maturity.hpp:65
                                                                    +
                                                                    LogisticMaturityInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the logistic maturity interface
                                                                    Definition: rcpp_maturity.hpp:72
                                                                    +
                                                                    LogisticMaturityInterface::evaluate
                                                                    virtual double evaluate(double x)
                                                                    evaluate the logistic maturity function
                                                                    Definition: rcpp_maturity.hpp:78
                                                                    +
                                                                    MaturityInterfaceBase
                                                                    MaturityInterfaceBase class should be inherited to define different Rcpp interfaces for each possible...
                                                                    Definition: rcpp_maturity.hpp:24
                                                                    MaturityInterfaceBase::evaluate
                                                                    virtual double evaluate(double x)=0
                                                                    evaluate the function
                                                                    -
                                                                    MaturityInterfaceBase::live_objects
                                                                    static std::map< uint32_t, MaturityInterfaceBase * > live_objects
                                                                    Definition: rcpp_maturity.hpp:28
                                                                    +
                                                                    MaturityInterfaceBase::live_objects
                                                                    static std::map< uint32_t, MaturityInterfaceBase * > live_objects
                                                                    Definition: rcpp_maturity.hpp:30
                                                                    MaturityInterfaceBase::get_id
                                                                    virtual uint32_t get_id()=0
                                                                    get the ID of the interface base object
                                                                    -
                                                                    MaturityInterfaceBase::id
                                                                    uint32_t id
                                                                    Definition: rcpp_maturity.hpp:25
                                                                    -
                                                                    MaturityInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_maturity.hpp:24
                                                                    -
                                                                    ParameterVector
                                                                    Rcpp representation of a Parameter vector interface between R and cpp.
                                                                    Definition: rcpp_interface_base.hpp:120
                                                                    -
                                                                    ParameterVector::resize
                                                                    void resize(size_t size)
                                                                    resize to length "size"
                                                                    Definition: rcpp_interface_base.hpp:242
                                                                    -
                                                                    ParameterVector::size
                                                                    size_t size()
                                                                    returns vector length
                                                                    Definition: rcpp_interface_base.hpp:234
                                                                    -
                                                                    ParameterVector::id_m
                                                                    uint32_t id_m
                                                                    Definition: rcpp_interface_base.hpp:124
                                                                    -
                                                                    fims_info::Information::maturity_models_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::MaturityBase< Type > > >::iterator maturity_models_iterator
                                                                    Definition: information.hpp:87
                                                                    -
                                                                    fims_info::Information::maturity_models
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::MaturityBase< Type > > > maturity_models
                                                                    Definition: information.hpp:83
                                                                    -
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:135
                                                                    -
                                                                    FIMS_WARNING_LOG
                                                                    #define FIMS_WARNING_LOG(MESSAGE)
                                                                    Definition: def.hpp:559
                                                                    -
                                                                    FIMS_INFO_LOG
                                                                    #define FIMS_INFO_LOG(MESSAGE)
                                                                    Definition: def.hpp:557
                                                                    -
                                                                    rcpp_interface_base.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    fims_popdy::LogisticMaturity
                                                                    LogisticMaturity class that returns the logistic function value from fims_math.
                                                                    Definition: logistic.hpp:25
                                                                    -
                                                                    fims_popdy::LogisticMaturity::slope
                                                                    fims::Vector< Type > slope
                                                                    Definition: logistic.hpp:28
                                                                    -
                                                                    fims_popdy::LogisticMaturity::inflection_point
                                                                    fims::Vector< Type > inflection_point
                                                                    Definition: logistic.hpp:26
                                                                    -
                                                                    fims_popdy::LogisticMaturity::evaluate
                                                                    virtual const Type evaluate(const Type &x)
                                                                    Method of the logistic maturity class that implements the logistic function from FIMS math.
                                                                    Definition: logistic.hpp:45
                                                                    +
                                                                    MaturityInterfaceBase::id
                                                                    uint32_t id
                                                                    Definition: rcpp_maturity.hpp:27
                                                                    +
                                                                    MaturityInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_maturity.hpp:26
                                                                    +
                                                                    Parameter
                                                                    RcppInterface class that defines the interface between R and C++ for parameter types.
                                                                    Definition: rcpp_interface_base.hpp:26
                                                                    +
                                                                    Parameter::estimated_m
                                                                    bool estimated_m
                                                                    Definition: rcpp_interface_base.hpp:35
                                                                    +
                                                                    Parameter::value_m
                                                                    double value_m
                                                                    Definition: rcpp_interface_base.hpp:28
                                                                    +
                                                                    Parameter::is_random_effect_m
                                                                    bool is_random_effect_m
                                                                    Definition: rcpp_interface_base.hpp:33
                                                                    +
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:126
                                                                    +
                                                                    fims_popdy::LogisticMaturity
                                                                    LogisticMaturity class that returns the logistic function value from fims_math.
                                                                    Definition: logistic.hpp:23
                                                                    +
                                                                    fims_popdy::LogisticMaturity::slope
                                                                    Type slope
                                                                    Definition: logistic.hpp:26
                                                                    +
                                                                    fims_popdy::LogisticMaturity::inflection_point
                                                                    Type inflection_point
                                                                    Definition: logistic.hpp:24
                                                                    +
                                                                    fims_popdy::LogisticMaturity::evaluate
                                                                    virtual const Type evaluate(const Type &x)
                                                                    Method of the logistic maturity class that implements the logistic function from FIMS math.
                                                                    Definition: logistic.hpp:41
                                                                    diff --git a/docs/rcpp__natural__mortality_8hpp_source.html b/docs/rcpp__natural__mortality_8hpp_source.html index bc62e63..7c5d1f5 100644 --- a/docs/rcpp__natural__mortality_8hpp_source.html +++ b/docs/rcpp__natural__mortality_8hpp_source.html @@ -76,11 +76,19 @@
                                                                    rcpp_natural_mortality.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    8 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_NATURAL_MORTALITY_HPP
                                                                    -
                                                                    9 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_NATURAL_MORTALITY_HPP
                                                                    -
                                                                    10 
                                                                    -
                                                                    11 #endif
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: rcpp_natural_mortality.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  *
                                                                    +
                                                                    5  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    6  * Fisheries Integrated Modeling System project. See LICENSE file
                                                                    +
                                                                    7  * for reuse information.
                                                                    +
                                                                    8  *
                                                                    +
                                                                    9  */
                                                                    +
                                                                    10 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_NATURAL_MORTALITY_HPP
                                                                    +
                                                                    11 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_NATURAL_MORTALITY_HPP
                                                                    +
                                                                    12 
                                                                    +
                                                                    13 #endif
                                                                    diff --git a/docs/rcpp__population_8hpp_source.html b/docs/rcpp__population_8hpp_source.html index 85ea485..d31c34f 100644 --- a/docs/rcpp__population_8hpp_source.html +++ b/docs/rcpp__population_8hpp_source.html @@ -76,16 +76,22 @@
                                                                    rcpp_population.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: rcpp_population.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    5  * Fisheries Integrated Modeling System project. See LICENSE file
                                                                    +
                                                                    6  * for reuse information.
                                                                    +
                                                                    7  */
                                                                    8 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_POPULATION_HPP
                                                                    9 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_POPULATION_HPP
                                                                    10 
                                                                    11 #include "../../../population_dynamics/population/population.hpp"
                                                                    -
                                                                    12 #include "rcpp_interface_base.hpp"
                                                                    +
                                                                    12 #include "rcpp_interface_base.hpp"
                                                                    13 
                                                                    22 class PopulationInterfaceBase : public FIMSRcppInterfaceBase {
                                                                    23  public:
                                                                    -
                                                                    24  static uint32_t id_g;
                                                                    +
                                                                    24  static uint32_t id_g;
                                                                    25  uint32_t id;
                                                                    26  // live objects in C++ are objects that have been created and live in memory
                                                                    27  static std::map<uint32_t, PopulationInterfaceBase*>
                                                                    @@ -113,351 +119,135 @@
                                                                    57  uint32_t nfleets;
                                                                    58  uint32_t nseasons;
                                                                    59  uint32_t nyears;
                                                                    -
                                                                    60  uint32_t nlengths;
                                                                    -
                                                                    61  uint32_t maturity_id;
                                                                    -
                                                                    62  uint32_t growth_id;
                                                                    -
                                                                    63  uint32_t recruitment_id;
                                                                    -
                                                                    64  ParameterVector log_M;
                                                                    -
                                                                    65  ParameterVector log_init_naa;
                                                                    -
                                                                    66  ParameterVector numbers_at_age;
                                                                    -
                                                                    67  Rcpp::NumericVector ages;
                                                                    -
                                                                    68  Rcpp::NumericVector proportion_female;
                                                                    +
                                                                    60  uint32_t maturity_id;
                                                                    +
                                                                    61  uint32_t growth_id;
                                                                    +
                                                                    62  uint32_t recruitment_id;
                                                                    +
                                                                    63  Rcpp::NumericVector log_M;
                                                                    +
                                                                    64  Rcpp::NumericVector log_init_naa;
                                                                    +
                                                                    65  Rcpp::NumericVector ages;
                                                                    +
                                                                    66  Rcpp::NumericVector proportion_female;
                                                                    +
                                                                    68  bool estimate_M;
                                                                    +
                                                                    69  bool estimate_initNAA;
                                                                    70  bool estimate_prop_female;
                                                                    -
                                                                    74  Rcpp::NumericVector derived_ssb;
                                                                    -
                                                                    75  Rcpp::NumericVector derived_naa;
                                                                    -
                                                                    76  Rcpp::NumericVector derived_biomass;
                                                                    -
                                                                    77  Rcpp::NumericVector derived_recruitment;
                                                                    -
                                                                    79  Rcpp::NumericVector estimated_log_M;
                                                                    -
                                                                    80  Rcpp::NumericVector estimated_log_init_naa;
                                                                    -
                                                                    81  Rcpp::NumericVector estimated_proportion_female;
                                                                    -
                                                                    82  std::string name;
                                                                    -
                                                                    84  PopulationInterface() : PopulationInterfaceBase() {}
                                                                    -
                                                                    85 
                                                                    -
                                                                    86  virtual ~PopulationInterface() {}
                                                                    -
                                                                    87 
                                                                    -
                                                                    88  virtual uint32_t get_id() { return this->id; }
                                                                    -
                                                                    89 
                                                                    -
                                                                    95  void SetMaturity(uint32_t maturity_id) { this->maturity_id = maturity_id; }
                                                                    -
                                                                    96 
                                                                    -
                                                                    102  void SetGrowth(uint32_t growth_id) { this->growth_id = growth_id; }
                                                                    -
                                                                    103 
                                                                    -
                                                                    109  void SetRecruitment(uint32_t recruitment_id) {
                                                                    -
                                                                    110  this->recruitment_id = recruitment_id;
                                                                    -
                                                                    111  }
                                                                    -
                                                                    112 
                                                                    -
                                                                    114  virtual void evaluate() {
                                                                    -
                                                                    115  fims_popdy::Population<double> population;
                                                                    -
                                                                    116  return population.Evaluate();
                                                                    -
                                                                    117  }
                                                                    -
                                                                    118 
                                                                    -
                                                                    123  virtual void finalize() {
                                                                    -
                                                                    124 
                                                                    -
                                                                    125  if (this->finalized) {
                                                                    -
                                                                    126  //log warning that finalize has been called more than once.
                                                                    -
                                                                    127  FIMS_WARNING_LOG("Population " + fims::to_string(this->id) + " has been finalized already.");
                                                                    -
                                                                    128  }
                                                                    -
                                                                    129 
                                                                    -
                                                                    130  this->finalized = true; //indicate this has been called already
                                                                    -
                                                                    131 
                                                                    -
                                                                    132  std::shared_ptr<fims_info::Information<double> > info =
                                                                    -
                                                                    133  fims_info::Information<double>::GetInstance();
                                                                    -
                                                                    134 
                                                                    -
                                                                    135 
                                                                    -
                                                                    136 
                                                                    -
                                                                    137 
                                                                    -
                                                                    138  this->estimated_log_M = Rcpp::NumericVector(this->log_M.size());
                                                                    -
                                                                    139  for (size_t i = 0; i < this->log_M.size(); i++) {
                                                                    -
                                                                    140  this->estimated_log_M[i] = this->log_M[i].initial_value_m;
                                                                    -
                                                                    141  }
                                                                    -
                                                                    142 
                                                                    -
                                                                    143  this->estimated_log_init_naa = Rcpp::NumericVector(this->log_init_naa.size());
                                                                    -
                                                                    144  for (size_t i = 0; i < this->log_init_naa.size(); i++) {
                                                                    -
                                                                    145  this->estimated_log_init_naa[i] = this->log_init_naa[i].initial_value_m;
                                                                    -
                                                                    146  }
                                                                    -
                                                                    147 
                                                                    -
                                                                    148  this->estimated_proportion_female = Rcpp::NumericVector(this->proportion_female.size());
                                                                    -
                                                                    149  for (size_t i = 0; i < this->proportion_female.size(); i++) {
                                                                    -
                                                                    150  this->estimated_proportion_female[i] = this->proportion_female[i];
                                                                    -
                                                                    151  }
                                                                    -
                                                                    152 
                                                                    -
                                                                    153  fims_info::Information<double>::population_iterator it;
                                                                    -
                                                                    154 
                                                                    -
                                                                    155 
                                                                    -
                                                                    156  it = info->populations.find(this->id);
                                                                    -
                                                                    157 
                                                                    -
                                                                    158  std::shared_ptr<fims_popdy::Population<double> > pop =
                                                                    -
                                                                    159  info->populations[this->id];
                                                                    -
                                                                    160  it = info->populations.find(this->id);
                                                                    -
                                                                    161  if (it == info->populations.end()) {
                                                                    -
                                                                    162  FIMS_WARNING_LOG("Population " + fims::to_string(this->id) + " not found in Information.");
                                                                    -
                                                                    163  return;
                                                                    -
                                                                    164  } else {
                                                                    -
                                                                    165 
                                                                    -
                                                                    166  if (this->estimated_log_M) {
                                                                    -
                                                                    167  for (size_t i = 0; i < this->log_M.size(); i++) {
                                                                    -
                                                                    168  this->estimated_log_M[i] = pop->log_M[i];
                                                                    -
                                                                    169  }
                                                                    -
                                                                    170  }
                                                                    -
                                                                    171 
                                                                    -
                                                                    172  if (this->estimated_log_init_naa) {
                                                                    -
                                                                    173  for (size_t i = 0; i < this->log_init_naa.size(); i++) {
                                                                    -
                                                                    174  this->estimated_log_init_naa[i] = pop->log_init_naa[i];
                                                                    -
                                                                    175  }
                                                                    -
                                                                    176  }
                                                                    -
                                                                    177 
                                                                    -
                                                                    178  if (this->estimate_prop_female) {
                                                                    -
                                                                    179  for (size_t i = 0; i < this->proportion_female.size(); i++) {
                                                                    -
                                                                    180  this->estimated_proportion_female[i] = pop->proportion_female[i];
                                                                    -
                                                                    181  }
                                                                    -
                                                                    182  }
                                                                    -
                                                                    183 
                                                                    -
                                                                    184  this->derived_naa = Rcpp::NumericVector(pop->numbers_at_age.size());
                                                                    -
                                                                    185  this->derived_ssb = Rcpp::NumericVector(pop->spawning_biomass.size());
                                                                    -
                                                                    186  this->derived_biomass = Rcpp::NumericVector(pop->biomass.size());
                                                                    -
                                                                    187  this->derived_recruitment = Rcpp::NumericVector(pop->expected_recruitment.size());
                                                                    -
                                                                    188 
                                                                    -
                                                                    189  //set naa from Information/
                                                                    -
                                                                    190  for (size_t i = 0; i < this->derived_naa.size(); i++) {
                                                                    -
                                                                    191  this->derived_naa[i] = pop->numbers_at_age[i];
                                                                    -
                                                                    192  }
                                                                    -
                                                                    193 
                                                                    -
                                                                    194  //set ssb from Information/
                                                                    -
                                                                    195  for (size_t i = 0; i < this->derived_ssb.size(); i++) {
                                                                    -
                                                                    196  this->derived_ssb[i] = pop->spawning_biomass[i];
                                                                    -
                                                                    197  }
                                                                    -
                                                                    198 
                                                                    -
                                                                    199  //set biomass from Information
                                                                    -
                                                                    200  for (size_t i = 0; i < this->derived_biomass.size(); i++) {
                                                                    -
                                                                    201  this->derived_biomass[i] = pop->biomass[i];
                                                                    -
                                                                    202  }
                                                                    -
                                                                    203 
                                                                    -
                                                                    204  //set recruitment from Information/
                                                                    -
                                                                    205  for (size_t i = 0; i < this->derived_recruitment.size(); i++) {
                                                                    -
                                                                    206  this->derived_recruitment[i] = pop->expected_recruitment[i];
                                                                    -
                                                                    207  }
                                                                    -
                                                                    208 
                                                                    -
                                                                    209  }
                                                                    -
                                                                    210 
                                                                    -
                                                                    211  }
                                                                    -
                                                                    212 
                                                                    -
                                                                    216  virtual std::string to_json() {
                                                                    -
                                                                    217  std::stringstream ss;
                                                                    -
                                                                    218 
                                                                    -
                                                                    219  ss << "\"module\" : {\n";
                                                                    -
                                                                    220  ss << " \"name\" : \"Population\",\n";
                                                                    -
                                                                    221 
                                                                    -
                                                                    222  ss << " \"type\" : \"population\",\n";
                                                                    -
                                                                    223  ss << " \"tag\" : \"" << this->name << "\",\n";
                                                                    -
                                                                    224  ss << " \"id\": " << this->id << ",\n";
                                                                    -
                                                                    225  ss << " \"recruitment_id\": " << this->recruitment_id << ",\n";
                                                                    -
                                                                    226  ss << " \"growth_id\": " << this->growth_id << ",\n";
                                                                    -
                                                                    227  ss << " \"maturity_id\": " << this->maturity_id << ",\n";
                                                                    -
                                                                    228 
                                                                    -
                                                                    229  ss << " \"parameter\": {\n";
                                                                    -
                                                                    230  ss << " \"name\": \"log_M\",\n";
                                                                    -
                                                                    231  ss << " \"id\":" << -999 << ",\n";
                                                                    -
                                                                    232  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    233  ss << " \"values\": " << this->log_M << "\n},\n";
                                                                    -
                                                                    234 
                                                                    -
                                                                    235  ss << " \"parameter\": {\n";
                                                                    -
                                                                    236  ss << " \"name\": \"log_init_naa\",\n";
                                                                    -
                                                                    237  ss << " \"id\":" << -999 << ",\n";
                                                                    -
                                                                    238  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    239  ss << " \"values\":" << this->log_init_naa << " \n},\n";
                                                                    -
                                                                    240 
                                                                    -
                                                                    241  ss << " \"parameter\": {\n";
                                                                    -
                                                                    242  ss << " \"name\": \"proportion_female\",\n";
                                                                    -
                                                                    243  ss << " \"id\":" << -999 << ",\n";
                                                                    -
                                                                    244  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    245  ss << " \"values\":" << this->proportion_female << "\n},\n";
                                                                    -
                                                                    246 
                                                                    -
                                                                    247 
                                                                    -
                                                                    248  ss << " \"derived_quantity\": {\n";
                                                                    -
                                                                    249  ss << " \"name\": \"ssb\",\n";
                                                                    -
                                                                    250  ss << " \"values\":[";
                                                                    -
                                                                    251  if (this->derived_ssb.size() == 0) {
                                                                    -
                                                                    252  ss << "]\n";
                                                                    -
                                                                    253  } else {
                                                                    -
                                                                    254  for (size_t i = 0; i < this->derived_ssb.size() - 1; i++) {
                                                                    -
                                                                    255  ss << this->derived_ssb[i] << ", ";
                                                                    -
                                                                    256  }
                                                                    -
                                                                    257  ss << this->derived_ssb[this->derived_ssb.size() - 1] << "]\n";
                                                                    -
                                                                    258  }
                                                                    -
                                                                    259  ss << " },\n";
                                                                    -
                                                                    260 
                                                                    -
                                                                    261  ss << " \"derived_quantity\": {\n";
                                                                    -
                                                                    262  ss << " \"name\": \"naa\",\n";
                                                                    -
                                                                    263  ss << " \"values\":[";
                                                                    -
                                                                    264  if (this->derived_naa.size() == 0) {
                                                                    -
                                                                    265  ss << "]\n";
                                                                    -
                                                                    266  } else {
                                                                    -
                                                                    267  for (size_t i = 0; i < this->derived_naa.size() - 1; i++) {
                                                                    -
                                                                    268  ss << this->derived_naa[i] << ", ";
                                                                    -
                                                                    269  }
                                                                    -
                                                                    270  ss << this->derived_naa[this->derived_naa.size() - 1] << "]\n";
                                                                    -
                                                                    271  }
                                                                    -
                                                                    272  ss << " },\n";
                                                                    -
                                                                    273 
                                                                    -
                                                                    274  ss << " \"derived_quantity\": {\n";
                                                                    -
                                                                    275  ss << " \"name\": \"biomass\",\n";
                                                                    -
                                                                    276  ss << " \"values\":[";
                                                                    -
                                                                    277  if (this->derived_biomass.size() == 0) {
                                                                    -
                                                                    278  ss << "]\n";
                                                                    -
                                                                    279  } else {
                                                                    -
                                                                    280  for (size_t i = 0; i < this->derived_biomass.size() - 1; i++) {
                                                                    -
                                                                    281  ss << this->derived_biomass[i] << ", ";
                                                                    -
                                                                    282  }
                                                                    -
                                                                    283  ss << this->derived_biomass[this->derived_biomass.size() - 1] << "]\n";
                                                                    -
                                                                    284  }
                                                                    -
                                                                    285  ss << " },\n";
                                                                    -
                                                                    286 
                                                                    -
                                                                    287  ss << " \"derived_quantity\": {\n";
                                                                    -
                                                                    288  ss << " \"name\": \"recruitment\",\n";
                                                                    -
                                                                    289  ss << " \"values\":[";
                                                                    -
                                                                    290  if (this->derived_recruitment.size() == 0) {
                                                                    -
                                                                    291  ss << "]\n";
                                                                    -
                                                                    292  } else {
                                                                    -
                                                                    293  for (size_t i = 0; i < this->derived_recruitment.size() - 1; i++) {
                                                                    -
                                                                    294  ss << this->derived_recruitment[i] << ", ";
                                                                    -
                                                                    295  }
                                                                    -
                                                                    296  ss << this->derived_recruitment[this->derived_recruitment.size() - 1] << "]\n";
                                                                    -
                                                                    297  }
                                                                    -
                                                                    298  ss << " }\n";
                                                                    -
                                                                    299 
                                                                    -
                                                                    300  ss << "}";
                                                                    -
                                                                    301 
                                                                    -
                                                                    302  return ss.str();
                                                                    -
                                                                    303  }
                                                                    -
                                                                    304 
                                                                    -
                                                                    305 
                                                                    -
                                                                    306 #ifdef TMB_MODEL
                                                                    -
                                                                    307 
                                                                    -
                                                                    308  template <typename Type>
                                                                    -
                                                                    309  bool add_to_fims_tmb_internal() {
                                                                    -
                                                                    310  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    -
                                                                    311  fims_info::Information<Type>::GetInstance();
                                                                    -
                                                                    312 
                                                                    -
                                                                    313  std::shared_ptr<fims_popdy::Population<Type> > population =
                                                                    -
                                                                    314  std::make_shared<fims_popdy::Population<Type> >();
                                                                    -
                                                                    315 
                                                                    -
                                                                    316  // set relative info
                                                                    -
                                                                    317  population->id = this->id;
                                                                    -
                                                                    318  population->nyears = this->nyears;
                                                                    -
                                                                    319  population->nfleets = this->nfleets;
                                                                    -
                                                                    320  population->nseasons = this->nseasons;
                                                                    -
                                                                    321  population->nages = this->nages;
                                                                    -
                                                                    322  if (this->nages == this->ages.size()) {
                                                                    -
                                                                    323  population->ages.resize(this->nages);
                                                                    -
                                                                    324  } else {
                                                                    -
                                                                    325  warning("The ages vector is not of size nages.");
                                                                    -
                                                                    326  }
                                                                    -
                                                                    327 
                                                                    -
                                                                    328  population->growth_id = this->growth_id;
                                                                    -
                                                                    329  population->recruitment_id = this->recruitment_id;
                                                                    -
                                                                    330  population->maturity_id = this->maturity_id;
                                                                    -
                                                                    331  population->log_M.resize(this->log_M.size());
                                                                    -
                                                                    332  population->log_init_naa.resize(this->log_init_naa.size());
                                                                    -
                                                                    333  for (size_t i = 0; i < log_M.size(); i++) {
                                                                    -
                                                                    334  population->log_M[i] = this->log_M[i].initial_value_m;
                                                                    -
                                                                    335  if (this->log_M[i].estimated_m) {
                                                                    -
                                                                    336  info->RegisterParameterName("log_M");
                                                                    -
                                                                    337  info->RegisterParameter(population->log_M[i]);
                                                                    -
                                                                    338  }
                                                                    -
                                                                    339  }
                                                                    -
                                                                    340  info->variable_map[this->log_M.id_m] = &(population)->log_M;
                                                                    -
                                                                    341 
                                                                    -
                                                                    342  for (size_t i = 0; i < log_init_naa.size(); i++) {
                                                                    -
                                                                    343  population->log_init_naa[i] = this->log_init_naa[i].initial_value_m;
                                                                    -
                                                                    344  if (this->log_init_naa[i].estimated_m) {
                                                                    -
                                                                    345  info->RegisterParameterName("log_init_naa");
                                                                    -
                                                                    346  info->RegisterParameter(population->log_init_naa[i]);
                                                                    -
                                                                    347  }
                                                                    -
                                                                    348  }
                                                                    -
                                                                    349  info->variable_map[this->log_init_naa.id_m] = &(population)->log_init_naa;
                                                                    -
                                                                    350  for (int i = 0; i < ages.size(); i++) {
                                                                    -
                                                                    351  population->ages[i] = this->ages[i];
                                                                    -
                                                                    352  }
                                                                    -
                                                                    353  for (int i = 0; i < proportion_female.size(); i++) {
                                                                    -
                                                                    354  population->proportion_female[i] = this->proportion_female[i];
                                                                    -
                                                                    355  if (estimate_prop_female) {
                                                                    -
                                                                    356  info->RegisterParameter(population->proportion_female[i]);
                                                                    -
                                                                    357  }
                                                                    -
                                                                    358  }
                                                                    -
                                                                    359 
                                                                    -
                                                                    360  population->numbers_at_age.resize((nyears + 1) * nages);
                                                                    -
                                                                    361  info->variable_map[this->numbers_at_age.id_m] = &(population)->numbers_at_age;
                                                                    -
                                                                    362 
                                                                    -
                                                                    363  // add to Information
                                                                    -
                                                                    364  info->populations[population->id] = population;
                                                                    -
                                                                    365 
                                                                    -
                                                                    366  return true;
                                                                    -
                                                                    367  }
                                                                    -
                                                                    368 
                                                                    -
                                                                    371  virtual bool add_to_fims_tmb() {
                                                                    -
                                                                    372  FIMS_INFO_LOG("adding Population object to TMB");
                                                                    -
                                                                    373  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    -
                                                                    374  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    -
                                                                    375  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    -
                                                                    376  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    -
                                                                    377 
                                                                    -
                                                                    378  return true;
                                                                    -
                                                                    379  }
                                                                    -
                                                                    380 
                                                                    -
                                                                    381 #endif
                                                                    -
                                                                    382 };
                                                                    -
                                                                    383 
                                                                    -
                                                                    384 #endif
                                                                    -
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:336
                                                                    -
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:342
                                                                    -
                                                                    FIMSRcppInterfaceBase::finalized
                                                                    bool finalized
                                                                    Definition: rcpp_interface_base.hpp:339
                                                                    -
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:345
                                                                    -
                                                                    ParameterVector
                                                                    Rcpp representation of a Parameter vector interface between R and cpp.
                                                                    Definition: rcpp_interface_base.hpp:120
                                                                    -
                                                                    ParameterVector::resize
                                                                    void resize(size_t size)
                                                                    resize to length "size"
                                                                    Definition: rcpp_interface_base.hpp:242
                                                                    -
                                                                    ParameterVector::size
                                                                    size_t size()
                                                                    returns vector length
                                                                    Definition: rcpp_interface_base.hpp:234
                                                                    -
                                                                    ParameterVector::id_m
                                                                    uint32_t id_m
                                                                    Definition: rcpp_interface_base.hpp:124
                                                                    +
                                                                    72  PopulationInterface() : PopulationInterfaceBase() {}
                                                                    +
                                                                    73 
                                                                    +
                                                                    74  virtual ~PopulationInterface() {}
                                                                    +
                                                                    75 
                                                                    +
                                                                    76  virtual uint32_t get_id() { return this->id; }
                                                                    +
                                                                    77 
                                                                    +
                                                                    83  void SetMaturity(uint32_t maturity_id) { this->maturity_id = maturity_id; }
                                                                    +
                                                                    84 
                                                                    +
                                                                    90  void SetGrowth(uint32_t growth_id) { this->growth_id = growth_id; }
                                                                    +
                                                                    91 
                                                                    +
                                                                    97  void SetRecruitment(uint32_t recruitment_id) {
                                                                    +
                                                                    98  this->recruitment_id = recruitment_id;
                                                                    +
                                                                    99  }
                                                                    +
                                                                    100 
                                                                    +
                                                                    102  virtual void evaluate() {
                                                                    +
                                                                    103  fims_popdy::Population<double> population;
                                                                    +
                                                                    104  return population.Evaluate();
                                                                    +
                                                                    105  }
                                                                    +
                                                                    106 
                                                                    +
                                                                    107 #ifdef TMB_MODEL
                                                                    +
                                                                    108 
                                                                    +
                                                                    109  template <typename Type>
                                                                    +
                                                                    110  bool add_to_fims_tmb_internal() {
                                                                    +
                                                                    111  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    +
                                                                    112  fims_info::Information<Type>::GetInstance();
                                                                    +
                                                                    113 
                                                                    +
                                                                    114  std::shared_ptr<fims_popdy::Population<Type> > population =
                                                                    +
                                                                    115  std::make_shared<fims_popdy::Population<Type> >();
                                                                    +
                                                                    116 
                                                                    +
                                                                    117  // set relative info
                                                                    +
                                                                    118  population->id = this->id;
                                                                    +
                                                                    119  population->nyears = this->nyears;
                                                                    +
                                                                    120  population->nfleets = this->nfleets;
                                                                    +
                                                                    121  population->nseasons = this->nseasons;
                                                                    +
                                                                    122  population->nages = this->nages;
                                                                    +
                                                                    123  if (this->nages == this->ages.size()) {
                                                                    +
                                                                    124  population->ages.resize(this->nages);
                                                                    +
                                                                    125  } else {
                                                                    +
                                                                    126  warning("The ages vector is not of size nages.");
                                                                    +
                                                                    127  }
                                                                    +
                                                                    128 
                                                                    +
                                                                    129  population->growth_id = this->growth_id;
                                                                    +
                                                                    130  population->recruitment_id = this->recruitment_id;
                                                                    +
                                                                    131  population->maturity_id = this->maturity_id;
                                                                    +
                                                                    132  population->log_M.resize(this->log_M.size());
                                                                    +
                                                                    133  population->log_init_naa.resize(this->log_init_naa.size());
                                                                    +
                                                                    134  for (int i = 0; i < log_M.size(); i++) {
                                                                    +
                                                                    135  population->log_M[i] = this->log_M[i];
                                                                    +
                                                                    136  if (estimate_M) {
                                                                    +
                                                                    137  info->RegisterParameter(population->log_M[i]);
                                                                    +
                                                                    138  }
                                                                    +
                                                                    139  }
                                                                    +
                                                                    140 
                                                                    +
                                                                    141  for (int i = 0; i < log_init_naa.size(); i++) {
                                                                    +
                                                                    142  population->log_init_naa[i] = this->log_init_naa[i];
                                                                    +
                                                                    143  if (estimate_initNAA) {
                                                                    +
                                                                    144  info->RegisterParameter(population->log_init_naa[i]);
                                                                    +
                                                                    145  }
                                                                    +
                                                                    146  }
                                                                    +
                                                                    147  for (int i = 0; i < ages.size(); i++) {
                                                                    +
                                                                    148  population->ages[i] = this->ages[i];
                                                                    +
                                                                    149  }
                                                                    +
                                                                    150  for (int i = 0; i < proportion_female.size(); i++) {
                                                                    +
                                                                    151  population->proportion_female[i] = this->proportion_female[i];
                                                                    +
                                                                    152  if (estimate_prop_female) {
                                                                    +
                                                                    153  info->RegisterParameter(population->proportion_female[i]);
                                                                    +
                                                                    154  }
                                                                    +
                                                                    155  }
                                                                    +
                                                                    156 
                                                                    +
                                                                    157  // add to Information
                                                                    +
                                                                    158  info->populations[population->id] = population;
                                                                    +
                                                                    159 
                                                                    +
                                                                    160  return true;
                                                                    +
                                                                    161  }
                                                                    +
                                                                    162 
                                                                    +
                                                                    165  virtual bool add_to_fims_tmb() {
                                                                    +
                                                                    166  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    +
                                                                    167  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    +
                                                                    168  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    +
                                                                    169  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    +
                                                                    170 
                                                                    +
                                                                    171  return true;
                                                                    +
                                                                    172  }
                                                                    +
                                                                    173 
                                                                    +
                                                                    174 #endif
                                                                    +
                                                                    175 };
                                                                    +
                                                                    176 
                                                                    +
                                                                    177 #endif
                                                                    +
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:61
                                                                    +
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:64
                                                                    +
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:67
                                                                    PopulationInterfaceBase
                                                                    PopulationInterfaceBase class should be inherited to define different Rcpp interfaces for each possib...
                                                                    Definition: rcpp_population.hpp:22
                                                                    PopulationInterfaceBase::id
                                                                    uint32_t id
                                                                    Definition: rcpp_population.hpp:25
                                                                    PopulationInterfaceBase::get_id
                                                                    virtual uint32_t get_id()=0
                                                                    get_id method for child classes to inherit
                                                                    PopulationInterfaceBase::live_objects
                                                                    static std::map< uint32_t, PopulationInterfaceBase * > live_objects
                                                                    Definition: rcpp_population.hpp:28
                                                                    PopulationInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_population.hpp:24
                                                                    PopulationInterface
                                                                    Rcpp interface for a new Population. To instantiate from R: population <- new(population)
                                                                    Definition: rcpp_population.hpp:54
                                                                    -
                                                                    PopulationInterface::SetMaturity
                                                                    void SetMaturity(uint32_t maturity_id)
                                                                    Set the unique id for the Maturity object.
                                                                    Definition: rcpp_population.hpp:95
                                                                    -
                                                                    PopulationInterface::recruitment_id
                                                                    uint32_t recruitment_id
                                                                    Definition: rcpp_population.hpp:63
                                                                    -
                                                                    PopulationInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get_id method for child classes to inherit
                                                                    Definition: rcpp_population.hpp:88
                                                                    +
                                                                    PopulationInterface::SetMaturity
                                                                    void SetMaturity(uint32_t maturity_id)
                                                                    Set the unique id for the Maturity object.
                                                                    Definition: rcpp_population.hpp:83
                                                                    +
                                                                    PopulationInterface::recruitment_id
                                                                    uint32_t recruitment_id
                                                                    Definition: rcpp_population.hpp:62
                                                                    +
                                                                    PopulationInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get_id method for child classes to inherit
                                                                    Definition: rcpp_population.hpp:76
                                                                    PopulationInterface::nyears
                                                                    uint32_t nyears
                                                                    Definition: rcpp_population.hpp:59
                                                                    -
                                                                    PopulationInterface::derived_ssb
                                                                    Rcpp::NumericVector derived_ssb
                                                                    Definition: rcpp_population.hpp:74
                                                                    -
                                                                    PopulationInterface::log_init_naa
                                                                    ParameterVector log_init_naa
                                                                    Definition: rcpp_population.hpp:65
                                                                    +
                                                                    PopulationInterface::log_init_naa
                                                                    Rcpp::NumericVector log_init_naa
                                                                    Definition: rcpp_population.hpp:64
                                                                    PopulationInterface::nages
                                                                    uint32_t nages
                                                                    Definition: rcpp_population.hpp:56
                                                                    PopulationInterface::estimate_prop_female
                                                                    bool estimate_prop_female
                                                                    Definition: rcpp_population.hpp:70
                                                                    PopulationInterface::nfleets
                                                                    uint32_t nfleets
                                                                    Definition: rcpp_population.hpp:57
                                                                    PopulationInterface::nseasons
                                                                    uint32_t nseasons
                                                                    Definition: rcpp_population.hpp:58
                                                                    -
                                                                    PopulationInterface::growth_id
                                                                    uint32_t growth_id
                                                                    Definition: rcpp_population.hpp:62
                                                                    -
                                                                    PopulationInterface::SetRecruitment
                                                                    void SetRecruitment(uint32_t recruitment_id)
                                                                    Set the unique id for the Maturity object.
                                                                    Definition: rcpp_population.hpp:109
                                                                    -
                                                                    PopulationInterface::estimated_log_init_naa
                                                                    Rcpp::NumericVector estimated_log_init_naa
                                                                    Definition: rcpp_population.hpp:80
                                                                    -
                                                                    PopulationInterface::name
                                                                    std::string name
                                                                    Definition: rcpp_population.hpp:82
                                                                    -
                                                                    PopulationInterface::evaluate
                                                                    virtual void evaluate()
                                                                    evaluate the population function
                                                                    Definition: rcpp_population.hpp:114
                                                                    -
                                                                    PopulationInterface::log_M
                                                                    ParameterVector log_M
                                                                    Definition: rcpp_population.hpp:64
                                                                    -
                                                                    PopulationInterface::proportion_female
                                                                    Rcpp::NumericVector proportion_female
                                                                    Definition: rcpp_population.hpp:68
                                                                    -
                                                                    PopulationInterface::estimated_proportion_female
                                                                    Rcpp::NumericVector estimated_proportion_female
                                                                    Definition: rcpp_population.hpp:81
                                                                    -
                                                                    PopulationInterface::numbers_at_age
                                                                    ParameterVector numbers_at_age
                                                                    Definition: rcpp_population.hpp:66
                                                                    -
                                                                    PopulationInterface::to_json
                                                                    virtual std::string to_json()
                                                                    Convert the data to json representation for the output.
                                                                    Definition: rcpp_population.hpp:216
                                                                    -
                                                                    PopulationInterface::ages
                                                                    Rcpp::NumericVector ages
                                                                    Definition: rcpp_population.hpp:67
                                                                    -
                                                                    PopulationInterface::derived_recruitment
                                                                    Rcpp::NumericVector derived_recruitment
                                                                    Definition: rcpp_population.hpp:77
                                                                    -
                                                                    PopulationInterface::derived_naa
                                                                    Rcpp::NumericVector derived_naa
                                                                    Definition: rcpp_population.hpp:75
                                                                    -
                                                                    PopulationInterface::maturity_id
                                                                    uint32_t maturity_id
                                                                    Definition: rcpp_population.hpp:61
                                                                    -
                                                                    PopulationInterface::estimated_log_M
                                                                    Rcpp::NumericVector estimated_log_M
                                                                    Definition: rcpp_population.hpp:79
                                                                    -
                                                                    PopulationInterface::finalize
                                                                    virtual void finalize()
                                                                    finalize function. Extracts derived quantities back to the Rcpp interface object from the Information...
                                                                    Definition: rcpp_population.hpp:123
                                                                    -
                                                                    PopulationInterface::SetGrowth
                                                                    void SetGrowth(uint32_t growth_id)
                                                                    Set the unique id for the growth object.
                                                                    Definition: rcpp_population.hpp:102
                                                                    -
                                                                    PopulationInterface::derived_biomass
                                                                    Rcpp::NumericVector derived_biomass
                                                                    Definition: rcpp_population.hpp:76
                                                                    -
                                                                    PopulationInterface::nlengths
                                                                    uint32_t nlengths
                                                                    Definition: rcpp_population.hpp:60
                                                                    -
                                                                    fims_info::Information::populations
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > > populations
                                                                    Definition: information.hpp:102
                                                                    -
                                                                    fims_info::Information::population_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > >::iterator population_iterator
                                                                    Definition: information.hpp:106
                                                                    -
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:135
                                                                    -
                                                                    FIMS_WARNING_LOG
                                                                    #define FIMS_WARNING_LOG(MESSAGE)
                                                                    Definition: def.hpp:559
                                                                    -
                                                                    FIMS_INFO_LOG
                                                                    #define FIMS_INFO_LOG(MESSAGE)
                                                                    Definition: def.hpp:557
                                                                    -
                                                                    rcpp_interface_base.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    fims_popdy::Population
                                                                    Population class. Contains subpopulations that are divided into generic partitions (eg....
                                                                    Definition: population.hpp:30
                                                                    -
                                                                    fims_popdy::Population::Evaluate
                                                                    void Evaluate()
                                                                    Executes the population loop.
                                                                    Definition: population.hpp:489
                                                                    +
                                                                    PopulationInterface::growth_id
                                                                    uint32_t growth_id
                                                                    Definition: rcpp_population.hpp:61
                                                                    +
                                                                    PopulationInterface::SetRecruitment
                                                                    void SetRecruitment(uint32_t recruitment_id)
                                                                    Set the unique id for the Maturity object.
                                                                    Definition: rcpp_population.hpp:97
                                                                    +
                                                                    PopulationInterface::evaluate
                                                                    virtual void evaluate()
                                                                    evaluate the population function
                                                                    Definition: rcpp_population.hpp:102
                                                                    +
                                                                    PopulationInterface::proportion_female
                                                                    Rcpp::NumericVector proportion_female
                                                                    Definition: rcpp_population.hpp:66
                                                                    +
                                                                    PopulationInterface::estimate_initNAA
                                                                    bool estimate_initNAA
                                                                    Definition: rcpp_population.hpp:69
                                                                    +
                                                                    PopulationInterface::ages
                                                                    Rcpp::NumericVector ages
                                                                    Definition: rcpp_population.hpp:65
                                                                    +
                                                                    PopulationInterface::maturity_id
                                                                    uint32_t maturity_id
                                                                    Definition: rcpp_population.hpp:60
                                                                    +
                                                                    PopulationInterface::estimate_M
                                                                    bool estimate_M
                                                                    Definition: rcpp_population.hpp:68
                                                                    +
                                                                    PopulationInterface::SetGrowth
                                                                    void SetGrowth(uint32_t growth_id)
                                                                    Set the unique id for the growth object.
                                                                    Definition: rcpp_population.hpp:90
                                                                    +
                                                                    PopulationInterface::log_M
                                                                    Rcpp::NumericVector log_M
                                                                    Definition: rcpp_population.hpp:63
                                                                    +
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:126
                                                                    +
                                                                    fims_popdy::Population
                                                                    Population class. Contains subpopulations that are divided into generic partitions (eg....
                                                                    Definition: population.hpp:36
                                                                    +
                                                                    fims_popdy::Population::Evaluate
                                                                    void Evaluate()
                                                                    Executes the population loop.
                                                                    Definition: population.hpp:561
                                                                    diff --git a/docs/rcpp__recruitment_8hpp_source.html b/docs/rcpp__recruitment_8hpp_source.html index 7e81682..88fa5e4 100644 --- a/docs/rcpp__recruitment_8hpp_source.html +++ b/docs/rcpp__recruitment_8hpp_source.html @@ -76,276 +76,197 @@
                                                                    rcpp_recruitment.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    8 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_RECRUITMENT_HPP
                                                                    -
                                                                    9 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_RECRUITMENT_HPP
                                                                    -
                                                                    10 
                                                                    -
                                                                    11 #include "../../../population_dynamics/recruitment/recruitment.hpp"
                                                                    -
                                                                    12 #include "rcpp_interface_base.hpp"
                                                                    -
                                                                    13 
                                                                    -
                                                                    22 class RecruitmentInterfaceBase : public FIMSRcppInterfaceBase {
                                                                    -
                                                                    23  public:
                                                                    -
                                                                    24  static uint32_t id_g;
                                                                    -
                                                                    25  uint32_t id;
                                                                    -
                                                                    26  // live objects in C++ are objects that have been created and live in memory
                                                                    -
                                                                    27  static std::map<uint32_t, RecruitmentInterfaceBase*> live_objects;
                                                                    -
                                                                    30  // static std::vector<double> log_recruit_devs; /**< vector of log recruitment
                                                                    -
                                                                    31  // deviations*/
                                                                    -
                                                                    32  // static bool constrain_deviations; /**< whether or not the rec devs are
                                                                    -
                                                                    33  // constrained*/
                                                                    -
                                                                    34 
                                                                    -
                                                                    35  RecruitmentInterfaceBase() {
                                                                    -
                                                                    36  this->id = RecruitmentInterfaceBase::id_g++;
                                                                    -
                                                                    37  /* Create instance of map: key is id and value is pointer to
                                                                    -
                                                                    38  RecruitmentInterfaceBase */
                                                                    -
                                                                    39  RecruitmentInterfaceBase::live_objects[this->id] = this;
                                                                    -
                                                                    40  FIMSRcppInterfaceBase::fims_interface_objects.push_back(this);
                                                                    -
                                                                    41  }
                                                                    -
                                                                    42 
                                                                    -
                                                                    43  virtual ~RecruitmentInterfaceBase() {}
                                                                    -
                                                                    44 
                                                                    -
                                                                    47  virtual uint32_t get_id() = 0;
                                                                    -
                                                                    48 
                                                                    -
                                                                    51  virtual double evaluate(double spawners, double ssbzero) = 0;
                                                                    -
                                                                    52 
                                                                    -
                                                                    53 };
                                                                    -
                                                                    54 
                                                                    -
                                                                    55 uint32_t RecruitmentInterfaceBase::id_g = 1;
                                                                    -
                                                                    56 std::map<uint32_t, RecruitmentInterfaceBase*>
                                                                    -
                                                                    57  RecruitmentInterfaceBase::live_objects;
                                                                    -
                                                                    58 
                                                                    -
                                                                    64 class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
                                                                    -
                                                                    65  public:
                                                                    -
                                                                    66  ParameterVector logit_steep;
                                                                    -
                                                                    67  ParameterVector log_rzero;
                                                                    -
                                                                    68  ParameterVector log_devs;
                                                                    -
                                                                    69  bool estimate_log_devs = false;
                                                                    -
                                                                    71  double estimated_logit_steep;
                                                                    -
                                                                    72  double estimated_log_rzero;
                                                                    -
                                                                    73  Rcpp::NumericVector estimated_log_devs;
                                                                    -
                                                                    75  BevertonHoltRecruitmentInterface() : RecruitmentInterfaceBase() {}
                                                                    -
                                                                    76 
                                                                    -
                                                                    77  virtual ~BevertonHoltRecruitmentInterface() {}
                                                                    -
                                                                    78 
                                                                    -
                                                                    79  virtual uint32_t get_id() { return this->id; }
                                                                    -
                                                                    80 
                                                                    -
                                                                    81  virtual double evaluate(double spawners, double ssbzero) {
                                                                    -
                                                                    82  fims_popdy::SRBevertonHolt<double> BevHolt;
                                                                    -
                                                                    83  BevHolt.logit_steep.resize(1);
                                                                    -
                                                                    84  BevHolt.logit_steep[0] = this->logit_steep[0].initial_value_m;
                                                                    -
                                                                    85  if (this->logit_steep[0].initial_value_m == 1.0) {
                                                                    -
                                                                    86  warning(
                                                                    -
                                                                    87  "Steepness is subject to a logit transformation, so its value is "
                                                                    -
                                                                    88  "0.7848469. Fixing it at 1.0 is not currently possible.");
                                                                    -
                                                                    89  }
                                                                    -
                                                                    90  BevHolt.log_rzero.resize(1);
                                                                    -
                                                                    91  BevHolt.log_rzero[0] = this->log_rzero[0].initial_value_m;
                                                                    -
                                                                    92 
                                                                    -
                                                                    93  return BevHolt.evaluate(spawners, ssbzero);
                                                                    -
                                                                    94  }
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: rcpp_recruitment.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    5  * Fisheries Integrated Modeling System project. See LICENSE
                                                                    +
                                                                    6  * file for reuse information.
                                                                    +
                                                                    7  *
                                                                    +
                                                                    8  */
                                                                    +
                                                                    9 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_RECRUITMENT_HPP
                                                                    +
                                                                    10 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_RECRUITMENT_HPP
                                                                    +
                                                                    11 
                                                                    +
                                                                    12 #include "../../../population_dynamics/recruitment/recruitment.hpp"
                                                                    +
                                                                    13 #include "rcpp_interface_base.hpp"
                                                                    +
                                                                    14 
                                                                    +
                                                                    23 class RecruitmentInterfaceBase : public FIMSRcppInterfaceBase {
                                                                    +
                                                                    24  public:
                                                                    +
                                                                    25  static uint32_t id_g;
                                                                    +
                                                                    26  uint32_t id;
                                                                    +
                                                                    27  // live objects in C++ are objects that have been created and live in memory
                                                                    +
                                                                    28  static std::map<uint32_t, RecruitmentInterfaceBase*> live_objects;
                                                                    +
                                                                    31  // static std::vector<double> log_recruit_devs; /**< vector of log recruitment
                                                                    +
                                                                    32  // deviations*/
                                                                    +
                                                                    33  // static bool constrain_deviations; /**< whether or not the rec devs are
                                                                    +
                                                                    34  // constrained*/
                                                                    +
                                                                    35 
                                                                    +
                                                                    36  RecruitmentInterfaceBase() {
                                                                    +
                                                                    37  this->id = RecruitmentInterfaceBase::id_g++;
                                                                    +
                                                                    38  /* Create instance of map: key is id and value is pointer to
                                                                    +
                                                                    39  RecruitmentInterfaceBase */
                                                                    +
                                                                    40  RecruitmentInterfaceBase::live_objects[this->id] = this;
                                                                    +
                                                                    41  FIMSRcppInterfaceBase::fims_interface_objects.push_back(this);
                                                                    +
                                                                    42  }
                                                                    +
                                                                    43 
                                                                    +
                                                                    44  virtual ~RecruitmentInterfaceBase() {}
                                                                    +
                                                                    45 
                                                                    +
                                                                    48  virtual uint32_t get_id() = 0;
                                                                    +
                                                                    49 
                                                                    +
                                                                    52  virtual double evaluate(double spawners, double ssbzero) = 0;
                                                                    +
                                                                    53 
                                                                    +
                                                                    59  virtual double evaluate_nll() = 0;
                                                                    +
                                                                    60 };
                                                                    +
                                                                    61 
                                                                    +
                                                                    62 uint32_t RecruitmentInterfaceBase::id_g = 1;
                                                                    +
                                                                    63 std::map<uint32_t, RecruitmentInterfaceBase*>
                                                                    +
                                                                    64  RecruitmentInterfaceBase::live_objects;
                                                                    +
                                                                    65 
                                                                    +
                                                                    71 class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
                                                                    +
                                                                    72  public:
                                                                    +
                                                                    73  Parameter logit_steep;
                                                                    +
                                                                    74  Parameter log_rzero;
                                                                    +
                                                                    75  Parameter
                                                                    +
                                                                    76  log_sigma_recruit;
                                                                    +
                                                                    77  Rcpp::NumericVector log_devs;
                                                                    +
                                                                    78  bool estimate_log_devs = false;
                                                                    +
                                                                    80  BevertonHoltRecruitmentInterface() : RecruitmentInterfaceBase() {}
                                                                    +
                                                                    81 
                                                                    +
                                                                    82  virtual ~BevertonHoltRecruitmentInterface() {}
                                                                    +
                                                                    83 
                                                                    +
                                                                    84  virtual uint32_t get_id() { return this->id; }
                                                                    +
                                                                    85 
                                                                    +
                                                                    86  virtual double evaluate(double spawners, double ssbzero) {
                                                                    +
                                                                    87  fims_popdy::SRBevertonHolt<double> BevHolt;
                                                                    +
                                                                    88 
                                                                    +
                                                                    89  BevHolt.logit_steep = this->logit_steep.value_m;
                                                                    +
                                                                    90  if (this->logit_steep.value_m == 1.0) {
                                                                    +
                                                                    91  warning(
                                                                    +
                                                                    92  "Steepness is subject to a logit transformation, so its value is "
                                                                    +
                                                                    93  "0.7848469. Fixing it at 1.0 is not currently possible.");
                                                                    +
                                                                    94  }
                                                                    95 
                                                                    -
                                                                    100  virtual void finalize() {
                                                                    -
                                                                    101 
                                                                    -
                                                                    102  if (this->finalized) {
                                                                    -
                                                                    103  //log warning that finalize has been called more than once.
                                                                    -
                                                                    104  FIMS_WARNING_LOG("Beverton-Holt Recruitment " + fims::to_string(this->id) + " has been finalized already.");
                                                                    -
                                                                    105  }
                                                                    -
                                                                    106 
                                                                    -
                                                                    107  this->finalized = true; //indicate this has been called already
                                                                    -
                                                                    108 
                                                                    -
                                                                    109  std::shared_ptr<fims_info::Information<double> > info =
                                                                    -
                                                                    110  fims_info::Information<double>::GetInstance();
                                                                    -
                                                                    111 
                                                                    -
                                                                    112 
                                                                    -
                                                                    113  fims_info::Information<double>::recruitment_models_iterator it;
                                                                    +
                                                                    96  BevHolt.log_rzero = this->log_rzero.value_m;
                                                                    +
                                                                    97 
                                                                    +
                                                                    98  return BevHolt.evaluate(spawners, ssbzero);
                                                                    +
                                                                    99  }
                                                                    +
                                                                    100 
                                                                    +
                                                                    101  virtual double evaluate_nll() {
                                                                    +
                                                                    102  fims_popdy::SRBevertonHolt<double> NLL;
                                                                    +
                                                                    103 
                                                                    +
                                                                    104  NLL.log_sigma_recruit = this->log_sigma_recruit.value_m;
                                                                    +
                                                                    105  NLL.log_recruit_devs.resize(log_devs.size()); // Vector from TMB
                                                                    +
                                                                    106  for (int i = 0; i < log_devs.size(); i++) {
                                                                    +
                                                                    107  NLL.log_recruit_devs[i] = log_devs[i];
                                                                    +
                                                                    108  }
                                                                    +
                                                                    109  RECRUITMENT_LOG << "Log recruit devs being passed to C++ are " << log_devs
                                                                    +
                                                                    110  << std::endl;
                                                                    +
                                                                    111  NLL.estimate_log_recruit_devs = this->estimate_log_devs;
                                                                    +
                                                                    112  return NLL.evaluate_nll();
                                                                    +
                                                                    113  }
                                                                    114 
                                                                    -
                                                                    115  it = info->recruitment_models.find(this->id);
                                                                    +
                                                                    115 #ifdef TMB_MODEL
                                                                    116 
                                                                    -
                                                                    117  if (it == info->recruitment_models.end()) {
                                                                    -
                                                                    118  FIMS_WARNING_LOG("Beverton-Holt Recruitment " + fims::to_string(this->id) + " not found in Information.");
                                                                    -
                                                                    119  return;
                                                                    -
                                                                    120  } else {
                                                                    +
                                                                    117  template <typename Type>
                                                                    +
                                                                    118  bool add_to_fims_tmb_internal() {
                                                                    +
                                                                    119  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    +
                                                                    120  fims_info::Information<Type>::GetInstance();
                                                                    121 
                                                                    -
                                                                    122  std::shared_ptr<fims_popdy::SRBevertonHolt<double> > recr =
                                                                    -
                                                                    123  std::dynamic_pointer_cast<fims_popdy::SRBevertonHolt<double> >(it->second);
                                                                    +
                                                                    122  std::shared_ptr<fims_popdy::SRBevertonHolt<Type> > recruitment =
                                                                    +
                                                                    123  std::make_shared<fims_popdy::SRBevertonHolt<Type> >();
                                                                    124 
                                                                    -
                                                                    125  for (size_t i = 0; i < this->logit_steep.size(); i++) {
                                                                    -
                                                                    126  if (this->logit_steep[i].estimated_m) {
                                                                    -
                                                                    127  this->logit_steep[i].final_value_m = recr->logit_steep[i];
                                                                    -
                                                                    128  } else {
                                                                    -
                                                                    129  this->logit_steep[i].final_value_m = this->logit_steep[i].initial_value_m;
                                                                    -
                                                                    130  }
                                                                    -
                                                                    131  }
                                                                    -
                                                                    132 
                                                                    -
                                                                    133  for (size_t i = 0; i < log_rzero.size(); i++) {
                                                                    -
                                                                    134  if (log_rzero[i].estimated_m) {
                                                                    -
                                                                    135  this->log_rzero[i].final_value_m = recr->log_rzero[i];
                                                                    -
                                                                    136  } else {
                                                                    -
                                                                    137  this->log_rzero[i].final_value_m = this->log_rzero[i].initial_value_m;
                                                                    -
                                                                    138  }
                                                                    -
                                                                    139  }
                                                                    -
                                                                    140 
                                                                    -
                                                                    141  for (size_t i = 0; i < this->estimated_log_devs.size(); i++) {
                                                                    -
                                                                    142  if (this->log_devs[i].estimated_m) {
                                                                    -
                                                                    143  this->log_devs[i].final_value_m = recr->log_recruit_devs[i];
                                                                    -
                                                                    144  } else {
                                                                    -
                                                                    145  this->log_devs[i].final_value_m = this->log_devs[i].initial_value_m;
                                                                    -
                                                                    146  }
                                                                    -
                                                                    147  }
                                                                    -
                                                                    148  }
                                                                    -
                                                                    149 
                                                                    -
                                                                    150 
                                                                    -
                                                                    151  }
                                                                    -
                                                                    152 
                                                                    -
                                                                    156  virtual std::string to_json() {
                                                                    -
                                                                    157  std::stringstream ss;
                                                                    -
                                                                    158 
                                                                    -
                                                                    159  ss << "\"module\" : {\n";
                                                                    -
                                                                    160  ss << " \"name\": \"recruitment\",\n";
                                                                    -
                                                                    161  ss << " \"type\": \"Beverton-Holt\",\n";
                                                                    -
                                                                    162  ss << " \"id\": " << this->id << ",\n";
                                                                    -
                                                                    163 
                                                                    -
                                                                    164  ss << " \"parameter\": {\n";
                                                                    -
                                                                    165  ss << " \"name\": \"logit_steep\",\n";
                                                                    -
                                                                    166  ss << " \"id\":" << this->logit_steep.id_m << ",\n";
                                                                    -
                                                                    167  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    168  ss << " \"values\":" << this->logit_steep << ",\n},\n";
                                                                    -
                                                                    169 
                                                                    -
                                                                    170  ss << " \"parameter\": {\n";
                                                                    -
                                                                    171  ss << " \"name\": \"log_rzero\",\n";
                                                                    -
                                                                    172  ss << " \"id\":" << this->log_rzero.id_m << ",\n";
                                                                    -
                                                                    173  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    174  ss << " \"values\":" << this->log_rzero << ",\n },\n";
                                                                    -
                                                                    175 
                                                                    -
                                                                    176  ss << " \"parameter\": {\n";
                                                                    -
                                                                    177  ss << " \"name\": \"log_devs\",\n";
                                                                    -
                                                                    178  ss << " \"id\":" << this->log_devs.id_m << ",\n";
                                                                    -
                                                                    179  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    180  ss << " \"values\":" << this->log_devs << ",\n },\n";
                                                                    +
                                                                    125  // set relative info
                                                                    +
                                                                    126  recruitment->id = this->id;
                                                                    +
                                                                    127  recruitment->logit_steep = this->logit_steep.value_m;
                                                                    +
                                                                    128  if (this->logit_steep.estimated_m) {
                                                                    +
                                                                    129  if (this->logit_steep.is_random_effect_m) {
                                                                    +
                                                                    130  info->RegisterRandomEffect(recruitment->logit_steep);
                                                                    +
                                                                    131  } else {
                                                                    +
                                                                    132  info->RegisterParameter(recruitment->logit_steep);
                                                                    +
                                                                    133  }
                                                                    +
                                                                    134  }
                                                                    +
                                                                    135  recruitment->log_rzero = this->log_rzero.value_m;
                                                                    +
                                                                    136  if (this->log_rzero.estimated_m) {
                                                                    +
                                                                    137  if (this->log_rzero.is_random_effect_m) {
                                                                    +
                                                                    138  info->RegisterRandomEffect(recruitment->log_rzero);
                                                                    +
                                                                    139  } else {
                                                                    +
                                                                    140  info->RegisterParameter(recruitment->log_rzero);
                                                                    +
                                                                    141  }
                                                                    +
                                                                    142  }
                                                                    +
                                                                    143  recruitment->log_sigma_recruit = this->log_sigma_recruit.value_m;
                                                                    +
                                                                    144  if (this->log_sigma_recruit.estimated_m) {
                                                                    +
                                                                    145  if (this->log_sigma_recruit.is_random_effect_m) {
                                                                    +
                                                                    146  info->RegisterRandomEffect(recruitment->log_sigma_recruit);
                                                                    +
                                                                    147  } else {
                                                                    +
                                                                    148  info->RegisterParameter(recruitment->log_sigma_recruit);
                                                                    +
                                                                    149  }
                                                                    +
                                                                    150  }
                                                                    +
                                                                    151 
                                                                    +
                                                                    152  recruitment->log_recruit_devs.resize(this->log_devs.size());
                                                                    +
                                                                    153  if (this->estimate_log_devs) {
                                                                    +
                                                                    154  for (size_t i = 0; i < recruitment->log_recruit_devs.size(); i++) {
                                                                    +
                                                                    155  recruitment->log_recruit_devs[i] = this->log_devs[i];
                                                                    +
                                                                    156  info->RegisterParameter(recruitment->log_recruit_devs[i]);
                                                                    +
                                                                    157  }
                                                                    +
                                                                    158  } else {
                                                                    +
                                                                    159  recruitment->estimate_log_recruit_devs = estimate_log_devs;
                                                                    +
                                                                    160  for (size_t i = 0; i < recruitment->log_recruit_devs.size(); i++) {
                                                                    +
                                                                    161  recruitment->log_recruit_devs[i] = this->log_devs[i];
                                                                    +
                                                                    162  }
                                                                    +
                                                                    163  }
                                                                    +
                                                                    164 
                                                                    +
                                                                    165  // add to Information
                                                                    +
                                                                    166  info->recruitment_models[recruitment->id] = recruitment;
                                                                    +
                                                                    167 
                                                                    +
                                                                    168  return true;
                                                                    +
                                                                    169  }
                                                                    +
                                                                    170 
                                                                    +
                                                                    173  virtual bool add_to_fims_tmb() {
                                                                    +
                                                                    174  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    +
                                                                    175  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    +
                                                                    176  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    +
                                                                    177  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    +
                                                                    178 
                                                                    +
                                                                    179  return true;
                                                                    +
                                                                    180  }
                                                                    181 
                                                                    -
                                                                    182 
                                                                    -
                                                                    183  return ss.str();
                                                                    -
                                                                    184  }
                                                                    -
                                                                    185 
                                                                    -
                                                                    186 #ifdef TMB_MODEL
                                                                    -
                                                                    187 
                                                                    -
                                                                    188  template <typename Type>
                                                                    -
                                                                    189  bool add_to_fims_tmb_internal() {
                                                                    -
                                                                    190  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    -
                                                                    191  fims_info::Information<Type>::GetInstance();
                                                                    -
                                                                    192 
                                                                    -
                                                                    193  std::shared_ptr<fims_popdy::SRBevertonHolt<Type> > recruitment =
                                                                    -
                                                                    194  std::make_shared<fims_popdy::SRBevertonHolt<Type> >();
                                                                    -
                                                                    195 
                                                                    -
                                                                    196  // set relative info
                                                                    -
                                                                    197  recruitment->id = this->id;
                                                                    -
                                                                    198  //set logit_steep
                                                                    -
                                                                    199  recruitment->logit_steep.resize(this->logit_steep.size());
                                                                    -
                                                                    200  for (size_t i = 0; i < this->logit_steep.size(); i++) {
                                                                    -
                                                                    201 
                                                                    -
                                                                    202  recruitment->logit_steep[i] = this->logit_steep[i].initial_value_m;
                                                                    -
                                                                    203 
                                                                    -
                                                                    204  if (this->logit_steep[i].estimated_m) {
                                                                    -
                                                                    205  info->RegisterParameterName("logit_steep");
                                                                    -
                                                                    206  if (this->logit_steep[i].is_random_effect_m) {
                                                                    -
                                                                    207  info->RegisterRandomEffect(recruitment->logit_steep[i]);
                                                                    -
                                                                    208  } else {
                                                                    -
                                                                    209  info->RegisterParameter(recruitment->logit_steep[i]);
                                                                    -
                                                                    210  }
                                                                    -
                                                                    211  }
                                                                    -
                                                                    212 
                                                                    -
                                                                    213  }
                                                                    -
                                                                    214 
                                                                    -
                                                                    215  info->variable_map[this->logit_steep.id_m] = &(recruitment)->logit_steep;
                                                                    -
                                                                    216 
                                                                    -
                                                                    217 
                                                                    -
                                                                    218  //set log_rzero
                                                                    -
                                                                    219  recruitment->log_rzero.resize(this->log_rzero.size());
                                                                    -
                                                                    220  for (size_t i = 0; i < this->log_rzero.size(); i++) {
                                                                    -
                                                                    221 
                                                                    -
                                                                    222  recruitment->log_rzero[i] = this->log_rzero[i].initial_value_m;
                                                                    -
                                                                    223 
                                                                    -
                                                                    224  if (this->log_rzero[i].estimated_m) {
                                                                    -
                                                                    225  info->RegisterParameterName("log_rzero");
                                                                    -
                                                                    226  if (this->log_rzero[i].is_random_effect_m) {
                                                                    -
                                                                    227  info->RegisterRandomEffect(recruitment->log_rzero[i]);
                                                                    -
                                                                    228  } else {
                                                                    -
                                                                    229  info->RegisterParameter(recruitment->log_rzero[i]);
                                                                    -
                                                                    230  }
                                                                    -
                                                                    231  }
                                                                    -
                                                                    232  }
                                                                    -
                                                                    233 
                                                                    -
                                                                    234  info->variable_map[this->log_rzero.id_m] = &(recruitment)->log_rzero;
                                                                    -
                                                                    235 
                                                                    -
                                                                    236  //set log_recruit_devs
                                                                    -
                                                                    237  recruitment->log_recruit_devs.resize(this->log_devs.size());
                                                                    -
                                                                    238  for (size_t i = 0; i < this->log_devs.size(); i++) {
                                                                    -
                                                                    239  recruitment->log_recruit_devs[i] = this->log_devs[i].initial_value_m;
                                                                    -
                                                                    240  if (this->log_devs[i].estimated_m) {
                                                                    -
                                                                    241  info->RegisterParameter(recruitment->log_recruit_devs[i]);
                                                                    -
                                                                    242  } else {
                                                                    -
                                                                    243  recruitment->estimate_log_recruit_devs = false;
                                                                    -
                                                                    244  }
                                                                    -
                                                                    245 
                                                                    -
                                                                    246  }
                                                                    -
                                                                    247  info->variable_map[this->log_devs.id_m] = &(recruitment)->log_recruit_devs;
                                                                    -
                                                                    248 
                                                                    -
                                                                    249  // add to Information
                                                                    -
                                                                    250  info->recruitment_models[recruitment->id] = recruitment;
                                                                    -
                                                                    251 
                                                                    -
                                                                    252  return true;
                                                                    -
                                                                    253  }
                                                                    -
                                                                    254 
                                                                    -
                                                                    257  virtual bool add_to_fims_tmb() {
                                                                    -
                                                                    258  FIMS_INFO_LOG("adding Recruitment object to TMB");
                                                                    -
                                                                    259  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    -
                                                                    260  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    -
                                                                    261  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    -
                                                                    262  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    -
                                                                    263 
                                                                    -
                                                                    264  return true;
                                                                    -
                                                                    265  }
                                                                    -
                                                                    266 
                                                                    -
                                                                    267 #endif
                                                                    -
                                                                    268 };
                                                                    -
                                                                    269 
                                                                    -
                                                                    270 #endif
                                                                    -
                                                                    BevertonHoltRecruitmentInterface
                                                                    Rcpp interface for Beverton-Holt as an S4 object. To instantiate from R: beverton_holt <- new(beverto...
                                                                    Definition: rcpp_recruitment.hpp:64
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::log_devs
                                                                    ParameterVector log_devs
                                                                    Definition: rcpp_recruitment.hpp:68
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::logit_steep
                                                                    ParameterVector logit_steep
                                                                    Definition: rcpp_recruitment.hpp:66
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::to_json
                                                                    virtual std::string to_json()
                                                                    Convert the data to json representation for the output.
                                                                    Definition: rcpp_recruitment.hpp:156
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::estimated_logit_steep
                                                                    double estimated_logit_steep
                                                                    Definition: rcpp_recruitment.hpp:71
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::finalize
                                                                    virtual void finalize()
                                                                    finalize function. Extracts derived quantities back to the Rcpp interface object from the Information...
                                                                    Definition: rcpp_recruitment.hpp:100
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::evaluate
                                                                    virtual double evaluate(double spawners, double ssbzero)
                                                                    evaluate method for child recruitment interface objects to inherit
                                                                    Definition: rcpp_recruitment.hpp:81
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::estimated_log_rzero
                                                                    double estimated_log_rzero
                                                                    Definition: rcpp_recruitment.hpp:72
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::estimated_log_devs
                                                                    Rcpp::NumericVector estimated_log_devs
                                                                    Definition: rcpp_recruitment.hpp:73
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::log_rzero
                                                                    ParameterVector log_rzero
                                                                    Definition: rcpp_recruitment.hpp:67
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_recruitment.hpp:79
                                                                    -
                                                                    BevertonHoltRecruitmentInterface::estimate_log_devs
                                                                    bool estimate_log_devs
                                                                    Definition: rcpp_recruitment.hpp:69
                                                                    -
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:336
                                                                    -
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:342
                                                                    -
                                                                    FIMSRcppInterfaceBase::finalized
                                                                    bool finalized
                                                                    Definition: rcpp_interface_base.hpp:339
                                                                    -
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:345
                                                                    -
                                                                    ParameterVector
                                                                    Rcpp representation of a Parameter vector interface between R and cpp.
                                                                    Definition: rcpp_interface_base.hpp:120
                                                                    -
                                                                    ParameterVector::resize
                                                                    void resize(size_t size)
                                                                    resize to length "size"
                                                                    Definition: rcpp_interface_base.hpp:242
                                                                    -
                                                                    ParameterVector::size
                                                                    size_t size()
                                                                    returns vector length
                                                                    Definition: rcpp_interface_base.hpp:234
                                                                    -
                                                                    ParameterVector::id_m
                                                                    uint32_t id_m
                                                                    Definition: rcpp_interface_base.hpp:124
                                                                    -
                                                                    RecruitmentInterfaceBase
                                                                    RecruitmentInterfaceBase class should be inherited to define different Rcpp interfaces for each possi...
                                                                    Definition: rcpp_recruitment.hpp:22
                                                                    -
                                                                    RecruitmentInterfaceBase::live_objects
                                                                    static std::map< uint32_t, RecruitmentInterfaceBase * > live_objects
                                                                    Definition: rcpp_recruitment.hpp:27
                                                                    -
                                                                    RecruitmentInterfaceBase::id
                                                                    uint32_t id
                                                                    Definition: rcpp_recruitment.hpp:25
                                                                    +
                                                                    182 #endif
                                                                    +
                                                                    183 };
                                                                    +
                                                                    184 
                                                                    +
                                                                    185 #endif
                                                                    +
                                                                    BevertonHoltRecruitmentInterface
                                                                    Rcpp interface for Beverton-Holt as an S4 object. To instantiate from R: beverton_holt <- new(beverto...
                                                                    Definition: rcpp_recruitment.hpp:71
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::evaluate_nll
                                                                    virtual double evaluate_nll()
                                                                    evaluate recruitment nll
                                                                    Definition: rcpp_recruitment.hpp:101
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::logit_steep
                                                                    Parameter logit_steep
                                                                    Definition: rcpp_recruitment.hpp:73
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::evaluate
                                                                    virtual double evaluate(double spawners, double ssbzero)
                                                                    evaluate method for child recruitment interface objects to inherit
                                                                    Definition: rcpp_recruitment.hpp:86
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::log_devs
                                                                    Rcpp::NumericVector log_devs
                                                                    Definition: rcpp_recruitment.hpp:77
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    get the ID of the interface base object
                                                                    Definition: rcpp_recruitment.hpp:84
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::log_sigma_recruit
                                                                    Parameter log_sigma_recruit
                                                                    Definition: rcpp_recruitment.hpp:76
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::log_rzero
                                                                    Parameter log_rzero
                                                                    Definition: rcpp_recruitment.hpp:74
                                                                    +
                                                                    BevertonHoltRecruitmentInterface::estimate_log_devs
                                                                    bool estimate_log_devs
                                                                    Definition: rcpp_recruitment.hpp:78
                                                                    +
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:61
                                                                    +
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:64
                                                                    +
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:67
                                                                    +
                                                                    Parameter
                                                                    RcppInterface class that defines the interface between R and C++ for parameter types.
                                                                    Definition: rcpp_interface_base.hpp:26
                                                                    +
                                                                    Parameter::estimated_m
                                                                    bool estimated_m
                                                                    Definition: rcpp_interface_base.hpp:35
                                                                    +
                                                                    Parameter::value_m
                                                                    double value_m
                                                                    Definition: rcpp_interface_base.hpp:28
                                                                    +
                                                                    Parameter::is_random_effect_m
                                                                    bool is_random_effect_m
                                                                    Definition: rcpp_interface_base.hpp:33
                                                                    +
                                                                    RecruitmentInterfaceBase
                                                                    RecruitmentInterfaceBase class should be inherited to define different Rcpp interfaces for each possi...
                                                                    Definition: rcpp_recruitment.hpp:23
                                                                    +
                                                                    RecruitmentInterfaceBase::live_objects
                                                                    static std::map< uint32_t, RecruitmentInterfaceBase * > live_objects
                                                                    Definition: rcpp_recruitment.hpp:28
                                                                    +
                                                                    RecruitmentInterfaceBase::id
                                                                    uint32_t id
                                                                    Definition: rcpp_recruitment.hpp:26
                                                                    RecruitmentInterfaceBase::get_id
                                                                    virtual uint32_t get_id()=0
                                                                    get the ID of the interface base object
                                                                    RecruitmentInterfaceBase::evaluate
                                                                    virtual double evaluate(double spawners, double ssbzero)=0
                                                                    evaluate method for child recruitment interface objects to inherit
                                                                    -
                                                                    RecruitmentInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_recruitment.hpp:24
                                                                    -
                                                                    fims_info::Information::recruitment_models_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > >::iterator recruitment_models_iterator
                                                                    Definition: information.hpp:63
                                                                    -
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:135
                                                                    -
                                                                    fims_info::Information::recruitment_models
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > > recruitment_models
                                                                    Definition: information.hpp:59
                                                                    -
                                                                    FIMS_WARNING_LOG
                                                                    #define FIMS_WARNING_LOG(MESSAGE)
                                                                    Definition: def.hpp:559
                                                                    -
                                                                    FIMS_INFO_LOG
                                                                    #define FIMS_INFO_LOG(MESSAGE)
                                                                    Definition: def.hpp:557
                                                                    -
                                                                    rcpp_interface_base.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    fims_popdy::RecruitmentBase::log_rzero
                                                                    fims::Vector< Type > log_rzero
                                                                    Definition: recruitment_base.hpp:36
                                                                    -
                                                                    fims_popdy::SRBevertonHolt
                                                                    BevertonHolt class that returns the Beverton Holt SR from fims_math.
                                                                    Definition: sr_beverton_holt.hpp:25
                                                                    -
                                                                    fims_popdy::SRBevertonHolt::evaluate
                                                                    virtual const Type evaluate(const Type &spawners, const Type &phi_0)
                                                                    Beverton Holt implementation of the stock recruitment function.
                                                                    Definition: sr_beverton_holt.hpp:45
                                                                    -
                                                                    fims_popdy::SRBevertonHolt::logit_steep
                                                                    fims::Vector< Type > logit_steep
                                                                    Definition: sr_beverton_holt.hpp:29
                                                                    +
                                                                    RecruitmentInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_recruitment.hpp:25
                                                                    +
                                                                    RecruitmentInterfaceBase::evaluate_nll
                                                                    virtual double evaluate_nll()=0
                                                                    evaluate recruitment nll
                                                                    +
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:126
                                                                    +
                                                                    RECRUITMENT_LOG
                                                                    std::ofstream RECRUITMENT_LOG("logs/recruitment.log")
                                                                    +
                                                                    fims_popdy::RecruitmentBase::evaluate_nll
                                                                    virtual const Type evaluate_nll()
                                                                    Calculates the negative log likelihood of recruitment deviations.
                                                                    Definition: recruitment_base.hpp:72
                                                                    +
                                                                    fims_popdy::RecruitmentBase::log_sigma_recruit
                                                                    Type log_sigma_recruit
                                                                    Definition: recruitment_base.hpp:40
                                                                    +
                                                                    fims_popdy::RecruitmentBase::estimate_log_recruit_devs
                                                                    bool estimate_log_recruit_devs
                                                                    Definition: recruitment_base.hpp:44
                                                                    +
                                                                    fims_popdy::RecruitmentBase::log_rzero
                                                                    Type log_rzero
                                                                    Definition: recruitment_base.hpp:42
                                                                    +
                                                                    fims_popdy::RecruitmentBase::log_recruit_devs
                                                                    fims::Vector< Type > log_recruit_devs
                                                                    Definition: recruitment_base.hpp:36
                                                                    +
                                                                    fims_popdy::SRBevertonHolt
                                                                    BevertonHolt class that returns the Beverton Holt SR from fims_math.
                                                                    Definition: sr_beverton_holt.hpp:27
                                                                    +
                                                                    fims_popdy::SRBevertonHolt::logit_steep
                                                                    Type logit_steep
                                                                    Definition: sr_beverton_holt.hpp:31
                                                                    +
                                                                    fims_popdy::SRBevertonHolt::evaluate
                                                                    virtual const Type evaluate(const Type &spawners, const Type &phi_0)
                                                                    Beverton Holt implementation of the stock recruitment function.
                                                                    Definition: sr_beverton_holt.hpp:47
                                                                    diff --git a/docs/rcpp__selectivity_8hpp_source.html b/docs/rcpp__selectivity_8hpp_source.html index 09dd628..3c56436 100644 --- a/docs/rcpp__selectivity_8hpp_source.html +++ b/docs/rcpp__selectivity_8hpp_source.html @@ -76,472 +76,233 @@
                                                                    rcpp_selectivity.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    8 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_SELECTIVITY_HPP
                                                                    -
                                                                    9 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_SELECTIVITY_HPP
                                                                    -
                                                                    10 
                                                                    -
                                                                    11 #include "../../../population_dynamics/selectivity/selectivity.hpp"
                                                                    -
                                                                    12 #include "rcpp_interface_base.hpp"
                                                                    -
                                                                    13 
                                                                    -
                                                                    22 class SelectivityInterfaceBase : public FIMSRcppInterfaceBase {
                                                                    -
                                                                    23  public:
                                                                    -
                                                                    24  static uint32_t id_g;
                                                                    -
                                                                    25  uint32_t id;
                                                                    -
                                                                    26  // live objects in C++ are objects that have been created and live in memory
                                                                    -
                                                                    27  static std::map<uint32_t, SelectivityInterfaceBase*>
                                                                    -
                                                                    28  live_objects;
                                                                    -
                                                                    31  SelectivityInterfaceBase() {
                                                                    -
                                                                    32  this->id = SelectivityInterfaceBase::id_g++;
                                                                    -
                                                                    33  /* Create instance of map: key is id and value is pointer to
                                                                    -
                                                                    34  SelectivityInterfaceBase */
                                                                    -
                                                                    35  SelectivityInterfaceBase::live_objects[this->id] = this;
                                                                    -
                                                                    36  FIMSRcppInterfaceBase::fims_interface_objects.push_back(this);
                                                                    -
                                                                    37  }
                                                                    -
                                                                    38 
                                                                    -
                                                                    39  virtual ~SelectivityInterfaceBase() {}
                                                                    -
                                                                    40 
                                                                    -
                                                                    43  virtual uint32_t get_id() = 0;
                                                                    -
                                                                    44 
                                                                    -
                                                                    49  virtual double evaluate(double x) = 0;
                                                                    -
                                                                    50 };
                                                                    -
                                                                    51 
                                                                    -
                                                                    52 uint32_t SelectivityInterfaceBase::id_g = 1;
                                                                    -
                                                                    53 std::map<uint32_t, SelectivityInterfaceBase*>
                                                                    -
                                                                    54  SelectivityInterfaceBase::live_objects;
                                                                    -
                                                                    55 
                                                                    -
                                                                    60 class LogisticSelectivityInterface : public SelectivityInterfaceBase {
                                                                    -
                                                                    61  public:
                                                                    -
                                                                    62  ParameterVector
                                                                    -
                                                                    63  inflection_point;
                                                                    -
                                                                    64  ParameterVector slope;
                                                                    -
                                                                    66  LogisticSelectivityInterface() : SelectivityInterfaceBase() {}
                                                                    -
                                                                    67 
                                                                    -
                                                                    68  virtual ~LogisticSelectivityInterface() {}
                                                                    -
                                                                    69 
                                                                    -
                                                                    71  virtual uint32_t get_id() { return this->id; }
                                                                    -
                                                                    72 
                                                                    -
                                                                    77  virtual double evaluate(double x) {
                                                                    -
                                                                    78  fims_popdy::LogisticSelectivity<double> LogisticSel;
                                                                    -
                                                                    79  LogisticSel.inflection_point.resize(1);
                                                                    -
                                                                    80  LogisticSel.inflection_point[0] = this->inflection_point[0].initial_value_m;
                                                                    -
                                                                    81  LogisticSel.slope.resize(1);
                                                                    -
                                                                    82  LogisticSel.slope[0] = this->slope[0].initial_value_m;
                                                                    -
                                                                    83  return LogisticSel.evaluate(x);
                                                                    -
                                                                    84  }
                                                                    -
                                                                    89  virtual void finalize() {
                                                                    -
                                                                    90 
                                                                    -
                                                                    91  if (this->finalized) {
                                                                    -
                                                                    92  //log warning that finalize has been called more than once.
                                                                    -
                                                                    93  FIMS_WARNING_LOG("Logistic Selectivity " + fims::to_string(this->id) + " has been finalized already.");
                                                                    -
                                                                    94  }
                                                                    -
                                                                    95 
                                                                    -
                                                                    96  this->finalized = true; //indicate this has been called already
                                                                    -
                                                                    97 
                                                                    -
                                                                    98  std::shared_ptr<fims_info::Information<double> > info =
                                                                    -
                                                                    99  fims_info::Information<double>::GetInstance();
                                                                    -
                                                                    100 
                                                                    -
                                                                    101 
                                                                    -
                                                                    102  fims_info::Information<double>::selectivity_models_iterator it;
                                                                    -
                                                                    103 
                                                                    -
                                                                    104 
                                                                    -
                                                                    105  //search for maturity in Information
                                                                    -
                                                                    106  it = info->selectivity_models.find(this->id);
                                                                    -
                                                                    107  //if not found, just return
                                                                    -
                                                                    108  if (it == info->selectivity_models.end()) {
                                                                    -
                                                                    109  FIMS_WARNING_LOG("Logistic Selectivity " + fims::to_string(this->id) + " not found in Information.");
                                                                    -
                                                                    110  return;
                                                                    -
                                                                    111  } else {
                                                                    -
                                                                    112  std::shared_ptr<fims_popdy::LogisticSelectivity<double> > sel =
                                                                    -
                                                                    113  std::dynamic_pointer_cast<fims_popdy::LogisticSelectivity<double> >(it->second);
                                                                    -
                                                                    114 
                                                                    -
                                                                    115  for (size_t i = 0; i < inflection_point.size(); i++) {
                                                                    -
                                                                    116  if (this->inflection_point[i].estimated_m) {
                                                                    -
                                                                    117  this->inflection_point[i].final_value_m = sel->inflection_point[i];
                                                                    -
                                                                    118  } else {
                                                                    -
                                                                    119  this->inflection_point[i].final_value_m = this->inflection_point[i].initial_value_m;
                                                                    -
                                                                    120  }
                                                                    -
                                                                    121  }
                                                                    -
                                                                    122 
                                                                    -
                                                                    123  for (size_t i = 0; i < slope.size(); i++) {
                                                                    -
                                                                    124  if (this->slope[i].estimated_m) {
                                                                    -
                                                                    125  this->slope[i].final_value_m = sel->slope[i];
                                                                    -
                                                                    126  } else {
                                                                    -
                                                                    127  this->slope[i].final_value_m = this->slope[i].initial_value_m;
                                                                    -
                                                                    128  }
                                                                    -
                                                                    129 
                                                                    -
                                                                    130  }
                                                                    -
                                                                    131 
                                                                    -
                                                                    132  }
                                                                    -
                                                                    133  }
                                                                    -
                                                                    134 
                                                                    -
                                                                    138  virtual std::string to_json() {
                                                                    -
                                                                    139  std::stringstream ss;
                                                                    -
                                                                    140 
                                                                    -
                                                                    141  ss << "\"module\" : {\n";
                                                                    -
                                                                    142  ss << " \"name\":\"selectivity\",\n";
                                                                    -
                                                                    143  ss << " \"type\": \"Logistic\",\n";
                                                                    -
                                                                    144  ss << " \"id\": " << this->id << ",\n";
                                                                    -
                                                                    145 
                                                                    -
                                                                    146  ss << " \"parameter\": {\n";
                                                                    -
                                                                    147  ss << " \"name\": \"inflection_point\",\n";
                                                                    -
                                                                    148  ss << " \"id\":" << this->inflection_point.id_m << ",\n";
                                                                    -
                                                                    149  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    150  ss << " \"values\":" << this->inflection_point << ",\n },\n";
                                                                    -
                                                                    151 
                                                                    -
                                                                    152  ss << " \"parameter\": {\n";
                                                                    -
                                                                    153  ss << " \"name\": \"slope\",\n";
                                                                    -
                                                                    154  ss << " \"id\":" << this->slope.id_m << ",\n";
                                                                    -
                                                                    155  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    156  ss << " \"values\":" << this->slope << ",\n}\n";
                                                                    -
                                                                    157 
                                                                    -
                                                                    158 
                                                                    -
                                                                    159  ss << "}";
                                                                    -
                                                                    160 
                                                                    -
                                                                    161  return ss.str();
                                                                    -
                                                                    162  }
                                                                    -
                                                                    163 
                                                                    -
                                                                    164 
                                                                    -
                                                                    165 #ifdef TMB_MODEL
                                                                    -
                                                                    166 
                                                                    -
                                                                    167  template <typename Type>
                                                                    -
                                                                    168  bool add_to_fims_tmb_internal() {
                                                                    -
                                                                    169  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    -
                                                                    170  fims_info::Information<Type>::GetInstance();
                                                                    -
                                                                    171 
                                                                    -
                                                                    172  std::shared_ptr<fims_popdy::LogisticSelectivity<Type> > selectivity =
                                                                    -
                                                                    173  std::make_shared<fims_popdy::LogisticSelectivity<Type> >();
                                                                    -
                                                                    174  std::stringstream ss;
                                                                    -
                                                                    175  // set relative info
                                                                    -
                                                                    176  selectivity->id = this->id;
                                                                    -
                                                                    177  selectivity->inflection_point.resize(this->inflection_point.size());
                                                                    -
                                                                    178  for (size_t i = 0; i < this->inflection_point.size(); i++) {
                                                                    -
                                                                    179  selectivity->inflection_point[i] = this->inflection_point[i].initial_value_m;
                                                                    -
                                                                    180  if (this->inflection_point[i].estimated_m) {
                                                                    -
                                                                    181  ss.str("");
                                                                    -
                                                                    182  ss << "selectivity.inflection_point ." << this->id << "." << i;
                                                                    -
                                                                    183  info->RegisterParameterName(ss.str());
                                                                    -
                                                                    184  if (this->inflection_point[i].is_random_effect_m) {
                                                                    -
                                                                    185  info->RegisterRandomEffect(selectivity->inflection_point[i]);
                                                                    -
                                                                    186  } else {
                                                                    -
                                                                    187  info->RegisterParameter(selectivity->inflection_point[i]);
                                                                    -
                                                                    188  }
                                                                    -
                                                                    189  }
                                                                    -
                                                                    190  }
                                                                    -
                                                                    191 
                                                                    -
                                                                    192  info->variable_map[this->inflection_point.id_m] = &(selectivity)->inflection_point;
                                                                    -
                                                                    193  selectivity->slope.resize(this->slope.size());
                                                                    -
                                                                    194  for (size_t i = 0; i < this->slope.size(); i++) {
                                                                    -
                                                                    195  selectivity->slope[i] = this->slope[i].initial_value_m;
                                                                    -
                                                                    196  if (this->slope[i].estimated_m) {
                                                                    -
                                                                    197  ss.str("");
                                                                    -
                                                                    198  ss << "selectivity.slope." << this->id << "." << i;
                                                                    -
                                                                    199  info->RegisterParameterName(ss.str());
                                                                    -
                                                                    200  if (this->slope[i].is_random_effect_m) {
                                                                    -
                                                                    201  info->RegisterRandomEffect(selectivity->slope[i]);
                                                                    -
                                                                    202  } else {
                                                                    -
                                                                    203  info->RegisterParameter(selectivity->slope[i]);
                                                                    -
                                                                    204  }
                                                                    -
                                                                    205  }
                                                                    -
                                                                    206  }
                                                                    -
                                                                    207  info->variable_map[this->slope.id_m] = &(selectivity)->slope;
                                                                    -
                                                                    208 
                                                                    -
                                                                    209  // add to Information
                                                                    -
                                                                    210  info->selectivity_models[selectivity->id] = selectivity;
                                                                    -
                                                                    211 
                                                                    -
                                                                    212  return true;
                                                                    -
                                                                    213  }
                                                                    -
                                                                    214 
                                                                    -
                                                                    217  virtual bool add_to_fims_tmb() {
                                                                    -
                                                                    218  FIMS_INFO_LOG("adding Selectivity object to TMB");
                                                                    -
                                                                    219  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    -
                                                                    220  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    -
                                                                    221  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    -
                                                                    222  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    -
                                                                    223 
                                                                    -
                                                                    224  return true;
                                                                    -
                                                                    225  }
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * File: rcpp_selectivity.hpp
                                                                    +
                                                                    3  *
                                                                    +
                                                                    4  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    5  * Fisheries Integrated Modeling System project. See LICENSE
                                                                    +
                                                                    6  * file for reuse information.
                                                                    +
                                                                    7  *
                                                                    +
                                                                    8  */
                                                                    +
                                                                    9 #ifndef FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_SELECTIVITY_HPP
                                                                    +
                                                                    10 #define FIMS_INTERFACE_RCPP_RCPP_OBJECTS_RCPP_SELECTIVITY_HPP
                                                                    +
                                                                    11 
                                                                    +
                                                                    12 #include "../../../population_dynamics/selectivity/selectivity.hpp"
                                                                    +
                                                                    13 #include "rcpp_interface_base.hpp"
                                                                    +
                                                                    14 
                                                                    +
                                                                    23 class SelectivityInterfaceBase : public FIMSRcppInterfaceBase {
                                                                    +
                                                                    24  public:
                                                                    +
                                                                    25  static uint32_t id_g;
                                                                    +
                                                                    26  uint32_t id;
                                                                    +
                                                                    27  // live objects in C++ are objects that have been created and live in memory
                                                                    +
                                                                    28  static std::map<uint32_t, SelectivityInterfaceBase*>
                                                                    +
                                                                    29  live_objects;
                                                                    +
                                                                    32  SelectivityInterfaceBase() {
                                                                    +
                                                                    33  this->id = SelectivityInterfaceBase::id_g++;
                                                                    +
                                                                    34  /* Create instance of map: key is id and value is pointer to
                                                                    +
                                                                    35  SelectivityInterfaceBase */
                                                                    +
                                                                    36  SelectivityInterfaceBase::live_objects[this->id] = this;
                                                                    +
                                                                    37  FIMSRcppInterfaceBase::fims_interface_objects.push_back(this);
                                                                    +
                                                                    38  }
                                                                    +
                                                                    39 
                                                                    +
                                                                    40  virtual ~SelectivityInterfaceBase() {}
                                                                    +
                                                                    41 
                                                                    +
                                                                    44  virtual uint32_t get_id() = 0;
                                                                    +
                                                                    45 
                                                                    +
                                                                    50  virtual double evaluate(double x) = 0;
                                                                    +
                                                                    51 };
                                                                    +
                                                                    52 
                                                                    +
                                                                    53 uint32_t SelectivityInterfaceBase::id_g = 1;
                                                                    +
                                                                    54 std::map<uint32_t, SelectivityInterfaceBase*>
                                                                    +
                                                                    55  SelectivityInterfaceBase::live_objects;
                                                                    +
                                                                    56 
                                                                    +
                                                                    61 class LogisticSelectivityInterface : public SelectivityInterfaceBase {
                                                                    +
                                                                    62  public:
                                                                    +
                                                                    63  Parameter
                                                                    +
                                                                    64  inflection_point;
                                                                    +
                                                                    65  Parameter slope;
                                                                    +
                                                                    67  LogisticSelectivityInterface() : SelectivityInterfaceBase() {}
                                                                    +
                                                                    68 
                                                                    +
                                                                    69  virtual ~LogisticSelectivityInterface() {}
                                                                    +
                                                                    70 
                                                                    +
                                                                    72  virtual uint32_t get_id() { return this->id; }
                                                                    +
                                                                    73 
                                                                    +
                                                                    78  virtual double evaluate(double x) {
                                                                    +
                                                                    79  fims_popdy::LogisticSelectivity<double> LogisticSel;
                                                                    +
                                                                    80  LogisticSel.inflection_point = this->inflection_point.value_m;
                                                                    +
                                                                    81  LogisticSel.slope = this->slope.value_m;
                                                                    +
                                                                    82  return LogisticSel.evaluate(x);
                                                                    +
                                                                    83  }
                                                                    +
                                                                    84 
                                                                    +
                                                                    85 #ifdef TMB_MODEL
                                                                    +
                                                                    86 
                                                                    +
                                                                    87  template <typename Type>
                                                                    +
                                                                    88  bool add_to_fims_tmb_internal() {
                                                                    +
                                                                    89  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    +
                                                                    90  fims_info::Information<Type>::GetInstance();
                                                                    +
                                                                    91 
                                                                    +
                                                                    92  std::shared_ptr<fims_popdy::LogisticSelectivity<Type> > selectivity =
                                                                    +
                                                                    93  std::make_shared<fims_popdy::LogisticSelectivity<Type> >();
                                                                    +
                                                                    94 
                                                                    +
                                                                    95  // set relative info
                                                                    +
                                                                    96  selectivity->id = this->id;
                                                                    +
                                                                    97  selectivity->inflection_point = this->inflection_point.value_m;
                                                                    +
                                                                    98  if (this->inflection_point.estimated_m) {
                                                                    +
                                                                    99  if (this->inflection_point.is_random_effect_m) {
                                                                    +
                                                                    100  info->RegisterRandomEffect(selectivity->inflection_point);
                                                                    +
                                                                    101  } else {
                                                                    +
                                                                    102  info->RegisterParameter(selectivity->inflection_point);
                                                                    +
                                                                    103  }
                                                                    +
                                                                    104  }
                                                                    +
                                                                    105  selectivity->slope = this->slope.value_m;
                                                                    +
                                                                    106  if (this->slope.estimated_m) {
                                                                    +
                                                                    107  if (this->slope.is_random_effect_m) {
                                                                    +
                                                                    108  info->RegisterRandomEffect(selectivity->slope);
                                                                    +
                                                                    109  } else {
                                                                    +
                                                                    110  info->RegisterParameter(selectivity->slope);
                                                                    +
                                                                    111  }
                                                                    +
                                                                    112  }
                                                                    +
                                                                    113 
                                                                    +
                                                                    114  // add to Information
                                                                    +
                                                                    115  info->selectivity_models[selectivity->id] = selectivity;
                                                                    +
                                                                    116 
                                                                    +
                                                                    117  return true;
                                                                    +
                                                                    118  }
                                                                    +
                                                                    119 
                                                                    +
                                                                    122  virtual bool add_to_fims_tmb() {
                                                                    +
                                                                    123  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    +
                                                                    124  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    +
                                                                    125  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    +
                                                                    126  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    +
                                                                    127 
                                                                    +
                                                                    128  return true;
                                                                    +
                                                                    129  }
                                                                    +
                                                                    130 
                                                                    +
                                                                    131 #endif
                                                                    +
                                                                    132 };
                                                                    +
                                                                    133 
                                                                    +
                                                                    138 class DoubleLogisticSelectivityInterface : public SelectivityInterfaceBase {
                                                                    +
                                                                    139  public:
                                                                    +
                                                                    140  Parameter inflection_point_asc;
                                                                    +
                                                                    142  Parameter slope_asc;
                                                                    +
                                                                    143  Parameter inflection_point_desc;
                                                                    +
                                                                    145  Parameter slope_desc;
                                                                    +
                                                                    147  DoubleLogisticSelectivityInterface() : SelectivityInterfaceBase() {}
                                                                    +
                                                                    148 
                                                                    +
                                                                    149  virtual ~DoubleLogisticSelectivityInterface() {}
                                                                    +
                                                                    150 
                                                                    +
                                                                    152  virtual uint32_t get_id() { return this->id; }
                                                                    +
                                                                    153 
                                                                    +
                                                                    158  virtual double evaluate(double x) {
                                                                    +
                                                                    159  fims_popdy::DoubleLogisticSelectivity<double> DoubleLogisticSel;
                                                                    +
                                                                    160  DoubleLogisticSel.inflection_point_asc = this->inflection_point_asc.value_m;
                                                                    +
                                                                    161  DoubleLogisticSel.slope_asc = this->slope_asc.value_m;
                                                                    +
                                                                    162  DoubleLogisticSel.inflection_point_desc =
                                                                    +
                                                                    163  this->inflection_point_desc.value_m;
                                                                    +
                                                                    164  DoubleLogisticSel.slope_desc = this->slope_desc.value_m;
                                                                    +
                                                                    165  return DoubleLogisticSel.evaluate(x);
                                                                    +
                                                                    166  }
                                                                    +
                                                                    167 
                                                                    +
                                                                    168 #ifdef TMB_MODEL
                                                                    +
                                                                    169 
                                                                    +
                                                                    170  template <typename Type>
                                                                    +
                                                                    171  bool add_to_fims_tmb_internal() {
                                                                    +
                                                                    172  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    +
                                                                    173  fims_info::Information<Type>::GetInstance();
                                                                    +
                                                                    174 
                                                                    +
                                                                    175  std::shared_ptr<fims_popdy::DoubleLogisticSelectivity<Type> > selectivity =
                                                                    +
                                                                    176  std::make_shared<fims_popdy::DoubleLogisticSelectivity<Type> >();
                                                                    +
                                                                    177 
                                                                    +
                                                                    178  // set relative info
                                                                    +
                                                                    179  selectivity->id = this->id;
                                                                    +
                                                                    180  selectivity->inflection_point_asc = this->inflection_point_asc.value_m;
                                                                    +
                                                                    181  if (this->inflection_point_asc.estimated_m) {
                                                                    +
                                                                    182  if (this->inflection_point_asc.is_random_effect_m) {
                                                                    +
                                                                    183  info->RegisterRandomEffect(selectivity->inflection_point_asc);
                                                                    +
                                                                    184  } else {
                                                                    +
                                                                    185  info->RegisterParameter(selectivity->inflection_point_asc);
                                                                    +
                                                                    186  }
                                                                    +
                                                                    187  }
                                                                    +
                                                                    188  selectivity->slope_asc = this->slope_asc.value_m;
                                                                    +
                                                                    189  if (this->slope_asc.estimated_m) {
                                                                    +
                                                                    190  if (this->slope_asc.is_random_effect_m) {
                                                                    +
                                                                    191  info->RegisterRandomEffect(selectivity->slope_asc);
                                                                    +
                                                                    192  } else {
                                                                    +
                                                                    193  info->RegisterParameter(selectivity->slope_asc);
                                                                    +
                                                                    194  }
                                                                    +
                                                                    195  }
                                                                    +
                                                                    196  selectivity->inflection_point_desc = this->inflection_point_desc.value_m;
                                                                    +
                                                                    197  if (this->inflection_point_desc.estimated_m) {
                                                                    +
                                                                    198  if (this->inflection_point_desc.is_random_effect_m) {
                                                                    +
                                                                    199  info->RegisterRandomEffect(selectivity->inflection_point_desc);
                                                                    +
                                                                    200  } else {
                                                                    +
                                                                    201  info->RegisterParameter(selectivity->inflection_point_desc);
                                                                    +
                                                                    202  }
                                                                    +
                                                                    203  }
                                                                    +
                                                                    204  selectivity->slope_desc = this->slope_desc.value_m;
                                                                    +
                                                                    205  if (this->slope_desc.estimated_m) {
                                                                    +
                                                                    206  if (this->slope_desc.is_random_effect_m) {
                                                                    +
                                                                    207  info->RegisterRandomEffect(selectivity->slope_desc);
                                                                    +
                                                                    208  } else {
                                                                    +
                                                                    209  info->RegisterParameter(selectivity->slope_desc);
                                                                    +
                                                                    210  }
                                                                    +
                                                                    211  }
                                                                    +
                                                                    212 
                                                                    +
                                                                    213  // add to Information
                                                                    +
                                                                    214  info->selectivity_models[selectivity->id] = selectivity;
                                                                    +
                                                                    215 
                                                                    +
                                                                    216  return true;
                                                                    +
                                                                    217  }
                                                                    +
                                                                    218 
                                                                    +
                                                                    221  virtual bool add_to_fims_tmb() {
                                                                    +
                                                                    222  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    +
                                                                    223  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    +
                                                                    224  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    +
                                                                    225  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    226 
                                                                    -
                                                                    227 #endif
                                                                    -
                                                                    228 };
                                                                    +
                                                                    227  return true;
                                                                    +
                                                                    228  }
                                                                    229 
                                                                    -
                                                                    234 class DoubleLogisticSelectivityInterface : public SelectivityInterfaceBase {
                                                                    -
                                                                    235  public:
                                                                    -
                                                                    236  ParameterVector inflection_point_asc;
                                                                    -
                                                                    238  ParameterVector slope_asc;
                                                                    -
                                                                    239  ParameterVector inflection_point_desc;
                                                                    -
                                                                    241  ParameterVector slope_desc;
                                                                    -
                                                                    244  DoubleLogisticSelectivityInterface() : SelectivityInterfaceBase() {}
                                                                    -
                                                                    245 
                                                                    -
                                                                    246  virtual ~DoubleLogisticSelectivityInterface() {}
                                                                    -
                                                                    247 
                                                                    -
                                                                    249  virtual uint32_t get_id() { return this->id; }
                                                                    -
                                                                    250 
                                                                    -
                                                                    255  virtual double evaluate(double x) {
                                                                    -
                                                                    256  fims_popdy::DoubleLogisticSelectivity<double> DoubleLogisticSel;
                                                                    -
                                                                    257  DoubleLogisticSel.inflection_point_asc.resize(1);
                                                                    -
                                                                    258  DoubleLogisticSel.inflection_point_asc[0] = this->inflection_point_asc[0].initial_value_m;
                                                                    -
                                                                    259  DoubleLogisticSel.slope_asc.resize(1);
                                                                    -
                                                                    260  DoubleLogisticSel.slope_asc[0] = this->slope_asc[0].initial_value_m;
                                                                    -
                                                                    261  DoubleLogisticSel.inflection_point_desc.resize(1);
                                                                    -
                                                                    262  DoubleLogisticSel.inflection_point_desc[0] =
                                                                    -
                                                                    263  this->inflection_point_desc[0].initial_value_m;
                                                                    -
                                                                    264  DoubleLogisticSel.slope_desc.resize(1);
                                                                    -
                                                                    265  DoubleLogisticSel.slope_desc[0] = this->slope_desc[0].initial_value_m;
                                                                    -
                                                                    266  return DoubleLogisticSel.evaluate(x);
                                                                    -
                                                                    267  }
                                                                    -
                                                                    272  virtual void finalize() {
                                                                    -
                                                                    273 
                                                                    -
                                                                    274  if (this->finalized) {
                                                                    -
                                                                    275  //log warning that finalize has been called more than once.
                                                                    -
                                                                    276  FIMS_WARNING_LOG("Double Logistic Selectivity " + fims::to_string(this->id) + " has been finalized already.");
                                                                    -
                                                                    277  }
                                                                    -
                                                                    278 
                                                                    -
                                                                    279  this->finalized = true; //indicate this has been called already
                                                                    -
                                                                    280 
                                                                    -
                                                                    281  std::shared_ptr<fims_info::Information<double> > info =
                                                                    -
                                                                    282  fims_info::Information<double>::GetInstance();
                                                                    -
                                                                    283 
                                                                    -
                                                                    284 
                                                                    -
                                                                    285 
                                                                    -
                                                                    286  fims_info::Information<double>::selectivity_models_iterator it;
                                                                    -
                                                                    287 
                                                                    -
                                                                    288  //search for maturity in Information
                                                                    -
                                                                    289  it = info->selectivity_models.find(this->id);
                                                                    -
                                                                    290  //if not found, just return
                                                                    -
                                                                    291  if (it == info->selectivity_models.end()) {
                                                                    -
                                                                    292  FIMS_WARNING_LOG("Double Logistic Selectivity " + fims::to_string(this->id) + " not found in Information.");
                                                                    -
                                                                    293  return;
                                                                    -
                                                                    294  } else {
                                                                    -
                                                                    295  std::shared_ptr<fims_popdy::DoubleLogisticSelectivity<double> > sel =
                                                                    -
                                                                    296  std::dynamic_pointer_cast<fims_popdy::DoubleLogisticSelectivity<double> >(it->second);
                                                                    -
                                                                    297 
                                                                    -
                                                                    298 
                                                                    -
                                                                    299  for (size_t i = 0; i < inflection_point_asc.size(); i++) {
                                                                    -
                                                                    300  if (this->inflection_point_asc[i].estimated_m) {
                                                                    -
                                                                    301  this->inflection_point_asc[i].final_value_m = sel->inflection_point_asc[i];
                                                                    -
                                                                    302  } else {
                                                                    -
                                                                    303  this->inflection_point_asc[i].final_value_m = this->inflection_point_asc[i].initial_value_m;
                                                                    -
                                                                    304  }
                                                                    -
                                                                    305 
                                                                    -
                                                                    306  }
                                                                    -
                                                                    307 
                                                                    -
                                                                    308  for (size_t i = 0; i < slope_asc.size(); i++) {
                                                                    -
                                                                    309  if (this->slope_asc[i].estimated_m) {
                                                                    -
                                                                    310  this->slope_asc[i].final_value_m = sel->slope_asc[i];
                                                                    -
                                                                    311  } else {
                                                                    -
                                                                    312  this->slope_asc[i].final_value_m = this->slope_asc[i].initial_value_m;
                                                                    -
                                                                    313  }
                                                                    -
                                                                    314 
                                                                    -
                                                                    315  }
                                                                    -
                                                                    316 
                                                                    -
                                                                    317  for (size_t i = 0; i < inflection_point_desc.size(); i++) {
                                                                    -
                                                                    318  if (this->inflection_point_desc[i].estimated_m) {
                                                                    -
                                                                    319  this->inflection_point_desc[i].final_value_m = sel->inflection_point_desc[i];
                                                                    -
                                                                    320  } else {
                                                                    -
                                                                    321  this->inflection_point_desc[i].final_value_m = this->inflection_point_desc[i].initial_value_m;
                                                                    -
                                                                    322  }
                                                                    -
                                                                    323 
                                                                    -
                                                                    324  }
                                                                    -
                                                                    325 
                                                                    -
                                                                    326  for (size_t i = 0; i < slope_desc.size(); i++) {
                                                                    -
                                                                    327  if (this->slope_desc[i].estimated_m) {
                                                                    -
                                                                    328  this->slope_desc[i].final_value_m = sel->slope_desc[i];
                                                                    -
                                                                    329  } else {
                                                                    -
                                                                    330  this->slope_desc[i].final_value_m = this->slope_desc[i].initial_value_m;
                                                                    -
                                                                    331  }
                                                                    -
                                                                    332 
                                                                    -
                                                                    333  }
                                                                    -
                                                                    334 
                                                                    -
                                                                    335 
                                                                    -
                                                                    336 
                                                                    -
                                                                    337  }
                                                                    -
                                                                    338  }
                                                                    -
                                                                    339 
                                                                    -
                                                                    343  virtual std::string to_json() {
                                                                    -
                                                                    344  std::stringstream ss;
                                                                    -
                                                                    345 
                                                                    -
                                                                    346  ss << "\"module\" : {\n";
                                                                    -
                                                                    347  ss << " \"name\": \"selectivity\",\n";
                                                                    -
                                                                    348  ss << " \"type\": \"DoubleLogistic\",\n";
                                                                    -
                                                                    349  ss << " \"id\": " << this->id << ",\n";
                                                                    -
                                                                    350 
                                                                    -
                                                                    351  ss << " \"parameter\": {\n";
                                                                    -
                                                                    352  ss << " \"name\": \"inflection_point_asc\",\n";
                                                                    -
                                                                    353  ss << " \"id\":" << this->inflection_point_asc.id_m << ",\n";
                                                                    -
                                                                    354  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    355  ss << " \"values\":" << this->inflection_point_asc << ",\n},\n";
                                                                    -
                                                                    356 
                                                                    -
                                                                    357  ss << " \"parameter\": {\n";
                                                                    -
                                                                    358  ss << " \"name\": \"slope_asc\",\n";
                                                                    -
                                                                    359  ss << " \"id\":" << this->slope_asc.id_m << ",\n";
                                                                    -
                                                                    360  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    361  ss << " \"values\":" << this->slope_asc << ",\n},\n";
                                                                    -
                                                                    362 
                                                                    -
                                                                    363  ss << " \"parameter\": {\n";
                                                                    -
                                                                    364  ss << " \"name\": \"inflection_point_desc\",\n";
                                                                    -
                                                                    365  ss << " \"id\":" << this->inflection_point_desc.id_m << ",\n";
                                                                    -
                                                                    366  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    367  ss << " \"values\":" << this->inflection_point_desc << ",\n},\n";
                                                                    -
                                                                    368 
                                                                    -
                                                                    369  ss << " \"parameter\": {\n";
                                                                    -
                                                                    370  ss << " \"name\": \"slope_desc\",\n";
                                                                    -
                                                                    371  ss << " \"id\":" << this->slope_desc.id_m << ",\n";
                                                                    -
                                                                    372  ss << " \"type\": \"vector\",\n";
                                                                    -
                                                                    373  ss << " \"values\":" << this->slope_desc << ",\n}\n";
                                                                    -
                                                                    374 
                                                                    -
                                                                    375 
                                                                    -
                                                                    376  ss << "}";
                                                                    -
                                                                    377 
                                                                    -
                                                                    378  return ss.str();
                                                                    -
                                                                    379  }
                                                                    -
                                                                    380 
                                                                    -
                                                                    381 
                                                                    -
                                                                    382 #ifdef TMB_MODEL
                                                                    -
                                                                    383 
                                                                    -
                                                                    384  template <typename Type>
                                                                    -
                                                                    385  bool add_to_fims_tmb_internal() {
                                                                    -
                                                                    386  std::shared_ptr<fims_info::Information<Type> > info =
                                                                    -
                                                                    387  fims_info::Information<Type>::GetInstance();
                                                                    -
                                                                    388 
                                                                    -
                                                                    389  std::shared_ptr<fims_popdy::DoubleLogisticSelectivity<Type> > selectivity =
                                                                    -
                                                                    390  std::make_shared<fims_popdy::DoubleLogisticSelectivity<Type> >();
                                                                    -
                                                                    391 
                                                                    -
                                                                    392  std::stringstream ss;
                                                                    -
                                                                    393  // set relative info
                                                                    -
                                                                    394  selectivity->id = this->id;
                                                                    -
                                                                    395  selectivity->inflection_point_asc.resize(this->inflection_point_asc.size());
                                                                    -
                                                                    396  for (size_t i = 0; i < this->inflection_point_asc.size(); i++) {
                                                                    -
                                                                    397  selectivity->inflection_point_asc[i] = this->inflection_point_asc[i].initial_value_m;
                                                                    -
                                                                    398  if (this->inflection_point_asc[i].estimated_m) {
                                                                    -
                                                                    399  ss.str("");
                                                                    -
                                                                    400  ss << "selectivity.inflection_point_asc." << this->id << "." << i;
                                                                    -
                                                                    401  info->RegisterParameterName(ss.str());
                                                                    -
                                                                    402  if (this->inflection_point_asc[i].is_random_effect_m) {
                                                                    -
                                                                    403  info->RegisterRandomEffect(selectivity->inflection_point_asc[i]);
                                                                    -
                                                                    404  } else {
                                                                    -
                                                                    405  info->RegisterParameter(selectivity->inflection_point_asc[i]);
                                                                    -
                                                                    406  }
                                                                    -
                                                                    407  }
                                                                    -
                                                                    408  }
                                                                    -
                                                                    409 
                                                                    -
                                                                    410  info->variable_map[this->inflection_point_asc.id_m] = &(selectivity)->inflection_point_asc;
                                                                    -
                                                                    411 
                                                                    -
                                                                    412 
                                                                    -
                                                                    413  selectivity->slope_asc.resize(this->slope_asc.size());
                                                                    -
                                                                    414  for (size_t i = 0; i < this->slope_asc.size(); i++) {
                                                                    -
                                                                    415  selectivity->slope_asc[i] = this->slope_asc[i].initial_value_m;
                                                                    -
                                                                    416  if (this->slope_asc[i].estimated_m) {
                                                                    -
                                                                    417  ss.str("");
                                                                    -
                                                                    418  ss << "selectivity.slope_asc." << this->id << "." << i;
                                                                    -
                                                                    419  info->RegisterParameterName(ss.str());
                                                                    -
                                                                    420  if (this->slope_asc[i].is_random_effect_m) {
                                                                    -
                                                                    421  info->RegisterRandomEffect(selectivity->slope_asc[i]);
                                                                    -
                                                                    422  } else {
                                                                    -
                                                                    423  info->RegisterParameter(selectivity->slope_asc[i]);
                                                                    -
                                                                    424  }
                                                                    -
                                                                    425  }
                                                                    -
                                                                    426  }
                                                                    -
                                                                    427  info->variable_map[this->slope_asc.id_m] = &(selectivity)->slope_asc;
                                                                    -
                                                                    428 
                                                                    -
                                                                    429  selectivity->inflection_point_desc.resize(this->inflection_point_desc.size());
                                                                    -
                                                                    430  for (size_t i = 0; i < this->inflection_point_desc.size(); i++) {
                                                                    -
                                                                    431  selectivity->inflection_point_desc[i] = this->inflection_point_desc[i].initial_value_m;
                                                                    -
                                                                    432  if (this->inflection_point_desc[i].estimated_m) {
                                                                    -
                                                                    433  ss.str("");
                                                                    -
                                                                    434  ss << "selectivity.inflection_point_desc." << this->id << "." << i;
                                                                    -
                                                                    435  info->RegisterParameterName(ss.str());
                                                                    -
                                                                    436  if (this->inflection_point_desc[i].is_random_effect_m) {
                                                                    -
                                                                    437  info->RegisterRandomEffect(selectivity->inflection_point_desc[i]);
                                                                    -
                                                                    438  } else {
                                                                    -
                                                                    439  info->RegisterParameter(selectivity->inflection_point_desc[i]);
                                                                    -
                                                                    440  }
                                                                    -
                                                                    441  }
                                                                    -
                                                                    442  }
                                                                    -
                                                                    443 
                                                                    -
                                                                    444  info->variable_map[this->inflection_point_desc.id_m] = &(selectivity)->inflection_point_desc;
                                                                    -
                                                                    445  selectivity->slope_desc.resize(this->slope_desc.size());
                                                                    -
                                                                    446  for (size_t i = 0; i < this->slope_desc.size(); i++) {
                                                                    -
                                                                    447  selectivity->slope_desc[i] = this->slope_desc[i].initial_value_m;
                                                                    -
                                                                    448  if (this->slope_desc[i].estimated_m) {
                                                                    -
                                                                    449  ss.str("");
                                                                    -
                                                                    450  ss << "selectivity.slope_desc." << this->id << "." << i;
                                                                    -
                                                                    451  info->RegisterParameterName(ss.str());
                                                                    -
                                                                    452  if (this->slope_desc[i].is_random_effect_m) {
                                                                    -
                                                                    453  info->RegisterRandomEffect(selectivity->slope_desc[i]);
                                                                    -
                                                                    454  } else {
                                                                    -
                                                                    455  info->RegisterParameter(selectivity->slope_desc[i]);
                                                                    -
                                                                    456  }
                                                                    -
                                                                    457  }
                                                                    -
                                                                    458  }
                                                                    -
                                                                    459 
                                                                    -
                                                                    460 
                                                                    -
                                                                    461  info->variable_map[this->slope_desc.id_m] = &(selectivity)->slope_desc;
                                                                    -
                                                                    462 
                                                                    -
                                                                    463  // add to Information
                                                                    -
                                                                    464  info->selectivity_models[selectivity->id] = selectivity;
                                                                    -
                                                                    465 
                                                                    -
                                                                    466  return true;
                                                                    -
                                                                    467  }
                                                                    -
                                                                    468 
                                                                    -
                                                                    471  virtual bool add_to_fims_tmb() {
                                                                    -
                                                                    472  this->add_to_fims_tmb_internal<TMB_FIMS_REAL_TYPE>();
                                                                    -
                                                                    473  this->add_to_fims_tmb_internal<TMB_FIMS_FIRST_ORDER>();
                                                                    -
                                                                    474  this->add_to_fims_tmb_internal<TMB_FIMS_SECOND_ORDER>();
                                                                    -
                                                                    475  this->add_to_fims_tmb_internal<TMB_FIMS_THIRD_ORDER>();
                                                                    -
                                                                    476 
                                                                    -
                                                                    477  return true;
                                                                    -
                                                                    478  }
                                                                    -
                                                                    479 
                                                                    -
                                                                    480 #endif
                                                                    -
                                                                    481 };
                                                                    -
                                                                    482 
                                                                    -
                                                                    483 #endif
                                                                    -
                                                                    DoubleLogisticSelectivityInterface
                                                                    Rcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity ...
                                                                    Definition: rcpp_selectivity.hpp:234
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::slope_desc
                                                                    ParameterVector slope_desc
                                                                    Definition: rcpp_selectivity.hpp:241
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::inflection_point_desc
                                                                    ParameterVector inflection_point_desc
                                                                    Definition: rcpp_selectivity.hpp:239
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::slope_asc
                                                                    ParameterVector slope_asc
                                                                    Definition: rcpp_selectivity.hpp:238
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::evaluate
                                                                    virtual double evaluate(double x)
                                                                    evaluate the double logistic selectivity function
                                                                    Definition: rcpp_selectivity.hpp:255
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::inflection_point_asc
                                                                    ParameterVector inflection_point_asc
                                                                    Definition: rcpp_selectivity.hpp:236
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the double logistic selectivity interface
                                                                    Definition: rcpp_selectivity.hpp:249
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::to_json
                                                                    virtual std::string to_json()
                                                                    Convert the data to json representation for the output.
                                                                    Definition: rcpp_selectivity.hpp:343
                                                                    -
                                                                    DoubleLogisticSelectivityInterface::finalize
                                                                    virtual void finalize()
                                                                    finalize function. Extracts derived quantities back to the Rcpp interface object from the Information...
                                                                    Definition: rcpp_selectivity.hpp:272
                                                                    -
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:336
                                                                    -
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:342
                                                                    -
                                                                    FIMSRcppInterfaceBase::finalized
                                                                    bool finalized
                                                                    Definition: rcpp_interface_base.hpp:339
                                                                    -
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:345
                                                                    -
                                                                    LogisticSelectivityInterface
                                                                    Rcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity ...
                                                                    Definition: rcpp_selectivity.hpp:60
                                                                    -
                                                                    LogisticSelectivityInterface::finalize
                                                                    virtual void finalize()
                                                                    finalize function. Extracts derived quantities back to the Rcpp interface object from the Information...
                                                                    Definition: rcpp_selectivity.hpp:89
                                                                    -
                                                                    LogisticSelectivityInterface::inflection_point
                                                                    ParameterVector inflection_point
                                                                    Definition: rcpp_selectivity.hpp:63
                                                                    -
                                                                    LogisticSelectivityInterface::to_json
                                                                    virtual std::string to_json()
                                                                    Convert the data to json representation for the output.
                                                                    Definition: rcpp_selectivity.hpp:138
                                                                    -
                                                                    LogisticSelectivityInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the logistic selectivity interface
                                                                    Definition: rcpp_selectivity.hpp:71
                                                                    -
                                                                    LogisticSelectivityInterface::slope
                                                                    ParameterVector slope
                                                                    Definition: rcpp_selectivity.hpp:64
                                                                    -
                                                                    LogisticSelectivityInterface::evaluate
                                                                    virtual double evaluate(double x)
                                                                    evaluate the logistic selectivity function
                                                                    Definition: rcpp_selectivity.hpp:77
                                                                    -
                                                                    ParameterVector
                                                                    Rcpp representation of a Parameter vector interface between R and cpp.
                                                                    Definition: rcpp_interface_base.hpp:120
                                                                    -
                                                                    ParameterVector::resize
                                                                    void resize(size_t size)
                                                                    resize to length "size"
                                                                    Definition: rcpp_interface_base.hpp:242
                                                                    -
                                                                    ParameterVector::size
                                                                    size_t size()
                                                                    returns vector length
                                                                    Definition: rcpp_interface_base.hpp:234
                                                                    -
                                                                    ParameterVector::id_m
                                                                    uint32_t id_m
                                                                    Definition: rcpp_interface_base.hpp:124
                                                                    -
                                                                    SelectivityInterfaceBase
                                                                    SelectivityInterfaceBase class should be inherited to define different Rcpp interfaces for each possi...
                                                                    Definition: rcpp_selectivity.hpp:22
                                                                    +
                                                                    230 #endif
                                                                    +
                                                                    231 };
                                                                    +
                                                                    232 
                                                                    +
                                                                    233 #endif
                                                                    +
                                                                    DoubleLogisticSelectivityInterface
                                                                    Rcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity ...
                                                                    Definition: rcpp_selectivity.hpp:138
                                                                    +
                                                                    DoubleLogisticSelectivityInterface::evaluate
                                                                    virtual double evaluate(double x)
                                                                    evaluate the double logistic selectivity function
                                                                    Definition: rcpp_selectivity.hpp:158
                                                                    +
                                                                    DoubleLogisticSelectivityInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the double logistic selectivity interface
                                                                    Definition: rcpp_selectivity.hpp:152
                                                                    +
                                                                    DoubleLogisticSelectivityInterface::slope_asc
                                                                    Parameter slope_asc
                                                                    Definition: rcpp_selectivity.hpp:142
                                                                    +
                                                                    DoubleLogisticSelectivityInterface::inflection_point_asc
                                                                    Parameter inflection_point_asc
                                                                    Definition: rcpp_selectivity.hpp:140
                                                                    +
                                                                    DoubleLogisticSelectivityInterface::slope_desc
                                                                    Parameter slope_desc
                                                                    Definition: rcpp_selectivity.hpp:145
                                                                    +
                                                                    DoubleLogisticSelectivityInterface::inflection_point_desc
                                                                    Parameter inflection_point_desc
                                                                    Definition: rcpp_selectivity.hpp:143
                                                                    +
                                                                    FIMSRcppInterfaceBase
                                                                    Base class for all interface objects.
                                                                    Definition: rcpp_interface_base.hpp:61
                                                                    +
                                                                    FIMSRcppInterfaceBase::fims_interface_objects
                                                                    static std::vector< FIMSRcppInterfaceBase * > fims_interface_objects
                                                                    Definition: rcpp_interface_base.hpp:64
                                                                    +
                                                                    FIMSRcppInterfaceBase::add_to_fims_tmb
                                                                    virtual bool add_to_fims_tmb()
                                                                    virtual method to inherit to add objects to the TMB model
                                                                    Definition: rcpp_interface_base.hpp:67
                                                                    +
                                                                    LogisticSelectivityInterface
                                                                    Rcpp interface for logistic selectivity as an S4 object. To instantiate from R: logistic_selectivity ...
                                                                    Definition: rcpp_selectivity.hpp:61
                                                                    +
                                                                    LogisticSelectivityInterface::slope
                                                                    Parameter slope
                                                                    Definition: rcpp_selectivity.hpp:65
                                                                    +
                                                                    LogisticSelectivityInterface::inflection_point
                                                                    Parameter inflection_point
                                                                    Definition: rcpp_selectivity.hpp:64
                                                                    +
                                                                    LogisticSelectivityInterface::get_id
                                                                    virtual uint32_t get_id()
                                                                    returns the id for the logistic selectivity interface
                                                                    Definition: rcpp_selectivity.hpp:72
                                                                    +
                                                                    LogisticSelectivityInterface::evaluate
                                                                    virtual double evaluate(double x)
                                                                    evaluate the logistic selectivity function
                                                                    Definition: rcpp_selectivity.hpp:78
                                                                    +
                                                                    Parameter
                                                                    RcppInterface class that defines the interface between R and C++ for parameter types.
                                                                    Definition: rcpp_interface_base.hpp:26
                                                                    +
                                                                    Parameter::estimated_m
                                                                    bool estimated_m
                                                                    Definition: rcpp_interface_base.hpp:35
                                                                    +
                                                                    Parameter::value_m
                                                                    double value_m
                                                                    Definition: rcpp_interface_base.hpp:28
                                                                    +
                                                                    Parameter::is_random_effect_m
                                                                    bool is_random_effect_m
                                                                    Definition: rcpp_interface_base.hpp:33
                                                                    +
                                                                    SelectivityInterfaceBase
                                                                    SelectivityInterfaceBase class should be inherited to define different Rcpp interfaces for each possi...
                                                                    Definition: rcpp_selectivity.hpp:23
                                                                    SelectivityInterfaceBase::get_id
                                                                    virtual uint32_t get_id()=0
                                                                    get the ID of the interface base object
                                                                    -
                                                                    SelectivityInterfaceBase::live_objects
                                                                    static std::map< uint32_t, SelectivityInterfaceBase * > live_objects
                                                                    Definition: rcpp_selectivity.hpp:28
                                                                    -
                                                                    SelectivityInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_selectivity.hpp:24
                                                                    +
                                                                    SelectivityInterfaceBase::live_objects
                                                                    static std::map< uint32_t, SelectivityInterfaceBase * > live_objects
                                                                    Definition: rcpp_selectivity.hpp:29
                                                                    +
                                                                    SelectivityInterfaceBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: rcpp_selectivity.hpp:25
                                                                    SelectivityInterfaceBase::evaluate
                                                                    virtual double evaluate(double x)=0
                                                                    evaluate the function
                                                                    -
                                                                    SelectivityInterfaceBase::id
                                                                    uint32_t id
                                                                    Definition: rcpp_selectivity.hpp:25
                                                                    -
                                                                    fims_info::Information::selectivity_models_iterator
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::SelectivityBase< Type > > >::iterator selectivity_models_iterator
                                                                    Definition: information.hpp:71
                                                                    -
                                                                    fims_info::Information::selectivity_models
                                                                    std::map< uint32_t, std::shared_ptr< fims_popdy::SelectivityBase< Type > > > selectivity_models
                                                                    Definition: information.hpp:67
                                                                    -
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:135
                                                                    -
                                                                    FIMS_WARNING_LOG
                                                                    #define FIMS_WARNING_LOG(MESSAGE)
                                                                    Definition: def.hpp:559
                                                                    -
                                                                    FIMS_INFO_LOG
                                                                    #define FIMS_INFO_LOG(MESSAGE)
                                                                    Definition: def.hpp:557
                                                                    -
                                                                    rcpp_interface_base.hpp
                                                                    TODO: provide a brief description.
                                                                    -
                                                                    fims_popdy::DoubleLogisticSelectivity
                                                                    DoubleLogisticSelectivity class that returns the double logistic function value from fims_math.
                                                                    Definition: double_logistic.hpp:24
                                                                    -
                                                                    fims_popdy::DoubleLogisticSelectivity::inflection_point_asc
                                                                    fims::Vector< Type > inflection_point_asc
                                                                    Definition: double_logistic.hpp:25
                                                                    -
                                                                    fims_popdy::DoubleLogisticSelectivity::slope_asc
                                                                    fims::Vector< Type > slope_asc
                                                                    Definition: double_logistic.hpp:28
                                                                    -
                                                                    fims_popdy::DoubleLogisticSelectivity::slope_desc
                                                                    fims::Vector< Type > slope_desc
                                                                    Definition: double_logistic.hpp:34
                                                                    -
                                                                    fims_popdy::DoubleLogisticSelectivity::inflection_point_desc
                                                                    fims::Vector< Type > inflection_point_desc
                                                                    Definition: double_logistic.hpp:31
                                                                    -
                                                                    fims_popdy::DoubleLogisticSelectivity::evaluate
                                                                    virtual const Type evaluate(const Type &x)
                                                                    Method of the double logistic selectivity class that implements the double logistic function from FIM...
                                                                    Definition: double_logistic.hpp:57
                                                                    +
                                                                    SelectivityInterfaceBase::id
                                                                    uint32_t id
                                                                    Definition: rcpp_selectivity.hpp:26
                                                                    +
                                                                    fims_info::Information::GetInstance
                                                                    static std::shared_ptr< Information< Type > > GetInstance()
                                                                    Definition: information.hpp:126
                                                                    +
                                                                    fims_popdy::DoubleLogisticSelectivity
                                                                    DoubleLogisticSelectivity class that returns the double logistic function value from fims_math.
                                                                    Definition: double_logistic.hpp:21
                                                                    +
                                                                    fims_popdy::DoubleLogisticSelectivity::inflection_point_asc
                                                                    Type inflection_point_asc
                                                                    Definition: double_logistic.hpp:22
                                                                    +
                                                                    fims_popdy::DoubleLogisticSelectivity::inflection_point_desc
                                                                    Type inflection_point_desc
                                                                    Definition: double_logistic.hpp:28
                                                                    +
                                                                    fims_popdy::DoubleLogisticSelectivity::slope_asc
                                                                    Type slope_asc
                                                                    Definition: double_logistic.hpp:25
                                                                    +
                                                                    fims_popdy::DoubleLogisticSelectivity::slope_desc
                                                                    Type slope_desc
                                                                    Definition: double_logistic.hpp:31
                                                                    +
                                                                    fims_popdy::DoubleLogisticSelectivity::evaluate
                                                                    virtual const Type evaluate(const Type &x)
                                                                    Method of the double logistic selectivity class that implements the double logistic function from FIM...
                                                                    Definition: double_logistic.hpp:49
                                                                    fims_popdy::LogisticSelectivity
                                                                    LogisticSelectivity class that returns the logistic function value from fims_math.
                                                                    Definition: logistic.hpp:24
                                                                    -
                                                                    fims_popdy::LogisticSelectivity::slope
                                                                    fims::Vector< Type > slope
                                                                    Definition: logistic.hpp:27
                                                                    -
                                                                    fims_popdy::LogisticSelectivity::evaluate
                                                                    virtual const Type evaluate(const Type &x)
                                                                    Method of the logistic selectivity class that implements the logistic function from FIMS math.
                                                                    Definition: logistic.hpp:47
                                                                    -
                                                                    fims_popdy::LogisticSelectivity::inflection_point
                                                                    fims::Vector< Type > inflection_point
                                                                    Definition: logistic.hpp:25
                                                                    +
                                                                    fims_popdy::LogisticSelectivity::slope
                                                                    Type slope
                                                                    Definition: logistic.hpp:27
                                                                    +
                                                                    fims_popdy::LogisticSelectivity::inflection_point
                                                                    Type inflection_point
                                                                    Definition: logistic.hpp:25
                                                                    +
                                                                    fims_popdy::LogisticSelectivity::evaluate
                                                                    virtual const Type evaluate(const Type &x)
                                                                    Method of the logistic selectivity class that implements the logistic function from FIMS math.
                                                                    Definition: logistic.hpp:43
                                                                    diff --git a/docs/recruitment_8hpp_source.html b/docs/recruitment_8hpp_source.html index 76d7b5a..f01ac58 100644 --- a/docs/recruitment_8hpp_source.html +++ b/docs/recruitment_8hpp_source.html @@ -76,16 +76,27 @@
                                                                    recruitment.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    11 #ifndef FIMS_POPULATION_DYNAMICS_RECRUITMENT_HPP
                                                                    -
                                                                    12 #define FIMS_POPULATION_DYNAMICS_RECRUITMENT_HPP
                                                                    -
                                                                    13 
                                                                    -
                                                                    14 #include "functors/recruitment_base.hpp"
                                                                    -
                                                                    15 #include "functors/sr_beverton_holt.hpp"
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  *
                                                                    +
                                                                    3  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    4  * Fisheries Integrated Modeling System project. See LICENSE in the
                                                                    +
                                                                    5  * source folder for reuse information.
                                                                    +
                                                                    6  *
                                                                    +
                                                                    7  * Recruitment module file
                                                                    +
                                                                    8  * The purpose of this file is to include any .hpp files within the
                                                                    +
                                                                    9  * subfolders so that only this file needs to included in the model.hpp file.
                                                                    +
                                                                    10  *
                                                                    +
                                                                    11  * DEFINE guards for recruitment module outline to define the
                                                                    +
                                                                    12  * recruitment hpp file if not already defined.
                                                                    +
                                                                    13  */
                                                                    +
                                                                    14 #ifndef FIMS_POPULATION_DYNAMICS_RECRUITMENT_HPP
                                                                    +
                                                                    15 #define FIMS_POPULATION_DYNAMICS_RECRUITMENT_HPP
                                                                    16 
                                                                    -
                                                                    17 #endif /* FIMS_POPULATION_DYNAMICS_RECRUITMENT_HPP */
                                                                    -
                                                                    recruitment_base.hpp
                                                                    Serves as the parent class where recruitment functions are called.
                                                                    -
                                                                    sr_beverton_holt.hpp
                                                                    Calls the Beverton–Holt stock–recruitment function from fims_math and does the calculation.
                                                                    +
                                                                    17 #include "functors/recruitment_base.hpp"
                                                                    +
                                                                    18 #include "functors/sr_beverton_holt.hpp"
                                                                    +
                                                                    19 
                                                                    +
                                                                    20 #endif /* FIMS_POPULATION_DYNAMICS_RECRUITMENT_HPP */
                                                                    +
                                                                    recruitment_base.hpp
                                                                    diff --git a/docs/recruitment__base_8hpp.html b/docs/recruitment__base_8hpp.html index b2e9c0f..fe7d1a1 100644 --- a/docs/recruitment__base_8hpp.html +++ b/docs/recruitment__base_8hpp.html @@ -78,14 +78,11 @@
                                                                    recruitment_base.hpp File Reference
                                                                    - -

                                                                    Serves as the parent class where recruitment functions are called. -More...

                                                                    #include <cmath>
                                                                    #include "../../../common/fims_math.hpp"
                                                                    -#include "../../../common/fims_vector.hpp"
                                                                    -#include "../../../common/model_object.hpp"
                                                                    -#include "../../../distributions/distributions.hpp"
                                                                    +#include "../../../common/fims_vector.hpp"
                                                                    +#include "../../../common/model_object.hpp"
                                                                    +#include "../../../distributions/distributions.hpp"

                                                                    Go to the source code of this file.

                                                                    @@ -96,8 +93,9 @@
                                                                     

                                                                    Detailed Description

                                                                    -

                                                                    Serves as the parent class where recruitment functions are called.

                                                                    -

                                                                    Defines guards for recruitment base outline to define the recruitment hpp file if not already defined.

                                                                    Copyright
                                                                    This file is part of the NOAA, National Marine Fisheries Service Fisheries Integrated Modeling System project. See LICENSE in the source folder for reuse information.
                                                                    +

                                                                    This File is part of the NOAA, National Marine Fisheries Service Fisheries Integrated Modeling System project. See LICENSE in the source folder for reuse information.

                                                                    +

                                                                    Recruitment base file The purpose of this file is to serve as the parent class where recruitment functions are called.

                                                                    +

                                                                    DEFINE guards for recruitment base outline to define the recruitment hpp file if not already defined.

                                                                    diff --git a/docs/recruitment__base_8hpp_source.html b/docs/recruitment__base_8hpp_source.html index 3b6a9b2..29be6f1 100644 --- a/docs/recruitment__base_8hpp_source.html +++ b/docs/recruitment__base_8hpp_source.html @@ -77,71 +77,94 @@
                                                                    Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    10 #ifndef FIMS_POPULATION_DYNAMICS_RECRUITMENT_BASE_HPP
                                                                    -
                                                                    11 #define FIMS_POPULATION_DYNAMICS_RECRUITMENT_BASE_HPP
                                                                    -
                                                                    12 
                                                                    -
                                                                    13 #include <cmath> // for using std::pow and M_PI
                                                                    -
                                                                    14 
                                                                    -
                                                                    15 #include "../../../common/fims_math.hpp" // for using fims_math::log()
                                                                    -
                                                                    16 #include "../../../common/fims_vector.hpp"
                                                                    -
                                                                    17 #include "../../../common/model_object.hpp"
                                                                    -
                                                                    18 #include "../../../distributions/distributions.hpp"
                                                                    -
                                                                    19 
                                                                    -
                                                                    20 namespace fims_popdy {
                                                                    -
                                                                    21 
                                                                    -
                                                                    27 template <class Type>
                                                                    -
                                                                    28 struct RecruitmentBase : public fims_model_object::FIMSObject<Type> {
                                                                    -
                                                                    29  static uint32_t id_g;
                                                                    -
                                                                    31  fims::Vector<Type>
                                                                    -
                                                                    32  log_recruit_devs;
                                                                    -
                                                                    33  bool constrain_deviations = false;
                                                                    -
                                                                    36  fims::Vector<Type> log_rzero;
                                                                    -
                                                                    38  bool estimate_log_recruit_devs = true;
                                                                    -
                                                                    43  RecruitmentBase() { this->id = RecruitmentBase::id_g++; }
                                                                    -
                                                                    44 
                                                                    -
                                                                    45  virtual ~RecruitmentBase() {}
                                                                    -
                                                                    46 
                                                                    -
                                                                    51  void Prepare() { this->PrepareConstrainedDeviations(); }
                                                                    +
                                                                    14 #ifndef FIMS_POPULATION_DYNAMICS_RECRUITMENT_BASE_HPP
                                                                    +
                                                                    15 #define FIMS_POPULATION_DYNAMICS_RECRUITMENT_BASE_HPP
                                                                    +
                                                                    16 
                                                                    +
                                                                    17 #include <cmath> // for using std::pow and M_PI
                                                                    +
                                                                    18 
                                                                    +
                                                                    19 #include "../../../common/fims_math.hpp" // for using fims_math::log()
                                                                    +
                                                                    20 #include "../../../common/fims_vector.hpp"
                                                                    +
                                                                    21 #include "../../../common/model_object.hpp"
                                                                    +
                                                                    22 #include "../../../distributions/distributions.hpp"
                                                                    +
                                                                    23 
                                                                    +
                                                                    24 namespace fims_popdy {
                                                                    +
                                                                    25 
                                                                    +
                                                                    31 template <class Type>
                                                                    +
                                                                    32 struct RecruitmentBase : public fims_model_object::FIMSObject<Type> {
                                                                    +
                                                                    33  static uint32_t id_g;
                                                                    +
                                                                    35  fims::Vector<Type>
                                                                    +
                                                                    36  log_recruit_devs;
                                                                    +
                                                                    37  bool constrain_deviations = false;
                                                                    +
                                                                    40  Type log_sigma_recruit;
                                                                    +
                                                                    42  Type log_rzero;
                                                                    +
                                                                    44  bool estimate_log_recruit_devs = true;
                                                                    +
                                                                    49  RecruitmentBase() { this->id = RecruitmentBase::id_g++; }
                                                                    +
                                                                    50 
                                                                    +
                                                                    51  virtual ~RecruitmentBase() {}
                                                                    52 
                                                                    -
                                                                    59  virtual const Type evaluate(
                                                                    -
                                                                    60  const Type &spawners,
                                                                    -
                                                                    61  const Type &ssbzero) = 0; // need to add input parameter values
                                                                    -
                                                                    62 
                                                                    -
                                                                    63 
                                                                    -
                                                                    70  void PrepareConstrainedDeviations() {
                                                                    -
                                                                    71  if (!this->constrain_deviations) {
                                                                    -
                                                                    72  return;
                                                                    -
                                                                    73  }
                                                                    -
                                                                    74 
                                                                    -
                                                                    75  Type sum = 0.0;
                                                                    -
                                                                    76 
                                                                    -
                                                                    77  for (size_t i = 0; i < this->log_recruit_devs.size(); i++) {
                                                                    -
                                                                    78  sum += this->log_recruit_devs[i];
                                                                    -
                                                                    79  }
                                                                    -
                                                                    80 
                                                                    -
                                                                    81  for (size_t i = 0; i < this->log_recruit_devs.size(); i++) {
                                                                    -
                                                                    82  this->log_recruit_devs[i] -= sum / (this->log_recruit_devs.size());
                                                                    -
                                                                    83  }
                                                                    -
                                                                    84  }
                                                                    -
                                                                    85 };
                                                                    -
                                                                    86 
                                                                    -
                                                                    87 template <class Type>
                                                                    -
                                                                    88 uint32_t RecruitmentBase<Type>::id_g = 0;
                                                                    -
                                                                    89 } // namespace fims_popdy
                                                                    +
                                                                    57  void Prepare() { this->PrepareConstrainedDeviations(); }
                                                                    +
                                                                    58 
                                                                    +
                                                                    65  virtual const Type evaluate(
                                                                    +
                                                                    66  const Type &spawners,
                                                                    +
                                                                    67  const Type &ssbzero) = 0; // need to add input parameter values
                                                                    +
                                                                    68 
                                                                    +
                                                                    72  virtual const Type evaluate_nll() {
                                                                    +
                                                                    73  Type nll = 0.0;
                                                                    +
                                                                    75  if (!this->estimate_log_recruit_devs) {
                                                                    +
                                                                    76  return nll;
                                                                    +
                                                                    77  } else {
                                                                    +
                                                                    78 #ifdef TMB_MODEL
                                                                    +
                                                                    79  fims_distributions::Dnorm<Type> dnorm;
                                                                    +
                                                                    80  dnorm.sd = fims_math::exp(this->log_sigma_recruit);
                                                                    +
                                                                    81  for (size_t i = 0; i < this->log_recruit_devs.size(); i++) {
                                                                    +
                                                                    82  dnorm.x = this->log_recruit_devs[i];
                                                                    +
                                                                    83  dnorm.mean = 0.0;
                                                                    +
                                                                    84  nll -= dnorm.evaluate(true);
                                                                    +
                                                                    85  }
                                                                    +
                                                                    86 #endif
                                                                    +
                                                                    87  return nll;
                                                                    +
                                                                    88  }
                                                                    +
                                                                    89  }
                                                                    90 
                                                                    -
                                                                    91 #endif /* FIMS_POPULATION_DYNAMICS_RECRUITMENT_BASE_HPP */
                                                                    -
                                                                    fims::Vector
                                                                    Definition: fims_vector.hpp:25
                                                                    -
                                                                    fims_model_object::FIMSObject
                                                                    FIMSObject struct that defines member types and returns the unique id.
                                                                    Definition: model_object.hpp:24
                                                                    -
                                                                    fims_popdy::RecruitmentBase
                                                                    Base class for all recruitment functors.
                                                                    Definition: recruitment_base.hpp:28
                                                                    -
                                                                    fims_popdy::RecruitmentBase::log_rzero
                                                                    fims::Vector< Type > log_rzero
                                                                    Definition: recruitment_base.hpp:36
                                                                    -
                                                                    fims_popdy::RecruitmentBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: recruitment_base.hpp:29
                                                                    -
                                                                    fims_popdy::RecruitmentBase::PrepareConstrainedDeviations
                                                                    void PrepareConstrainedDeviations()
                                                                    Prepare constrained recruitment deviations. Based on ADMB sum-to-zero constraint implementation....
                                                                    Definition: recruitment_base.hpp:70
                                                                    -
                                                                    fims_popdy::RecruitmentBase::Prepare
                                                                    void Prepare()
                                                                    Prepares the recruitment deviations vector.
                                                                    Definition: recruitment_base.hpp:51
                                                                    +
                                                                    97  void PrepareConstrainedDeviations() {
                                                                    +
                                                                    98  if (!this->constrain_deviations) {
                                                                    +
                                                                    99  return;
                                                                    +
                                                                    100  }
                                                                    +
                                                                    101 
                                                                    +
                                                                    102  Type sum = 0.0;
                                                                    +
                                                                    103 
                                                                    +
                                                                    104  for (size_t i = 0; i < this->log_recruit_devs.size(); i++) {
                                                                    +
                                                                    105  sum += this->log_recruit_devs[i];
                                                                    +
                                                                    106  }
                                                                    +
                                                                    107 
                                                                    +
                                                                    108  RECRUITMENT_LOG << "log_recruit_devs: \n";
                                                                    +
                                                                    109  for (size_t i = 0; i < this->log_recruit_devs.size(); i++) {
                                                                    +
                                                                    110  this->log_recruit_devs[i] -= sum / (this->log_recruit_devs.size());
                                                                    +
                                                                    111  RECRUITMENT_LOG << this->log_recruit_devs[i] << std::endl;
                                                                    +
                                                                    112  }
                                                                    +
                                                                    113  }
                                                                    +
                                                                    114 };
                                                                    +
                                                                    115 
                                                                    +
                                                                    116 template <class Type>
                                                                    +
                                                                    117 uint32_t RecruitmentBase<Type>::id_g = 0;
                                                                    +
                                                                    118 } // namespace fims_popdy
                                                                    +
                                                                    119 
                                                                    +
                                                                    120 #endif /* FIMS_POPULATION_DYNAMICS_RECRUITMENT_BASE_HPP */
                                                                    +
                                                                    fims::Vector
                                                                    Definition: fims_vector.hpp:18
                                                                    +
                                                                    RECRUITMENT_LOG
                                                                    std::ofstream RECRUITMENT_LOG("logs/recruitment.log")
                                                                    +
                                                                    fims_model_object::FIMSObject
                                                                    FIMSObject struct that defines member types and returns the unique id.
                                                                    Definition: model_object.hpp:25
                                                                    +
                                                                    fims_popdy::RecruitmentBase
                                                                    Base class for all recruitment functors.
                                                                    Definition: recruitment_base.hpp:32
                                                                    +
                                                                    fims_popdy::RecruitmentBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: recruitment_base.hpp:33
                                                                    +
                                                                    fims_popdy::RecruitmentBase::PrepareConstrainedDeviations
                                                                    void PrepareConstrainedDeviations()
                                                                    Prepare constrained recruitment deviations. Based on ADMB sum-to-zero constraint implementation....
                                                                    Definition: recruitment_base.hpp:97
                                                                    +
                                                                    fims_popdy::RecruitmentBase::evaluate_nll
                                                                    virtual const Type evaluate_nll()
                                                                    Calculates the negative log likelihood of recruitment deviations.
                                                                    Definition: recruitment_base.hpp:72
                                                                    +
                                                                    fims_popdy::RecruitmentBase::Prepare
                                                                    void Prepare()
                                                                    Prepares the recruitment deviations vector.
                                                                    Definition: recruitment_base.hpp:57
                                                                    fims_popdy::RecruitmentBase::evaluate
                                                                    virtual const Type evaluate(const Type &spawners, const Type &ssbzero)=0
                                                                    Calculates the expected recruitment for a given spawning input.
                                                                    -
                                                                    fims_popdy::RecruitmentBase::estimate_log_recruit_devs
                                                                    bool estimate_log_recruit_devs
                                                                    Definition: recruitment_base.hpp:38
                                                                    -
                                                                    fims_popdy::RecruitmentBase::constrain_deviations
                                                                    bool constrain_deviations
                                                                    Definition: recruitment_base.hpp:33
                                                                    -
                                                                    fims_popdy::RecruitmentBase::RecruitmentBase
                                                                    RecruitmentBase()
                                                                    Constructor.
                                                                    Definition: recruitment_base.hpp:43
                                                                    -
                                                                    fims_popdy::RecruitmentBase::log_recruit_devs
                                                                    fims::Vector< Type > log_recruit_devs
                                                                    Definition: recruitment_base.hpp:32
                                                                    +
                                                                    fims_popdy::RecruitmentBase::log_sigma_recruit
                                                                    Type log_sigma_recruit
                                                                    Definition: recruitment_base.hpp:40
                                                                    +
                                                                    fims_popdy::RecruitmentBase::estimate_log_recruit_devs
                                                                    bool estimate_log_recruit_devs
                                                                    Definition: recruitment_base.hpp:44
                                                                    +
                                                                    fims_popdy::RecruitmentBase::constrain_deviations
                                                                    bool constrain_deviations
                                                                    Definition: recruitment_base.hpp:37
                                                                    +
                                                                    fims_popdy::RecruitmentBase::log_rzero
                                                                    Type log_rzero
                                                                    Definition: recruitment_base.hpp:42
                                                                    +
                                                                    fims_popdy::RecruitmentBase::RecruitmentBase
                                                                    RecruitmentBase()
                                                                    Constructor.
                                                                    Definition: recruitment_base.hpp:49
                                                                    +
                                                                    fims_popdy::RecruitmentBase::log_recruit_devs
                                                                    fims::Vector< Type > log_recruit_devs
                                                                    Definition: recruitment_base.hpp:36
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searchData= [ - ['parameter_5fnames_906',['parameter_names',['../classfims__info_1_1Information.html#ac1fbb03c15a0c6ca3d634b8761804823',1,'fims_info::Information']]], - ['parameters_907',['parameters',['../classfims__info_1_1Information.html#ab32f7d2e0f24b8c8f651a1cdf99cac17',1,'fims_info::Information::parameters()'],['../structfims__model__object_1_1FIMSObject.html#ac625a90f1af6d01d8c476d0a1ecb5343',1,'fims_model_object::FIMSObject::parameters()']]], - ['populations_908',['populations',['../classfims__info_1_1Information.html#a13bc1ac7074aeb44f7ceb0d2b9bb8531',1,'fims_info::Information']]], - ['proportion_5fcatch_5fnumbers_5fat_5fage_909',['proportion_catch_numbers_at_age',['../classFleetInterface.html#a5f8e1067606b8c3cf264c06a113316d1',1,'FleetInterface::proportion_catch_numbers_at_age()'],['../structfims__popdy_1_1Fleet.html#af5bd44e0948bdc39ae4a8453db16f103',1,'fims_popdy::Fleet::proportion_catch_numbers_at_age()']]], - ['proportion_5fcatch_5fnumbers_5fat_5flength_910',['proportion_catch_numbers_at_length',['../classFleetInterface.html#a32cae4719c817e0949fb089f6b59bab7',1,'FleetInterface::proportion_catch_numbers_at_length()'],['../structfims__popdy_1_1Fleet.html#ac23696298ec8a976fdfb27873bbadc31',1,'fims_popdy::Fleet::proportion_catch_numbers_at_length()']]], - ['proportion_5ffemale_911',['proportion_female',['../classPopulationInterface.html#aa530597de608776c84fe26ecc81b5e66',1,'PopulationInterface::proportion_female()'],['../structfims__popdy_1_1Population.html#ae47bb5ebf7a3f1b14f69b9cfd7ad8ecf',1,'fims_popdy::Population::proportion_female()']]], - ['proportion_5fmature_5fat_5fage_912',['proportion_mature_at_age',['../structfims__popdy_1_1Population.html#a3dde506dfcd218d4ae8373880747a433',1,'fims_popdy::Population']]] + ['p_583',['p',['../classDmultinomDistributionsInterface.html#a563a86aac155b9a5477bb405e5d31b6a',1,'DmultinomDistributionsInterface']]], + ['parameters_584',['parameters',['../classfims__info_1_1Information.html#ab32f7d2e0f24b8c8f651a1cdf99cac17',1,'fims_info::Information::parameters()'],['../structfims__model__object_1_1FIMSObject.html#ac625a90f1af6d01d8c476d0a1ecb5343',1,'fims_model_object::FIMSObject::parameters()']]], + ['populations_585',['populations',['../classfims__info_1_1Information.html#a13bc1ac7074aeb44f7ceb0d2b9bb8531',1,'fims_info::Information']]], + ['proportion_5ffemale_586',['proportion_female',['../classPopulationInterface.html#aa530597de608776c84fe26ecc81b5e66',1,'PopulationInterface::proportion_female()'],['../structfims__popdy_1_1Population.html#ae47bb5ebf7a3f1b14f69b9cfd7ad8ecf',1,'fims_popdy::Population::proportion_female()']]], + ['proportion_5fmature_5fat_5fage_587',['proportion_mature_at_age',['../structfims__popdy_1_1Population.html#a3dde506dfcd218d4ae8373880747a433',1,'fims_popdy::Population']]] ]; diff --git a/docs/search/variables_f.js b/docs/search/variables_f.js index 2040a20..0edfdfe 100644 --- a/docs/search/variables_f.js +++ b/docs/search/variables_f.js @@ -1,4 +1,4 @@ var searchData= [ - ['q_913',['q',['../structfims__popdy_1_1Fleet.html#a9dbf02a91350fb062adc9ded0a89c66e',1,'fims_popdy::Fleet']]] + ['q_588',['q',['../structfims__popdy_1_1Fleet.html#a3d3b3fd71ba4856b080c263024bfe2d7',1,'fims_popdy::Fleet']]] ]; diff --git a/docs/selectivity_2functors_2logistic_8hpp_source.html b/docs/selectivity_2functors_2logistic_8hpp_source.html index 28d0177..e008e62 100644 --- a/docs/selectivity_2functors_2logistic_8hpp_source.html +++ b/docs/selectivity_2functors_2logistic_8hpp_source.html @@ -76,51 +76,45 @@
                                                                    logistic.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    9 #ifndef POPULATION_DYNAMICS_SELECTIVITY_LOGISTIC_HPP
                                                                    -
                                                                    10 #define POPULATION_DYNAMICS_SELECTIVITY_LOGISTIC_HPP
                                                                    -
                                                                    11 
                                                                    -
                                                                    12 //#include "../../../interface/interface.hpp"
                                                                    -
                                                                    13 #include "../../../common/fims_math.hpp"
                                                                    -
                                                                    14 #include "../../../common/fims_vector.hpp"
                                                                    -
                                                                    15 #include "selectivity_base.hpp"
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    3  * Fisheries Integrated Modeling System project.
                                                                    +
                                                                    4  * Refer to the LICENSE file for reuse information.
                                                                    +
                                                                    5  *
                                                                    +
                                                                    6  * The purpose of this file is to declare the LogisticSelectivity class
                                                                    +
                                                                    7  * which implements the logistic function from fims_math in the selectivity
                                                                    +
                                                                    8  * module.
                                                                    +
                                                                    9  */
                                                                    +
                                                                    10 #ifndef POPULATION_DYNAMICS_SELECTIVITY_LOGISTIC_HPP
                                                                    +
                                                                    11 #define POPULATION_DYNAMICS_SELECTIVITY_LOGISTIC_HPP
                                                                    +
                                                                    12 
                                                                    +
                                                                    13 //#include "../../../interface/interface.hpp"
                                                                    +
                                                                    14 #include "../../../common/fims_math.hpp"
                                                                    +
                                                                    15 #include "selectivity_base.hpp"
                                                                    16 
                                                                    17 namespace fims_popdy {
                                                                    18 
                                                                    23 template <typename Type>
                                                                    24 struct LogisticSelectivity : public SelectivityBase<Type> {
                                                                    -
                                                                    25  fims::Vector<Type> inflection_point;
                                                                    -
                                                                    27  fims::Vector<Type> slope;
                                                                    -
                                                                    30  LogisticSelectivity() : SelectivityBase<Type>()
                                                                    -
                                                                    31  {
                                                                    -
                                                                    32  }
                                                                    +
                                                                    25  Type inflection_point;
                                                                    +
                                                                    27  Type slope;
                                                                    +
                                                                    30  LogisticSelectivity() : SelectivityBase<Type>() {}
                                                                    +
                                                                    31 
                                                                    +
                                                                    32  virtual ~LogisticSelectivity() {}
                                                                    33 
                                                                    -
                                                                    34  virtual ~LogisticSelectivity()
                                                                    -
                                                                    35  {
                                                                    -
                                                                    36  }
                                                                    -
                                                                    37 
                                                                    -
                                                                    47  virtual const Type evaluate(const Type& x)
                                                                    -
                                                                    48  {
                                                                    -
                                                                    49  return fims_math::logistic<Type>(inflection_point[0], slope[0], x);
                                                                    -
                                                                    50  }
                                                                    -
                                                                    51 
                                                                    -
                                                                    62  virtual const Type evaluate(const Type& x, size_t pos)
                                                                    -
                                                                    63  {
                                                                    -
                                                                    64  return fims_math::logistic<Type>(inflection_point.get_force_scalar(pos), slope.get_force_scalar(pos), x);
                                                                    -
                                                                    65  }
                                                                    -
                                                                    66 };
                                                                    -
                                                                    67 
                                                                    -
                                                                    68 } // namespace fims_popdy
                                                                    -
                                                                    69 
                                                                    -
                                                                    70 #endif /* POPULATION_DYNAMICS_SELECTIVITY_LOGISTIC_HPP */
                                                                    -
                                                                    fims::Vector
                                                                    Definition: fims_vector.hpp:25
                                                                    -
                                                                    selectivity_base.hpp
                                                                    Declares the SelectivityBase class which is the base class for all selectivity functors.
                                                                    +
                                                                    43  virtual const Type evaluate(const Type& x) {
                                                                    +
                                                                    44  return fims_math::logistic<Type>(inflection_point, slope, x);
                                                                    +
                                                                    45  }
                                                                    +
                                                                    46 };
                                                                    +
                                                                    47 
                                                                    +
                                                                    48 } // namespace fims_popdy
                                                                    +
                                                                    49 
                                                                    +
                                                                    50 #endif /* POPULATION_DYNAMICS_SELECTIVITY_LOGISTIC_HPP */
                                                                    fims_popdy::LogisticSelectivity
                                                                    LogisticSelectivity class that returns the logistic function value from fims_math.
                                                                    Definition: logistic.hpp:24
                                                                    -
                                                                    fims_popdy::LogisticSelectivity::slope
                                                                    fims::Vector< Type > slope
                                                                    Definition: logistic.hpp:27
                                                                    -
                                                                    fims_popdy::LogisticSelectivity::evaluate
                                                                    virtual const Type evaluate(const Type &x)
                                                                    Method of the logistic selectivity class that implements the logistic function from FIMS math.
                                                                    Definition: logistic.hpp:47
                                                                    -
                                                                    fims_popdy::LogisticSelectivity::evaluate
                                                                    virtual const Type evaluate(const Type &x, size_t pos)
                                                                    Method of the logistic selectivity class that implements the logistic function from FIMS math.
                                                                    Definition: logistic.hpp:62
                                                                    -
                                                                    fims_popdy::LogisticSelectivity::inflection_point
                                                                    fims::Vector< Type > inflection_point
                                                                    Definition: logistic.hpp:25
                                                                    -
                                                                    fims_popdy::SelectivityBase
                                                                    Base class for all selectivity functors.
                                                                    Definition: selectivity_base.hpp:24
                                                                    +
                                                                    fims_popdy::LogisticSelectivity::slope
                                                                    Type slope
                                                                    Definition: logistic.hpp:27
                                                                    +
                                                                    fims_popdy::LogisticSelectivity::inflection_point
                                                                    Type inflection_point
                                                                    Definition: logistic.hpp:25
                                                                    +
                                                                    fims_popdy::LogisticSelectivity::evaluate
                                                                    virtual const Type evaluate(const Type &x)
                                                                    Method of the logistic selectivity class that implements the logistic function from FIMS math.
                                                                    Definition: logistic.hpp:43
                                                                    +
                                                                    fims_popdy::SelectivityBase
                                                                    Base class for all selectivity functors.
                                                                    Definition: selectivity_base.hpp:27
                                                                    diff --git a/docs/selectivity_8hpp_source.html b/docs/selectivity_8hpp_source.html index 373f01c..d995d6d 100644 --- a/docs/selectivity_8hpp_source.html +++ b/docs/selectivity_8hpp_source.html @@ -76,16 +76,27 @@
                                                                    selectivity.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    11 #ifndef FIMS_POPULATION_DYNAMICS_SELECTIVITY_HPP
                                                                    -
                                                                    12 #define FIMS_POPULATION_DYNAMICS_SELECTIVITY_HPP
                                                                    -
                                                                    13 
                                                                    -
                                                                    14 #include "functors/double_logistic.hpp"
                                                                    -
                                                                    15 #include "functors/logistic.hpp"
                                                                    -
                                                                    16 #include "functors/selectivity_base.hpp"
                                                                    -
                                                                    17 
                                                                    -
                                                                    18 #endif /* FIMS_POPULATION_DYNAMICS_SELECTIVITY_HPP */
                                                                    -
                                                                    selectivity_base.hpp
                                                                    Declares the SelectivityBase class which is the base class for all selectivity functors.
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  *
                                                                    +
                                                                    3  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    4  * Fisheries Integrated Modeling System project. See LICENSE in the
                                                                    +
                                                                    5  * source folder for reuse information.
                                                                    +
                                                                    6  *
                                                                    +
                                                                    7  * Selectivity module file
                                                                    +
                                                                    8  * The purpose of this file is to include any .hpp files within the
                                                                    +
                                                                    9  * subfolders so that only this file needs to included in the model.hpp file.
                                                                    +
                                                                    10  *
                                                                    +
                                                                    11  * DEFINE guards for selectivity module outline to define the
                                                                    +
                                                                    12  * selectivity hpp file if not already defined.
                                                                    +
                                                                    13  */
                                                                    +
                                                                    14 #ifndef FIMS_POPULATION_DYNAMICS_SELECTIVITY_HPP
                                                                    +
                                                                    15 #define FIMS_POPULATION_DYNAMICS_SELECTIVITY_HPP
                                                                    +
                                                                    16 
                                                                    +
                                                                    17 #include "functors/double_logistic.hpp"
                                                                    +
                                                                    18 #include "functors/logistic.hpp"
                                                                    +
                                                                    19 #include "functors/selectivity_base.hpp"
                                                                    +
                                                                    20 
                                                                    +
                                                                    21 #endif /* FIMS_POPULATION_DYNAMICS_SELECTIVITY_HPP */
                                                                    diff --git a/docs/selectivity__base_8hpp_source.html b/docs/selectivity__base_8hpp_source.html index b1adf9c..8f2c754 100644 --- a/docs/selectivity__base_8hpp_source.html +++ b/docs/selectivity__base_8hpp_source.html @@ -76,47 +76,56 @@
                                                                    selectivity_base.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    11 #ifndef POPULATION_DYNAMICS_SELECTIVITY_BASE_HPP
                                                                    -
                                                                    12 #define POPULATION_DYNAMICS_SELECTIVITY_BASE_HPP
                                                                    -
                                                                    13 
                                                                    -
                                                                    14 #include "../../../common/model_object.hpp"
                                                                    -
                                                                    15 
                                                                    -
                                                                    16 namespace fims_popdy {
                                                                    -
                                                                    17 
                                                                    -
                                                                    23 template <typename Type>
                                                                    -
                                                                    24 struct SelectivityBase : public fims_model_object::FIMSObject<Type> {
                                                                    -
                                                                    25  // id_g is the ID of the instance of the SelectivityBase class.
                                                                    -
                                                                    26  // this is like a memory tracker.
                                                                    -
                                                                    27  // Assigning each one its own ID is a way to keep track of
                                                                    -
                                                                    28  // all the instances of the SelectivityBase class.
                                                                    -
                                                                    29  static uint32_t
                                                                    -
                                                                    30  id_g;
                                                                    -
                                                                    34  SelectivityBase() {
                                                                    -
                                                                    35  // increment id of the singleton selectivity class
                                                                    -
                                                                    36  this->id = SelectivityBase::id_g++;
                                                                    -
                                                                    37  }
                                                                    -
                                                                    38 
                                                                    -
                                                                    39  virtual ~SelectivityBase() {}
                                                                    -
                                                                    40 
                                                                    -
                                                                    46  virtual const Type evaluate(const Type& x) = 0;
                                                                    -
                                                                    47 
                                                                    -
                                                                    54  virtual const Type evaluate(const Type& x, size_t pos) = 0;
                                                                    -
                                                                    55 };
                                                                    -
                                                                    56 
                                                                    -
                                                                    57 // default id of the singleton selectivity class
                                                                    -
                                                                    58 template <typename Type>
                                                                    -
                                                                    59 uint32_t SelectivityBase<Type>::id_g = 0;
                                                                    -
                                                                    60 
                                                                    -
                                                                    61 } // namespace fims_popdy
                                                                    -
                                                                    62 
                                                                    -
                                                                    63 #endif /* POPULATION_DYNAMICS_SELECTIVITY_BASE_HPP */
                                                                    -
                                                                    fims_model_object::FIMSObject
                                                                    FIMSObject struct that defines member types and returns the unique id.
                                                                    Definition: model_object.hpp:24
                                                                    -
                                                                    fims_popdy::SelectivityBase
                                                                    Base class for all selectivity functors.
                                                                    Definition: selectivity_base.hpp:24
                                                                    -
                                                                    fims_popdy::SelectivityBase::evaluate
                                                                    virtual const Type evaluate(const Type &x, size_t pos)=0
                                                                    Calculates the selectivity.
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  *
                                                                    +
                                                                    3  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    4  * Fisheries Integrated Modeling System project. See LICENSE in the
                                                                    +
                                                                    5  * source folder for reuse information.
                                                                    +
                                                                    6  *
                                                                    +
                                                                    7  * SelectivityBase file
                                                                    +
                                                                    8  * The purpose of this file is to declare the SelectivityBase class
                                                                    +
                                                                    9  * which is the base class for all selectivity functors.
                                                                    +
                                                                    10  *
                                                                    +
                                                                    11  * DEFINE guards for selectivity module outline to define the
                                                                    +
                                                                    12  * selectivity hpp file if not already defined.
                                                                    +
                                                                    13  */
                                                                    +
                                                                    14 #ifndef POPULATION_DYNAMICS_SELECTIVITY_BASE_HPP
                                                                    +
                                                                    15 #define POPULATION_DYNAMICS_SELECTIVITY_BASE_HPP
                                                                    +
                                                                    16 
                                                                    +
                                                                    17 #include "../../../common/model_object.hpp"
                                                                    +
                                                                    18 
                                                                    +
                                                                    19 namespace fims_popdy {
                                                                    +
                                                                    20 
                                                                    +
                                                                    26 template <typename Type>
                                                                    +
                                                                    27 struct SelectivityBase : public fims_model_object::FIMSObject<Type> {
                                                                    +
                                                                    28  // id_g is the ID of the instance of the SelectivityBase class.
                                                                    +
                                                                    29  // this is like a memory tracker.
                                                                    +
                                                                    30  // Assigning each one its own ID is a way to keep track of
                                                                    +
                                                                    31  // all the instances of the SelectivityBase class.
                                                                    +
                                                                    32  static uint32_t
                                                                    +
                                                                    33  id_g;
                                                                    +
                                                                    37  SelectivityBase() {
                                                                    +
                                                                    38  // increment id of the singleton selectivity class
                                                                    +
                                                                    39  this->id = SelectivityBase::id_g++;
                                                                    +
                                                                    40  }
                                                                    +
                                                                    41 
                                                                    +
                                                                    42  virtual ~SelectivityBase() {}
                                                                    +
                                                                    43 
                                                                    +
                                                                    49  virtual const Type evaluate(const Type& x) = 0;
                                                                    +
                                                                    50 };
                                                                    +
                                                                    51 
                                                                    +
                                                                    52 // default id of the singleton selectivity class
                                                                    +
                                                                    53 template <typename Type>
                                                                    +
                                                                    54 uint32_t SelectivityBase<Type>::id_g = 0;
                                                                    +
                                                                    55 
                                                                    +
                                                                    56 } // namespace fims_popdy
                                                                    +
                                                                    57 
                                                                    +
                                                                    58 #endif /* POPULATION_DYNAMICS_SELECTIVITY_BASE_HPP */
                                                                    +
                                                                    fims_model_object::FIMSObject
                                                                    FIMSObject struct that defines member types and returns the unique id.
                                                                    Definition: model_object.hpp:25
                                                                    +
                                                                    fims_popdy::SelectivityBase
                                                                    Base class for all selectivity functors.
                                                                    Definition: selectivity_base.hpp:27
                                                                    fims_popdy::SelectivityBase::evaluate
                                                                    virtual const Type evaluate(const Type &x)=0
                                                                    Calculates the selectivity.
                                                                    -
                                                                    fims_popdy::SelectivityBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: selectivity_base.hpp:30
                                                                    -
                                                                    fims_popdy::SelectivityBase::SelectivityBase
                                                                    SelectivityBase()
                                                                    Constructor.
                                                                    Definition: selectivity_base.hpp:34
                                                                    +
                                                                    fims_popdy::SelectivityBase::id_g
                                                                    static uint32_t id_g
                                                                    Definition: selectivity_base.hpp:33
                                                                    +
                                                                    fims_popdy::SelectivityBase::SelectivityBase
                                                                    SelectivityBase()
                                                                    Constructor.
                                                                    Definition: selectivity_base.hpp:37
                                                                    diff --git a/docs/sr__beverton__holt_8hpp_source.html b/docs/sr__beverton__holt_8hpp_source.html index e4b7213..dbb4a32 100644 --- a/docs/sr__beverton__holt_8hpp_source.html +++ b/docs/sr__beverton__holt_8hpp_source.html @@ -76,53 +76,62 @@
                                                                    sr_beverton_holt.hpp
                                                                    -Go to the documentation of this file.
                                                                    1 
                                                                    -
                                                                    10 #ifndef FIMS_POPULATION_DYNAMICS_RECRUITMENT_SR_BEVERTON_HOLT_HPP
                                                                    -
                                                                    11 #define FIMS_POPULATION_DYNAMICS_RECRUITMENT_SR_BEVERTON_HOLT_HPP
                                                                    -
                                                                    12 
                                                                    -
                                                                    13 #include "recruitment_base.hpp"
                                                                    -
                                                                    14 #include "../../../common/fims_vector.hpp"
                                                                    +
                                                                    1 /*
                                                                    +
                                                                    2  *
                                                                    +
                                                                    3  * This File is part of the NOAA, National Marine Fisheries Service
                                                                    +
                                                                    4  * Fisheries Integrated Modeling System project. See LICENSE in the
                                                                    +
                                                                    5  * source folder for reuse information.
                                                                    +
                                                                    6  *
                                                                    +
                                                                    7  * Beverton Holt stock recruitment function
                                                                    +
                                                                    8  * The purpose of this file is to call the Beverton Holt stock
                                                                    +
                                                                    9  * recruitment function from fims_math and does the calculation.
                                                                    +
                                                                    10  * Inherits from recruitment base.
                                                                    +
                                                                    11  *
                                                                    +
                                                                    12  */
                                                                    +
                                                                    13 #ifndef FIMS_POPULATION_DYNAMICS_RECRUITMENT_SR_BEVERTON_HOLT_HPP
                                                                    +
                                                                    14 #define FIMS_POPULATION_DYNAMICS_RECRUITMENT_SR_BEVERTON_HOLT_HPP
                                                                    15 
                                                                    -
                                                                    16 namespace fims_popdy {
                                                                    +
                                                                    16 #include "recruitment_base.hpp"
                                                                    17 
                                                                    -
                                                                    24 template <typename Type>
                                                                    -
                                                                    25 struct SRBevertonHolt : public RecruitmentBase<Type> {
                                                                    -
                                                                    26  // Here we define the members that will be used in the Beverton Holt SR
                                                                    -
                                                                    27  // function. These members are needed by Beverton Holt but will not be common
                                                                    -
                                                                    28  // to all recruitment functions like spawners is below.
                                                                    -
                                                                    29  fims::Vector<Type> logit_steep;
                                                                    -
                                                                    32  SRBevertonHolt() : RecruitmentBase<Type>() {}
                                                                    -
                                                                    33 
                                                                    -
                                                                    34  virtual ~SRBevertonHolt() {}
                                                                    +
                                                                    18 namespace fims_popdy {
                                                                    +
                                                                    19 
                                                                    +
                                                                    26 template <typename Type>
                                                                    +
                                                                    27 struct SRBevertonHolt : public RecruitmentBase<Type> {
                                                                    +
                                                                    28  // Here we define the members that will be used in the Beverton Holt SR
                                                                    +
                                                                    29  // function. These members are needed by Beverton Holt but will not be common
                                                                    +
                                                                    30  // to all recruitment functions like spawners is below.
                                                                    +
                                                                    31  Type logit_steep;
                                                                    +
                                                                    34  SRBevertonHolt() : RecruitmentBase<Type>() {}
                                                                    35 
                                                                    -
                                                                    45  virtual const Type evaluate(const Type& spawners, const Type& phi_0) {
                                                                    -
                                                                    46  Type recruits;
                                                                    -
                                                                    47  Type steep;
                                                                    -
                                                                    48  Type steep_lo = 0.2;
                                                                    -
                                                                    49  Type steep_hi = 1.0;
                                                                    -
                                                                    50  Type rzero;
                                                                    -
                                                                    51 
                                                                    -
                                                                    52  // Transform input parameters
                                                                    -
                                                                    53  steep = fims_math::inv_logit(steep_lo, steep_hi, this->logit_steep[0]);
                                                                    -
                                                                    54  rzero = fims_math::exp(this->log_rzero[0]);
                                                                    -
                                                                    55 
                                                                    -
                                                                    56  recruits = (0.8 * rzero * steep * spawners) /
                                                                    -
                                                                    57  (0.2 * phi_0 * rzero * (1.0 - steep) + spawners * (steep - 0.2));
                                                                    -
                                                                    58 
                                                                    -
                                                                    59  return recruits;
                                                                    -
                                                                    60  }
                                                                    -
                                                                    61 };
                                                                    -
                                                                    62 
                                                                    -
                                                                    63 } // namespace fims_popdy
                                                                    +
                                                                    36  virtual ~SRBevertonHolt() {}
                                                                    +
                                                                    37 
                                                                    +
                                                                    47  virtual const Type evaluate(const Type& spawners, const Type& phi_0) {
                                                                    +
                                                                    48  Type recruits;
                                                                    +
                                                                    49  Type steep;
                                                                    +
                                                                    50  Type steep_lo = 0.2;
                                                                    +
                                                                    51  Type steep_hi = 1.0;
                                                                    +
                                                                    52  Type rzero;
                                                                    +
                                                                    53 
                                                                    +
                                                                    54  // Transform input parameters
                                                                    +
                                                                    55  steep = fims_math::inv_logit(steep_lo, steep_hi, this->logit_steep);
                                                                    +
                                                                    56  rzero = fims_math::exp(this->log_rzero);
                                                                    +
                                                                    57 
                                                                    +
                                                                    58  recruits = (0.8 * rzero * steep * spawners) /
                                                                    +
                                                                    59  (0.2 * phi_0 * rzero * (1.0 - steep) + spawners * (steep - 0.2));
                                                                    +
                                                                    60 
                                                                    +
                                                                    61  return recruits;
                                                                    +
                                                                    62  }
                                                                    +
                                                                    63 };
                                                                    64 
                                                                    -
                                                                    65 #endif /* FIMS_POPULATION_DYNAMICS_RECRUITMENT_SR_BEVERTON_HOLT_HPP */
                                                                    -
                                                                    fims::Vector
                                                                    Definition: fims_vector.hpp:25
                                                                    -
                                                                    recruitment_base.hpp
                                                                    Serves as the parent class where recruitment functions are called.
                                                                    -
                                                                    fims_popdy::RecruitmentBase
                                                                    Base class for all recruitment functors.
                                                                    Definition: recruitment_base.hpp:28
                                                                    -
                                                                    fims_popdy::RecruitmentBase::log_rzero
                                                                    fims::Vector< Type > log_rzero
                                                                    Definition: recruitment_base.hpp:36
                                                                    -
                                                                    fims_popdy::SRBevertonHolt
                                                                    BevertonHolt class that returns the Beverton Holt SR from fims_math.
                                                                    Definition: sr_beverton_holt.hpp:25
                                                                    -
                                                                    fims_popdy::SRBevertonHolt::evaluate
                                                                    virtual const Type evaluate(const Type &spawners, const Type &phi_0)
                                                                    Beverton Holt implementation of the stock recruitment function.
                                                                    Definition: sr_beverton_holt.hpp:45
                                                                    -
                                                                    fims_popdy::SRBevertonHolt::logit_steep
                                                                    fims::Vector< Type > logit_steep
                                                                    Definition: sr_beverton_holt.hpp:29
                                                                    +
                                                                    65 } // namespace fims_popdy
                                                                    +
                                                                    66 
                                                                    +
                                                                    67 #endif /* FIMS_POPULATION_DYNAMICS_RECRUITMENT_SR_BEVERTON_HOLT_HPP */
                                                                    +
                                                                    recruitment_base.hpp
                                                                    +
                                                                    fims_popdy::RecruitmentBase
                                                                    Base class for all recruitment functors.
                                                                    Definition: recruitment_base.hpp:32
                                                                    +
                                                                    fims_popdy::RecruitmentBase::log_rzero
                                                                    Type log_rzero
                                                                    Definition: recruitment_base.hpp:42
                                                                    +
                                                                    fims_popdy::SRBevertonHolt
                                                                    BevertonHolt class that returns the Beverton Holt SR from fims_math.
                                                                    Definition: sr_beverton_holt.hpp:27
                                                                    +
                                                                    fims_popdy::SRBevertonHolt::logit_steep
                                                                    Type logit_steep
                                                                    Definition: sr_beverton_holt.hpp:31
                                                                    +
                                                                    fims_popdy::SRBevertonHolt::evaluate
                                                                    virtual const Type evaluate(const Type &spawners, const Type &phi_0)
                                                                    Beverton Holt implementation of the stock recruitment function.
                                                                    Definition: sr_beverton_holt.hpp:47
                                                                    diff --git a/docs/structfims__data__object_1_1DataObject-members.html b/docs/structfims__data__object_1_1DataObject-members.html index bdad203..bdb82da 100644 --- a/docs/structfims__data__object_1_1DataObject-members.html +++ b/docs/structfims__data__object_1_1DataObject-members.html @@ -83,34 +83,33 @@ at(size_t i, size_t j)fims_data_object::DataObject< Type >inline at(size_t i, size_t j, size_t k)fims_data_object::DataObject< Type >inline at(size_t i, size_t j, size_t k, size_t l)fims_data_object::DataObject< Type >inline - CheckDimensions(size_t actual, size_t expected)fims_model_object::FIMSObject< Type >inline - datafims_data_object::DataObject< Type > - DataObject(size_t imax)fims_data_object::DataObject< Type >inline - DataObject(size_t imax, size_t jmax)fims_data_object::DataObject< Type >inline - DataObject(size_t imax, size_t jmax, size_t kmax)fims_data_object::DataObject< Type >inline - DataObject(size_t imax, size_t jmax, size_t kmax, size_t lmax)fims_data_object::DataObject< Type >inline - dimensionsfims_data_object::DataObject< Type > - fixed_effects_parametersfims_model_object::FIMSObject< Type > - get_dimensions() constfims_data_object::DataObject< Type >inline - get_imax() constfims_data_object::DataObject< Type >inline - get_jmax() constfims_data_object::DataObject< Type >inline - get_kmax() constfims_data_object::DataObject< Type >inline - get_lmax() constfims_data_object::DataObject< Type >inline - GetId() constfims_model_object::FIMSObject< Type >inline - idfims_model_object::FIMSObject< Type > - id_gfims_data_object::DataObject< Type >static - imaxfims_data_object::DataObject< Type > - jmaxfims_data_object::DataObject< Type > - kmaxfims_data_object::DataObject< Type > - lmaxfims_data_object::DataObject< Type > - na_valuefims_data_object::DataObject< Type > - operator()(size_t i)fims_data_object::DataObject< Type >inline - operator()(size_t i, size_t j)fims_data_object::DataObject< Type >inline - operator()(size_t i, size_t j, size_t k)fims_data_object::DataObject< Type >inline - operator()(size_t i, size_t j, size_t k, size_t l)fims_data_object::DataObject< Type >inline - parametersfims_model_object::FIMSObject< Type > - random_effects_parametersfims_model_object::FIMSObject< Type > - ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual + datafims_data_object::DataObject< Type > + DataObject(size_t imax)fims_data_object::DataObject< Type >inline + DataObject(size_t imax, size_t jmax)fims_data_object::DataObject< Type >inline + DataObject(size_t imax, size_t jmax, size_t kmax)fims_data_object::DataObject< Type >inline + DataObject(size_t imax, size_t jmax, size_t kmax, size_t lmax)fims_data_object::DataObject< Type >inline + dimensionsfims_data_object::DataObject< Type > + fixed_effects_parametersfims_model_object::FIMSObject< Type > + get_dimensions() constfims_data_object::DataObject< Type >inline + get_imax() constfims_data_object::DataObject< Type >inline + get_jmax() constfims_data_object::DataObject< Type >inline + get_kmax() constfims_data_object::DataObject< Type >inline + get_lmax() constfims_data_object::DataObject< Type >inline + GetId() constfims_model_object::FIMSObject< Type >inline + idfims_model_object::FIMSObject< Type > + id_gfims_data_object::DataObject< Type >static + imaxfims_data_object::DataObject< Type > + jmaxfims_data_object::DataObject< Type > + kmaxfims_data_object::DataObject< Type > + lmaxfims_data_object::DataObject< Type > + na_valuefims_data_object::DataObject< Type > + operator()(size_t i)fims_data_object::DataObject< Type >inline + operator()(size_t i, size_t j)fims_data_object::DataObject< Type >inline + operator()(size_t i, size_t j, size_t k)fims_data_object::DataObject< Type >inline + operator()(size_t i, size_t j, size_t k, size_t l)fims_data_object::DataObject< Type >inline + parametersfims_model_object::FIMSObject< Type > + random_effects_parametersfims_model_object::FIMSObject< Type > + ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                    diff --git a/docs/structfims__data__object_1_1DataObject.html b/docs/structfims__data__object_1_1DataObject.html index 98fc45e..e038807 100644 --- a/docs/structfims__data__object_1_1DataObject.html +++ b/docs/structfims__data__object_1_1DataObject.html @@ -139,14 +139,11 @@ uint32_t GetId () const  Getter that returns the unique id for parameters in the model.
                                                                      -bool CheckDimensions (size_t actual, size_t expected) - Check the dimensions of an object. More...
                                                                    -  - - + + @@ -884,8 +881,8 @@

                                                                    Member Data Documentation

                                                                    - -

                                                                    ◆ data

                                                                    + +

                                                                    ◆ data

                                                                    @@ -893,7 +890,7 @@

                                                                    - +

                                                                    Public Attributes

                                                                    fims::Vector< Type > data
                                                                     
                                                                    std::vector< Type > data
                                                                     
                                                                    size_t dimensions
                                                                     
                                                                    size_t imax
                                                                    fims::Vector<Type> fims_data_object::DataObject< Type >::datastd::vector<Type> fims_data_object::DataObject< Type >::data
                                                                    diff --git a/docs/structfims__model__object_1_1FIMSObject-members.html b/docs/structfims__model__object_1_1FIMSObject-members.html index 3c30cf9..a070835 100644 --- a/docs/structfims__model__object_1_1FIMSObject-members.html +++ b/docs/structfims__model__object_1_1FIMSObject-members.html @@ -79,13 +79,12 @@

                                                                    This is the complete list of members for fims_model_object::FIMSObject< Type >, including all inherited members.

                                                                    - - - - - - - + + + + + +
                                                                    CheckDimensions(size_t actual, size_t expected)fims_model_object::FIMSObject< Type >inline
                                                                    fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    GetId() constfims_model_object::FIMSObject< Type >inline
                                                                    idfims_model_object::FIMSObject< Type >
                                                                    parametersfims_model_object::FIMSObject< Type >
                                                                    random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                    fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    GetId() constfims_model_object::FIMSObject< Type >inline
                                                                    idfims_model_object::FIMSObject< Type >
                                                                    parametersfims_model_object::FIMSObject< Type >
                                                                    random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                    diff --git a/docs/structfims__model__object_1_1FIMSObject.html b/docs/structfims__model__object_1_1FIMSObject.html index 5f55649..95036eb 100644 --- a/docs/structfims__model__object_1_1FIMSObject.html +++ b/docs/structfims__model__object_1_1FIMSObject.html @@ -91,14 +91,14 @@
                                                                    -fims_data_object::DataObject< Type > -fims_distributions::DensityComponentBase< Type > -fims_popdy::Fleet< Type > -fims_popdy::GrowthBase< Type > -fims_popdy::MaturityBase< Type > -fims_popdy::Population< Type > -fims_popdy::RecruitmentBase< Type > -fims_popdy::SelectivityBase< Type > +fims_data_object::DataObject< Type > +fims_distributions::DistributionsBase< Type > +fims_popdy::Fleet< Type > +fims_popdy::GrowthBase< Type > +fims_popdy::MaturityBase< Type > +fims_popdy::Population< Type > +fims_popdy::RecruitmentBase< Type > +fims_popdy::SelectivityBase< Type >
                                                                    @@ -108,9 +108,6 @@ uint32_t  - - -
                                                                    GetId () const
                                                                     Getter that returns the unique id for parameters in the model.
                                                                     
                                                                    bool CheckDimensions (size_t actual, size_t expected)
                                                                     Check the dimensions of an object. More...
                                                                     
                                                                    @@ -128,58 +125,7 @@ struct fims_model_object::FIMSObject< Type >

                                                                    FIMSObject struct that defines member types and returns the unique id.

                                                                    -

                                                                    Member Function Documentation

                                                                    - -

                                                                    ◆ CheckDimensions()

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<typename Type >
                                                                    -

                                                                    Public Attributes

                                                                    - - - - -
                                                                    - - - - - - - - - - - - - - - - - - -
                                                                    bool fims_model_object::FIMSObject< Type >::CheckDimensions (size_t actual,
                                                                    size_t expected 
                                                                    )
                                                                    -                                                                     		-inline
                                                                    -
                                                                    - -

                                                                    Check the dimensions of an object.

                                                                    -
                                                                    Parameters
                                                                    - - - -
                                                                    actualThe actual dimensions.
                                                                    expectedThe expected dimensions.
                                                                    -
                                                                    -
                                                                    -
                                                                    Returns
                                                                    true
                                                                    -
                                                                    -false
                                                                    - -
                                                                    - -

                                                                    Member Data Documentation

                                                                    +

                                                                    Member Data Documentation

                                                                    ◆ fixed_effects_parameters

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z7Do4m|5@SHnu?t$=@4hpY5EY=3Lg(MUfqn)-Y3jH{X8ymWp!e+b#p2O)4$5i-fA?f zQ53;FIh&=k*p07FN0veaKBLb+a-l8rxAJNd#~o0qB4VozU#6^jnRtrlGp8? zlaRF=S3gL$*bkV5rNbWy2?s5WXG4@1ZL^xLZu{P@#)8rcg6l3-jmLGh891r{3BKgKDrp5 zI23jThis is the complete list of members for fims_popdy::DoubleLogisticSelectivity< Type >, including all inherited members.

                                                                    - - - - + + - - + + - - + + diff --git a/docs/structfims__popdy_1_1DoubleLogisticSelectivity.html b/docs/structfims__popdy_1_1DoubleLogisticSelectivity.html index 69a9959..0ac277d 100644 --- a/docs/structfims__popdy_1_1DoubleLogisticSelectivity.html +++ b/docs/structfims__popdy_1_1DoubleLogisticSelectivity.html @@ -101,9 +101,6 @@ - - - @@ -114,20 +111,17 @@ uint32_t  - - -
                                                                    CheckDimensions(size_t actual, size_t expected)fims_model_object::FIMSObject< Type >inline
                                                                    DoubleLogisticSelectivity() (defined in fims_popdy::DoubleLogisticSelectivity< Type >)fims_popdy::DoubleLogisticSelectivity< Type >inline
                                                                    evaluate(const Type &x)fims_popdy::DoubleLogisticSelectivity< Type >inlinevirtual
                                                                    evaluate(const Type &x, size_t pos)fims_popdy::DoubleLogisticSelectivity< Type >inlinevirtual
                                                                    DoubleLogisticSelectivity() (defined in fims_popdy::DoubleLogisticSelectivity< Type >)fims_popdy::DoubleLogisticSelectivity< Type >inline
                                                                    evaluate(const Type &x)fims_popdy::DoubleLogisticSelectivity< Type >inlinevirtual
                                                                    fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    GetId() constfims_model_object::FIMSObject< Type >inline
                                                                    idfims_model_object::FIMSObject< Type >
                                                                    id_gfims_popdy::SelectivityBase< Type >static
                                                                    inflection_point_ascfims_popdy::DoubleLogisticSelectivity< Type >
                                                                    inflection_point_descfims_popdy::DoubleLogisticSelectivity< Type >
                                                                    inflection_point_ascfims_popdy::DoubleLogisticSelectivity< Type >
                                                                    inflection_point_descfims_popdy::DoubleLogisticSelectivity< Type >
                                                                    parametersfims_model_object::FIMSObject< Type >
                                                                    random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    SelectivityBase()fims_popdy::SelectivityBase< Type >inline
                                                                    slope_ascfims_popdy::DoubleLogisticSelectivity< Type >
                                                                    slope_descfims_popdy::DoubleLogisticSelectivity< Type >
                                                                    slope_ascfims_popdy::DoubleLogisticSelectivity< Type >
                                                                    slope_descfims_popdy::DoubleLogisticSelectivity< Type >
                                                                    ~DoubleLogisticSelectivity() (defined in fims_popdy::DoubleLogisticSelectivity< Type >)fims_popdy::DoubleLogisticSelectivity< Type >inlinevirtual
                                                                    ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                    ~SelectivityBase() (defined in fims_popdy::SelectivityBase< Type >)fims_popdy::SelectivityBase< Type >inlinevirtual
                                                                    virtual const Type evaluate (const Type &x)
                                                                     Method of the double logistic selectivity class that implements the double logistic function from FIMS math. More...
                                                                     
                                                                    virtual const Type evaluate (const Type &x, size_t pos)
                                                                     Method of the double logistic selectivity class that implements the double logistic function from FIMS math. More...
                                                                     
                                                                    - Public Member Functions inherited from fims_popdy::SelectivityBase< Type >
                                                                     SelectivityBase ()
                                                                    GetId () const
                                                                     Getter that returns the unique id for parameters in the model.
                                                                     
                                                                    bool CheckDimensions (size_t actual, size_t expected)
                                                                     Check the dimensions of an object. More...
                                                                     
                                                                    - - - - - - - - + + + + + + + + @@ -151,7 +145,7 @@

                                                                    DoubleLogisticSelectivity class that returns the double logistic function value from fims_math.

                                                                    Member Function Documentation

                                                                    -

                                                                    ◆ evaluate() [1/2]

                                                                    +

                                                                    ◆ evaluate()

                                                                    @@ -177,7 +171,7 @@

                                                                    Method of the double logistic selectivity class that implements the double logistic function from FIMS math.

                                                                    -

                                                                    \( \frac{1.0}{ 1.0 + exp(-1.0 * slope\_asc (x - inflection_point\_asc))} \left(1.0-\frac{1.0}{ 1.0 + exp(-1.0 * slope\_desc (x - inflection_point\_desc))} \right)\)

                                                                    +

                                                                    \( \frac{1.0}{ 1.0 + exp(-1.0 * slope_{asc} (x - inflection_point_{asc}))} \left(1.0-\frac{1.0}{ 1.0 + exp(-1.0 * slope_{desc} (x - inflection_point_{desc}))} \right)\)

                                                                    Parameters

                                                                    Public Attributes

                                                                    fims::Vector< Type > inflection_point_asc
                                                                     
                                                                    fims::Vector< Type > slope_asc
                                                                     
                                                                    fims::Vector< Type > inflection_point_desc
                                                                     
                                                                    fims::Vector< Type > slope_desc
                                                                     
                                                                    Type inflection_point_asc
                                                                     
                                                                    Type slope_asc
                                                                     
                                                                    Type inflection_point_desc
                                                                     
                                                                    Type slope_desc
                                                                     
                                                                    - Public Attributes inherited from fims_model_object::FIMSObject< Type >
                                                                    uint32_t id
                                                                     
                                                                    @@ -187,61 +181,11 @@

                                                                    fims_popdy::SelectivityBase< Type >.

                                                                    - - - -

                                                                    ◆ evaluate() [2/2]

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<typename Type >
                                                                    -
                                                                    xThe independent variable in the double logistic function (e.g., age or size in selectivity).
                                                                    - - - - -
                                                                    - - - - - - - - - - - - - - - - - - -
                                                                    virtual const Type fims_popdy::DoubleLogisticSelectivity< Type >::evaluate (const Type & x,
                                                                    size_t pos 
                                                                    )
                                                                    -                                                                     		-inlinevirtual
                                                                    -
                                                                    - -

                                                                    Method of the double logistic selectivity class that implements the double logistic function from FIMS math.

                                                                    -

                                                                    \( \frac{1.0}{ 1.0 + exp(-1.0 * slope\_asc_t (x - inflection_point\_asc_t))} \left(1.0-\frac{1.0}{ 1.0 + exp(-1.0 * slope\_desc_t (x - inflection_point\_desc_t))} \right)\)

                                                                    -
                                                                    Parameters
                                                                    - - - -
                                                                    xThe independent variable in the double logistic function (e.g., age or size in selectivity).
                                                                    posPosition index, e.g., which year.
                                                                    -
                                                                    -
                                                                    - -

                                                                    Implements fims_popdy::SelectivityBase< Type >.

                                                                    -

                                                                    Member Data Documentation

                                                                    - -

                                                                    ◆ inflection_point_asc

                                                                    + +

                                                                    ◆ inflection_point_asc

                                                                    @@ -249,7 +193,7 @@

                                                                    - fims::Vector<Type> fims_popdy::DoubleLogisticSelectivity< Type >::inflection_point_asc + Type fims_popdy::DoubleLogisticSelectivity< Type >::inflection_point_asc

                                                                    @@ -257,8 +201,8 @@

                                                                    -

                                                                    ◆ inflection_point_desc

                                                                    + +

                                                                    ◆ inflection_point_desc

                                                                    @@ -266,7 +210,7 @@

                                                                    - fims::Vector<Type> fims_popdy::DoubleLogisticSelectivity< Type >::inflection_point_desc + Type fims_popdy::DoubleLogisticSelectivity< Type >::inflection_point_desc

                                                                    @@ -274,8 +218,8 @@

                                                                    -

                                                                    ◆ slope_asc

                                                                    + +

                                                                    ◆ slope_asc

                                                                    @@ -283,7 +227,7 @@

                                                                    - fims::Vector<Type> fims_popdy::DoubleLogisticSelectivity< Type >::slope_asc + Type fims_popdy::DoubleLogisticSelectivity< Type >::slope_asc

                                                                    @@ -291,8 +235,8 @@

                                                                    -

                                                                    ◆ slope_desc

                                                                    + +

                                                                    ◆ slope_desc

                                                                    @@ -300,7 +244,7 @@

                                                                    - fims::Vector<Type> fims_popdy::DoubleLogisticSelectivity< Type >::slope_desc + Type fims_popdy::DoubleLogisticSelectivity< Type >::slope_desc

                                                                    diff --git a/docs/structfims__popdy_1_1EWAAgrowth-members.html b/docs/structfims__popdy_1_1EWAAgrowth-members.html index 548a3d3..d80b79d 100644 --- a/docs/structfims__popdy_1_1EWAAgrowth-members.html +++ b/docs/structfims__popdy_1_1EWAAgrowth-members.html @@ -79,18 +79,16 @@

                                                                    This is the complete list of members for fims_popdy::EWAAgrowth< Type >, including all inherited members.

                                                                    - - - - - - - - - - - - + + + + + + + + + + diff --git a/docs/structfims__popdy_1_1EWAAgrowth.html b/docs/structfims__popdy_1_1EWAAgrowth.html index 3e91868..8be24e5 100644 --- a/docs/structfims__popdy_1_1EWAAgrowth.html +++ b/docs/structfims__popdy_1_1EWAAgrowth.html @@ -73,7 +73,6 @@
                                                                    -Public Types | Public Member Functions | Public Attributes | List of all members
                                                                    @@ -97,11 +96,6 @@
                                                                    CheckDimensions(size_t actual, size_t expected)fims_model_object::FIMSObject< Type >inline
                                                                    evaluate(const double &a)fims_popdy::EWAAgrowth< Type >inlinevirtual
                                                                    ewaafims_popdy::EWAAgrowth< Type >
                                                                    EWAAgrowth() (defined in fims_popdy::EWAAgrowth< Type >)fims_popdy::EWAAgrowth< Type >inline
                                                                    fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    GetId() constfims_model_object::FIMSObject< Type >inline
                                                                    GrowthBase()fims_popdy::GrowthBase< Type >inline
                                                                    idfims_model_object::FIMSObject< Type >
                                                                    id_gfims_popdy::GrowthBase< Type >static
                                                                    parametersfims_model_object::FIMSObject< Type >
                                                                    random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    weight_iterator typedeffims_popdy::EWAAgrowth< Type >
                                                                    evaluate(const double &a)fims_popdy::EWAAgrowth< Type >inlinevirtual
                                                                    ewaafims_popdy::EWAAgrowth< Type >
                                                                    EWAAgrowth() (defined in fims_popdy::EWAAgrowth< Type >)fims_popdy::EWAAgrowth< Type >inline
                                                                    fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    GetId() constfims_model_object::FIMSObject< Type >inline
                                                                    GrowthBase()fims_popdy::GrowthBase< Type >inline
                                                                    idfims_model_object::FIMSObject< Type >
                                                                    id_gfims_popdy::GrowthBase< Type >static
                                                                    parametersfims_model_object::FIMSObject< Type >
                                                                    random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    ~EWAAgrowth() (defined in fims_popdy::EWAAgrowth< Type >)fims_popdy::EWAAgrowth< Type >inlinevirtual
                                                                    ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                    ~GrowthBase() (defined in fims_popdy::GrowthBase< Type >)fims_popdy::GrowthBase< Type >inlinevirtual
                                                                    - - - -

                                                                    -Public Types

                                                                    typedef std::map< double, double >::iterator weight_iterator
                                                                     
                                                                    @@ -117,9 +111,6 @@ uint32_t  - - -

                                                                    Public Member Functions

                                                                    virtual const Type evaluate (const double &a)
                                                                    GetId () const
                                                                     Getter that returns the unique id for parameters in the model.
                                                                     
                                                                    bool CheckDimensions (size_t actual, size_t expected)
                                                                     Check the dimensions of an object. More...
                                                                     
                                                                    @@ -146,25 +137,7 @@ struct fims_popdy::EWAAgrowth< Type >

                                                                    EWAAgrowth class that returns the EWAA function value.

                                                                    -

                                                                    Member Typedef Documentation

                                                                    - -

                                                                    ◆ weight_iterator

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<typename Type >
                                                                    -

                                                                    Public Attributes

                                                                    - - - -
                                                                    typedef std::map<double, double>::iterator fims_popdy::EWAAgrowth< Type >::weight_iterator
                                                                    -
                                                                    -

                                                                    Iterator for ewaa map object >

                                                                    - -
                                                                    -
                                                                    -

                                                                    Member Function Documentation

                                                                    +

                                                                    Member Function Documentation

                                                                    ◆ evaluate()

                                                                    diff --git a/docs/structfims__popdy_1_1Fleet-members.html b/docs/structfims__popdy_1_1Fleet-members.html index 50d0c7a..99ffc9c 100644 --- a/docs/structfims__popdy_1_1Fleet-members.html +++ b/docs/structfims__popdy_1_1Fleet-members.html @@ -80,49 +80,39 @@

                                                                    This is the complete list of members for fims_popdy::Fleet< Type >, including all inherited members.

                                                                    - + - - - - - - - - + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - + + - - - - - + diff --git a/docs/structfims__popdy_1_1Fleet.html b/docs/structfims__popdy_1_1Fleet.html index 500de52..86f4e39 100644 --- a/docs/structfims__popdy_1_1Fleet.html +++ b/docs/structfims__popdy_1_1Fleet.html @@ -106,26 +106,21 @@ virtual  - - - + + + - + - - - - - - + + + + - - -
                                                                    age_compositionfims_popdy::Fleet< Type >
                                                                    age_length_conversion_matrixfims_popdy::Fleet< Type >
                                                                    agecomp_likelihoodfims_popdy::Fleet< Type >
                                                                    catch_at_agefims_popdy::Fleet< Type >
                                                                    catch_indexfims_popdy::Fleet< Type >
                                                                    catch_numbers_at_agefims_popdy::Fleet< Type >
                                                                    catch_numbers_at_lengthfims_popdy::Fleet< Type >
                                                                    catch_weight_at_agefims_popdy::Fleet< Type >
                                                                    CheckDimensions(size_t actual, size_t expected)fims_model_object::FIMSObject< Type >inline
                                                                    evaluate_age_comp()fims_popdy::Fleet< Type >inline
                                                                    evaluate_index()fims_popdy::Fleet< Type >inline
                                                                    evaluate_length_comp()fims_popdy::Fleet< Type >inline
                                                                    expected_catchfims_popdy::Fleet< Type >
                                                                    expected_catch_lpdffims_popdy::Fleet< Type >
                                                                    catch_weight_at_agefims_popdy::Fleet< Type >
                                                                    evaluate_age_comp_nll()fims_popdy::Fleet< Type >inlinevirtual
                                                                    evaluate_index_nll()fims_popdy::Fleet< Type >inlinevirtual
                                                                    expected_catchfims_popdy::Fleet< Type >
                                                                    expected_indexfims_popdy::Fleet< Type >
                                                                    expected_index_lpdffims_popdy::Fleet< Type >
                                                                    fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    Fleet()fims_popdy::Fleet< Type >inline
                                                                    fleet_observed_agecomp_data_id_mfims_popdy::Fleet< Type >
                                                                    fleet_observed_index_data_id_mfims_popdy::Fleet< Type >
                                                                    fleet_observed_lengthcomp_data_id_mfims_popdy::Fleet< Type >
                                                                    fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    Fleet()fims_popdy::Fleet< Type >inline
                                                                    fleet_agecomp_likelihood_id_mfims_popdy::Fleet< Type >
                                                                    fleet_index_likelihood_id_mfims_popdy::Fleet< Type >
                                                                    fleet_observed_agecomp_data_id_mfims_popdy::Fleet< Type >
                                                                    fleet_observed_index_data_id_mfims_popdy::Fleet< Type >
                                                                    fleet_selectivity_id_mfims_popdy::Fleet< Type >
                                                                    Fmortfims_popdy::Fleet< Type >
                                                                    GetId() constfims_model_object::FIMSObject< Type >inline
                                                                    idfims_model_object::FIMSObject< Type >
                                                                    id_gfims_popdy::Fleet< Type >static
                                                                    Initialize(int nyears, int nages, int nlengths=0)fims_popdy::Fleet< Type >inline
                                                                    is_surveyfims_popdy::Fleet< Type >
                                                                    length_compositionfims_popdy::Fleet< Type >
                                                                    log_expected_indexfims_popdy::Fleet< Type >
                                                                    log_Fmortfims_popdy::Fleet< Type >
                                                                    log_qfims_popdy::Fleet< Type >
                                                                    index_likelihoodfims_popdy::Fleet< Type >
                                                                    Initialize(int nyears, int nages)fims_popdy::Fleet< Type >inline
                                                                    is_surveyfims_popdy::Fleet< Type >
                                                                    log_Fmortfims_popdy::Fleet< Type >
                                                                    log_obs_errorfims_popdy::Fleet< Type >
                                                                    log_qfims_popdy::Fleet< Type >
                                                                    nagesfims_popdy::Fleet< Type >
                                                                    nlengthsfims_popdy::Fleet< Type >
                                                                    nyearsfims_popdy::Fleet< Type >
                                                                    observed_agecomp_datafims_popdy::Fleet< Type >
                                                                    observed_catch_lpdffims_popdy::Fleet< Type >
                                                                    nyearsfims_popdy::Fleet< Type >
                                                                    observed_agecomp_datafims_popdy::Fleet< Type >
                                                                    observed_index_datafims_popdy::Fleet< Type >
                                                                    observed_index_lpdffims_popdy::Fleet< Type >
                                                                    observed_lengthcomp_datafims_popdy::Fleet< Type >
                                                                    parametersfims_model_object::FIMSObject< Type >
                                                                    Prepare()fims_popdy::Fleet< Type >inline
                                                                    proportion_catch_numbers_at_agefims_popdy::Fleet< Type >
                                                                    proportion_catch_numbers_at_lengthfims_popdy::Fleet< Type >
                                                                    qfims_popdy::Fleet< Type >
                                                                    qfims_popdy::Fleet< Type >
                                                                    random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    selectivityfims_popdy::Fleet< Type >
                                                                    ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                    ~Fleet ()
                                                                     Destructor.
                                                                     
                                                                    void Initialize (int nyears, int nages, int nlengths=0)
                                                                     Intialize Fleet Class. More...
                                                                     
                                                                    void Initialize (int nyears, int nages)
                                                                     Intialize Fleet Class. More...
                                                                     
                                                                    void Prepare ()
                                                                     Prepare to run the fleet module. Called at each model iteration, and used to exponentiate the log q and Fmort parameters prior to evaluation. More...
                                                                     Prepare to run the fleet module. Called at each model itartion, and used to exponentiate the log q and Fmort parameters prior to evaluation. More...
                                                                     
                                                                    void evaluate_age_comp ()
                                                                     
                                                                    void evaluate_length_comp ()
                                                                     
                                                                    void evaluate_index ()
                                                                     
                                                                    virtual const Type evaluate_age_comp_nll ()
                                                                     
                                                                    virtual const Type evaluate_index_nll ()
                                                                     
                                                                    - Public Member Functions inherited from fims_model_object::FIMSObject< Type >
                                                                    uint32_t GetId () const
                                                                     Getter that returns the unique id for parameters in the model.
                                                                     
                                                                    bool CheckDimensions (size_t actual, size_t expected)
                                                                     Check the dimensions of an object. More...
                                                                     
                                                                    @@ -133,8 +128,14 @@ - - + + + + + + + + @@ -147,50 +148,28 @@ - - - - - - + + + + - - + + - - - - - - - - - - - - - - - - - - - - @@ -222,8 +201,8 @@

                                                                    Member Function Documentation

                                                                    - -

                                                                    ◆ evaluate_age_comp()

                                                                    + +

                                                                    ◆ evaluate_age_comp_nll()

                                                                    @@ -234,7 +213,7 @@

                                                                    Public Attributes

                                                                     
                                                                    size_t nages
                                                                     
                                                                    size_t nlengths
                                                                     
                                                                    int fleet_index_likelihood_id_m
                                                                     
                                                                    std::shared_ptr< fims_distributions::DistributionsBase< Type > > index_likelihood
                                                                     
                                                                    int fleet_agecomp_likelihood_id_m
                                                                     
                                                                    std::shared_ptr< fims_distributions::DistributionsBase< Type > > agecomp_likelihood
                                                                     
                                                                    int fleet_selectivity_id_m = -999
                                                                     
                                                                    std::shared_ptr< SelectivityBase< Type > > selectivity
                                                                     
                                                                    std::shared_ptr< fims_data_object::DataObject< Type > > observed_agecomp_data
                                                                     
                                                                    int fleet_observed_lengthcomp_data_id_m = -999
                                                                     
                                                                    std::shared_ptr< fims_data_object::DataObject< Type > > observed_lengthcomp_data
                                                                     
                                                                    fims::Vector< Type > log_Fmort
                                                                     
                                                                    fims::Vector< Type > log_q
                                                                     
                                                                    Type log_q
                                                                     
                                                                    fims::Vector< Type > log_obs_error
                                                                     
                                                                    fims::Vector< Type > Fmort
                                                                     
                                                                    fims::Vector< Type > q
                                                                     
                                                                    Type q
                                                                     
                                                                    fims::Vector< Type > catch_at_age
                                                                     
                                                                    fims::Vector< Type > catch_index
                                                                     
                                                                    fims::Vector< Type > age_composition
                                                                     
                                                                    fims::Vector< Type > length_composition
                                                                     
                                                                    fims::Vector< Type > age_length_conversion_matrix
                                                                     
                                                                    fims::Vector< Type > observed_catch_lpdf
                                                                     
                                                                    fims::Vector< Type > observed_index_lpdf
                                                                     
                                                                    fims::Vector< Type > expected_catch
                                                                     
                                                                    fims::Vector< Type > expected_index
                                                                     
                                                                    fims::Vector< Type > log_expected_index
                                                                     
                                                                    fims::Vector< Type > expected_catch_lpdf
                                                                     
                                                                    fims::Vector< Type > expected_index_lpdf
                                                                     
                                                                    fims::Vector< Type > catch_numbers_at_age
                                                                     
                                                                    fims::Vector< Type > catch_numbers_at_length
                                                                     
                                                                    fims::Vector< Type > proportion_catch_numbers_at_age
                                                                     
                                                                    fims::Vector< Type > proportion_catch_numbers_at_length
                                                                     
                                                                    fims::Vector< Type > catch_weight_at_age
                                                                     
                                                                    bool is_survey = false
                                                                    - + @@ -242,16 +221,16 @@

                                                                    -inline +inlinevirtual

                                                                    void fims_popdy::Fleet< Type >::evaluate_age_comp virtual const Type fims_popdy::Fleet< Type >::evaluate_age_comp_nll ( )
                                                                    -

                                                                    Evaluate the proportion of catch numbers at age.

                                                                    +

                                                                    < The negative log likelihood value

                                                                    - -

                                                                    ◆ evaluate_index()

                                                                    + +

                                                                    ◆ evaluate_index_nll()

                                                                    @@ -262,7 +241,7 @@

                                                                    - + @@ -270,44 +249,16 @@

                                                                    -inline +inlinevirtual

                                                                    void fims_popdy::Fleet< Type >::evaluate_index virtual const Type fims_popdy::Fleet< Type >::evaluate_index_nll ( )

                                                                    -

                                                                    Evaluate the log of the expected index.

                                                                    +

                                                                    < The negative log likelihood value

                                                                    - -

                                                                    ◆ evaluate_length_comp()

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<class Type >
                                                                    - - - - - -
                                                                    - - - - - - - -
                                                                    void fims_popdy::Fleet< Type >::evaluate_length_comp ()
                                                                    -                                                                     		-inline
                                                                    -
                                                                    -

                                                                    Evaluate the proportion of catch numbers at length.

                                                                    - -
                                                                    -
                                                                    - -

                                                                    ◆ Initialize()

                                                                    + +

                                                                    ◆ Initialize()

                                                                    @@ -327,13 +278,7 @@

                                                                    int  - nages, - - - - - int  - nlengths = 0  + nages  @@ -353,7 +298,6 @@

                                                                    nyearsThe number of years in the model. nagesThe number of ages in the model. - nlengthsThe number of lengths in the model. @@ -385,18 +329,12 @@

                                                                    -

                                                                    Prepare to run the fleet module. Called at each model iteration, and used to exponentiate the log q and Fmort parameters prior to evaluation.

                                                                    +

                                                                    Prepare to run the fleet module. Called at each model itartion, and used to exponentiate the log q and Fmort parameters prior to evaluation.

                                                                    <derived quantity catch at age

                                                                    <derived quantity catch index

                                                                    -

                                                                    <model expected number at age

                                                                    -

                                                                    <model expected number at length

                                                                    <model expected total catch

                                                                    <model expected index of abundance

                                                                    -

                                                                    <model expected index of abundance

                                                                    -

                                                                    <model expected catch at age

                                                                    <model expected catch at age

                                                                    -

                                                                    <model expected catch at length

                                                                    -

                                                                    <model expected catch at length

                                                                    <model expected weight at age

                                                                    @@ -419,8 +357,8 @@

                                                                    -

                                                                    ◆ age_length_conversion_matrix

                                                                    + +

                                                                    ◆ agecomp_likelihood

                                                                    @@ -428,11 +366,11 @@

                                                                    - fims::Vector<Type> fims_popdy::Fleet< Type >::age_length_conversion_matrix + std::shared_ptr<fims_distributions::DistributionsBase<Type> > fims_popdy::Fleet< Type >::agecomp_likelihood

                                                                    -

                                                                    derived quantity age-length transition matrix

                                                                    +

                                                                    agecomp likelihood component

                                                                    @@ -485,23 +423,6 @@

                                                                    model expected catch at age

                                                                    -

                                                                    -
                                                                    - -

                                                                    ◆ catch_numbers_at_length

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<class Type >
                                                                    - - - - -
                                                                    fims::Vector<Type> fims_popdy::Fleet< Type >::catch_numbers_at_length
                                                                    -
                                                                    -

                                                                    model expected catch at length

                                                                    -
                                                                    @@ -538,8 +459,8 @@

                                                                    -

                                                                    ◆ expected_catch_lpdf

                                                                    + +

                                                                    ◆ expected_index

                                                                    @@ -547,16 +468,16 @@

                                                                    - fims::Vector<Type> fims_popdy::Fleet< Type >::expected_catch_lpdf + fims::Vector<Type> fims_popdy::Fleet< Type >::expected_index

                                                                    -

                                                                    model expected total catch linked to log probability density function

                                                                    +

                                                                    model expected index of abundance

                                                                    - -

                                                                    ◆ expected_index

                                                                    + +

                                                                    ◆ fleet_agecomp_likelihood_id_m

                                                                    @@ -564,16 +485,18 @@

                                                                    - fims::Vector<Type> fims_popdy::Fleet< Type >::expected_index + int fims_popdy::Fleet< Type >::fleet_agecomp_likelihood_id_m

                                                                    -

                                                                    model expected index of abundance

                                                                    +Initial value:
                                                                    =
                                                                    +
                                                                    -999
                                                                    +

                                                                    id of agecomp likelihood component

                                                                    - -

                                                                    ◆ expected_index_lpdf

                                                                    + +

                                                                    ◆ fleet_index_likelihood_id_m

                                                                    @@ -581,11 +504,13 @@

                                                                    - fims::Vector<Type> fims_popdy::Fleet< Type >::expected_index_lpdf + int fims_popdy::Fleet< Type >::fleet_index_likelihood_id_m

                                                                    -

                                                                    model expected index of abundance linked to log probability density function

                                                                    +Initial value:
                                                                    =
                                                                    +
                                                                    -999
                                                                    +

                                                                    id of index likelihood component. The "fleet_" prefix indicates it belongs to the Fleet struct, and the "_m" postfix signifies that it's a member variable.

                                                                    @@ -621,23 +546,6 @@

                                                                    id of index data

                                                                    -

                                                                    -
                                                                    - -

                                                                    ◆ fleet_observed_lengthcomp_data_id_m

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<class Type >
                                                                    - - - - -
                                                                    int fims_popdy::Fleet< Type >::fleet_observed_lengthcomp_data_id_m = -999
                                                                    -
                                                                    -

                                                                    id of length comp data

                                                                    -
                                                                    @@ -699,8 +607,8 @@

                                                                    -

                                                                    ◆ is_survey

                                                                    + +

                                                                    ◆ index_likelihood

                                                                    @@ -708,16 +616,16 @@

                                                                    - bool fims_popdy::Fleet< Type >::is_survey = false + std::shared_ptr<fims_distributions::DistributionsBase<Type> > fims_popdy::Fleet< Type >::index_likelihood

                                                                    -

                                                                    is this fleet object a survey

                                                                    +

                                                                    index likelihood component

                                                                    - -

                                                                    ◆ length_composition

                                                                    + +

                                                                    ◆ is_survey

                                                                    @@ -725,16 +633,16 @@

                                                                    - fims::Vector<Type> fims_popdy::Fleet< Type >::length_composition + bool fims_popdy::Fleet< Type >::is_survey = false

                                                                    -

                                                                    derived quantity length composition

                                                                    +

                                                                    is this fleet object a survey

                                                                    - -

                                                                    ◆ log_expected_index

                                                                    + +

                                                                    ◆ log_Fmort

                                                                    @@ -742,16 +650,16 @@

                                                                    - fims::Vector<Type> fims_popdy::Fleet< Type >::log_expected_index + fims::Vector<Type> fims_popdy::Fleet< Type >::log_Fmort

                                                                    -

                                                                    model expected index of abundance

                                                                    +

                                                                    estimated parameter: log Fishing mortality

                                                                    - -

                                                                    ◆ log_Fmort

                                                                    + +

                                                                    ◆ log_obs_error

                                                                    @@ -759,16 +667,16 @@

                                                                    - fims::Vector<Type> fims_popdy::Fleet< Type >::log_Fmort + fims::Vector<Type> fims_popdy::Fleet< Type >::log_obs_error

                                                                    -

                                                                    estimated parameter: log Fishing mortality

                                                                    +

                                                                    estimated parameters: observation error associated with index

                                                                    - -

                                                                    ◆ log_q

                                                                    + +

                                                                    ◆ log_q

                                                                    @@ -776,7 +684,7 @@

                                                                    - fims::Vector<Type> fims_popdy::Fleet< Type >::log_q + Type fims_popdy::Fleet< Type >::log_q

                                                                    @@ -799,23 +707,6 @@

                                                                    the number of ages in the model

                                                                    -

                                                                    -
                                                                    - -

                                                                    ◆ nlengths

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<class Type >
                                                                    - - - - -
                                                                    size_t fims_popdy::Fleet< Type >::nlengths
                                                                    -
                                                                    -

                                                                    the number of lengths in the model

                                                                    -
                                                                    @@ -850,23 +741,6 @@

                                                                    observed agecomp data

                                                                    - - -                                                                     -

                                                                    ◆ observed_catch_lpdf

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<class Type >
                                                                    - - - - -
                                                                    fims::Vector<Type> fims_popdy::Fleet< Type >::observed_catch_lpdf
                                                                    -
                                                                    -

                                                                    observed total catch linked to log probability density function

                                                                    -
                                                                    @@ -886,76 +760,8 @@

                                                                    -

                                                                    ◆ observed_index_lpdf

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<class Type >
                                                                    - - - - -
                                                                    fims::Vector<Type> fims_popdy::Fleet< Type >::observed_index_lpdf
                                                                    -
                                                                    -

                                                                    observed index of abundance linked to log probability density function

                                                                    - -
                                                                    -
                                                                    - -

                                                                    ◆ observed_lengthcomp_data

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<class Type >
                                                                    - - - - -
                                                                    std::shared_ptr<fims_data_object::DataObject<Type> > fims_popdy::Fleet< Type >::observed_lengthcomp_data
                                                                    -
                                                                    -

                                                                    observed lengthcomp data

                                                                    - -
                                                                    -
                                                                    - -

                                                                    ◆ proportion_catch_numbers_at_age

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<class Type >
                                                                    - - - - -
                                                                    fims::Vector<Type> fims_popdy::Fleet< Type >::proportion_catch_numbers_at_age
                                                                    -
                                                                    -

                                                                    model expected catch at age

                                                                    - -
                                                                    -
                                                                    - -

                                                                    ◆ proportion_catch_numbers_at_length

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<class Type >
                                                                    - - - - -
                                                                    fims::Vector<Type> fims_popdy::Fleet< Type >::proportion_catch_numbers_at_length
                                                                    -
                                                                    -

                                                                    model expected catch at length

                                                                    - -
                                                                    -
                                                                    - -

                                                                    ◆ q

                                                                    + +

                                                                    ◆ q

                                                                    @@ -963,7 +769,7 @@

                                                                    - fims::Vector<Type> fims_popdy::Fleet< Type >::q + Type fims_popdy::Fleet< Type >::q

                                                                    diff --git a/docs/structfims__popdy_1_1GrowthBase-members.html b/docs/structfims__popdy_1_1GrowthBase-members.html index bac64de..73b5c3d 100644 --- a/docs/structfims__popdy_1_1GrowthBase-members.html +++ b/docs/structfims__popdy_1_1GrowthBase-members.html @@ -79,17 +79,16 @@

                                                                    This is the complete list of members for fims_popdy::GrowthBase< Type >, including all inherited members.

                                                                    - - - - - - - - - - - + + + + + + + + + +
                                                                    CheckDimensions(size_t actual, size_t expected)fims_model_object::FIMSObject< Type >inline
                                                                    evaluate(const double &a)=0fims_popdy::GrowthBase< Type >pure virtual
                                                                    fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    GetId() constfims_model_object::FIMSObject< Type >inline
                                                                    GrowthBase()fims_popdy::GrowthBase< Type >inline
                                                                    idfims_model_object::FIMSObject< Type >
                                                                    id_gfims_popdy::GrowthBase< Type >static
                                                                    parametersfims_model_object::FIMSObject< Type >
                                                                    random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                    ~GrowthBase() (defined in fims_popdy::GrowthBase< Type >)fims_popdy::GrowthBase< Type >inlinevirtual
                                                                    evaluate(const double &a)=0fims_popdy::GrowthBase< Type >pure virtual
                                                                    fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    GetId() constfims_model_object::FIMSObject< Type >inline
                                                                    GrowthBase()fims_popdy::GrowthBase< Type >inline
                                                                    idfims_model_object::FIMSObject< Type >
                                                                    id_gfims_popdy::GrowthBase< Type >static
                                                                    parametersfims_model_object::FIMSObject< Type >
                                                                    random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                    ~GrowthBase() (defined in fims_popdy::GrowthBase< Type >)fims_popdy::GrowthBase< Type >inlinevirtual
                                                                    diff --git a/docs/structfims__popdy_1_1GrowthBase.html b/docs/structfims__popdy_1_1GrowthBase.html index e6be5d0..cbb6ad7 100644 --- a/docs/structfims__popdy_1_1GrowthBase.html +++ b/docs/structfims__popdy_1_1GrowthBase.html @@ -110,9 +110,6 @@ uint32_t GetId () const  Getter that returns the unique id for parameters in the model.
                                                                      -bool CheckDimensions (size_t actual, size_t expected) - Check the dimensions of an object. More...
                                                                    -  diff --git a/docs/structfims__popdy_1_1LogisticMaturity-members.html b/docs/structfims__popdy_1_1LogisticMaturity-members.html index 8d58cee..d1f5026 100644 --- a/docs/structfims__popdy_1_1LogisticMaturity-members.html +++ b/docs/structfims__popdy_1_1LogisticMaturity-members.html @@ -79,19 +79,17 @@

                                                                    This is the complete list of members for fims_popdy::LogisticMaturity< Type >, including all inherited members.

                                                                    Static Public Attributes

                                                                    - - - + - + - +
                                                                    CheckDimensions(size_t actual, size_t expected)fims_model_object::FIMSObject< Type >inline
                                                                    evaluate(const Type &x)fims_popdy::LogisticMaturity< Type >inlinevirtual
                                                                    evaluate(const Type &x, size_t pos)fims_popdy::LogisticMaturity< Type >inlinevirtual
                                                                    evaluate(const Type &x)fims_popdy::LogisticMaturity< Type >inlinevirtual
                                                                    fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    GetId() constfims_model_object::FIMSObject< Type >inline
                                                                    idfims_model_object::FIMSObject< Type >
                                                                    id_gfims_popdy::MaturityBase< Type >static
                                                                    inflection_pointfims_popdy::LogisticMaturity< Type >
                                                                    inflection_pointfims_popdy::LogisticMaturity< Type >
                                                                    LogisticMaturity() (defined in fims_popdy::LogisticMaturity< Type >)fims_popdy::LogisticMaturity< Type >inline
                                                                    MaturityBase()fims_popdy::MaturityBase< Type >inline
                                                                    parametersfims_model_object::FIMSObject< Type >
                                                                    random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    slopefims_popdy::LogisticMaturity< Type >
                                                                    slopefims_popdy::LogisticMaturity< Type >
                                                                    ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                    diff --git a/docs/structfims__popdy_1_1LogisticMaturity.html b/docs/structfims__popdy_1_1LogisticMaturity.html index 2eba88a..e7b392b 100644 --- a/docs/structfims__popdy_1_1LogisticMaturity.html +++ b/docs/structfims__popdy_1_1LogisticMaturity.html @@ -101,9 +101,6 @@ virtual const Type evaluate (const Type &x)  Method of the logistic maturity class that implements the logistic function from FIMS math. More...
                                                                      -virtual const Type evaluate (const Type &x, size_t pos) - Method of the logistic maturity class that implements the logistic function from FIMS math. More...
                                                                    -  - Public Member Functions inherited from fims_popdy::MaturityBase< Type >  MaturityBase () @@ -114,16 +111,13 @@ uint32_t GetId () const  Getter that returns the unique id for parameters in the model.
                                                                      -bool CheckDimensions (size_t actual, size_t expected) - Check the dimensions of an object. More...
                                                                    -  - - - - + + + + @@ -147,7 +141,7 @@

                                                                    LogisticMaturity class that returns the logistic function value from fims_math.

                                                                    Member Function Documentation

                                                                    -

                                                                    ◆ evaluate() [1/2]

                                                                    +

                                                                    ◆ evaluate()

                                                                    @@ -185,63 +179,11 @@

                                                                    fims_popdy::MaturityBase< Type >.

                                                                    -

                                                                    -
                                                                    - -

                                                                    ◆ evaluate() [2/2]

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<typename Type >
                                                                    -

                                                                    Public Attributes

                                                                    fims::Vector< Type > inflection_point
                                                                     
                                                                    fims::Vector< Type > slope
                                                                     
                                                                    Type inflection_point
                                                                     
                                                                    Type slope
                                                                     
                                                                    - Public Attributes inherited from fims_model_object::FIMSObject< Type >
                                                                    uint32_t id
                                                                     
                                                                    - - - - -
                                                                    - - - - - - - - - - - - - - - - - - -
                                                                    virtual const Type fims_popdy::LogisticMaturity< Type >::evaluate (const Type & x,
                                                                    size_t pos 
                                                                    )
                                                                    -                                                                     		-inlinevirtual
                                                                    -
                                                                    - -

                                                                    Method of the logistic maturity class that implements the logistic function from FIMS math.

                                                                    -

                                                                    -\[ \frac{1.0}{ 1.0 + exp(-1.0 * slope_t (x - {inflection\_point}_t))} \] -

                                                                    -
                                                                    Parameters
                                                                    - - - -
                                                                    xThe independent variable in the logistic function (e.g., age or size in selectivity).
                                                                    posPosition index, e.g., which year.
                                                                    -
                                                                    -
                                                                    - -

                                                                    Implements fims_popdy::MaturityBase< Type >.

                                                                    -

                                                                    Member Data Documentation

                                                                    - -

                                                                    ◆ inflection_point

                                                                    + +

                                                                    ◆ inflection_point

                                                                    @@ -249,7 +191,7 @@

                                                                    - fims::Vector<Type> fims_popdy::LogisticMaturity< Type >::inflection_point + Type fims_popdy::LogisticMaturity< Type >::inflection_point

                                                                    @@ -257,8 +199,8 @@

                                                                    -

                                                                    ◆ slope

                                                                    + +

                                                                    ◆ slope

                                                                    @@ -266,7 +208,7 @@

                                                                    - fims::Vector<Type> fims_popdy::LogisticMaturity< Type >::slope + Type fims_popdy::LogisticMaturity< Type >::slope

                                                                    diff --git a/docs/structfims__popdy_1_1LogisticSelectivity-members.html b/docs/structfims__popdy_1_1LogisticSelectivity-members.html index 06baea0..dd92927 100644 --- a/docs/structfims__popdy_1_1LogisticSelectivity-members.html +++ b/docs/structfims__popdy_1_1LogisticSelectivity-members.html @@ -79,19 +79,17 @@

                                                                    This is the complete list of members for fims_popdy::LogisticSelectivity< Type >, including all inherited members.

                                                                    - - - + - + - + diff --git a/docs/structfims__popdy_1_1LogisticSelectivity.html b/docs/structfims__popdy_1_1LogisticSelectivity.html index a066773..1fcae1e 100644 --- a/docs/structfims__popdy_1_1LogisticSelectivity.html +++ b/docs/structfims__popdy_1_1LogisticSelectivity.html @@ -101,9 +101,6 @@ - - - @@ -114,16 +111,13 @@ uint32_t  - - -
                                                                    CheckDimensions(size_t actual, size_t expected)fims_model_object::FIMSObject< Type >inline
                                                                    evaluate(const Type &x)fims_popdy::LogisticSelectivity< Type >inlinevirtual
                                                                    evaluate(const Type &x, size_t pos)fims_popdy::LogisticSelectivity< Type >inlinevirtual
                                                                    evaluate(const Type &x)fims_popdy::LogisticSelectivity< Type >inlinevirtual
                                                                    fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    GetId() constfims_model_object::FIMSObject< Type >inline
                                                                    idfims_model_object::FIMSObject< Type >
                                                                    id_gfims_popdy::SelectivityBase< Type >static
                                                                    inflection_pointfims_popdy::LogisticSelectivity< Type >
                                                                    inflection_pointfims_popdy::LogisticSelectivity< Type >
                                                                    LogisticSelectivity() (defined in fims_popdy::LogisticSelectivity< Type >)fims_popdy::LogisticSelectivity< Type >inline
                                                                    parametersfims_model_object::FIMSObject< Type >
                                                                    random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    SelectivityBase()fims_popdy::SelectivityBase< Type >inline
                                                                    slopefims_popdy::LogisticSelectivity< Type >
                                                                    slopefims_popdy::LogisticSelectivity< Type >
                                                                    ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                    ~LogisticSelectivity() (defined in fims_popdy::LogisticSelectivity< Type >)fims_popdy::LogisticSelectivity< Type >inlinevirtual
                                                                    ~SelectivityBase() (defined in fims_popdy::SelectivityBase< Type >)fims_popdy::SelectivityBase< Type >inlinevirtual
                                                                    virtual const Type evaluate (const Type &x)
                                                                     Method of the logistic selectivity class that implements the logistic function from FIMS math. More...
                                                                     
                                                                    virtual const Type evaluate (const Type &x, size_t pos)
                                                                     Method of the logistic selectivity class that implements the logistic function from FIMS math. More...
                                                                     
                                                                    - Public Member Functions inherited from fims_popdy::SelectivityBase< Type >
                                                                     SelectivityBase ()
                                                                    GetId () const
                                                                     Getter that returns the unique id for parameters in the model.
                                                                     
                                                                    bool CheckDimensions (size_t actual, size_t expected)
                                                                     Check the dimensions of an object. More...
                                                                     
                                                                    - - - - + + + + @@ -147,7 +141,7 @@

                                                                    LogisticSelectivity class that returns the logistic function value from fims_math.

                                                                    Member Function Documentation

                                                                    -

                                                                    ◆ evaluate() [1/2]

                                                                    +

                                                                    ◆ evaluate()

                                                                    @@ -174,7 +168,7 @@

                                                                    -\[ \frac{1.0}{ 1.0 + exp(-1.0 * slope (x - inflection\_point))} \] +\[ \frac{1.0}{ 1.0 + exp(-1.0 * slope (x - inflection_point))} \]

                                                                    Parameters

                                                                    Public Attributes

                                                                    fims::Vector< Type > inflection_point
                                                                     
                                                                    fims::Vector< Type > slope
                                                                     
                                                                    Type inflection_point
                                                                     
                                                                    Type slope
                                                                     
                                                                    - Public Attributes inherited from fims_model_object::FIMSObject< Type >
                                                                    uint32_t id
                                                                     
                                                                    @@ -185,63 +179,11 @@

                                                                    fims_popdy::SelectivityBase< Type >.

                                                                    - - - -

                                                                    ◆ evaluate() [2/2]

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<typename Type >
                                                                    -
                                                                    - - - - -
                                                                    - - - - - - - - - - - - - - - - - - -
                                                                    virtual const Type fims_popdy::LogisticSelectivity< Type >::evaluate (const Type & x,
                                                                    size_t pos 
                                                                    )
                                                                    -                                                                     		-inlinevirtual
                                                                    -
                                                                    - -

                                                                    Method of the logistic selectivity class that implements the logistic function from FIMS math.

                                                                    -

                                                                    -\[ \frac{1.0}{ 1.0 + exp(-1.0 * slope_t (x - {inflection\_point}_t))} \] -

                                                                    -
                                                                    Parameters
                                                                    - - - -
                                                                    xThe independent variable in the logistic function (e.g., age or size in selectivity).
                                                                    posPosition index, e.g., which year.
                                                                    -
                                                                    -
                                                                    - -

                                                                    Implements fims_popdy::SelectivityBase< Type >.

                                                                    -

                                                                    Member Data Documentation

                                                                    - -

                                                                    ◆ inflection_point

                                                                    + +

                                                                    ◆ inflection_point

                                                                    @@ -249,7 +191,7 @@

                                                                    - fims::Vector<Type> fims_popdy::LogisticSelectivity< Type >::inflection_point + Type fims_popdy::LogisticSelectivity< Type >::inflection_point

                                                                    @@ -257,8 +199,8 @@

                                                                    -

                                                                    ◆ slope

                                                                    + +

                                                                    ◆ slope

                                                                    @@ -266,7 +208,7 @@

                                                                    - fims::Vector<Type> fims_popdy::LogisticSelectivity< Type >::slope + Type fims_popdy::LogisticSelectivity< Type >::slope

                                                                    diff --git a/docs/structfims__popdy_1_1MaturityBase-members.html b/docs/structfims__popdy_1_1MaturityBase-members.html index b43aa31..fd2c510 100644 --- a/docs/structfims__popdy_1_1MaturityBase-members.html +++ b/docs/structfims__popdy_1_1MaturityBase-members.html @@ -79,9 +79,7 @@

                                                                    This is the complete list of members for fims_popdy::MaturityBase< Type >, including all inherited members.

                                                                    - - - + diff --git a/docs/structfims__popdy_1_1MaturityBase.html b/docs/structfims__popdy_1_1MaturityBase.html index 0e7e79f..138b3d5 100644 --- a/docs/structfims__popdy_1_1MaturityBase.html +++ b/docs/structfims__popdy_1_1MaturityBase.html @@ -105,17 +105,11 @@ - - - - - -
                                                                    CheckDimensions(size_t actual, size_t expected)fims_model_object::FIMSObject< Type >inline
                                                                    evaluate(const Type &x)=0fims_popdy::MaturityBase< Type >pure virtual
                                                                    evaluate(const Type &x, size_t pos)=0fims_popdy::MaturityBase< Type >pure virtual
                                                                    evaluate(const Type &x)=0fims_popdy::MaturityBase< Type >pure virtual
                                                                    fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    GetId() constfims_model_object::FIMSObject< Type >inline
                                                                    idfims_model_object::FIMSObject< Type >
                                                                    virtual const Type evaluate (const Type &x)=0
                                                                     Calculates the maturity. More...
                                                                     
                                                                    virtual const Type evaluate (const Type &x, size_t pos)=0
                                                                     Calculates the selectivity. More...
                                                                     
                                                                    - Public Member Functions inherited from fims_model_object::FIMSObject< Type >
                                                                    uint32_t GetId () const
                                                                     Getter that returns the unique id for parameters in the model.
                                                                     
                                                                    bool CheckDimensions (size_t actual, size_t expected)
                                                                     Check the dimensions of an object. More...
                                                                     
                                                                    @@ -147,7 +141,7 @@

                                                                    Member Function Documentation

                                                                    -

                                                                    ◆ evaluate() [1/2]

                                                                    +

                                                                    ◆ evaluate()

                                                                    @@ -182,55 +176,6 @@

                                                                    fims_popdy::LogisticMaturity< Type >.

                                                                    -

                                                                    -
                                                                    - -

                                                                    ◆ evaluate() [2/2]

                                                                    - -
                                                                    -
                                                                    -
                                                                    -template<typename Type >
                                                                    -

                                                                    Static Public Attributes

                                                                    - - - - -
                                                                    - - - - - - - - - - - - - - - - - - -
                                                                    virtual const Type fims_popdy::MaturityBase< Type >::evaluate (const Type & x,
                                                                    size_t pos 
                                                                    )
                                                                    -                                                                     		-pure virtual
                                                                    -
                                                                    - -

                                                                    Calculates the selectivity.

                                                                    -
                                                                    Parameters
                                                                    - - - -
                                                                    xThe independent variable in the logistic function (e.g., age or size in selectivity).
                                                                    posPosition index, e.g., which year.
                                                                    -
                                                                    -
                                                                    - -

                                                                    Implemented in fims_popdy::LogisticMaturity< Type >.

                                                                    -

                                                                    Member Data Documentation

                                                                    diff --git a/docs/structfims__popdy_1_1Population-members.html b/docs/structfims__popdy_1_1Population-members.html index 9be956e..72c86ac 100644 --- a/docs/structfims__popdy_1_1Population-members.html +++ b/docs/structfims__popdy_1_1Population-members.html @@ -96,47 +96,46 @@ CalculateUnfishedBiomass(size_t i_age_year, size_t year, size_t age)fims_popdy::Population< Type >inline CalculateUnfishedNumbersAA(size_t i_age_year, size_t i_agem1_yearm1, size_t age)fims_popdy::Population< Type >inline CalculateUnfishedSpawningBiomass(size_t i_age_year, size_t year, size_t age)fims_popdy::Population< Type >inline - CheckDimensions(size_t actual, size_t expected)fims_model_object::FIMSObject< Type >inline - Evaluate()fims_popdy::Population< Type >inline - expected_catchfims_popdy::Population< Type > - expected_numbers_at_agefims_popdy::Population< Type > - expected_recruitmentfims_popdy::Population< Type > - fixed_effects_parametersfims_model_object::FIMSObject< Type > - fleet_idfims_popdy::Population< Type > - fleetsfims_popdy::Population< Type > - GetId() constfims_model_object::FIMSObject< Type >inline - growthfims_popdy::Population< Type > - growth_idfims_popdy::Population< Type > - idfims_model_object::FIMSObject< Type > - id_gfims_popdy::Population< Type >static - Initialize(int nyears, int nseasons, int nages)fims_popdy::Population< Type >inline - log_init_naafims_popdy::Population< Type > - log_Mfims_popdy::Population< Type > - Mfims_popdy::Population< Type > - maturityfims_popdy::Population< Type > - maturity_idfims_popdy::Population< Type > - mortality_Ffims_popdy::Population< Type > - mortality_Zfims_popdy::Population< Type > - nagesfims_popdy::Population< Type > - nfleetsfims_popdy::Population< Type > - nseasonsfims_popdy::Population< Type > - numbers_at_agefims_popdy::Population< Type > - nyearsfims_popdy::Population< Type > - parametersfims_model_object::FIMSObject< Type > - Population() (defined in fims_popdy::Population< Type >)fims_popdy::Population< Type >inline - Prepare()fims_popdy::Population< Type >inline - proportion_femalefims_popdy::Population< Type > - proportion_mature_at_agefims_popdy::Population< Type > - random_effects_parametersfims_model_object::FIMSObject< Type > - recruitmentfims_popdy::Population< Type > - recruitment_idfims_popdy::Population< Type > - spawning_biomassfims_popdy::Population< Type > - unfished_biomassfims_popdy::Population< Type > - unfished_numbers_at_agefims_popdy::Population< Type > - unfished_spawning_biomassfims_popdy::Population< Type > - weight_at_agefims_popdy::Population< Type > - yearsfims_popdy::Population< Type > - ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual + Evaluate()fims_popdy::Population< Type >inline + expected_catchfims_popdy::Population< Type > + expected_numbers_at_agefims_popdy::Population< Type > + expected_recruitmentfims_popdy::Population< Type > + fixed_effects_parametersfims_model_object::FIMSObject< Type > + fleet_idfims_popdy::Population< Type > + fleetsfims_popdy::Population< Type > + GetId() constfims_model_object::FIMSObject< Type >inline + growthfims_popdy::Population< Type > + growth_idfims_popdy::Population< Type > + idfims_model_object::FIMSObject< Type > + id_gfims_popdy::Population< Type >static + Initialize(int nyears, int nseasons, int nages)fims_popdy::Population< Type >inline + log_init_naafims_popdy::Population< Type > + log_Mfims_popdy::Population< Type > + Mfims_popdy::Population< Type > + maturityfims_popdy::Population< Type > + maturity_idfims_popdy::Population< Type > + mortality_Ffims_popdy::Population< Type > + mortality_Zfims_popdy::Population< Type > + nagesfims_popdy::Population< Type > + nfleetsfims_popdy::Population< Type > + nseasonsfims_popdy::Population< Type > + numbers_at_agefims_popdy::Population< Type > + nyearsfims_popdy::Population< Type > + parametersfims_model_object::FIMSObject< Type > + Population() (defined in fims_popdy::Population< Type >)fims_popdy::Population< Type >inline + Prepare()fims_popdy::Population< Type >inline + proportion_femalefims_popdy::Population< Type > + proportion_mature_at_agefims_popdy::Population< Type > + random_effects_parametersfims_model_object::FIMSObject< Type > + recruitmentfims_popdy::Population< Type > + recruitment_idfims_popdy::Population< Type > + spawning_biomassfims_popdy::Population< Type > + unfished_biomassfims_popdy::Population< Type > + unfished_numbers_at_agefims_popdy::Population< Type > + unfished_spawning_biomassfims_popdy::Population< Type > + weight_at_agefims_popdy::Population< Type > + yearsfims_popdy::Population< Type > + ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual

                                                                    diff --git a/docs/structfims__popdy_1_1Population.html b/docs/structfims__popdy_1_1Population.html index c7312c1..dc12cc2 100644 --- a/docs/structfims__popdy_1_1Population.html +++ b/docs/structfims__popdy_1_1Population.html @@ -159,9 +159,6 @@ uint32_t GetId () const  Getter that returns the unique id for parameters in the model.
                                                                      -bool CheckDimensions (size_t actual, size_t expected) - Check the dimensions of an object. More...
                                                                    -  diff --git a/docs/structfims__popdy_1_1RecruitmentBase-members.html b/docs/structfims__popdy_1_1RecruitmentBase-members.html index 0e009d5..9b167a9 100644 --- a/docs/structfims__popdy_1_1RecruitmentBase-members.html +++ b/docs/structfims__popdy_1_1RecruitmentBase-members.html @@ -79,23 +79,24 @@

                                                                    This is the complete list of members for fims_popdy::RecruitmentBase< Type >, including all inherited members.

                                                                    Public Attributes

                                                                    - - - - + + + + - - - - - - - - + + + + + + + + +
                                                                    CheckDimensions(size_t actual, size_t expected)fims_model_object::FIMSObject< Type >inline
                                                                    constrain_deviationsfims_popdy::RecruitmentBase< Type >
                                                                    estimate_log_recruit_devsfims_popdy::RecruitmentBase< Type >
                                                                    evaluate(const Type &spawners, const Type &ssbzero)=0fims_popdy::RecruitmentBase< Type >pure virtual
                                                                    constrain_deviationsfims_popdy::RecruitmentBase< Type >
                                                                    estimate_log_recruit_devsfims_popdy::RecruitmentBase< Type >
                                                                    evaluate(const Type &spawners, const Type &ssbzero)=0fims_popdy::RecruitmentBase< Type >pure virtual
                                                                    evaluate_nll()fims_popdy::RecruitmentBase< Type >inlinevirtual
                                                                    fixed_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    GetId() constfims_model_object::FIMSObject< Type >inline
                                                                    idfims_model_object::FIMSObject< Type >
                                                                    id_gfims_popdy::RecruitmentBase< Type >static
                                                                    log_recruit_devsfims_popdy::RecruitmentBase< Type >
                                                                    log_rzerofims_popdy::RecruitmentBase< Type >
                                                                    parametersfims_model_object::FIMSObject< Type >
                                                                    Prepare()fims_popdy::RecruitmentBase< Type >inline
                                                                    PrepareConstrainedDeviations()fims_popdy::RecruitmentBase< Type >inline
                                                                    random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    RecruitmentBase()fims_popdy::RecruitmentBase< Type >inline
                                                                    ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                    ~RecruitmentBase() (defined in fims_popdy::RecruitmentBase< Type >)fims_popdy::RecruitmentBase< Type >inlinevirtual
                                                                    log_rzerofims_popdy::RecruitmentBase< Type >
                                                                    log_sigma_recruitfims_popdy::RecruitmentBase< Type >
                                                                    parametersfims_model_object::FIMSObject< Type >
                                                                    Prepare()fims_popdy::RecruitmentBase< Type >inline
                                                                    PrepareConstrainedDeviations()fims_popdy::RecruitmentBase< Type >inline
                                                                    random_effects_parametersfims_model_object::FIMSObject< Type >
                                                                    RecruitmentBase()fims_popdy::RecruitmentBase< Type >inline
                                                                    ~FIMSObject() (defined in fims_model_object::FIMSObject< Type >)fims_model_object::FIMSObject< Type >inlinevirtual
                                                                    ~RecruitmentBase() (defined in fims_popdy::RecruitmentBase< Type >)fims_popdy::RecruitmentBase< Type >inlinevirtual
                                                                    diff --git a/docs/structfims__popdy_1_1RecruitmentBase.html b/docs/structfims__popdy_1_1RecruitmentBase.html index 52e6329..5b99e82 100644 --- a/docs/structfims__popdy_1_1RecruitmentBase.html +++ b/docs/structfims__popdy_1_1RecruitmentBase.html @@ -110,6 +110,9 @@ virtual const Type evaluate (const Type &spawners, const Type &ssbzero)=0  Calculates the expected recruitment for a given spawning input. More...
                                                                      +virtual const Type evaluate_nll () + Calculates the negative log likelihood of recruitment deviations. More...
                                                                    +  void PrepareConstrainedDeviations ()  Prepare constrained recruitment deviations. Based on ADMB sum-to-zero constraint implementation. We still need to adde an additional penalty to the PrepareConstrainedDeviations method. More discussion can be found here: https://groups.google.com/a/admb-project.org/g/users/c/63YJmYGEPuE.
                                                                    @@ -119,9 +122,6 @@ uint32_t GetId () const  Getter that returns the unique id for parameters in the model.
                                                                      -bool CheckDimensions (size_t actual, size_t expected) - Check the dimensions of an object. More...
                                                                    -  @@ -129,8 +129,10 @@ - - + + + + @@ -207,6 +209,36 @@

                                                                    fims_popdy::SRBevertonHolt< Type >.

                                                                    + + + +

                                                                    ◆ evaluate_nll()

                                                                    + +
                                                                    +
                                                                    +
                                                                    +template<class Type >
                                                                    +

                                                                    Public Attributes

                                                                     
                                                                    bool constrain_deviations = false
                                                                     
                                                                    fims::Vector< Type > log_rzero
                                                                     
                                                                    Type log_sigma_recruit
                                                                     
                                                                    Type log_rzero
                                                                     
                                                                    bool estimate_log_recruit_devs = true
                                                                     
                                                                    - Public Attributes inherited from fims_model_object::FIMSObject< Type >
                                                                    + + + + +
                                                                    + + + + + + + +
                                                                    virtual const Type fims_popdy::RecruitmentBase< Type >::evaluate_nll ()
                                                                    +                                                                     		+inlinevirtual
                                                                    +

                                                                    + +

                                                                    Calculates the negative log likelihood of recruitment deviations.

                                                                    +

                                                                    < The negative log likelihood value

                                                                    +

                                                                    Member Data Documentation

                                                                    @@ -286,8 +318,8 @@

                                                                    -

                                                                    ◆ log_rzero

                                                                    + +

                                                                    ◆ log_rzero

                                                                    @@ -295,12 +327,29 @@

                                                                    - fims::Vector<Type> fims_popdy::RecruitmentBase< Type >::log_rzero + Type fims_popdy::RecruitmentBase< Type >::log_rzero

                                                                    Log of unexploited recruitment.

                                                                    +
                                                                    +
                                                                    + +

                                                                    ◆ log_sigma_recruit

                                                                    + +
                                                                    +
                                                                    +
                                                                    +template<class Type >
                                                                    + + + + +
                                                                    Type fims_popdy::RecruitmentBase< Type >::log_sigma_recruit
                                                                    +
                                                                    +

                                                                    Log standard deviation of log recruitment deviations

                                                                    +
                                                                    The documentation for this struct was generated from the following file: