From 23e472b54c5f92a096255d3c53c0352494ce3c25 Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Tue, 9 Jul 2024 19:14:49 +0000 Subject: [PATCH] build based on 0680917 --- dev/.documenter-siteinfo.json | 2 +- dev/index.html | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 736959d..213ec93 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-09T18:09:30","documenter_version":"1.5.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-09T19:14:45","documenter_version":"1.5.0"}} \ No newline at end of file diff --git a/dev/index.html b/dev/index.html index 06e0da6..4c35eb1 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,20 +1,20 @@ -Home · Chron.jl

Chron

Documentation for the Chron.jl package.

Chron.intcal13 — Constant
intcal13
+Home · Chron.jl
Chron
Documentation for the Chron.jl package.
Chron.intcal13 — Constant
intcal13
 NamedTuple with 4 fields:
   dt            = Int64 1
   Age_Calendar  = StepRange{Int64, Int64}   1:1:50000
   Age_sigma     = Vector{Float64}(50000,)   [8.0 ... 274.0]
-  Age_14C       = Vector{Float64}(50000,)   [196.8 ... 46401.0]
The IntCal13 radiocarbon calibration curve
Reimer PJ, Bard E, Bayliss A, Beck JW, Blackwell PG, Bronk Ramsey C, Buck CE, Cheng H, Edwards RL, Friedrich M, Grootes PM, Guilderson TP, Haflidason H, , Hajdas I, Hatté C, Heaton TJ, Hogg AG, Hughen KA, Kaiser KF, Kromer B, Manning SW, Niu M, Reimer RW, Richards DA, Scott EM, Southon JR, Turney CSM, van der Plicht J. (2013) "IntCal13 and MARINE13 radiocarbon age calibration curves 0-50000 years calBP". Radiocarbon 55(4). doi: 10.2458/azujsrc.55.16947
source
Chron.intcal20 — Constant
intcal20
+  Age_14C       = Vector{Float64}(50000,)   [196.8 ... 46401.0]
The IntCal13 radiocarbon calibration curve
Reimer PJ, Bard E, Bayliss A, Beck JW, Blackwell PG, Bronk Ramsey C, Buck CE, Cheng H, Edwards RL, Friedrich M, Grootes PM, Guilderson TP, Haflidason H, , Hajdas I, Hatté C, Heaton TJ, Hogg AG, Hughen KA, Kaiser KF, Kromer B, Manning SW, Niu M, Reimer RW, Richards DA, Scott EM, Southon JR, Turney CSM, van der Plicht J. (2013) "IntCal13 and MARINE13 radiocarbon age calibration curves 0-50000 years calBP". Radiocarbon 55(4). doi: 10.2458/azujsrc.55.16947
source
Chron.intcal20 — Constant
intcal20
 NamedTuple with 4 fields:
   dt            = Int64 1
   Age_Calendar  = StepRange{Int64, Int64}   1:1:55000
   Age_sigma     = Vector{Float64}(55000,)   [11.0 ... 1024.0]
-  Age_14C       = Vector{Float64}(55000,)   [197.0 ... 50100.0]
The IntCal20 northern hemisphere radiocarbon calibration curve.
Reimer P, Austin WEN, Bard E, Bayliss A, Blackwell PG, Bronk Ramsey C, Butzin M, Cheng H, Edwards RL, Friedrich M, Grootes PM, Guilderson TP, Hajdas I, Heaton TJ, Hogg AG, Hughen KA, Kromer B, Manning SW, Muscheler R, Palmer JG, Pearson C, van der Plicht J, Reimer RW, Richards DA, Scott EM, Southon JR, Turney CSM, Wacker L, Adolphi F, Büntgen U, Capano M, Fahrni S, Fogtmann-Schulz A, Friedrich R, Köhler P, Kudsk S, Miyake F, Olsen J, Reinig F, Sakamoto M, Sookdeo A, Talamo S. (2020). "The IntCal20 Northern Hemisphere radiocarbon age calibration curve (0-55 cal kBP)". Radiocarbon 62. doi: 10.1017/RDC.2020.41.
source
Chron.marine20 — Constant
The Marine20 radiocarbon calibration curve.
Heaton TJ, Köhler P, Butzin M, et al. (2020) "Marine20—The Marine Radiocarbon Age Calibration Curve (0–55,000 cal BP)" Radiocarbon 62(4):779-820. doi: 10.1017/RDC.2020.68
source
Chron.shcal20 — Constant
shcal20
+  Age_14C       = Vector{Float64}(55000,)   [197.0 ... 50100.0]
The IntCal20 northern hemisphere radiocarbon calibration curve.
Reimer P, Austin WEN, Bard E, Bayliss A, Blackwell PG, Bronk Ramsey C, Butzin M, Cheng H, Edwards RL, Friedrich M, Grootes PM, Guilderson TP, Hajdas I, Heaton TJ, Hogg AG, Hughen KA, Kromer B, Manning SW, Muscheler R, Palmer JG, Pearson C, van der Plicht J, Reimer RW, Richards DA, Scott EM, Southon JR, Turney CSM, Wacker L, Adolphi F, Büntgen U, Capano M, Fahrni S, Fogtmann-Schulz A, Friedrich R, Köhler P, Kudsk S, Miyake F, Olsen J, Reinig F, Sakamoto M, Sookdeo A, Talamo S. (2020). "The IntCal20 Northern Hemisphere radiocarbon age calibration curve (0-55 cal kBP)". Radiocarbon 62. doi: 10.1017/RDC.2020.41.
source
Chron.marine20 — Constant
The Marine20 radiocarbon calibration curve.
Heaton TJ, Köhler P, Butzin M, et al. (2020) "Marine20—The Marine Radiocarbon Age Calibration Curve (0–55,000 cal BP)" Radiocarbon 62(4):779-820. doi: 10.1017/RDC.2020.68
source
Chron.shcal20 — Constant
shcal20
 NamedTuple with 4 fields:
   dt            = Int64 1
   Age_Calendar  = StepRange{Int64, Int64}   1:1:55000
   Age_sigma     = Vector{Float64}(55000,)   [10.0 ... 1008.0]
-  Age_14C       = Vector{Float64}(55000,)   [171.0 ... 50132.0]
The SHCal20 southern hemisphere radiocarbon calibration curve.
Hogg AG, Heaton TJ, Hua Q, Palmer JG, Turney CSM, Southon J, Bayliss A, Blackwell PG, Boswijk G, Bronk Ramsey C, Pearson C, Petchey F, Reimer P, Reimer R, Wacker L. (2020). "SHCal20 Southern Hemisphere calibration, 0-55,000 years cal BP". Radiocarbon 62. doi: 10.1017/RDC.2020.59
source
Chron.BilinearExponential — Type
BilinearExponential(loc, scl, shp, skw)
+  Age_14C       = Vector{Float64}(55000,)   [171.0 ... 50132.0]
The SHCal20 southern hemisphere radiocarbon calibration curve.
Hogg AG, Heaton TJ, Hua Q, Palmer JG, Turney CSM, Southon J, Bayliss A, Blackwell PG, Boswijk G, Bronk Ramsey C, Pearson C, Petchey F, Reimer P, Reimer R, Wacker L. (2020). "SHCal20 Southern Hemisphere calibration, 0-55,000 years cal BP". Radiocarbon 62. doi: 10.1017/RDC.2020.59
source
Chron.BilinearExponential — Type
BilinearExponential(loc, scl, shp, skw)
 BilinearExponential(p::AbstractVector)
 struct BilinearExponential{T<:Real} <: ContinuousUnivariateDistribution
     A::T
@@ -22,7 +22,7 @@
     scl::T
     shp::T
     skw::T
-end
A five-parameter pseudo-distribution which can be used to approximate various  asymmetric probability distributions found in geochronology (including as a result  of Bayesian eruption age estimation). 
This "bilinear exponential" distribution, as the name might suggest, is defined as an  exponential function with two log-linear segments, joined by an arctangent sigmoid:
\[ℯ^{A} * ℯ^{v*xₛ*shp*skw - (1-v)*xₛ*shp/skw}\]
where
\[v = 1/2 - atan(xₛ)/π\]
is a sigmoid, positive on the left-hand side, and
\[xₛ = (x - loc)/scl\]
is x scaled by the location parameter loc and scale parameter scl,  In addition to the scale parameter scl, the additional shape parameters shp and skw  (which control the sharpness and skew of the resulting distribution, respectively), are  all three required to be nonnegative.
If only four parameters (loc, scl, shp, skw) are specified, the normalization constant A  will be calculated such that the resulting distribution is normalized.
source
Chron.BootstrapCrystDistributionKDE — Method
BootstrapCrystDistributionKDE(smpl::ChronAgeData; cutoff=-0.05, [tpbloss=0])
Bootstrap an estimate of the pre-eruptive (or pre-depositional) mineral crystallization distribution shape from a Chron.ChronAgeData object containing data for several samples, using a kernel density estimate of stacked sample data.
If the samples provided as csv files in smpl.Path take the five-column form of U-Pb isotopic data files, the ages and uncertainties will be those of upper intercepts given a time of Pb-loss optionally specified as tpbloss.
Uncertainties will be treated as one or two-sigma absolute based on the value of smpl.inputSigmaLevel.
Examples
BootstrappedDistribution = BootstrapCrystDistributionKDE(smpl)
source
Chron.BootstrapCrystDistributionKDE — Method
BootstrapCrystDistributionKDE(data::AbstractArray, [sigma::AbstractArray]; cutoff=-0.05)
Bootstrap an estimate of the pre-eruptive (or pre-depositional) mineral crystallization distribution shape from a 1- or 2-d array of sample ages (one row per sample, one column per datum, padded with NaNs as needed) and an equivalent-size array of one-sigma uncertainties, using a kernel density estimate of stacked sample data.
Examples
# Bootstrap crystallization distribution for a synthetic dataset with ages
+end
A five-parameter pseudo-distribution which can be used to approximate various  asymmetric probability distributions found in geochronology (including as a result  of Bayesian eruption age estimation). 
This "bilinear exponential" distribution, as the name might suggest, is defined as an  exponential function with two log-linear segments, joined by an arctangent sigmoid:
\[ℯ^{A} * ℯ^{v*xₛ*shp*skw - (1-v)*xₛ*shp/skw}\]
where
\[v = 1/2 - atan(xₛ)/π\]
is a sigmoid, positive on the left-hand side, and
\[xₛ = (x - loc)/scl\]
is x scaled by the location parameter loc and scale parameter scl,  In addition to the scale parameter scl, the additional shape parameters shp and skw  (which control the sharpness and skew of the resulting distribution, respectively), are  all three required to be nonnegative.
If only four parameters (loc, scl, shp, skw) are specified, the normalization constant A  will be calculated such that the resulting distribution is normalized.
source
Chron.BootstrapCrystDistributionKDE — Method
BootstrapCrystDistributionKDE(smpl::ChronAgeData; cutoff=-0.05, [tpbloss=0])
Bootstrap an estimate of the pre-eruptive (or pre-depositional) mineral crystallization distribution shape from a Chron.ChronAgeData object containing data for several samples, using a kernel density estimate of stacked sample data.
If the samples provided as csv files in smpl.Path take the five-column form of U-Pb isotopic data files, the ages and uncertainties will be those of upper intercepts given a time of Pb-loss optionally specified as tpbloss.
Uncertainties will be treated as one or two-sigma absolute based on the value of smpl.inputSigmaLevel.
Examples
BootstrappedDistribution = BootstrapCrystDistributionKDE(smpl)
source
Chron.BootstrapCrystDistributionKDE — Method
BootstrapCrystDistributionKDE(data::AbstractArray, [sigma::AbstractArray]; cutoff=-0.05)
Bootstrap an estimate of the pre-eruptive (or pre-depositional) mineral crystallization distribution shape from a 1- or 2-d array of sample ages (one row per sample, one column per datum, padded with NaNs as needed) and an equivalent-size array of one-sigma uncertainties, using a kernel density estimate of stacked sample data.
Examples
# Bootstrap crystallization distribution for a synthetic dataset with ages
 # [1,2,3,...10] Ma and uncertainties of 1 Ma each
-BootstrappedDistribution = BootstrapCrystDistributionKDE(1:10, ones(10))
source
Chron.StratMetropolis — Function
StratMetropolis(smpl::ChronAgeData, [hiatus::HiatusData,] config::StratAgeModelConfiguration)
-StratMetropolis(smpl::GeneralAgeData, [hiatus::HiatusData,] config::StratAgeModelConfiguration)
Runs the main Chron.jl age-depth model routine for a stratigraphic set of samples defined by sample heights and simple Gaussian age constraints in the smpl struct, and an age-depth model configuration defined by the config struct.
Optionally, if a hiatus struct is provided, the model will additionally incorporate information about the durations of known hiatuses at the specified model heights.
Examples:
(mdl, agedist, lldist) = StratMetropolis(smpl, config)
(mdl, agedist, hiatusdist, lldist) = StratMetropolis(smpl, hiatus, config)
source
Chron.StratMetropolis14C — Method
StratMetropolis14C(smpl::ChronAgeData, [hiatus::HiatusData,] config::StratAgeModelConfiguration)
Runs the main Chron.jl age-depth model routine for a stratigraphic set of samples defined by sample heights and interpolated radiocarbon age constraints in the smpl struct, and an age-depth model configuration defined by the config struct.
Optionally, if a hiatus struct is provided, the model will additionally incorporate information about the durations of known hiatuses at the specified model heights.
Examples:
(mdl, agedist, lldist) = StratMetropolis14C(smpl, config)
(mdl, agedist, hiatusdist, lldist) = StratMetropolis14C(smpl, hiatus, config)
source
Chron.StratMetropolisDist — Function
StratMetropolisDist(smpl::ChronAgeData, [hiatus::HiatusData,] config::StratAgeModelConfiguration)
Runs the main Chron.jl age-depth model routine for a stratigraphic set of samples defined by sample heights and fitted asymmetric age distributions (BilinearExponential) in the smpl struct, and an age-depth model configuration defined by the config struct.
Optionally, if a hiatus struct is provided, the model will additionally incorporate information about the durations of known hiatuses at the specified model heights.
Examples:
(mdl, agedist, lldist) = StratMetropolisDist(smpl, config)
(mdl, agedist, hiatusdist, lldist) = StratMetropolisDist(smpl, hiatus, config)
source
Chron.screen_outliers — Method
screen_outliers(smpl::ChronAgeData; agemin=0.0, agemax=Inf, maxgap=100, make_plots=true, discordancemin=0, discordancemax=100)
Screen outliers from the ChronAgeData struct smpl (making new data files in a screened subdirectory within smpl.Path) rejecting samples that either
a) Are older than agemax or younger than agemin
b) Are on the old side of a gap of more than maxgap/N sigma (e.g., xenocrysts)
If make_plots is true, plots showing screening results will be made in smpl.Path/screened.
If the underlying data is in the form of U-Pb ratios, the discordancemin and discordancemax keyword arguments may also be used for additional screening.
source
Chron.tMinDistMetropolis — Method
tMinDistMetropolis(smpl::ChronAgeData, nsteps::Int, burnin::Int, dist::Array{Float64})
Calculate the minimum limiting (eruption/deposition) age of each sample defined in the smpl struct, using the Isoplot.metropolis_min function, assuming mineral ages for each sample are drawn from the source distribution dist. Fits a BilinearExponential function to the resulting stationary distribution for each sample and stores the results in smpl.Params for use by the StratMetropolisDist function.
If the samples provided as csv files in smpl.Path take the five-column form of U-Pb isotopic data files, these will be interpreted as the columns
| ²⁰⁷Pb/²³⁵U | uncert (absolute) | ²⁰⁶Pb/²³⁸U | uncert (absolute) | correlation |
and Pb-loss-aware eruption/deposition age estimation will be conducted. In all other cases, the first two columns of each data file will be interpreted as
| Age | Age uncert (absolute) |
and standard eruption/deposition age estimation will be conducted.
In all cases, uncertainties will be treated as one or two-sigma absolute based on the value of smpl.inputSigmaLevel.
Examples
smpl = tMinDistMetropolis(smpl, 10^6, 10^5, HalfNormalDistribution)
source

+BootstrappedDistribution = BootstrapCrystDistributionKDE(1:10, ones(10))
source
Chron.StratMetropolis — Function
StratMetropolis(smpl::ChronAgeData, [hiatus::HiatusData,] config::StratAgeModelConfiguration)
+StratMetropolis(smpl::GeneralAgeData, [hiatus::HiatusData,] config::StratAgeModelConfiguration)

Runs the main Chron.jl age-depth model routine for a stratigraphic set of samples defined by sample heights and simple Gaussian age constraints in the smpl struct, and an age-depth model configuration defined by the config struct.

Optionally, if a hiatus struct is provided, the model will additionally incorporate information about the durations of known hiatuses at the specified model heights.

Examples:

(mdl, agedist, lldist) = StratMetropolis(smpl, config)
(mdl, agedist, hiatusdist, lldist) = StratMetropolis(smpl, hiatus, config)
source
Chron.StratMetropolis14C — Method
StratMetropolis14C(smpl::ChronAgeData, [hiatus::HiatusData,] config::StratAgeModelConfiguration)

Runs the main Chron.jl age-depth model routine for a stratigraphic set of samples defined by sample heights and interpolated radiocarbon age constraints in the smpl struct, and an age-depth model configuration defined by the config struct.

Optionally, if a hiatus struct is provided, the model will additionally incorporate information about the durations of known hiatuses at the specified model heights.

Examples:

(mdl, agedist, lldist) = StratMetropolis14C(smpl, config)
(mdl, agedist, hiatusdist, lldist) = StratMetropolis14C(smpl, hiatus, config)
source
Chron.StratMetropolisDist — Function
StratMetropolisDist(smpl::ChronAgeData, [hiatus::HiatusData,] config::StratAgeModelConfiguration)

Runs the main Chron.jl age-depth model routine for a stratigraphic set of samples defined by sample heights and fitted asymmetric age distributions (BilinearExponential) in the smpl struct, and an age-depth model configuration defined by the config struct.

Optionally, if a hiatus struct is provided, the model will additionally incorporate information about the durations of known hiatuses at the specified model heights.

Examples:

(mdl, agedist, lldist) = StratMetropolisDist(smpl, config)
(mdl, agedist, hiatusdist, lldist) = StratMetropolisDist(smpl, hiatus, config)
source
Chron.screen_outliers — Method
screen_outliers(smpl::ChronAgeData; agemin=0.0, agemax=Inf, maxgap=100, make_plots=true, discordancemin=0, discordancemax=100)

Screen outliers from the ChronAgeData struct smpl (making new data files in a screened subdirectory within smpl.Path) rejecting samples that either

a) Are older than agemax or younger than agemin

b) Are on the old side of a gap of more than maxgap/N sigma (e.g., xenocrysts)

If make_plots is true, plots showing screening results will be made in smpl.Path/screened.

If the underlying data is in the form of U-Pb ratios, the discordancemin and discordancemax keyword arguments may also be used for additional screening.

source
Chron.tMinDistMetropolis — Method
tMinDistMetropolis(smpl::ChronAgeData, nsteps::Int, burnin::Int, dist::Array{Float64})

Calculate the minimum limiting (eruption/deposition) age of each sample defined in the smpl struct, using the Isoplot.metropolis_min function, assuming mineral ages for each sample are drawn from the source distribution dist. Fits a BilinearExponential function to the resulting stationary distribution for each sample and stores the results in smpl.Params for use by the StratMetropolisDist function.

If the samples provided as csv files in smpl.Path take the five-column form of U-Pb isotopic data files, these will be interpreted as the columns

| ²⁰⁷Pb/²³⁵U | uncert (absolute) | ²⁰⁶Pb/²³⁸U | uncert (absolute) | correlation |

and Pb-loss-aware eruption/deposition age estimation will be conducted. In all other cases, the first two columns of each data file will be interpreted as

| Age | Age uncert (absolute) |

and standard eruption/deposition age estimation will be conducted.

In all cases, uncertainties will be treated as one or two-sigma absolute based on the value of smpl.inputSigmaLevel.

Examples

smpl = tMinDistMetropolis(smpl, 10^6, 10^5, HalfNormalDistribution)
source