From fe1a580cb33768a7e78225bfd357db0c65247082 Mon Sep 17 00:00:00 2001 From: Rikard Nordgren Date: Thu, 24 May 2018 11:44:14 +0200 Subject: [PATCH] Update webpage for release --- docs/bugs.html | 5 +-- docs/docs.html | 87 ++++++++++++++++++++++------------------------ docs/download.html | 25 ++++++++++--- docs/index.html | 16 +++++---- docs/install.html | 3 ++ 5 files changed, 75 insertions(+), 61 deletions(-) diff --git a/docs/bugs.html b/docs/bugs.html index 409d687bf..40ee3237e 100644 --- a/docs/bugs.html +++ b/docs/bugs.html @@ -32,7 +32,7 @@

Known Bugs

Known Bugs and Workarounds.pdf.
-

Known Bugs in PsN 4.7.0

+

Known Bugs in PsN 4.8.0

You can also check the latest reported issues. You can browse the issues by using the label tab as well as the Milestone tab (for different versions of PsN) at the PsN Github repository.

diff --git a/docs/docs.html b/docs/docs.html index 8ceb24256..ca45905ff 100644 --- a/docs/docs.html +++ b/docs/docs.html @@ -28,17 +28,17 @@

Documentation

- You can download all pdf documents listed below as a tar.gz - or a zip archive. + You can download all pdf documents listed below as a tar.gz + or a zip archive.

Before running PsN

-
PsN Configuration.pdf
-
Known Bugs and Workarounds.pdf
+
PsN Configuration.pdf
+
Known Bugs and Workarounds.pdf

PsN common options

-
PsN common options.pdf
+
PsN common options.pdf
List of common options for PsN tools.
@@ -46,86 +46,86 @@

PsN Tools

-
benchmark
+
benchmark
Benchmarking of NONMEM settings.
-
boot scm
+
boot scm
Bootstrapped Stepwise Covariate Model-building.
-
bootstrap
+
bootstrap
Bootstrap using the percentile or BCa method.
-
cdd
+
cdd
Case Deletion Diagnostics.
covmat
Create an empirical covariance matrix based on a rawresults file.
-
execute
+
execute
NONMEM runs are started using one or multiple model files.
-
extended grid
+
extended grid
non-parametric estimation on the extended grid.
-
frem
+
frem
Full random effects model.
-
gls
+
gls
Generalized Least Squares approximations of the residual error model.
-
lasso
+
lasso
Covariate model building using the lasso method.
-
linearize
+
linearize
Linearize a model.
-
llp
+
llp
Log-Likelihood Profiling around maximum-likelihood parameter estimates.
-
mcmp
+
mcmp
Monte-Carlo Mapped Power.
-
mimp
+
mimp
Multiple imputation.
-
nca
+
nca
Non-compartmental analysis.
-
nmoutput2so
+
nmoutput2so
Convert output from NONMEM to the DDMoRe standardised output format (so).
-
nonpb
+
nonpb
Non-Parametric Bootstrap.
-
npc
+
npc
Numerical Predictive Check.
-
parallel retries
+
parallel retries
Run multiple copies of a single model with tweaked initial estimates in parallel.
-
pind
+
pind
Individual Probabilities.
-
precond
+
precond
Estimate a model using preconditioning.
-
pvar
+
pvar
Parametric variability.
-
randtest
+
randtest
Randomization testing.
rawresults
Create a rawresults file from a set of list files.
-
resmod
+
resmod
Residual modelling.
-
runrecord +
runrecord runrecord template
Runrecord.
-
scm
+
scm
Stepwise Covariate Model-building.
Some extensively commented example/template configuration files for scm:
All default parameterizations explicitly using code section
@@ -138,35 +138,32 @@

PsN Tools

Standard template
-
se_of_eta
-
Standard Errors of Etas.
- -
simeval
+
simeval
Simulation-Evaluation diagnostics of outliers. Was ebe pde.
-
sir
+
sir
Parameter uncertainty from Sampling Importance Resampling.
-
sse
+
sse
Stochastic Simulation and Estimation.
-
sumo
+
sumo
Summary of Output from NONMEM.
-
transform
+
transform
Transform model files, i.e. boxcox, remove_iov.
-
update inits
+
update inits
Update a model file with parameter estimates from NONMEM output.
-
vpc
+
vpc
Visual Predictive Check.
Two-page poster on Visual Predictive Checks for censored and categorical data.pdf
-Separate description of >automatic binning in vpc.pdf. +Separate description of >automatic binning in vpc.pdf.
-
xv scm
+
xv scm
Cross-validated Stepwise Covariate Model-building.
@@ -200,7 +197,7 @@

Input options to PsN tool

All PsN tools accept a set of options which allow you to modify the behaviour of the tool. Some options are required for the tool, other options are specific for a certain tool and cannot be used together with other tools and finally there are a lot of common options.

Specific options:

-For example, the bootstrap tool creates 200 new data sets from the original data +For example, the bootstrap tool creates 200 new data sets from the original data by default. However the number of data sets can be limited to for example 50, by changing the number in the -sample option in the bootstrap tool.

$ bootstrap -samples=50 file.mod

@@ -217,7 +214,7 @@

Common options:

In this example the threads option makes the bootstrap tool run six NONMEM runs in parallel (on a cluster of computers or on multiple processors). To list all common PsN options enter:

$ psn_options -h

-

The Common options user guide.pdf describes these options in much more +

The Common options user guide.pdf describes these options in much more detail.

PsN Directory structure

@@ -238,7 +235,7 @@

Restarting a PsN tool

run.

Documentation for developers and testers

-The Developers guide.pdf contains information for developers and for +The Developers guide.pdf contains information for developers and for those in need of informationabout how to run the PsN test suite. diff --git a/docs/download.html b/docs/download.html index 752189b92..1bded2b85 100644 --- a/docs/download.html +++ b/docs/download.html @@ -101,15 +101,15 @@

Download

- + - @@ -117,7 +117,7 @@

Download

-
Please see the release notes PsN 4.7.0 for details.

+
Please see the release notes PsN 4.8.0 for details.

@@ -134,6 +134,21 @@

Download

+ + + + + + + + + +
Latest release PsN 4.7.0Latest release PsN 4.8.0
(Released on May 23rd 2017)

+

(Released on May 25th 2018)


PsN is distributed as a zipped file or as a gzipped tarball.

- PsN 4.7.0.zip
- PsN 4.7.0.tar.gz

+ PsN 4.8.0.zip
+ PsN 4.8.0.tar.gz
Older releases
+ PsN 4.7.0 + Please see the release notes 4.7.0 for details. 2017-05-23
+ .zip + .tar.gz +
PsN 4.6.0 diff --git a/docs/index.html b/docs/index.html index a9943892d..054ad14ea 100644 --- a/docs/index.html +++ b/docs/index.html @@ -35,20 +35,22 @@

Perl-speaks-NONMEM

under Documentation and also learn about Known Bugs, how to submit a new bug and how to become a part of the PsN mailing list.

-

Latest release PsN 4.7.0

-(Released on May 23rd 2017). +

Latest release PsN 4.8.0

+(Released on May 25th 2018).
New features in this version include;
    -
  • Major extensions to simeval, a tool for simulation-evaluation diagnostics for outlier detection.
    • -
  • Updates to frem, a tool for full random effects modelling for covariate building.
    • -
  • A new tool, resmod, used for evaluating different residual models, the addition of support for R Markdown when using -rplots greatly facilitating the automatic creation of reports and support for NONMEM 7.4.1.
    • +
  • A new tool qa for fast and automatic assumption assessment and quality assurance of models
    • +
  • A new tool transform, to manipulate model files. For example to automatically add IOV or Box-Cox transform ETAs
    • +
  • A new optional directory structure using a subdirectory for each model via the option -model_subdir
    • +
  • The addition of support for vpc for mixture models
    • +
  • Second order approximation added to the linearize tool
    • +
  • The presentation of meta data in a new file, meta.yaml, which is in a both human and computer readable format

Perl-speaks-NONMEM
-©2018 by Mats Karlsson, Andrew Hooker, Rikard Nordgren and Svetlana Freiberga. All rights reserved.
+©2018 by Mats Karlsson, Rikard Nordgren, Svetlana Freiberga, Sebastian Ueckert and Gunnar Yngman. All rights reserved.
©2016-2017 by Mats Karlsson, Andrew Hooker, Rikard Nordgren, Kajsa Harling and Svetlana Freiberga.
©2013-2015 by Mats Karlsson, Andrew Hooker, Rikard Nordgren and Kajsa Harling.
©2008-2012 by Mats Karlsson, Niclas Jonsson, Andrew Hooker and Kajsa Harling.
diff --git a/docs/install.html b/docs/install.html index 4b066ecf8..14d804229 100644 --- a/docs/install.html +++ b/docs/install.html @@ -77,6 +77,7 @@

Installing Strawberry Perl Modules on Windows

cpan Math::Random
cpan MooseX::Params::Validate
cpan Statistics::Distributions
+cpan YAML::XS
cpan XML::LibXML
@@ -93,6 +94,7 @@

Installing ActivePerl Modules on Windows

ppm install statistics-distributions
ppm install archive-zip
ppm install file-copy-recursive
+ppm install YAML-XS
ppm install XML-LibXML @@ -124,6 +126,7 @@

Installing Perl modules on Linux/Unix/Mac OS

cpan Statistics::Distributions
cpan Archive::Zip
cpan File::Copy::Recursive
+cpan Yaml::XS
cpan Storable