From 0324b97893e8e738d5d7f280337e5cc69ef7647f Mon Sep 17 00:00:00 2001 From: Rikard Nordgren Date: Mon, 24 Jun 2024 21:18:43 +0200 Subject: [PATCH] Update webpage for release --- docs/docs.html | 92 +++++++++++++++++++++++----------------------- docs/download.html | 26 ++++++++++--- docs/index.html | 15 +++++++- docs/install.html | 6 +-- 4 files changed, 83 insertions(+), 56 deletions(-) diff --git a/docs/docs.html b/docs/docs.html index 1546ec60..4569d67d 100644 --- a/docs/docs.html +++ b/docs/docs.html @@ -31,12 +31,12 @@

Documentation

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.
@@ -44,95 +44,95 @@

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.
-
crossval
+
crossval
Cross validation.
-
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.
-
proseval
+
proseval
Prosepective evaluation of models.
-
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.
-
qa
+
qa
Quality assurance.
-
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
@@ -145,41 +145,41 @@

PsN Tools

Standard template
-
simeval
+
simeval
Simulation-Evaluation diagnostics of outliers. Was ebe pde.
-
scmplus
+
scmplus
An enhanced version of scm.
-
monitor
+
monitor
Monitor scm or scmplus runs.
-
scmreport
+
scmreport
Create a report after an scm or scmplus run.
-
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.
@@ -213,7 +213,7 @@

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

@@ -230,7 +230,7 @@

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

@@ -251,7 +251,7 @@

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 850c0259..1af06f20 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 5.3.1 for details.

+
Please see the release notes PsN 5.4.0 for details.

@@ -134,6 +134,22 @@

Download

+ + + + + + + + + + +
Latest release PsN 5.3.1Latest release PsN 5.4.0
(Released on April 26th 2023)

+

(Released on June 24th 2024)


PsN is distributed as a zipped file or as a gzipped tarball for Linux and macOS and as a special zipped bundle for Windows.

- PsN-5.3.1-windows-64bit.zip
- PsN 5.3.1.tar.gz

+ PsN-5.4.0-windows-64bit.zip
+ PsN 5.4.0.tar.gz
Older releases
+ PsN 5.3.1 + Please see the release notes 5.3.1 for details. 2023-04-26
+ PsN-5.3.1-windows-64bit.zip
+ PsN 5.3.1.tar.gz

+

PsN 5.3.0 diff --git a/docs/index.html b/docs/index.html index 5ea49af3..808ec157 100644 --- a/docs/index.html +++ b/docs/index.html @@ -34,11 +34,22 @@

Perl-speaks-NONMEM

Use the top menu for information on how to Download and Install PsN. You can read about the different parts of PsN 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.


-The latest release of PsN is version 5.3.1. Instructions on how to download it and a detailed list of changes can be found in the download section. A brief list of what is new can be found below in the news section. +The latest release of PsN is version 5.4.0. Instructions on how to download it and a detailed list of changes can be found in the download section. A brief list of what is new can be found below in the news section.

News

+

PsN 5.4.0 released (2023-06-24)

+ +Changes in this version include: +
    +
  • Various fixes to FREM
    • +
  • Reference correction for VPC
    • +
  • Use Math::Random::Free instead of Math::Random because of licensing issues
    • +
  • New environment variable PSNCONFPATH
    • +
+ +

PsN 5.3.1 released (2023-04-26)

Changes in this version include: @@ -119,7 +130,7 @@

PsN 4.8.0 released (2018-05-25)

Perl-speaks-NONMEM
-©2022-2023 by Mats Karlsson and Rikard Nordgren. All rights reserved.
+©2022-2024 by Mats Karlsson and Rikard Nordgren. All rights reserved.
©2020-2021 by Mats Karlsson, Rikard Nordgren and Sebastian Ueckert. All rights reserved.
©2018-2019 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.
diff --git a/docs/install.html b/docs/install.html index 910579bc..bfbd4de3 100644 --- a/docs/install.html +++ b/docs/install.html @@ -51,8 +51,8 @@

Windows

  1. Unpack the file you downloaded from the PsN Download Page. The unpacked directory can be put at any location on your computer.
    2. -
  2. Update your PATH environment variable to include the path to PsN-5.3.1\strawberry\perl\bin
    3. -
  3. Add your NONMEM version by editing the PsN configuration file at PsN-5.3.1\strawberry\perl\site\lib\PsN_5_3_1\psn.conf. Under [nm_versions] add for example default=C:\nm751,7.5.1 if your NONMEM version is 7.5.1 and can be found under C:\nm751
    4. +
  4. Update your PATH environment variable to include the path to PsN-5.4.0\strawberry\perl\bin
    5. +
  5. Add your NONMEM version by editing the PsN configuration file at PsN-5.4.0\strawberry\perl\site\lib\PsN_5_4_0\psn.conf. Under [nm_versions] add for example default=C:\nm751,7.5.1 if your NONMEM version is 7.5.1 and can be found under C:\nm751
@@ -282,7 +282,7 @@

On Linux and macOS

To check which PsN version is the default use the command
psn -version
A specific version may be called with its version number, for example
-execute-5.3.1 -help
+execute-5.4.0 -help