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Expand Up @@ -31,108 +31,108 @@ <h2>Documentation</h2>
<h3>Before running PsN</h3>
<dl>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/psn_configuration.pdf">PsN Configuration.pdf</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/known_bugs_and_workarounds.pdf">Known Bugs and Workarounds.pdf</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/psn_configuration.pdf">PsN Configuration.pdf</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/known_bugs_and_workarounds.pdf">Known Bugs and Workarounds.pdf</a></dt>

<h3>PsN common options</h3>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/common_options.pdf">PsN common options.pdf</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/common_options.pdf">PsN common options.pdf</a></dt>

<dd>List of common options for PsN tools.</dd>
</dl>
<h3>PsN Tools</h3>
<dl>


<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/benchmark_userguide.pdf">benchmark</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/benchmark_userguide.pdf">benchmark</a></dt>
<dd>Benchmarking of NONMEM settings.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/boot_scm_userguide.pdf">boot scm</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/boot_scm_userguide.pdf">boot scm</a></dt>
<dd>Bootstrapped Stepwise Covariate Model-building.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/bootstrap_userguide.pdf">bootstrap</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/bootstrap_userguide.pdf">bootstrap</a></dt>
<dd>Bootstrap using the percentile or BCa method.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/cdd_userguide.pdf">cdd</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/cdd_userguide.pdf">cdd</a></dt>
<dd>Case Deletion Diagnostics.</dd>

<dt>covmat</dt>
<dd>Create an empirical covariance matrix based on a rawresults file.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/crossval_userguide.pdf">crossval</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/crossval_userguide.pdf">crossval</a></dt>
<dd>Cross validation.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/execute_userguide.pdf">execute</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/execute_userguide.pdf">execute</a></dt>
<dd>NONMEM runs are started using one or multiple model files.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/extended_grid_userguide.pdf">extended grid</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/extended_grid_userguide.pdf">extended grid</a></dt>
<dd>non-parametric estimation on the extended grid.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/frem_userguide.pdf">frem</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/frem_userguide.pdf">frem</a></dt>
<dd>Full random effects model.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/gls_userguide.pdf">gls</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/gls_userguide.pdf">gls</a></dt>
<dd>Generalized Least Squares approximations of the residual error model.</dd>

<dt> <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/lasso_userguide.pdf">lasso</a> </dt>
<dt> <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/lasso_userguide.pdf">lasso</a> </dt>
<dd>Covariate model building using the lasso method.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/linearize_userguide.pdf">linearize</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/linearize_userguide.pdf">linearize</a></dt>
<dd>Linearize a model.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/llp_userguide.pdf">llp</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/llp_userguide.pdf">llp</a></dt>
<dd>Log-Likelihood Profiling around maximum-likelihood parameter estimates.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/mcmp_userguide.pdf">mcmp</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/mcmp_userguide.pdf">mcmp</a></dt>
<dd>Monte-Carlo Mapped Power.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/mimp_userguide.pdf">mimp</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/mimp_userguide.pdf">mimp</a></dt>
<dd>Multiple imputation.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/nca_userguide.pdf">nca</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/nca_userguide.pdf">nca</a></dt>
<dd>Non-compartmental analysis.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/nmoutput2so_userguide.pdf">nmoutput2so</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/nmoutput2so_userguide.pdf">nmoutput2so</a></dt>
<dd>Convert output from NONMEM to the DDMoRe standardised output format (so).</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/nonpb_userguide.pdf">nonpb</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/nonpb_userguide.pdf">nonpb</a></dt>
<dd>Non-Parametric Bootstrap.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/proseval_userguide.pdf">proseval</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/proseval_userguide.pdf">proseval</a></dt>
<dd>Prosepective evaluation of models.</dd>

<dt> <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/vpc_npc_userguide.pdf">npc</a></dt>
<dt> <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/vpc_npc_userguide.pdf">npc</a></dt>
<dd>Numerical Predictive Check.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/parallel_retries_userguide.pdf">parallel retries</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/parallel_retries_userguide.pdf">parallel retries</a></dt>
<dd>Run multiple copies of a single model with tweaked initial estimates in parallel.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/nonpb_userguide.pdf">pind</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/nonpb_userguide.pdf">pind</a></dt>
<dd>Individual Probabilities.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/precond_userguide.pdf">precond</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/precond_userguide.pdf">precond</a></dt>
<dd>Estimate a model using preconditioning.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/pvar_userguide.pdf">pvar</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/pvar_userguide.pdf">pvar</a></dt>
<dd>Parametric variability.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/qa_userguide.pdf">qa</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/qa_userguide.pdf">qa</a></dt>
<dd>Quality assurance.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/randtest_userguide.pdf">randtest</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/randtest_userguide.pdf">randtest</a></dt>
<dd>Randomization testing.</dd>

<dt>rawresults</dt>
<dd>Create a rawresults file from a set of list files.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/resmod_userguide.pdf">resmod</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/resmod_userguide.pdf">resmod</a></dt>
<dd>Residual modelling.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/runrecord_userguide.pdf">runrecord</a>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/runrecord_userguide.pdf">runrecord</a>
<a href="https://raw.githubusercontent.com/UUPharmacometrics/PsN/master/doc/runrecord_template.xls">runrecord template</a></dt>
<dd>Runrecord.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/scm_userguide.pdf">scm</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/scm_userguide.pdf">scm</a></dt>
<dd>Stepwise Covariate Model-building.<br>
Some extensively commented example/template configuration files for scm:<br>
<a href="https://raw.githubusercontent.com/UUPharmacometrics/PsN/master/doc/config_all_default_parameterizations_explicitly.scm" target="_blank">All default parameterizations explicitly using code section</a><br>
Expand All @@ -145,41 +145,41 @@ <h3>PsN Tools</h3>
<a href="https://raw.githubusercontent.com/UUPharmacometrics/PsN/master/doc/config_template_standard.scm" target="_blank">Standard template</a><br>
</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/simeval_userguide.pdf">simeval</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/simeval_userguide.pdf">simeval</a></dt>
<dd>Simulation-Evaluation diagnostics of outliers. Was ebe pde.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/scmplus_userguide.pdf">scmplus</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/scmplus_userguide.pdf">scmplus</a></dt>
<dd>An enhanced version of scm.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/monitor_userguide.pdf">monitor</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/monitor_userguide.pdf">monitor</a></dt>
<dd>Monitor scm or scmplus runs.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/scmreport_userguide.pdf">scmreport</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/scmreport_userguide.pdf">scmreport</a></dt>
<dd>Create a report after an scm or scmplus run.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/sir_userguide.pdf">sir</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/sir_userguide.pdf">sir</a></dt>
<dd>Parameter uncertainty from Sampling Importance Resampling.</dd>

<dt> <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/sse_userguide.pdf">sse</a> </dt>
<dt> <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/sse_userguide.pdf">sse</a> </dt>
<dd>Stochastic Simulation and Estimation.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/sumo_userguide.pdf">sumo</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/sumo_userguide.pdf">sumo</a></dt>
<dd>Summary of Output from NONMEM.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/transform_userguide.pdf">transform</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/transform_userguide.pdf">transform</a></dt>
<dd>Transform model files, i.e. boxcox, remove_iov.</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/update_inits_userguide.pdf">update inits</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/update_inits_userguide.pdf">update inits</a></dt>
<dd> Update a model file with parameter estimates from NONMEM output.</dd>

<dt> <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/vpc_npc_userguide.pdf">vpc</a></dt>
<dt> <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/vpc_npc_userguide.pdf">vpc</a></dt>
<dd>Visual Predictive Check.<br>
Two-page poster on <a href="http://www.page-meeting.org/pdf_assets/7002-Poster_PAGE_VPC_090618_final.pdf" target="_blank">Visual Predictive Checks for censored and
categorical data.pdf</a><br>
Separate description of <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/vpc_binning.pdf">>automatic binning in vpc.pdf.</a>
Separate description of <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/vpc_binning.pdf">>automatic binning in vpc.pdf.</a>
</dd>

<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/xv_scm_userguide.pdf">xv scm</a></dt>
<dt><a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/xv_scm_userguide.pdf">xv scm</a></dt>
<dd>Cross-validated Stepwise Covariate Model-building.</dd>
</dl>

Expand Down Expand Up @@ -213,7 +213,7 @@ <h3>Input options to PsN tool</h3>
All PsN tools accept a set of options which allow you to modify the behaviour of the tool. Some options are <b>required</b> for the tool, other options are <b>specific</b> for a certain tool and cannot be used
together with other tools and finally there are a lot of <b>common</b> options.
<h4>Specific options: </h4>
For example, the <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/bootstrap_userguide.pdf">bootstrap</a> tool creates 200 new data sets from the original data
For example, the <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/bootstrap_userguide.pdf">bootstrap</a> 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 <span class="style2">-sample</span> option in the bootstrap
tool.</p>
<p><code>$ bootstrap -samples=50 file.mod</code></p>
Expand All @@ -230,7 +230,7 @@ <h4>Common options: </h4>
<p> 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:</p>
<p><code>$ psn_options -h</code></p>
<p>The <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/common_options.pdf">Common options user guide.pdf</a> describes these options in much more
<p>The <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/common_options.pdf">Common options user guide.pdf</a> describes these options in much more
detail. </p>

<h3>PsN Directory structure</h3>
Expand All @@ -251,7 +251,7 @@ <h3>Restarting a PsN tool</h3>
run.</p>
<hr COLOR="darkred">
<h3>Documentation for developers and testers</h3>
The <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/developers_guide.pdf">Developers guide.pdf</a> contains information for developers and for
The <a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/developers_guide.pdf">Developers guide.pdf</a> contains information for developers and for
those in need of informationabout how to run the PsN test suite.


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Expand Up @@ -101,23 +101,23 @@ <h2>Download</h2>
<table class="downloads">
<tbody>
<tr>
<th colspan="3" style="text-align:left;">Latest release PsN 5.3.1</th>
<th colspan="3" style="text-align:left;">Latest release PsN 5.4.0</th>
</tr>
<td style="text-align:left;"> <small><i>(Released on April 26<sup>th</sup> 2023)</i></small><p>
<td style="text-align:left;"> <small><i>(Released on June 24<sup>th</sup> 2024)</i></small><p>
<tr>
<td style="text-align:left;">
<p><br>PsN is distributed as a zipped file or as a gzipped tarball for Linux and macOS and as a special zipped bundle for Windows.
<p>
<a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/PsN-5.3.1-windows-64bit.zip">PsN-5.3.1-windows-64bit.zip</a><br>
<a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/PsN-5.3.1.tar.gz">PsN 5.3.1.tar.gz</a><p>
<a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/PsN-5.4.0-windows-64bit.zip">PsN-5.4.0-windows-64bit.zip</a><br>
<a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.4.0/PsN-5.4.0.tar.gz">PsN 5.4.0.tar.gz</a><p>
</td>
</tr>
</tbody>
</table>
<tr>


<br>Please see the <a href="https://raw.githubusercontent.com/UUPharmacometrics/PsN/master/development/release_notes/release_notes_PsN_5_3_1.txt">release notes PsN 5.3.1</a> for details. </td><p>
<br>Please see the <a href="https://raw.githubusercontent.com/UUPharmacometrics/PsN/master/development/release_notes/release_notes_PsN_5_4_0.txt">release notes PsN 5.4.0</a> for details. </td><p>

</td>
<p>
Expand All @@ -134,6 +134,22 @@ <h2>Download</h2>
<th colspan="3" style="text-align:left;">Older releases</th>
</tr>


<tr>
<td style="text-align:left;">
PsN 5.3.1
</td>
<td rowspan="2" width="70%">Please see the <a href="https://raw.githubusercontent.com/UUPharmacometrics/PsN/master/development/release_notes/release_notes_PsN_5_3_1.txt" target="_blank">release notes 5.3.1</a> for details. </td>
<td rowspan="2">2023-04-26</td>
</tr>

<tr>
<td style="text-align:left;">
<a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/PsN-5.3.1-windows-64bit.zip">PsN-5.3.1-windows-64bit.zip</a><br>
<a href="https://github.com/UUPharmacometrics/PsN/releases/download/v5.3.1/PsN-5.3.1.tar.gz">PsN 5.3.1.tar.gz</a><p>
</td>
</tr>

<tr>
<td style="text-align:left;">
PsN 5.3.0
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