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It is inspired by the article on practical identifiabiliy in the frame of nonlinear -mixed-effects models by Duchesne et al (2021)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> - - - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Reference</a> -</li> -<li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> - Articles - - <span class="caret"></span> - </a> - <ul class="dropdown-menu" role="menu"><li> - <a href="../articles/mkin.html">Introduction to mkin</a> - </li> - <li class="divider"> - <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> - <li> - <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> - </li> - <li> - <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> - </li> - <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - </li> - <li class="divider"> - <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> - <li> - <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <a href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> - </li> - <li> - <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> - </li> - <li> - <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> - </li> - <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> - </li> - <li class="divider"> - <li class="dropdown-header">Performance</li> - <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - </li> - <li> - <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> - </li> - <li> - <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> - </li> - <li class="divider"> - <li class="dropdown-header">Miscellaneous</li> - <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> - </li> - <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> - </li> +mixed-effects models by Duchesne et al (2021)."><meta property="og:description" content="The purpose of this method is to check if a certain algorithm for fitting +nonlinear hierarchical models (also known as nonlinear mixed-effects models) +will reliably yield results that are sufficiently similar to each other, if +started with a certain range of reasonable starting parameters. It is +inspired by the article on practical identifiabiliy in the frame of nonlinear +mixed-effects models by Duchesne et al (2021)."></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> + + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">mkin</a> + + <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item dropdown"> + <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button> + <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/mkin.html">Introduction to mkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6></li> + <li><a class="dropdown-item" href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li> + <li><a class="dropdown-item" href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li> + <li><a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> + <li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> + <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li> + <li><a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li> + <li><a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a></li> </ul></li> -<li> - 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<div class="ref-description"> + <div class="ref-description section level2"> <p>The purpose of this method is to check if a certain algorithm for fitting nonlinear hierarchical models (also known as nonlinear mixed-effects models) will reliably yield results that are sufficiently similar to each other, if @@ -122,7 +79,8 @@ inspired by the article on practical identifiabiliy in the frame of nonlinear mixed-effects models by Duchesne et al (2021).</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">multistart</span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> <span> n <span class="op">=</span> <span class="fl">50</span>,</span> @@ -131,78 +89,74 @@ mixed-effects models by Duchesne et al (2021).</p> <span> <span class="va">...</span></span> <span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for saem.mmkin</span></span> +<span><span class="co"># S3 method for class 'saem.mmkin'</span></span> <span><span class="fu">multistart</span><span class="op">(</span><span class="va">object</span>, n <span class="op">=</span> <span class="fl">50</span>, cores <span class="op">=</span> <span class="fl">1</span>, cluster <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for multistart</span></span> +<span><span class="co"># S3 method for class 'multistart'</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="fu">best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for default</span></span> +<span><span class="co"># Default S3 method</span></span> <span><span class="fu">best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="fu">which.best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for default</span></span> +<span><span class="co"># Default S3 method</span></span> <span><span class="fu">which.best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> - <dl><dt>object</dt> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + + +<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt> <dd><p>The fit object to work with</p></dd> -<dt>n</dt> +<dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a></dt> <dd><p>How many different combinations of starting parameters should be used?</p></dd> -<dt>cores</dt> +<dt id="arg-cores">cores<a class="anchor" aria-label="anchor" href="#arg-cores"></a></dt> <dd><p>How many fits should be run in parallel (only on posix platforms)?</p></dd> -<dt>cluster</dt> +<dt id="arg-cluster">cluster<a class="anchor" aria-label="anchor" href="#arg-cluster"></a></dt> <dd><p>A cluster as returned by <a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">parallel::makeCluster</a> to be used for parallel execution.</p></dd> -<dt>...</dt> +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Passed to the update function.</p></dd> -<dt>x</dt> +<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dd><p>The multistart object to print</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> - - -<p>A list of <a href="saem.html">saem.mmkin</a> objects, with class attributes + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> + <p>A list of <a href="saem.html">saem.mmkin</a> objects, with class attributes 'multistart.saem.mmkin' and 'multistart'.</p> - - <p>The object with the highest likelihood</p> - - <p>The index of the object with the highest likelihood</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical identifiability in the frame of nonlinear mixed effects models: the example of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. doi: 10.1186/s12859-021-04373-4.</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><a href="parplot.html">parplot</a>, <a href="llhist.html">llhist</a></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">dmta_ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span></span> @@ -218,7 +172,7 @@ doi: 10.1186/s12859-021-04373-4.</p> <span class="r-in"><span><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">7</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f_saem_full</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f_saem_full_multi</span> <span class="op"><-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_full</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span>, las <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="multistart-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_full</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] "sd(log_k2)"</span> @@ -230,33 +184,29 @@ doi: 10.1186/s12859-021-04373-4.</p> <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">parallel</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">cl</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f_saem_reduced_multi</span> <span class="op"><-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cluster <span class="op">=</span> <span class="va">cl</span><span class="op">)</span></span></span> -<span class="r-in"><span><span class="fu"><a href="parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">2</span><span class="op">)</span>, las <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="multistart-2.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> - <p></p><p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> - </footer></div> + </footer></div> + - - </body></html> |