<!DOCTYPE html> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Fit nonlinear mixed models with SAEM — saem • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link 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src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Fit nonlinear mixed models with SAEM — saem"><meta property="og:description" content="This function uses saemix::saemix() as a backend for fitting nonlinear mixed effects models created from mmkin row objects using the Stochastic Approximation Expectation Maximisation algorithm (SAEM)."><!-- 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">1.1.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" 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> <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/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </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/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> <li> <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> </li> </ul></li> <li> <a href="../news/index.html">News</a> </li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Fit nonlinear mixed models with SAEM</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/saem.R" class="external-link"><code>R/saem.R</code></a></small> <div class="hidden name"><code>saem.Rd</code></div> </div> <div class="ref-description"> <p>This function uses <code><a href="https://rdrr.io/pkg/saemix/man/saemix.html" class="external-link">saemix::saemix()</a></code> as a backend for fitting nonlinear mixed effects models created from <a href="mmkin.html">mmkin</a> row objects using the Stochastic Approximation Expectation Maximisation algorithm (SAEM).</p> </div> <div id="ref-usage"> <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">saem</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span> <span class="co"># S3 method for mmkin</span> <span class="fu">saem</span><span class="op">(</span> <span class="va">object</span>, transformations <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="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>, degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>, conf.level <span class="op">=</span> <span class="fl">0.6</span>, solution_type <span class="op">=</span> <span class="st">"auto"</span>, nbiter.saemix <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">300</span>, <span class="fl">100</span><span class="op">)</span>, control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>displayProgress <span class="op">=</span> <span class="cn">FALSE</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, nbiter.saemix <span class="op">=</span> <span class="va">nbiter.saemix</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, fail_with_errors <span class="op">=</span> <span class="cn">TRUE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span> <span class="op">)</span> <span class="co"># S3 method for saem.mmkin</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>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span> <span class="fu">saemix_model</span><span class="op">(</span> <span class="va">object</span>, solution_type <span class="op">=</span> <span class="st">"auto"</span>, transformations <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="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>, degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>, conf.level <span class="op">=</span> <span class="fl">0.6</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span> <span class="op">)</span> <span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An <a href="mmkin.html">mmkin</a> row object containing several fits of the same <a href="mkinmod.html">mkinmod</a> model to different datasets</p></dd> <dt>...</dt> <dd><p>Further parameters passed to <a href="https://rdrr.io/pkg/saemix/man/saemixModel.html" class="external-link">saemix::saemixModel</a>.</p></dd> <dt>transformations</dt> <dd><p>Per default, all parameter transformations are done in mkin. If this argument is set to 'saemix', parameter transformations are done in 'saemix' for the supported cases. Currently this is only supported in cases where the initial concentration of the parent is not fixed, SFO or DFOP is used for the parent and there is either no metabolite or one.</p></dd> <dt>degparms_start</dt> <dd><p>Parameter values given as a named numeric vector will be used to override the starting values obtained from the 'mmkin' object.</p></dd> <dt>test_log_parms</dt> <dd><p>If TRUE, an attempt is made to use more robust starting values for population parameters fitted as log parameters in mkin (like rate constants) by only considering rate constants that pass the t-test when calculating mean degradation parameters using <a href="mean_degparms.html">mean_degparms</a>.</p></dd> <dt>conf.level</dt> <dd><p>Possibility to adjust the required confidence level for parameter that are tested if requested by 'test_log_parms'.</p></dd> <dt>solution_type</dt> <dd><p>Possibility to specify the solution type in case the automatic choice is not desired</p></dd> <dt>nbiter.saemix</dt> <dd><p>Convenience option to increase the number of iterations</p></dd> <dt>control</dt> <dd><p>Passed to <a href="https://rdrr.io/pkg/saemix/man/saemix.html" class="external-link">saemix::saemix</a>.</p></dd> <dt>fail_with_errors</dt> <dd><p>Should a failure to compute standard errors from the inverse of the Fisher Information Matrix be a failure?</p></dd> <dt>verbose</dt> <dd><p>Should we print information about created objects of type <a href="https://rdrr.io/pkg/saemix/man/SaemixModel-class.html" class="external-link">saemix::SaemixModel</a> and <a href="https://rdrr.io/pkg/saemix/man/SaemixData-class.html" class="external-link">saemix::SaemixData</a>?</p></dd> <dt>quiet</dt> <dd><p>Should we suppress the messages saemix prints at the beginning and the end of the optimisation process?</p></dd> <dt>x</dt> <dd><p>An saem.mmkin object to print</p></dd> <dt>digits</dt> <dd><p>Number of digits to use for printing</p></dd> </dl></div> <div id="value"> <h2>Value</h2> <p>An S3 object of class 'saem.mmkin', containing the fitted <a href="https://rdrr.io/pkg/saemix/man/SaemixObject-class.html" class="external-link">saemix::SaemixObject</a> as a list component named 'so'. The object also inherits from 'mixed.mmkin'. An <a href="https://rdrr.io/pkg/saemix/man/SaemixModel-class.html" class="external-link">saemix::SaemixModel</a> object. An <a href="https://rdrr.io/pkg/saemix/man/SaemixData-class.html" class="external-link">saemix::SaemixData</a> object.</p> </div> <div id="details"> <h2>Details</h2> <p>An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of datasets using <a href="mkinfit.html">mkinfit</a>.</p> <p>Starting values for the fixed effects (population mean parameters, argument psi0 of <code><a href="https://rdrr.io/pkg/saemix/man/saemixModel.html" class="external-link">saemix::saemixModel()</a></code> are the mean values of the parameters found using <a href="mmkin.html">mmkin</a>.</p> </div> <div id="see-also"> <h2>See also</h2> <div class="dont-index"><p><a href="summary.saem.mmkin.html">summary.saem.mmkin</a> <a href="plot.mixed.mmkin.html">plot.mixed.mmkin</a></p></div> </div> <div id="ref-examples"> <h2>Examples</h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># \dontrun{</span></span> <span class="r-in"><span class="va">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="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span> <span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><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="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span><span class="op">)</span></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span> <span class="r-in"><span class="va">f_mmkin_parent_p0_fixed</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">ds</span>,</span> <span class="r-in"> state.ini <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>parent <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, fixed_initials <span class="op">=</span> <span class="st">"parent"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-in"><span class="va">f_saem_p0_fixed</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent_p0_fixed</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"></span> <span class="r-in"><span class="va">f_mmkin_parent</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><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="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-in"><span class="va">f_saem_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"><span class="va">f_saem_fomc</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"><span class="va">f_saem_dfop</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"></span> <span class="r-in"><span class="co"># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span></span> <span class="r-in"><span class="co"># functions from saemix</span></span> <span class="r-in"><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">saemix</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: npde</span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-msg co"><span class="r-pr">#></span> Attaching package: ‘npde’</span> <span class="r-msg co"><span class="r-pr">#></span> The following object is masked from ‘package:nlmixr’:</span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-msg co"><span class="r-pr">#></span> warfarin</span> <span class="r-msg co"><span class="r-pr">#></span> Package saemix, version 3.0</span> <span class="r-msg co"><span class="r-pr">#></span> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-msg co"><span class="r-pr">#></span> Attaching package: ‘saemix’</span> <span class="r-msg co"><span class="r-pr">#></span> The following objects are masked from ‘package:npde’:</span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-msg co"><span class="r-pr">#></span> kurtosis, skewness</span> <span class="r-msg co"><span class="r-pr">#></span> The following object is masked from ‘package:RxODE’:</span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-msg co"><span class="r-pr">#></span> phi</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_saem_sfo</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_dfop</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in compare.saemix(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so):</span> object 'f_saem_sfo' not found</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"individual.fit"</span><span class="op">)</span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"npde"</span><span class="op">)</span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"vpc"</span><span class="op">)</span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span> <span class="r-in"></span> <span class="r-in"><span class="va">f_mmkin_parent_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_mmkin_parent</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> <span class="r-in"><span class="va">f_saem_fomc_tc</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent_tc</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_fomc_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in compare.saemix(f_saem_fomc$so, f_saem_fomc_tc$so):</span> object 'f_saem_fomc' not found</span> <span class="r-in"></span> <span class="r-in"><span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span> <span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span class="va">fomc_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span> <span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span class="va">dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span> <span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span class="co"># The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,</span></span> <span class="r-in"><span class="co"># and compiled ODEs for FOMC that are much slower</span></span> <span class="r-in"><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="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span> <span class="r-in"> <span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">sfo_sfo</span>, <span class="st">"FOMC-SFO"</span> <span class="op">=</span> <span class="va">fomc_sfo</span>, <span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo</span><span class="op">)</span>,</span> <span class="r-in"> <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-in"><span class="co"># saem fits of SFO-SFO and DFOP-SFO to these data take about five seconds</span></span> <span class="r-in"><span class="co"># each on this system, as we use analytical solutions written for saemix.</span></span> <span class="r-in"><span class="co"># When using the analytical solutions written for mkin this took around</span></span> <span class="r-in"><span class="co"># four minutes</span></span> <span class="r-in"><span class="va">f_saem_sfo_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"><span class="va">f_saem_dfop_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> <span class="r-in"><span class="co"># We can use print, plot and summary methods to check the results</span></span> <span class="r-in"><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">f_saem_dfop_sfo</span><span class="op">)</span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'print': object 'f_saem_dfop_sfo' not found</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_dfop_sfo' not found</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'object' in selecting a method for function 'summary': object 'f_saem_dfop_sfo' not found</span> <span class="r-in"></span> <span class="r-in"><span class="co"># The following takes about 6 minutes</span></span> <span class="r-in"><span class="co">#f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</span></span> <span class="r-in"><span class="co"># control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span></span> <span class="r-in"></span> <span class="r-in"><span class="co">#saemix::compare.saemix(list(</span></span> <span class="r-in"><span class="co"># f_saem_dfop_sfo$so,</span></span> <span class="r-in"><span class="co"># f_saem_dfop_sfo_deSolve$so))</span></span> <span class="r-in"></span> <span class="r-in"><span class="co"># If the model supports it, we can also use eigenvalue based solutions, which</span></span> <span class="r-in"><span class="co"># take a similar amount of time</span></span> <span class="r-in"><span class="co">#f_saem_sfo_sfo_eigen <- saem(f_mmkin["SFO-SFO", ], solution_type = "eigen",</span></span> <span class="r-in"><span class="co"># control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span></span> <span class="r-in"><span class="co"># }</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> <footer><div class="copyright"> <p></p><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> 2.0.2.</p> </div> </footer></div> </body></html>