<!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>Summary method for class "saem.mmkin" — summary.saem.mmkin • 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 rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script 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="Summary method for class " saem.mmkin summary.saem.mmkin><meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters for fixed effects (population), random effects (deviations from the population mean) and residual error model, as well as the resulting endpoints such as formation fractions and DT50 values. Optionally (default is FALSE), the data are listed in full."><meta name="robots" content="noindex"><!-- 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development 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/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>Summary method for class "saem.mmkin"</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.saem.mmkin.R" class="external-link"><code>R/summary.saem.mmkin.R</code></a></small> <div class="hidden name"><code>summary.saem.mmkin.Rd</code></div> </div> <div class="ref-description"> <p>Lists model equations, initial parameter values, optimised parameters for fixed effects (population), random effects (deviations from the population mean) and residual error model, as well as the resulting endpoints such as formation fractions and DT50 values. Optionally (default is FALSE), the data are listed in full.</p> </div> <div id="ref-usage"> <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for saem.mmkin</span> <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">object</span>, data <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span> <span class="co"># S3 method for summary.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>, verbose <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">verbose</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 object of class <a href="saem.html">saem.mmkin</a></p></dd> <dt>data</dt> <dd><p>logical, indicating whether the full data should be included in the summary.</p></dd> <dt>verbose</dt> <dd><p>Should the summary be verbose?</p></dd> <dt>distimes</dt> <dd><p>logical, indicating whether DT50 and DT90 values should be included.</p></dd> <dt>...</dt> <dd><p>optional arguments passed to methods like <code>print</code>.</p></dd> <dt>x</dt> <dd><p>an object of class summary.saem.mmkin</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>The summary function returns a list based on the <a href="https://rdrr.io/pkg/saemix/man/SaemixObject-class.html" class="external-link">saemix::SaemixObject</a>obtained in the fit, with at least the following additional components</p> <dl><dt>saemixversion, mkinversion, Rversion</dt> <dd><p>The saemix, mkin and R versions used</p></dd> <dt>date.fit, date.summary</dt> <dd><p>The dates where the fit and the summary were produced</p></dd> <dt>diffs</dt> <dd><p>The differential equations used in the degradation model</p></dd> <dt>use_of_ff</dt> <dd><p>Was maximum or minimum use made of formation fractions</p></dd> <dt>data</dt> <dd><p>The data</p></dd> <dt>confint_trans</dt> <dd><p>Transformed parameters as used in the optimisation, with confidence intervals</p></dd> <dt>confint_back</dt> <dd><p>Backtransformed parameters, with confidence intervals if available</p></dd> <dt>confint_errmod</dt> <dd><p>Error model parameters with confidence intervals</p></dd> <dt>ff</dt> <dd><p>The estimated formation fractions derived from the fitted model.</p></dd> <dt>distimes</dt> <dd><p>The DT50 and DT90 values for each observed variable.</p></dd> <dt>SFORB</dt> <dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd> </dl><p>The print method is called for its side effect, i.e. printing the summary.</p> </div> <div id="author"> <h2>Author</h2> <p>Johannes Ranke for the mkin specific parts saemix authors for the parts inherited from saemix.</p> </div> <div id="ref-examples"> <h2>Examples</h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># Generate five datasets following DFOP-SFO kinetics</span></span> <span class="r-in"><span class="va">sampling_times</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="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></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">"m1"</span><span class="op">)</span>,</span> <span class="r-in"> m1 <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>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">1234</span><span class="op">)</span></span> <span class="r-in"><span class="va">k1_in</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.1</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span></span> <span class="r-in"><span class="va">k2_in</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.02</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span></span> <span class="r-in"><span class="va">g_in</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">qlogis</a></span><span class="op">(</span><span class="fl">0.5</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span><span class="op">)</span></span> <span class="r-in"><span class="va">f_parent_to_m1_in</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">qlogis</a></span><span class="op">(</span><span class="fl">0.3</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span><span class="op">)</span></span> <span class="r-in"><span class="va">k_m1_in</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.02</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span></span> <span class="r-in"></span> <span class="r-in"><span class="va">pred_dfop_sfo</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">k1</span>, <span class="va">k2</span>, <span class="va">g</span>, <span class="va">f_parent_to_m1</span>, <span class="va">k_m1</span><span class="op">)</span> <span class="op">{</span></span> <span class="r-in"> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">dfop_sfo</span>,</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="va">k1</span>, k2 <span class="op">=</span> <span class="va">k2</span>, g <span class="op">=</span> <span class="va">g</span>, f_parent_to_m1 <span class="op">=</span> <span class="va">f_parent_to_m1</span>, k_m1 <span class="op">=</span> <span class="va">k_m1</span><span class="op">)</span>,</span> <span class="r-in"> <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>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> <span class="r-in"> <span class="va">sampling_times</span><span class="op">)</span></span> <span class="r-in"><span class="op">}</span></span> <span class="r-in"></span> <span class="r-in"><span class="va">ds_mean_dfop_sfo</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">5</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 class="r-in"> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">dfop_sfo</span>,</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="va">k1_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span>, k2 <span class="op">=</span> <span class="va">k2_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span>, g <span class="op">=</span> <span class="va">g_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span>,</span> <span class="r-in"> f_parent_to_m1 <span class="op">=</span> <span class="va">f_parent_to_m1_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span>, k_m1 <span class="op">=</span> <span class="va">k_m1_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span><span class="op">)</span>,</span> <span class="r-in"> <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>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> <span class="r-in"> <span class="va">sampling_times</span><span class="op">)</span></span> <span class="r-in"><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_mean_dfop_sfo</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">"ds"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span></span> <span class="r-in"></span> <span class="r-in"><span class="va">ds_syn_dfop_sfo</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">ds_mean_dfop_sfo</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">{</span></span> <span class="r-in"> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">ds</span>,</span> <span class="r-in"> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="fl">1</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="fl">0.07</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span>,</span> <span class="r-in"> n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span> <span class="r-in"><span class="op">}</span><span class="op">)</span></span> <span class="r-in"></span> <span class="r-in"><span class="co"># \dontrun{</span></span> <span class="r-in"><span class="co"># Evaluate using mmkin and saem</span></span> <span class="r-in"><span class="va">f_mmkin_dfop_sfo</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 class="va">dfop_sfo</span><span class="op">)</span>, <span class="va">ds_syn_dfop_sfo</span>,</span> <span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">5</span><span class="op">)</span></span> <span class="r-in"><span class="va">f_saem_dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin_dfop_sfo</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/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 class="co"># }</span></span> <span class="r-in"></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>