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diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html deleted file mode 100644 index 76d667b9..00000000 --- a/docs/dev/reference/nlme.mmkin.html +++ /dev/null @@ -1,464 +0,0 @@ -<!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>Create an nlme model for an mmkin row object — nlme.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="Create an nlme model for an mmkin row object — nlme.mmkin"><meta property="og:description" content="This functions sets up a nonlinear mixed effects model for an mmkin row -object. 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."><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">1.2.3</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/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> - </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>Create an nlme model for an mmkin row object</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nlme.mmkin.R" class="external-link"><code>R/nlme.mmkin.R</code></a></small> - <div class="hidden name"><code>nlme.mmkin.Rd</code></div> - </div> - - <div class="ref-description"> - <p>This functions sets up a nonlinear mixed effects model for an mmkin row -object. 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.</p> - </div> - - <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> -<span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span></span> -<span> <span class="va">model</span>,</span> -<span> data <span class="op">=</span> <span class="st">"auto"</span>,</span> -<span> fixed <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="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, <span class="kw">function</span><span class="op">(</span><span class="va">el</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/eval.html" class="external-link">eval</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/parse.html" class="external-link">parse</a></span><span class="op">(</span>text <span class="op">=</span></span> -<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="va">el</span>, <span class="fl">1</span>, sep <span class="op">=</span> <span class="st">"~"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>,</span> -<span> random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>,</span> -<span> <span class="va">groups</span>,</span> -<span> start <span class="op">=</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> -<span> correlation <span class="op">=</span> <span class="cn">NULL</span>,</span> -<span> weights <span class="op">=</span> <span class="cn">NULL</span>,</span> -<span> <span class="va">subset</span>,</span> -<span> method <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">"ML"</span>, <span class="st">"REML"</span><span class="op">)</span>,</span> -<span> na.action <span class="op">=</span> <span class="va">na.fail</span>,</span> -<span> <span class="va">naPattern</span>,</span> -<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><span class="op">)</span>,</span> -<span> verbose <span class="op">=</span> <span class="cn">FALSE</span></span> -<span><span class="op">)</span></span> -<span></span> -<span><span class="co"># S3 method for nlme.mmkin</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>, 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> -<span></span> -<span><span class="co"># S3 method for nlme.mmkin</span></span> -<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">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> - </div> - - <div id="arguments"> - <h2>Arguments</h2> - <dl><dt>model</dt> -<dd><p>An <a href="mmkin.html">mmkin</a> row object.</p></dd> - - -<dt>data</dt> -<dd><p>Ignored, data are taken from the mmkin model</p></dd> - - -<dt>fixed</dt> -<dd><p>Ignored, all degradation parameters fitted in the -mmkin model are used as fixed parameters</p></dd> - - -<dt>random</dt> -<dd><p>If not specified, no correlations between random effects are -set up for the optimised degradation model parameters. This is -achieved by using the <a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">nlme::pdDiag</a> method.</p></dd> - - -<dt>groups</dt> -<dd><p>See the documentation of nlme</p></dd> - - -<dt>start</dt> -<dd><p>If not specified, mean values of the fitted degradation -parameters taken from the mmkin object are used</p></dd> - - -<dt>correlation</dt> -<dd><p>See the documentation of nlme</p></dd> - - -<dt>weights</dt> -<dd><p>passed to nlme</p></dd> - - -<dt>subset</dt> -<dd><p>passed to nlme</p></dd> - - -<dt>method</dt> -<dd><p>passed to nlme</p></dd> - - -<dt>na.action</dt> -<dd><p>passed to nlme</p></dd> - - -<dt>naPattern</dt> -<dd><p>passed to nlme</p></dd> - - -<dt>control</dt> -<dd><p>passed to nlme</p></dd> - - -<dt>verbose</dt> -<dd><p>passed to nlme</p></dd> - - -<dt>x</dt> -<dd><p>An nlme.mmkin object to print</p></dd> - - -<dt>digits</dt> -<dd><p>Number of digits to use for printing</p></dd> - - -<dt>...</dt> -<dd><p>Update specifications passed to update.nlme</p></dd> - - -<dt>object</dt> -<dd><p>An nlme.mmkin object to update</p></dd> - -</dl></div> - <div id="value"> - <h2>Value</h2> - - -<p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object -with additional elements. It also inherits from 'mixed.mmkin'.</p> - </div> - <div id="details"> - <h2>Details</h2> - <p>Note that the convergence of the nlme algorithms depends on the quality -of the data. In degradation kinetics, we often only have few datasets -(e.g. data for few soils) and complicated degradation models, which may -make it impossible to obtain convergence with nlme.</p> - </div> - <div id="note"> - <h2>Note</h2> - <p>As the object inherits from <a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme::nlme</a>, there is a wealth of -methods that will automatically work on 'nlme.mmkin' objects, such as -<code><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">nlme::intervals()</a></code>, <code><a href="https://rdrr.io/pkg/nlme/man/anova.lme.html" class="external-link">nlme::anova.lme()</a></code> and <code><a href="https://rdrr.io/pkg/nlme/man/coef.lme.html" class="external-link">nlme::coef.lme()</a></code>.</p> - </div> - <div id="see-also"> - <h2>See also</h2> - <div class="dont-index"><p><code><a href="nlme.html">nlme_function()</a></code>, <a href="plot.mixed.mmkin.html">plot.mixed.mmkin</a>, <a href="summary.nlme.mmkin.html">summary.nlme.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><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> -<span class="r-in"><span> <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="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> -<span class="r-in"><span> <span class="va">f</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">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</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://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span></span> -<span class="r-in"><span> <span class="va">f_nlme_sfo</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> -<span class="r-in"><span> <span class="va">f_nlme_dfop</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span></span> -<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_dfop</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9268 <.0001</span> -<span class="r-in"><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">f_nlme_dfop</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Structural model:</span> -<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> -<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span> -<span class="r-out co"><span class="r-pr">#></span> * parent</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Data:</span> -<span class="r-out co"><span class="r-pr">#></span> 90 observations of 1 variable(s) grouped in 5 datasets</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Log-likelihood: -238.6</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> -<span class="r-out co"><span class="r-pr">#></span> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) </span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> 94.1702 -1.8002 -4.1474 0.0324 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Random effects:</span> -<span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)</span> -<span class="r-out co"><span class="r-pr">#></span> Level: ds</span> -<span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis Residual</span> -<span class="r-out co"><span class="r-pr">#></span> StdDev: 2.488 0.8447 1.33 0.4652 2.321</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="nlme.mmkin-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> $distimes</span> -<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 10.79857 100.7937 30.34192 4.193936 43.85441</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="va">ds_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span> -<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</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></span> -<span class="r-in"><span> <span class="va">m_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> -<span class="r-in"><span> 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>, use_of_ff <span class="op">=</span> <span class="st">"min"</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">m_sfo_sfo_ff</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> -<span class="r-in"><span> 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>, use_of_ff <span class="op">=</span> <span class="st">"max"</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">m_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> -<span class="r-in"><span> 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>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="va">f_2</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="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">m_sfo_sfo</span>,</span></span> -<span class="r-in"><span> <span class="st">"SFO-SFO-ff"</span> <span class="op">=</span> <span class="va">m_sfo_sfo_ff</span>,</span></span> -<span class="r-in"><span> <span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">m_dfop_sfo</span><span class="op">)</span>,</span></span> -<span class="r-in"><span> <span class="va">ds_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="va">f_nlme_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> -<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme_sfo_sfo</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="nlme.mmkin-2.png" alt="" width="700" height="433"></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="co"># With formation fractions this does not coverge with defaults</span></span></span> -<span class="r-in"><span> <span class="co"># f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ])</span></span></span> -<span class="r-in"><span> <span class="co">#plot(f_nlme_sfo_sfo_ff)</span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="co"># For the following, we need to increase pnlsMaxIter and the tolerance</span></span></span> -<span class="r-in"><span> <span class="co"># to get convergence</span></span></span> -<span class="r-in"><span> <span class="va">f_nlme_dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span></span> -<span class="r-in"><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>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="nlme.mmkin-3.png" alt="" width="700" height="433"></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span>, <span class="va">f_nlme_sfo_sfo</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</span> -<span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_sfo_sfo</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> $ff</span> -<span class="r-out co"><span class="r-pr">#></span> parent_sink parent_A1 A1_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 0.5912432 0.4087568 1.0000000 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> $distimes</span> -<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> -<span class="r-out co"><span class="r-pr">#></span> parent 19.13518 63.5657</span> -<span class="r-out co"><span class="r-pr">#></span> A1 66.02155 219.3189</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> $ff</span> -<span class="r-out co"><span class="r-pr">#></span> parent_A1 parent_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 0.2768575 0.7231425 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> $distimes</span> -<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 11.07091 104.6320 31.49737 4.462384 46.20825</span> -<span class="r-out co"><span class="r-pr">#></span> A1 162.30507 539.1658 NA NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">></span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span> <span class="co"># tc error model for nlme available</span></span></span> -<span class="r-in"><span> <span class="co"># Attempts to fit metabolite kinetics with the tc error model are possible,</span></span></span> -<span class="r-in"><span> <span class="co"># but need tweeking of control values and sometimes do not converge</span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="va">f_tc</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">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> -<span class="r-in"><span> <span class="va">f_nlme_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> -<span class="r-in"><span> <span class="va">f_nlme_dfop_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span></span> -<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_sfo_tc</span>, <span class="va">f_nlme_dfop</span>, <span class="va">f_nlme_dfop_tc</span><span class="op">)</span></span></span> -<span class="r-in"><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">f_nlme_dfop_tc</span><span class="op">)</span></span></span> -<span class="r-in"><span> <span class="op">}</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Structural model:</span> -<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> -<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span> -<span class="r-out co"><span class="r-pr">#></span> * parent</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Data:</span> -<span class="r-out co"><span class="r-pr">#></span> 90 observations of 1 variable(s) grouped in 5 datasets</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Log-likelihood: -238.4</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> -<span class="r-out co"><span class="r-pr">#></span> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) </span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> 94.04773 -1.82340 -4.16716 0.05686 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Random effects:</span> -<span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)</span> -<span class="r-out co"><span class="r-pr">#></span> Level: ds</span> -<span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis Residual</span> -<span class="r-out co"><span class="r-pr">#></span> StdDev: 2.474 0.85 1.337 0.4659 1</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Variance function:</span> -<span class="r-out co"><span class="r-pr">#></span> Structure: Constant plus proportion of variance covariate</span> -<span class="r-out co"><span class="r-pr">#></span> Formula: ~fitted(.) </span> -<span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> -<span class="r-out co"><span class="r-pr">#></span> const prop </span> -<span class="r-out co"><span class="r-pr">#></span> 2.23223593 0.01262367 </span> -<span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="va">f_2_obs</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_2</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span></span> -<span class="r-in"><span> <span class="va">f_nlme_sfo_sfo_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> -<span class="r-in"><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">f_nlme_sfo_sfo_obs</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Structural model:</span> -<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent_sink * parent - k_parent_A1 * parent</span> -<span class="r-out co"><span class="r-pr">#></span> d_A1/dt = + k_parent_A1 * parent - k_A1_sink * A1</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Data:</span> -<span class="r-out co"><span class="r-pr">#></span> 170 observations of 2 variable(s) grouped in 5 datasets</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Log-likelihood: -473</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> -<span class="r-out co"><span class="r-pr">#></span> list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1) </span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 87.976 -3.670 -4.164 -4.645 </span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Random effects:</span> -<span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1)</span> -<span class="r-out co"><span class="r-pr">#></span> Level: ds</span> -<span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink Residual</span> -<span class="r-out co"><span class="r-pr">#></span> StdDev: 3.992 1.777 1.055 0.4821 6.483</span> -<span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Variance function:</span> -<span class="r-out co"><span class="r-pr">#></span> Structure: Different standard deviations per stratum</span> -<span class="r-out co"><span class="r-pr">#></span> Formula: ~1 | name </span> -<span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> -<span class="r-out co"><span class="r-pr">#></span> parent A1 </span> -<span class="r-out co"><span class="r-pr">#></span> 1.0000000 0.2049994 </span> -<span class="r-in"><span> <span class="va">f_nlme_dfop_sfo_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span></span> -<span class="r-in"><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>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="va">f_2_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_2</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> -<span class="r-in"><span> <span class="co"># f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations</span></span></span> -<span class="r-in"><span> <span class="co"># f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ],</span></span></span> -<span class="r-in"><span> <span class="co"># control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm</span></span></span> -<span class="r-in"><span></span></span> -<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span>, <span class="va">f_nlme_dfop_sfo_obs</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio</span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32093</span> -<span class="r-out co"><span class="r-pr">#></span> p-value</span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs <.0001</span> -<span class="r-in"><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> - - - <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> 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