<!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>Benchmark timings for 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="Benchmark timings for saem.mmkin">
<meta property="og:description" content="mkin">
<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-article">
<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>
<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>
<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>
<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>
<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 toc-ignore">
<h1 data-toc-skip>Benchmark timings for saem.mmkin</h1>
<h4 data-toc-skip class="author">Johannes
Ranke</h4>
<h4 data-toc-skip class="date">Last change 17 February 2023
(rebuilt 2023-02-17)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small>
<div class="hidden name"><code>saem_benchmarks.rmd</code></div>
</div>
<p>Each system is characterized by operating system type, CPU type, mkin
version, saemix version and R version. A compiler was available, so if
no analytical solution was available, compiled ODE models are used.</p>
<p>Every fit is only performed once, so the accuracy of the benchmarks
is limited.</p>
<p>For the initial mmkin fits, we use all available cores.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">n_cores</span> <span class="op"><-</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<div class="section level2">
<h2 id="test-data">Test data<a class="anchor" aria-label="anchor" href="#test-data"></a>
</h2>
<p>Please refer to the vignette <code>dimethenamid_2018</code> for an
explanation of the following preprocessing.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">dmta_ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span>
<span> <span class="va">ds_i</span> <span class="op"><-</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span>
<span> <span class="va">ds_i</span><span class="op">[</span><span class="va">ds_i</span><span class="op">$</span><span class="va">name</span> <span class="op">==</span> <span class="st">"DMTAP"</span>, <span class="st">"name"</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"DMTA"</span></span>
<span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">*</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">f_time_norm</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span>
<span> <span class="va">ds_i</span></span>
<span><span class="op">}</span><span class="op">)</span></span>
<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="va">dmta_ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span>
<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span>
<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span>
<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="test-cases">Test cases<a class="anchor" aria-label="anchor" href="#test-cases"></a>
</h2>
<div class="section level3">
<h3 id="parent-only">Parent only<a class="anchor" aria-label="anchor" href="#parent-only"></a>
</h3>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">parent_mods</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="st">"SFORB"</span>, <span class="st">"HS"</span><span class="op">)</span></span>
<span><span class="va">parent_sep_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">parent_mods</span>, <span class="va">dmta_ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span></span>
<span><span class="va">parent_sep_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">parent_sep_const</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span>
<span></span>
<span><span class="va">t1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sfo_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
<span><span class="va">t2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
<span><span class="va">t3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
<span><span class="va">t4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hs_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
<span><span class="va">t5</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
<span><span class="va">t6</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
<span><span class="va">t7</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
<span><span class="va">t8</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hs_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span></span>
<span> <span class="va">sfo_const</span>, <span class="va">dfop_const</span>, <span class="va">sforb_const</span>, <span class="va">hs_const</span>,</span>
<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="right">npar</th>
<th align="right">AIC</th>
<th align="right">BIC</th>
<th align="right">Lik</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">sfo_const</td>
<td align="right">5</td>
<td align="right">796.3</td>
<td align="right">795.3</td>
<td align="right">-393.2</td>
</tr>
<tr class="even">
<td align="left">sfo_tc</td>
<td align="right">6</td>
<td align="right">798.3</td>
<td align="right">797.1</td>
<td align="right">-393.2</td>
</tr>
<tr class="odd">
<td align="left">dfop_const</td>
<td align="right">9</td>
<td align="right">709.4</td>
<td align="right">707.5</td>
<td align="right">-345.7</td>
</tr>
<tr class="even">
<td align="left">sforb_const</td>
<td align="right">9</td>
<td align="right">710.0</td>
<td align="right">708.1</td>
<td align="right">-346.0</td>
</tr>
<tr class="odd">
<td align="left">hs_const</td>
<td align="right">9</td>
<td align="right">713.7</td>
<td align="right">711.8</td>
<td align="right">-347.8</td>
</tr>
<tr class="even">
<td align="left">dfop_tc</td>
<td align="right">10</td>
<td align="right">669.8</td>
<td align="right">667.7</td>
<td align="right">-324.9</td>
</tr>
<tr class="odd">
<td align="left">sforb_tc</td>
<td align="right">10</td>
<td align="right">662.8</td>
<td align="right">660.7</td>
<td align="right">-321.4</td>
</tr>
<tr class="even">
<td align="left">hs_tc</td>
<td align="right">10</td>
<td align="right">667.3</td>
<td align="right">665.2</td>
<td align="right">-323.6</td>
</tr>
</tbody>
</table>
<p>The above model comparison suggests to use the SFORB model with
two-component error. For comparison, we keep the DFOP model with
two-component error, as it competes with SFORB for biphasic curves.</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_tc</span><span class="op">)</span></span></code></pre></div>
<pre><code><span><span class="co">## [1] "sd(log_k2)"</span></span></code></pre>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_tc</span><span class="op">)</span></span></code></pre></div>
<pre><code><span><span class="co">## [1] "sd(log_k_DMTA_bound_free)"</span></span></code></pre>
<p>For these two models, random effects for the transformed parameters
<code>k2</code> and <code>k_DMTA_bound_free</code> could not be
quantified.</p>
</div>
<div class="section level3">
<h3 id="one-metabolite">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite"></a>
</h3>
<p>We remove parameters that were found to be ill-defined in the parent
only fits.</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">one_met_mods</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> DFOP_SFO <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"M23"</span><span class="op">)</span>,</span>
<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>,</span>
<span> SFORB_SFO <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"M23"</span><span class="op">)</span>,</span>
<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="va">one_met_sep_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">one_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"const"</span>,</span>
<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="va">one_met_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">one_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span>
<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span></span>
<span><span class="va">t9</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">one_met_sep_tc</span><span class="op">[</span><span class="st">"DFOP_SFO"</span>, <span class="op">]</span>,</span>
<span> no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
<span><span class="va">t10</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">one_met_sep_tc</span><span class="op">[</span><span class="st">"SFORB_SFO"</span>, <span class="op">]</span>,</span>
<span> no_random_effect <span class="op">=</span> <span class="st">"log_k_DMTA_bound_free"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div>
</div>
<div class="section level3">
<h3 id="three-metabolites">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites"></a>
</h3>
<p>For the case of three metabolites, we only keep the SFORB model in
order to limit the time for compiling this vignette, and as fitting in
parallel may disturb the benchmark. Again, we do not include random
effects that were ill-defined in previous fits of subsets of the
degradation model.</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_sfo_tc</span><span class="op">)</span></span></code></pre></div>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">three_met_mods</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> SFORB_SFO3_plus <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</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">"M23"</span>, <span class="st">"M27"</span>, <span class="st">"M31"</span><span class="op">)</span><span class="op">)</span>,</span>
<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span>
<span> M27 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span>
<span> M31 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M27"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="va">three_met_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">three_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span>
<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span></span>
<span><span class="va">t11</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_sfo3_plus_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">three_met_sep_tc</span><span class="op">[</span><span class="st">"SFORB_SFO3_plus"</span>, <span class="op">]</span>,</span>
<span> no_random_effect <span class="op">=</span> <span class="st">"log_k_DMTA_bound_free"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div>
</div>
</div>
<div class="section level2">
<h2 id="results">Results<a class="anchor" aria-label="anchor" href="#results"></a>
</h2>
<p>Benchmarks for all available error models are shown. They are
intended for improving mkin, not for comparing CPUs or operating
systems. All trademarks belong to their respective owners.</p>
<div class="section level3">
<h3 id="parent-only-1">Parent only<a class="anchor" aria-label="anchor" href="#parent-only-1"></a>
</h3>
<p>Constant variance for SFO, DFOP, SFORB and HS.</p>
<table class="table">
<thead><tr class="header">
<th align="left">CPU</th>
<th align="left">OS</th>
<th align="left">mkin</th>
<th align="left">saemix</th>
<th align="right">t1</th>
<th align="right">t2</th>
<th align="right">t3</th>
<th align="right">t4</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Ryzen 7 1700</td>
<td align="left">Linux</td>
<td align="left">1.2.0</td>
<td align="left">3.2</td>
<td align="right">2.140</td>
<td align="right">4.626</td>
<td align="right">4.328</td>
<td align="right">4.998</td>
</tr>
<tr class="even">
<td align="left">Ryzen 7 1700</td>
<td align="left">Linux</td>
<td align="left">1.2.2</td>
<td align="left">3.2</td>
<td align="right">2.427</td>
<td align="right">4.550</td>
<td align="right">4.217</td>
<td align="right">4.851</td>
</tr>
<tr class="odd">
<td align="left">Ryzen 9 7950X</td>
<td align="left">Linux</td>
<td align="left">1.2.1</td>
<td align="left">3.2</td>
<td align="right">1.352</td>
<td align="right">2.813</td>
<td align="right">2.401</td>
<td align="right">2.074</td>
</tr>
<tr class="even">
<td align="left">Ryzen 9 7950X</td>
<td align="left">Linux</td>
<td align="left">1.2.2</td>
<td align="left">3.2</td>
<td align="right">1.328</td>
<td align="right">2.738</td>
<td align="right">2.336</td>
<td align="right">2.023</td>
</tr>
<tr class="odd">
<td align="left">Ryzen 9 7950X</td>
<td align="left">Linux</td>
<td align="left">1.2.3</td>
<td align="left">3.2</td>
<td align="right">1.118</td>
<td align="right">2.036</td>
<td align="right">2.010</td>
<td align="right">2.088</td>
</tr>
</tbody>
</table>
<p>Two-component error fits for SFO, DFOP, SFORB and HS.</p>
<table class="table">
<thead><tr class="header">
<th align="left">CPU</th>
<th align="left">OS</th>
<th align="left">mkin</th>
<th align="left">saemix</th>
<th align="right">t5</th>
<th align="right">t6</th>
<th align="right">t7</th>
<th align="right">t8</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Ryzen 7 1700</td>
<td align="left">Linux</td>
<td align="left">1.2.0</td>
<td align="left">3.2</td>
<td align="right">5.678</td>
<td align="right">7.441</td>
<td align="right">8.000</td>
<td align="right">7.980</td>
</tr>
<tr class="even">
<td align="left">Ryzen 7 1700</td>
<td align="left">Linux</td>
<td align="left">1.2.2</td>
<td align="left">3.2</td>
<td align="right">5.352</td>
<td align="right">7.201</td>
<td align="right">8.174</td>
<td align="right">8.401</td>
</tr>
<tr class="odd">
<td align="left">Ryzen 9 7950X</td>
<td align="left">Linux</td>
<td align="left">1.2.1</td>
<td align="left">3.2</td>
<td align="right">2.388</td>
<td align="right">3.033</td>
<td align="right">3.532</td>
<td align="right">3.310</td>
</tr>
<tr class="even">
<td align="left">Ryzen 9 7950X</td>
<td align="left">Linux</td>
<td align="left">1.2.2</td>
<td align="left">3.2</td>
<td align="right">2.341</td>
<td align="right">2.968</td>
<td align="right">3.465</td>
<td align="right">3.341</td>
</tr>
<tr class="odd">
<td align="left">Ryzen 9 7950X</td>
<td align="left">Linux</td>
<td align="left">1.2.3</td>
<td align="left">3.2</td>
<td align="right">2.159</td>
<td align="right">3.584</td>
<td align="right">3.307</td>
<td align="right">3.460</td>
</tr>
</tbody>
</table>
</div>
<div class="section level3">
<h3 id="one-metabolite-1">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite-1"></a>
</h3>
<p>Two-component error for DFOP-SFO and SFORB-SFO.</p>
<table class="table">
<thead><tr class="header">
<th align="left">CPU</th>
<th align="left">OS</th>
<th align="left">mkin</th>
<th align="left">saemix</th>
<th align="right">t9</th>
<th align="right">t10</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Ryzen 7 1700</td>
<td align="left">Linux</td>
<td align="left">1.2.0</td>
<td align="left">3.2</td>
<td align="right">24.465</td>
<td align="right">800.266</td>
</tr>
<tr class="even">
<td align="left">Ryzen 7 1700</td>
<td align="left">Linux</td>
<td align="left">1.2.2</td>
<td align="left">3.2</td>
<td align="right">25.193</td>
<td align="right">798.580</td>
</tr>
<tr class="odd">
<td align="left">Ryzen 9 7950X</td>
<td align="left">Linux</td>
<td align="left">1.2.1</td>
<td align="left">3.2</td>
<td align="right">11.247</td>
<td align="right">285.216</td>
</tr>
<tr class="even">
<td align="left">Ryzen 9 7950X</td>
<td align="left">Linux</td>
<td align="left">1.2.2</td>
<td align="left">3.2</td>
<td align="right">11.242</td>
<td align="right">284.258</td>
</tr>
<tr class="odd">
<td align="left">Ryzen 9 7950X</td>
<td align="left">Linux</td>
<td align="left">1.2.3</td>
<td align="left">3.2</td>
<td align="right">11.796</td>
<td align="right">216.012</td>
</tr>
</tbody>
</table>
</div>
<div class="section level3">
<h3 id="three-metabolites-1">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites-1"></a>
</h3>
<p>Two-component error for SFORB-SFO3-plus</p>
<table class="table">
<thead><tr class="header">
<th align="left">CPU</th>
<th align="left">OS</th>
<th align="left">mkin</th>
<th align="left">saemix</th>
<th align="right">t11</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Ryzen 7 1700</td>
<td align="left">Linux</td>
<td align="left">1.2.0</td>
<td align="left">3.2</td>
<td align="right">1289.198</td>
</tr>
<tr class="even">
<td align="left">Ryzen 7 1700</td>
<td align="left">Linux</td>
<td align="left">1.2.2</td>
<td align="left">3.2</td>
<td align="right">1312.445</td>
</tr>
<tr class="odd">
<td align="left">Ryzen 9 7950X</td>
<td align="left">Linux</td>
<td align="left">1.2.1</td>
<td align="left">3.2</td>
<td align="right">489.939</td>
</tr>
<tr class="even">
<td align="left">Ryzen 9 7950X</td>
<td align="left">Linux</td>
<td align="left">1.2.2</td>
<td align="left">3.2</td>
<td align="right">482.970</td>
</tr>
<tr class="odd">
<td align="left">Ryzen 9 7950X</td>
<td align="left">Linux</td>
<td align="left">1.2.3</td>
<td align="left">3.2</td>
<td align="right">392.364</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc"><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> 2.0.7.</p>
</div>
</footer>
</div>
</body>
</html>
