<!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 mkin • 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 mkin"> <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 mkin</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/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> </div> <p>Each system is characterized by the operating system type, the CPU type, the mkin version, and, as in June 2022 the current R version lead to worse performance, the 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>The following wrapper function for <code>mmkin</code> is used because the way the error model is specified was changed in mkin version 0.9.49.1.</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/packageDescription.html" class="external-link">packageVersion</a></span><span class="op">(</span><span class="st">"mkin"</span><span class="op">)</span> <span class="op">></span> <span class="st">"0.9.48.1"</span><span class="op">)</span> <span class="op">{</span></span> <span> <span class="va">mmkin_bench</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, <span class="va">error_model</span> <span class="op">=</span> <span class="st">"const"</span><span class="op">)</span> <span class="op">{</span></span> <span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, error_model <span class="op">=</span> <span class="va">error_model</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span> <span class="op">}</span></span> <span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span> <span> <span class="va">mmkin_bench</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, <span class="va">error_model</span> <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">{</span></span> <span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, reweight.method <span class="op">=</span> <span class="va">error_model</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span> <span class="op">}</span></span> <span><span class="op">}</span></span></code></pre></div> <div class="section level2"> <h2 id="test-cases">Test cases<a class="anchor" aria-label="anchor" href="#test-cases"></a> </h2> <p>Parent only:</p> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">FOCUS_C</span> <span class="op"><-</span> <span class="va">FOCUS_2006_C</span></span> <span><span class="va">FOCUS_D</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">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></span> <span><span class="va">parent_datasets</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">FOCUS_C</span>, <span class="va">FOCUS_D</span><span class="op">)</span></span> <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="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span><span class="op">)</span>, <span class="va">parent_datasets</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="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span><span class="op">)</span>, <span class="va">parent_datasets</span>,</span> <span> error_model <span class="op">=</span> <span class="st">"tc"</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> <p>One metabolite:</p> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> <span> parent <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">"m1"</span><span class="op">)</span>,</span> <span> m1 <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><span class="va">FOMC_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> <span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> <span> m1 <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><span class="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> <span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>, <span class="co"># erroneously used FOMC twice, not fixed for consistency</span></span> <span> m1 <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><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="fu">mmkin_bench</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">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</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">FOCUS_D</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="fu">mmkin_bench</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">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</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">FOCUS_D</span><span class="op">)</span>,</span> <span> error_model <span class="op">=</span> <span class="st">"tc"</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="fu">mmkin_bench</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">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</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">FOCUS_D</span><span class="op">)</span>,</span> <span> error_model <span class="op">=</span> <span class="st">"obs"</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> <p>Two metabolites, synthetic data:</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <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">"M1"</span><span class="op">)</span>,</span> <span> M1 <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">"M2"</span><span class="op">)</span>,</span> <span> M2 <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> 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> <span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <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="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span> <span> M1 <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> M2 <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> 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> <span><span class="va">SFO_lin_a</span> <span class="op"><-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> <span></span> <span><span class="va">DFOP_par_c</span> <span class="op"><-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> <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="fu">mmkin_bench</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">m_synth_SFO_lin</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">SFO_lin_a</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="fu">mmkin_bench</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">m_synth_DFOP_par</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_par_c</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> <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="fu">mmkin_bench</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">m_synth_SFO_lin</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">SFO_lin_a</span><span class="op">)</span>,</span> <span> error_model <span class="op">=</span> <span class="st">"tc"</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">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="fu">mmkin_bench</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">m_synth_DFOP_par</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_par_c</span><span class="op">)</span>,</span> <span> error_model <span class="op">=</span> <span class="st">"tc"</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> <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="fu">mmkin_bench</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">m_synth_SFO_lin</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">SFO_lin_a</span><span class="op">)</span>,</span> <span> error_model <span class="op">=</span> <span class="st">"obs"</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">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="fu">mmkin_bench</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">m_synth_DFOP_par</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_par_c</span><span class="op">)</span>,</span> <span> error_model <span class="op">=</span> <span class="st">"obs"</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 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">Parent only<a class="anchor" aria-label="anchor" href="#parent-only"></a> </h3> <p>Constant variance (t1) and two-component error model (t2) for four models fitted to two datasets, i.e. eight fits for each test.</p> <table class="table"> <thead><tr class="header"> <th align="left">OS</th> <th align="left">CPU</th> <th align="left">R</th> <th align="left">mkin</th> <th align="right">t1</th> <th align="right">t2</th> </tr></thead> <tbody> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.48.1</td> <td align="right">3.610</td> <td align="right">11.019</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.49.1</td> <td align="right">8.184</td> <td align="right">22.889</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.49.2</td> <td align="right">7.064</td> <td align="right">12.558</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.49.3</td> <td align="right">7.296</td> <td align="right">21.239</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.49.4</td> <td align="right">5.936</td> <td align="right">20.545</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.50.2</td> <td align="right">1.714</td> <td align="right">3.971</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.50.3</td> <td align="right">1.752</td> <td align="right">4.156</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.50.4</td> <td align="right">1.786</td> <td align="right">3.729</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">1.0.3</td> <td align="right">1.881</td> <td align="right">3.504</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">1.0.4</td> <td align="right">1.867</td> <td align="right">3.450</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.1.3</td> <td align="left">1.1.0</td> <td align="right">1.791</td> <td align="right">3.289</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.0</td> <td align="right">1.842</td> <td align="right">3.453</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">i7-4710MQ</td> <td align="left">4.2.1</td> <td align="left">1.1.0</td> <td align="right">1.959</td> <td align="right">4.116</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">i7-4710MQ</td> <td align="left">4.1.3</td> <td align="left">1.1.0</td> <td align="right">1.877</td> <td align="right">3.906</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">i7-4710MQ</td> <td align="left">4.2.1</td> <td align="left">1.1.1</td> <td align="right">1.644</td> <td align="right">3.172</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.1</td> <td align="right">1.770</td> <td align="right">3.377</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.2</td> <td align="right">1.957</td> <td align="right">3.633</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.2</td> <td align="left">1.2.0</td> <td align="right">2.140</td> <td align="right">3.774</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.2</td> <td align="left">1.2.2</td> <td align="right">2.187</td> <td align="right">3.851</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 9 7950X</td> <td align="left">4.2.2</td> <td align="left">1.2.0</td> <td align="right">1.288</td> <td align="right">1.794</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 9 7950X</td> <td align="left">4.2.2</td> <td align="left">1.2.2</td> <td align="right">1.276</td> <td align="right">1.804</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 9 7950X</td> <td align="left">4.2.2</td> <td align="left">1.2.3</td> <td align="right">1.370</td> <td align="right">1.883</td> </tr> </tbody> </table> </div> <div class="section level3"> <h3 id="one-metabolite">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite"></a> </h3> <p>Constant variance (t3), two-component error model (t4), and variance by variable (t5) for three models fitted to one dataset, i.e. three fits for each test.</p> <table class="table"> <thead><tr class="header"> <th align="left">OS</th> <th align="left">CPU</th> <th align="left">R</th> <th align="left">mkin</th> <th align="right">t3</th> <th align="right">t4</th> <th align="right">t5</th> </tr></thead> <tbody> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.48.1</td> <td align="right">3.764</td> <td align="right">14.347</td> <td align="right">9.495</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.49.1</td> <td align="right">4.649</td> <td align="right">13.789</td> <td align="right">6.395</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.49.2</td> <td align="right">4.786</td> <td align="right">8.461</td> <td align="right">5.675</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.49.3</td> <td align="right">4.510</td> <td align="right">13.805</td> <td align="right">7.386</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.49.4</td> <td align="right">4.446</td> <td align="right">15.335</td> <td align="right">6.002</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.50.2</td> <td align="right">1.402</td> <td align="right">6.174</td> <td align="right">2.764</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.50.3</td> <td align="right">1.430</td> <td align="right">6.615</td> <td align="right">2.878</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.50.4</td> <td align="right">1.397</td> <td align="right">7.251</td> <td align="right">2.810</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">1.0.3</td> <td align="right">1.430</td> <td align="right">6.344</td> <td align="right">2.798</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">1.0.4</td> <td align="right">1.415</td> <td align="right">6.364</td> <td align="right">2.820</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.1.3</td> <td align="left">1.1.0</td> <td align="right">1.310</td> <td align="right">6.279</td> <td align="right">2.681</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.0</td> <td align="right">3.802</td> <td align="right">21.247</td> <td align="right">8.461</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">i7-4710MQ</td> <td align="left">4.2.1</td> <td align="left">1.1.0</td> <td align="right">3.334</td> <td align="right">19.521</td> <td align="right">7.565</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">i7-4710MQ</td> <td align="left">4.1.3</td> <td align="left">1.1.0</td> <td align="right">1.578</td> <td align="right">8.058</td> <td align="right">3.339</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">i7-4710MQ</td> <td align="left">4.2.1</td> <td align="left">1.1.1</td> <td align="right">1.230</td> <td align="right">5.839</td> <td align="right">2.444</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.1</td> <td align="right">1.308</td> <td align="right">5.758</td> <td align="right">2.558</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.2</td> <td align="right">1.503</td> <td align="right">6.147</td> <td align="right">2.803</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.2</td> <td align="left">1.2.0</td> <td align="right">1.554</td> <td align="right">6.193</td> <td align="right">2.843</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.2</td> <td align="left">1.2.2</td> <td align="right">1.585</td> <td align="right">6.335</td> <td align="right">3.003</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 9 7950X</td> <td align="left">4.2.2</td> <td align="left">1.2.0</td> <td align="right">0.792</td> <td align="right">2.378</td> <td align="right">1.245</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 9 7950X</td> <td align="left">4.2.2</td> <td align="left">1.2.2</td> <td align="right">0.784</td> <td align="right">2.355</td> <td align="right">1.233</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 9 7950X</td> <td align="left">4.2.2</td> <td align="left">1.2.3</td> <td align="right">0.770</td> <td align="right">2.011</td> <td align="right">1.123</td> </tr> </tbody> </table> </div> <div class="section level3"> <h3 id="two-metabolites">Two metabolites<a class="anchor" aria-label="anchor" href="#two-metabolites"></a> </h3> <p>Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.</p> <table class="table"> <colgroup> <col width="8%"> <col width="19%"> <col width="8%"> <col width="12%"> <col width="8%"> <col width="8%"> <col width="8%"> <col width="9%"> <col width="8%"> <col width="9%"> </colgroup> <thead><tr class="header"> <th align="left">OS</th> <th align="left">CPU</th> <th align="left">R</th> <th align="left">mkin</th> <th align="right">t6</th> <th align="right">t7</th> <th align="right">t8</th> <th align="right">t9</th> <th align="right">t10</th> <th align="right">t11</th> </tr></thead> <tbody> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.48.1</td> <td align="right">2.623</td> <td align="right">4.587</td> <td align="right">7.525</td> <td align="right">16.621</td> <td align="right">8.576</td> <td align="right">31.267</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.49.1</td> <td align="right">2.542</td> <td align="right">4.128</td> <td align="right">4.632</td> <td align="right">8.171</td> <td align="right">3.676</td> <td align="right">5.636</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.49.2</td> <td align="right">2.723</td> <td align="right">4.478</td> <td align="right">4.862</td> <td align="right">7.618</td> <td align="right">3.579</td> <td align="right">5.574</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.49.3</td> <td align="right">2.643</td> <td align="right">4.374</td> <td align="right">7.020</td> <td align="right">11.124</td> <td align="right">5.388</td> <td align="right">7.365</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.49.4</td> <td align="right">2.635</td> <td align="right">4.259</td> <td align="right">4.737</td> <td align="right">7.763</td> <td align="right">3.427</td> <td align="right">5.626</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.50.2</td> <td align="right">0.777</td> <td align="right">1.236</td> <td align="right">1.332</td> <td align="right">2.872</td> <td align="right">2.069</td> <td align="right">2.987</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.50.3</td> <td align="right">0.858</td> <td align="right">1.264</td> <td align="right">1.333</td> <td align="right">2.984</td> <td align="right">2.113</td> <td align="right">3.073</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">0.9.50.4</td> <td align="right">0.783</td> <td align="right">1.282</td> <td align="right">1.486</td> <td align="right">3.815</td> <td align="right">1.958</td> <td align="right">3.105</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">1.0.3</td> <td align="right">0.763</td> <td align="right">1.244</td> <td align="right">1.457</td> <td align="right">3.054</td> <td align="right">1.923</td> <td align="right">2.839</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">NA</td> <td align="left">1.0.4</td> <td align="right">0.785</td> <td align="right">1.252</td> <td align="right">1.466</td> <td align="right">3.091</td> <td align="right">1.936</td> <td align="right">2.826</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.1.3</td> <td align="left">1.1.0</td> <td align="right">0.744</td> <td align="right">1.227</td> <td align="right">1.288</td> <td align="right">3.553</td> <td align="right">1.895</td> <td align="right">2.738</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.0</td> <td align="right">3.018</td> <td align="right">4.165</td> <td align="right">5.036</td> <td align="right">10.844</td> <td align="right">6.623</td> <td align="right">9.722</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">i7-4710MQ</td> <td align="left">4.2.1</td> <td align="left">1.1.0</td> <td align="right">2.522</td> <td align="right">3.792</td> <td align="right">4.143</td> <td align="right">11.268</td> <td align="right">5.935</td> <td align="right">8.728</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">i7-4710MQ</td> <td align="left">4.1.3</td> <td align="left">1.1.0</td> <td align="right">0.907</td> <td align="right">1.535</td> <td align="right">1.589</td> <td align="right">4.544</td> <td align="right">2.302</td> <td align="right">3.463</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">i7-4710MQ</td> <td align="left">4.2.1</td> <td align="left">1.1.1</td> <td align="right">0.678</td> <td align="right">1.095</td> <td align="right">1.149</td> <td align="right">3.247</td> <td align="right">1.658</td> <td align="right">2.472</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.1</td> <td align="right">0.696</td> <td align="right">1.124</td> <td align="right">1.321</td> <td align="right">2.786</td> <td align="right">1.744</td> <td align="right">2.566</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.2</td> <td align="right">0.861</td> <td align="right">1.295</td> <td align="right">1.507</td> <td align="right">3.102</td> <td align="right">1.961</td> <td align="right">2.852</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.2</td> <td align="left">1.2.0</td> <td align="right">0.913</td> <td align="right">1.345</td> <td align="right">1.539</td> <td align="right">3.011</td> <td align="right">1.987</td> <td align="right">2.802</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 7 1700</td> <td align="left">4.2.2</td> <td align="left">1.2.2</td> <td align="right">0.935</td> <td align="right">1.381</td> <td align="right">1.551</td> <td align="right">3.209</td> <td align="right">1.976</td> <td align="right">3.013</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 9 7950X</td> <td align="left">4.2.2</td> <td align="left">1.2.0</td> <td align="right">0.445</td> <td align="right">0.591</td> <td align="right">0.660</td> <td align="right">1.190</td> <td align="right">0.814</td> <td align="right">1.100</td> </tr> <tr class="odd"> <td align="left">Linux</td> <td align="left">Ryzen 9 7950X</td> <td align="left">4.2.2</td> <td align="left">1.2.2</td> <td align="right">0.443</td> <td align="right">0.586</td> <td align="right">0.661</td> <td align="right">1.176</td> <td align="right">0.803</td> <td align="right">1.097</td> </tr> <tr class="even"> <td align="left">Linux</td> <td align="left">Ryzen 9 7950X</td> <td align="left">4.2.2</td> <td align="left">1.2.3</td> <td align="right">0.418</td> <td align="right">0.530</td> <td align="right">0.591</td> <td align="right">1.006</td> <td align="right">0.716</td> <td align="right">0.949</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>