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<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 2023-11-02)</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 style="width:100%;" class="table">
<colgroup>
<col width="8%">
<col width="54%">
<col width="8%">
<col width="12%">
<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">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>
<tr class="odd">
<td align="left">Linux</td>
<td align="left">Ryzen 9 7950X</td>
<td align="left">4.2.3</td>
<td align="left">1.2.3</td>
<td align="right">1.406</td>
<td align="right">1.948</td>
</tr>
<tr class="even">
<td align="left">Linux</td>
<td align="left">Ryzen 9 7950X</td>
<td align="left">4.3.0</td>
<td align="left">1.2.4</td>
<td align="right">1.386</td>
<td align="right">1.960</td>
</tr>
<tr class="odd">
<td align="left">Linux</td>
<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
<td align="left">4.3.1</td>
<td align="left">1.2.5</td>
<td align="right">2.369</td>
<td align="right">3.632</td>
</tr>
<tr class="even">
<td align="left">Linux</td>
<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
<td align="left">4.3.1</td>
<td align="left">1.2.6</td>
<td align="right">2.856</td>
<td align="right">4.960</td>
</tr>
<tr class="odd">
<td align="left">Linux</td>
<td align="left">Ryzen 9 7950X</td>
<td align="left">4.3.2</td>
<td align="left">1.2.6</td>
<td align="right">1.400</td>
<td align="right">2.012</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">
<colgroup>
<col width="7%">
<col width="50%">
<col width="7%">
<col width="11%">
<col width="7%">
<col width="8%">
<col width="7%">
</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">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>
<tr class="odd">
<td align="left">Linux</td>
<td align="left">Ryzen 9 7950X</td>
<td align="left">4.2.3</td>
<td align="left">1.2.3</td>
<td align="right">0.793</td>
<td align="right">2.109</td>
<td align="right">1.178</td>
</tr>
<tr class="even">
<td align="left">Linux</td>
<td align="left">Ryzen 9 7950X</td>
<td align="left">4.3.0</td>
<td align="left">1.2.4</td>
<td align="right">0.779</td>
<td align="right">2.080</td>
<td align="right">1.106</td>
</tr>
<tr class="odd">
<td align="left">Linux</td>
<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
<td align="left">4.3.1</td>
<td align="left">1.2.5</td>
<td align="right">1.823</td>
<td align="right">5.555</td>
<td align="right">2.404</td>
</tr>
<tr class="even">
<td align="left">Linux</td>
<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
<td align="left">4.3.1</td>
<td align="left">1.2.6</td>
<td align="right">1.761</td>
<td align="right">5.405</td>
<td align="right">2.462</td>
</tr>
<tr class="odd">
<td align="left">Linux</td>
<td align="left">Ryzen 9 7950X</td>
<td align="left">4.3.2</td>
<td align="left">1.2.6</td>
<td align="right">0.790</td>
<td align="right">2.212</td>
<td align="right">1.173</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 style="width:100%;" class="table">
<colgroup>
<col width="5%">
<col width="40%">
<col width="5%">
<col width="8%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="6%">
<col width="5%">
<col width="6%">
</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>
<tr class="odd">
<td align="left">Linux</td>
<td align="left">Ryzen 9 7950X</td>
<td align="left">4.2.3</td>
<td align="left">1.2.3</td>
<td align="right">0.432</td>
<td align="right">0.549</td>
<td align="right">0.609</td>
<td align="right">1.052</td>
<td align="right">0.743</td>
<td align="right">0.989</td>
</tr>
<tr class="even">
<td align="left">Linux</td>
<td align="left">Ryzen 9 7950X</td>
<td align="left">4.3.0</td>
<td align="left">1.2.4</td>
<td align="right">0.410</td>
<td align="right">0.526</td>
<td align="right">0.553</td>
<td align="right">1.249</td>
<td align="right">0.712</td>
<td align="right">0.948</td>
</tr>
<tr class="odd">
<td align="left">Linux</td>
<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
<td align="left">4.3.1</td>
<td align="left">1.2.5</td>
<td align="right">0.798</td>
<td align="right">1.096</td>
<td align="right">1.217</td>
<td align="right">3.173</td>
<td align="right">1.634</td>
<td align="right">2.271</td>
</tr>
<tr class="even">
<td align="left">Linux</td>
<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
<td align="left">4.3.1</td>
<td align="left">1.2.6</td>
<td align="right">0.813</td>
<td align="right">1.136</td>
<td align="right">1.220</td>
<td align="right">3.114</td>
<td align="right">1.598</td>
<td align="right">2.255</td>
</tr>
<tr class="odd">
<td align="left">Linux</td>
<td align="left">Ryzen 9 7950X</td>
<td align="left">4.3.2</td>
<td align="left">1.2.6</td>
<td align="right">0.432</td>
<td align="right">0.551</td>
<td align="right">0.580</td>
<td align="right">1.322</td>
<td align="right">0.746</td>
<td align="right">0.996</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
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<nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
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<p></p>
<p>Developed by Johannes Ranke.</p>
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<p></p>
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