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      <h1 data-toc-skip>Benchmark timings for mkin</h1>
                        <h4 class="author">Johannes Ranke</h4>
            
            <h4 class="date">2020-05-12</h4>
      
      <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/benchmarks.Rmd"><code>vignettes/web_only/benchmarks.Rmd</code></a></small>
      <div class="hidden name"><code>benchmarks.Rmd</code></div>

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<p>Each system is characterized by its CPU type, the operating system type and the mkin version. Currently only values for one system are available.</p>
<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">cpu_model</span> <span class="kw">&lt;-</span> <span class="kw pkg">benchmarkme</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/benchmarkme/man/get_cpu.html">get_cpu</a></span>()$<span class="no">model_name</span>
<span class="no">operating_system</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html">Sys.info</a></span>()<span class="kw">[[</span><span class="st">"sysname"</span>]]
<span class="no">mkin_version</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html">as.character</a></span>(<span class="fu"><a href="https://rdrr.io/r/utils/packageDescription.html">packageVersion</a></span>(<span class="st">"mkin"</span>))
<span class="no">system_string</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="no">operating_system</span>, <span class="st">", "</span>, <span class="no">cpu_model</span>, <span class="st">", mkin version "</span>, <span class="no">mkin_version</span>)
<span class="fu"><a href="https://rdrr.io/r/base/load.html">load</a></span>(<span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span>)
<span class="no">mkin_benchmarks</span>[<span class="no">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"CPU"</span>, <span class="st">"OS"</span>, <span class="st">"mkin"</span>)] <span class="kw">&lt;-</span>
  <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">cpu_model</span>, <span class="no">operating_system</span>, <span class="no">mkin_version</span>)

<span class="kw">if</span> (<span class="no">mkin_version</span> <span class="kw">&gt;</span> <span class="st">"0.9.48.1"</span>) {
  <span class="no">mmkin_bench</span> <span class="kw">&lt;-</span> <span class="kw">function</span>(<span class="no">models</span>, <span class="no">datasets</span>, <span class="no">error_model</span> <span class="kw">=</span> <span class="st">"const"</span>) {
    <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span>(<span class="no">models</span>, <span class="no">datasets</span>, <span class="kw">error_model</span> <span class="kw">=</span> <span class="no">error_model</span>, <span class="kw">cores</span> <span class="kw">=</span> <span class="fl">1</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
  }
} <span class="kw">else</span> {
  <span class="no">mmkin_bench</span> <span class="kw">&lt;-</span> <span class="kw">function</span>(<span class="no">models</span>, <span class="no">datasets</span>, <span class="no">error_model</span> <span class="kw">=</span> <span class="kw">NULL</span>) {
    <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span>(<span class="no">models</span>, <span class="no">datasets</span>, <span class="kw">reweight.method</span> <span class="kw">=</span> <span class="no">error_model</span>, <span class="kw">cores</span> <span class="kw">=</span> <span class="fl">1</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
  }
}</pre></body></html></div>
<div id="test-cases" class="section level2">
<h2 class="hasAnchor">
<a href="#test-cases" class="anchor"></a>Test cases</h2>
<p>Parent only:</p>
<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">FOCUS_C</span> <span class="kw">&lt;-</span> <span class="no">FOCUS_2006_C</span>
<span class="no">FOCUS_D</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html">subset</a></span>(<span class="no">FOCUS_2006_D</span>, <span class="no">value</span> <span class="kw">!=</span> <span class="fl">0</span>)
<span class="no">parent_datasets</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_C</span>, <span class="no">FOCUS_D</span>)

<span class="no">t1</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="no">parent_datasets</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t2</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="no">parent_datasets</span>,
    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]</pre></body></html></div>
<p>One metabolite:</p>
<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">SFO_SFO</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(
  <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),
  <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="no">FOMC_SFO</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(
  <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),
  <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">DFOP_SFO</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(
  <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),
  <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="no">t3</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t4</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>),
    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t5</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>),
    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]</pre></body></html></div>
<p>Two metabolites, synthetic data:</p>
<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="no">m_synth_SFO_lin</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),
                           <span class="kw">M1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),
                           <span class="kw">M2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),
                           <span class="kw">use_of_ff</span> <span class="kw">=</span> <span class="st">"max"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)

<span class="no">m_synth_DFOP_par</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"M1"</span>, <span class="st">"M2"</span>)),
                           <span class="kw">M1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),
                           <span class="kw">M2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),
                           <span class="kw">use_of_ff</span> <span class="kw">=</span> <span class="st">"max"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)

<span class="no">SFO_lin_a</span> <span class="kw">&lt;-</span> <span class="no">synthetic_data_for_UBA_2014</span><span class="kw">[[</span><span class="fl">1</span>]]$<span class="no">data</span>

<span class="no">DFOP_par_c</span> <span class="kw">&lt;-</span> <span class="no">synthetic_data_for_UBA_2014</span><span class="kw">[[</span><span class="fl">12</span>]]$<span class="no">data</span>

<span class="no">t6</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t7</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]]

<span class="no">t8</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>),
    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t9</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>),
    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]

<span class="no">t10</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>),
    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
<span class="no">t11</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>),
    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]</pre></body></html></div>
<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="no">mkin_benchmarks</span>[<span class="no">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"t"</span>, <span class="fl">1</span>:<span class="fl">11</span>)] <span class="kw">&lt;-</span>
  <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">t1</span>, <span class="no">t2</span>, <span class="no">t3</span>, <span class="no">t4</span>, <span class="no">t5</span>, <span class="no">t6</span>, <span class="no">t7</span>, <span class="no">t8</span>, <span class="no">t9</span>, <span class="no">t10</span>, <span class="no">t11</span>)
<span class="fu"><a href="https://rdrr.io/r/base/save.html">save</a></span>(<span class="no">mkin_benchmarks</span>, <span class="kw">file</span> <span class="kw">=</span> <span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span>)</pre></body></html></div>
</div>
<div id="results" class="section level2">
<h2 class="hasAnchor">
<a href="#results" class="anchor"></a>Results</h2>
<p>Currently, we only have benchmark information on one system, therefore only the mkin version is shown with the results below. Timings are in seconds, shorter is better.</p>
<div class="sourceCode" id="cb12"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/colnames.html">rownames</a></span>(<span class="no">mkin_benchmarks</span>) <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html">as.character</a></span>(<span class="no">mkin_benchmarks</span>$<span class="no">mkin</span>)</pre></body></html></div>
<p>Benchmarks for all available error models are shown.</p>
<div id="parent-only" class="section level3">
<h3 class="hasAnchor">
<a href="#parent-only" class="anchor"></a>Parent only</h3>
<p>Constant variance and two-component error model:</p>
<div class="sourceCode" id="cb13"><html><body><pre class="r"><span class="fu">kable</span>(<span class="no">mkin_benchmarks</span>[, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"t1"</span>, <span class="st">"t2"</span>)])</pre></body></html></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="right">t1</th>
<th align="right">t2</th>
</tr></thead>
<tbody>
<tr class="odd">
<td>0.9.48.1</td>
<td align="right">3.610</td>
<td align="right">11.019</td>
</tr>
<tr class="even">
<td>0.9.49.1</td>
<td align="right">8.184</td>
<td align="right">22.889</td>
</tr>
<tr class="odd">
<td>0.9.49.2</td>
<td align="right">7.064</td>
<td align="right">12.558</td>
</tr>
<tr class="even">
<td>0.9.49.3</td>
<td align="right">7.296</td>
<td align="right">21.239</td>
</tr>
<tr class="odd">
<td>0.9.49.4</td>
<td align="right">5.936</td>
<td align="right">20.545</td>
</tr>
<tr class="even">
<td>0.9.50.2</td>
<td align="right">1.659</td>
<td align="right">3.900</td>
</tr>
</tbody>
</table>
</div>
<div id="one-metabolite" class="section level3">
<h3 class="hasAnchor">
<a href="#one-metabolite" class="anchor"></a>One metabolite</h3>
<p>Constant variance, variance by variable and two-component error model:</p>
<div class="sourceCode" id="cb14"><html><body><pre class="r"><span class="fu">kable</span>(<span class="no">mkin_benchmarks</span>[, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"t3"</span>, <span class="st">"t4"</span>, <span class="st">"t5"</span>)])</pre></body></html></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="right">t3</th>
<th align="right">t4</th>
<th align="right">t5</th>
</tr></thead>
<tbody>
<tr class="odd">
<td>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>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>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>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>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>0.9.50.2</td>
<td align="right">1.389</td>
<td align="right">6.106</td>
<td align="right">2.716</td>
</tr>
</tbody>
</table>
</div>
<div id="two-metabolites" class="section level3">
<h3 class="hasAnchor">
<a href="#two-metabolites" class="anchor"></a>Two metabolites</h3>
<p>Two different datasets, for each constant variance, variance by variable and two-component error model are shown:</p>
<div class="sourceCode" id="cb15"><html><body><pre class="r"><span class="fu">kable</span>(<span class="no">mkin_benchmarks</span>[, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"t"</span>, <span class="fl">6</span>:<span class="fl">11</span>)])</pre></body></html></div>
<table class="table">
<thead><tr class="header">
<th></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>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>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>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>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>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>0.9.50.2</td>
<td align="right">0.751</td>
<td align="right">1.209</td>
<td align="right">1.270</td>
<td align="right">2.859</td>
<td align="right">2.026</td>
<td align="right">2.963</td>
</tr>
</tbody>
</table>
</div>
</div>
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