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authorJohannes Ranke <johannes.ranke@jrwb.de>2025-02-14 09:15:20 +0100
committerJohannes Ranke <johannes.ranke@jrwb.de>2025-02-14 09:15:20 +0100
commit91a5834dd701211f929fd25419dc34561ce3b4e7 (patch)
tree860862d680fea23581d08b2948c5ac3e922a8447 /docs/dev/articles/web_only/saem_benchmarks.html
parentb0f08271d1dae8ffaf57f557c27eba1314ece1d5 (diff)
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+ <li><a class="dropdown-item" href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li>
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+ <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
+ <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
+ <li><a class="dropdown-item" href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li>
+ <li><a class="dropdown-item" href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li>
+ <li><a class="dropdown-item" href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li>
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+ <li><a class="dropdown-item" href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li>
+ <li><a class="dropdown-item" href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li>
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+
+ <h1>Benchmark timings for saem.mmkin</h1>
+ <h4 data-toc-skip class="author">Johannes
+Ranke</h4>
+
+ <h4 data-toc-skip class="date">Last change 17 February 2023
+(rebuilt 2025-02-14)</h4>
+
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small>
+ <div class="d-none name"><code>saem_benchmarks.rmd</code></div>
+ </div>
+
+
+
+<p>Each system is characterized by operating system type, CPU type, mkin
+version, saemix version and R version. A compiler was available, so if
+no analytical solution was available, compiled ODE models are used.</p>
+<p>Every fit is only performed once, so the accuracy of the benchmarks
+is limited.</p>
+<p>For the initial mmkin fits, we use all available cores.</p>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">n_cores</span> <span class="op">&lt;-</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
+<div class="section level2">
+<h2 id="test-data">Test data<a class="anchor" aria-label="anchor" href="#test-data"></a>
+</h2>
+<p>Please refer to the vignette <code>dimethenamid_2018</code> for an
+explanation of the following preprocessing.</p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">dmta_ds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span>
+<span> <span class="va">ds_i</span> <span class="op">&lt;-</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span>
+<span> <span class="va">ds_i</span><span class="op">[</span><span class="va">ds_i</span><span class="op">$</span><span class="va">name</span> <span class="op">==</span> <span class="st">"DMTAP"</span>, <span class="st">"name"</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="st">"DMTA"</span></span>
+<span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">&lt;-</span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">*</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">f_time_norm</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span>
+<span> <span class="va">ds_i</span></span>
+<span><span class="op">}</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span>
+<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span>
+<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="cn">NULL</span></span>
+<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="cn">NULL</span></span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="test-cases">Test cases<a class="anchor" aria-label="anchor" href="#test-cases"></a>
+</h2>
+<div class="section level3">
+<h3 id="parent-only">Parent only<a class="anchor" aria-label="anchor" href="#parent-only"></a>
+</h3>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">parent_mods</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span>, <span class="st">"SFORB"</span>, <span class="st">"HS"</span><span class="op">)</span></span>
+<span><span class="va">parent_sep_const</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">parent_mods</span>, <span class="va">dmta_ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span></span>
+<span><span class="va">parent_sep_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">parent_sep_const</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span>
+<span></span>
+<span><span class="va">t1</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sfo_const</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
+<span><span class="va">t2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_const</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
+<span><span class="va">t3</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_const</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
+<span><span class="va">t4</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hs_const</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
+<span><span class="va">t5</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sfo_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
+<span><span class="va">t6</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
+<span><span class="va">t7</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
+<span><span class="va">t8</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hs_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span></span>
+<span> <span class="va">sfo_const</span>, <span class="va">dfop_const</span>, <span class="va">sforb_const</span>, <span class="va">hs_const</span>,</span>
+<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div>
+<table class="table">
+<thead><tr class="header">
+<th align="left"></th>
+<th align="right">npar</th>
+<th align="right">AIC</th>
+<th align="right">BIC</th>
+<th align="right">Lik</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="left">sfo_const</td>
+<td align="right">5</td>
+<td align="right">796.3</td>
+<td align="right">795.3</td>
+<td align="right">-393.2</td>
+</tr>
+<tr class="even">
+<td align="left">sfo_tc</td>
+<td align="right">6</td>
+<td align="right">798.3</td>
+<td align="right">797.1</td>
+<td align="right">-393.2</td>
+</tr>
+<tr class="odd">
+<td align="left">dfop_const</td>
+<td align="right">9</td>
+<td align="right">709.4</td>
+<td align="right">707.5</td>
+<td align="right">-345.7</td>
+</tr>
+<tr class="even">
+<td align="left">sforb_const</td>
+<td align="right">9</td>
+<td align="right">710.0</td>
+<td align="right">708.1</td>
+<td align="right">-346.0</td>
+</tr>
+<tr class="odd">
+<td align="left">hs_const</td>
+<td align="right">9</td>
+<td align="right">713.7</td>
+<td align="right">711.8</td>
+<td align="right">-347.8</td>
+</tr>
+<tr class="even">
+<td align="left">dfop_tc</td>
+<td align="right">10</td>
+<td align="right">670.1</td>
+<td align="right">668.0</td>
+<td align="right">-325.0</td>
+</tr>
+<tr class="odd">
+<td align="left">sforb_tc</td>
+<td align="right">10</td>
+<td align="right">662.9</td>
+<td align="right">660.8</td>
+<td align="right">-321.4</td>
+</tr>
+<tr class="even">
+<td align="left">hs_tc</td>
+<td align="right">10</td>
+<td align="right">667.2</td>
+<td align="right">665.1</td>
+<td align="right">-323.6</td>
+</tr>
+</tbody>
+</table>
+<p>The above model comparison suggests to use the SFORB model with
+two-component error. For comparison, we keep the DFOP model with
+two-component error, as it competes with SFORB for biphasic curves.</p>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_tc</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## [1] "sd(log_k2)"</span></span></code></pre>
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_tc</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## [1] "sd(log_k_DMTA_bound_free)"</span></span></code></pre>
+<p>For these two models, random effects for the transformed parameters
+<code>k2</code> and <code>k_DMTA_bound_free</code> could not be
+quantified.</p>
+</div>
+<div class="section level3">
+<h3 id="one-metabolite">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite"></a>
+</h3>
+<p>We remove parameters that were found to be ill-defined in the parent
+only fits.</p>
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">one_met_mods</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
+<span> DFOP_SFO <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
+<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"M23"</span><span class="op">)</span>,</span>
+<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>,</span>
+<span> SFORB_SFO <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
+<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"M23"</span><span class="op">)</span>,</span>
+<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
+<span></span>
+<span><span class="va">one_met_sep_const</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">one_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"const"</span>,</span>
+<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span><span class="va">one_met_sep_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">one_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span>
+<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span></span>
+<span><span class="va">t9</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_sfo_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">one_met_sep_tc</span><span class="op">[</span><span class="st">"DFOP_SFO"</span>, <span class="op">]</span>,</span>
+<span> no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
+<span><span class="va">t10</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_sfo_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">one_met_sep_tc</span><span class="op">[</span><span class="st">"SFORB_SFO"</span>, <span class="op">]</span>,</span>
+<span> no_random_effect <span class="op">=</span> <span class="st">"log_k_DMTA_bound_free"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div>
+</div>
+<div class="section level3">
+<h3 id="three-metabolites">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites"></a>
+</h3>
+<p>For the case of three metabolites, we only keep the SFORB model in
+order to limit the time for compiling this vignette, and as fitting in
+parallel may disturb the benchmark. Again, we do not include random
+effects that were ill-defined in previous fits of subsets of the
+degradation model.</p>
+<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_sfo_tc</span><span class="op">)</span></span></code></pre></div>
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="va">three_met_mods</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
+<span> SFORB_SFO3_plus <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
+<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M23"</span>, <span class="st">"M27"</span>, <span class="st">"M31"</span><span class="op">)</span><span class="op">)</span>,</span>
+<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span>
+<span> M27 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span>
+<span> M31 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M27"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
+<span></span>
+<span><span class="va">three_met_sep_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">three_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span>
+<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span></span>
+<span><span class="va">t11</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_sfo3_plus_const</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">three_met_sep_tc</span><span class="op">[</span><span class="st">"SFORB_SFO3_plus"</span>, <span class="op">]</span>,</span>
+<span> no_random_effect <span class="op">=</span> <span class="st">"log_k_DMTA_bound_free"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div>
+</div>
+</div>
+<div class="section level2">
+<h2 id="results">Results<a class="anchor" aria-label="anchor" href="#results"></a>
+</h2>
+<p>Benchmarks for all available error models are shown. They are
+intended for improving mkin, not for comparing CPUs or operating
+systems. All trademarks belong to their respective owners.</p>
+<div class="section level3">
+<h3 id="parent-only-1">Parent only<a class="anchor" aria-label="anchor" href="#parent-only-1"></a>
+</h3>
+<p>Constant variance for SFO, DFOP, SFORB and HS.</p>
+<table class="table">
+<colgroup>
+<col width="48%">
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="7%">
+<col width="7%">
+<col width="7%">
+<col width="7%">
+</colgroup>
+<thead><tr class="header">
+<th align="left">CPU</th>
+<th align="left">OS</th>
+<th align="left">mkin</th>
+<th align="left">saemix</th>
+<th align="right">t1</th>
+<th align="right">t2</th>
+<th align="right">t3</th>
+<th align="right">t4</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="left">Ryzen 7 1700</td>
+<td align="left">Linux</td>
+<td align="left">1.2.0</td>
+<td align="left">3.2</td>
+<td align="right">2.140</td>
+<td align="right">4.626</td>
+<td align="right">4.328</td>
+<td align="right">4.998</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 7 1700</td>
+<td align="left">Linux</td>
+<td align="left">1.2.2</td>
+<td align="left">3.2</td>
+<td align="right">2.427</td>
+<td align="right">4.550</td>
+<td align="right">4.217</td>
+<td align="right">4.851</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.1</td>
+<td align="left">3.2</td>
+<td align="right">1.352</td>
+<td align="right">2.813</td>
+<td align="right">2.401</td>
+<td align="right">2.074</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.2</td>
+<td align="left">3.2</td>
+<td align="right">1.328</td>
+<td align="right">2.738</td>
+<td align="right">2.336</td>
+<td align="right">2.023</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.3</td>
+<td align="left">3.2</td>
+<td align="right">1.118</td>
+<td align="right">2.036</td>
+<td align="right">2.010</td>
+<td align="right">2.088</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.3</td>
+<td align="left">3.2</td>
+<td align="right">1.419</td>
+<td align="right">2.374</td>
+<td align="right">1.926</td>
+<td align="right">2.398</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.4</td>
+<td align="left">3.2</td>
+<td align="right">0.972</td>
+<td align="right">2.550</td>
+<td align="right">1.987</td>
+<td align="right">2.055</td>
+</tr>
+<tr class="even">
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">Linux</td>
+<td align="left">1.2.6</td>
+<td align="left">3.2</td>
+<td align="right">2.998</td>
+<td align="right">6.523</td>
+<td align="right">6.126</td>
+<td align="right">4.721</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.6</td>
+<td align="left">3.2</td>
+<td align="right">1.135</td>
+<td align="right">2.025</td>
+<td align="right">2.406</td>
+<td align="right">2.478</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.9</td>
+<td align="left">3.3</td>
+<td align="right">1.086</td>
+<td align="right">1.991</td>
+<td align="right">1.949</td>
+<td align="right">2.411</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.10</td>
+<td align="left">3.3</td>
+<td align="right">1.115</td>
+<td align="right">2.277</td>
+<td align="right">1.945</td>
+<td align="right">2.134</td>
+</tr>
+</tbody>
+</table>
+<p>Two-component error fits for SFO, DFOP, SFORB and HS.</p>
+<table class="table">
+<colgroup>
+<col width="48%">
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="7%">
+<col width="7%">
+<col width="7%">
+<col width="7%">
+</colgroup>
+<thead><tr class="header">
+<th align="left">CPU</th>
+<th align="left">OS</th>
+<th align="left">mkin</th>
+<th align="left">saemix</th>
+<th align="right">t5</th>
+<th align="right">t6</th>
+<th align="right">t7</th>
+<th align="right">t8</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="left">Ryzen 7 1700</td>
+<td align="left">Linux</td>
+<td align="left">1.2.0</td>
+<td align="left">3.2</td>
+<td align="right">5.678</td>
+<td align="right">7.441</td>
+<td align="right">8.000</td>
+<td align="right">7.980</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 7 1700</td>
+<td align="left">Linux</td>
+<td align="left">1.2.2</td>
+<td align="left">3.2</td>
+<td align="right">5.352</td>
+<td align="right">7.201</td>
+<td align="right">8.174</td>
+<td align="right">8.401</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.1</td>
+<td align="left">3.2</td>
+<td align="right">2.388</td>
+<td align="right">3.033</td>
+<td align="right">3.532</td>
+<td align="right">3.310</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.2</td>
+<td align="left">3.2</td>
+<td align="right">2.341</td>
+<td align="right">2.968</td>
+<td align="right">3.465</td>
+<td align="right">3.341</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.3</td>
+<td align="left">3.2</td>
+<td align="right">2.159</td>
+<td align="right">3.584</td>
+<td align="right">3.307</td>
+<td align="right">3.460</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.3</td>
+<td align="left">3.2</td>
+<td align="right">2.348</td>
+<td align="right">3.134</td>
+<td align="right">3.253</td>
+<td align="right">3.530</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.4</td>
+<td align="left">3.2</td>
+<td align="right">2.127</td>
+<td align="right">3.587</td>
+<td align="right">3.433</td>
+<td align="right">3.595</td>
+</tr>
+<tr class="even">
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">Linux</td>
+<td align="left">1.2.6</td>
+<td align="left">3.2</td>
+<td align="right">5.070</td>
+<td align="right">8.464</td>
+<td align="right">8.525</td>
+<td align="right">7.599</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.6</td>
+<td align="left">3.2</td>
+<td align="right">2.161</td>
+<td align="right">3.325</td>
+<td align="right">3.669</td>
+<td align="right">3.153</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.9</td>
+<td align="left">3.3</td>
+<td align="right">2.426</td>
+<td align="right">3.196</td>
+<td align="right">3.256</td>
+<td align="right">3.322</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.10</td>
+<td align="left">3.3</td>
+<td align="right">2.372</td>
+<td align="right">3.137</td>
+<td align="right">3.100</td>
+<td align="right">3.281</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="section level3">
+<h3 id="one-metabolite-1">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite-1"></a>
+</h3>
+<p>Two-component error for DFOP-SFO and SFORB-SFO.</p>
+<table style="width:100%;" class="table">
+<colgroup>
+<col width="53%">
+<col width="7%">
+<col width="9%">
+<col width="9%">
+<col width="9%">
+<col width="10%">
+</colgroup>
+<thead><tr class="header">
+<th align="left">CPU</th>
+<th align="left">OS</th>
+<th align="left">mkin</th>
+<th align="left">saemix</th>
+<th align="right">t9</th>
+<th align="right">t10</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="left">Ryzen 7 1700</td>
+<td align="left">Linux</td>
+<td align="left">1.2.0</td>
+<td align="left">3.2</td>
+<td align="right">24.465</td>
+<td align="right">800.266</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 7 1700</td>
+<td align="left">Linux</td>
+<td align="left">1.2.2</td>
+<td align="left">3.2</td>
+<td align="right">25.193</td>
+<td align="right">798.580</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.1</td>
+<td align="left">3.2</td>
+<td align="right">11.247</td>
+<td align="right">285.216</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.2</td>
+<td align="left">3.2</td>
+<td align="right">11.242</td>
+<td align="right">284.258</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.3</td>
+<td align="left">3.2</td>
+<td align="right">11.796</td>
+<td align="right">216.012</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.3</td>
+<td align="left">3.2</td>
+<td align="right">12.841</td>
+<td align="right">292.688</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.4</td>
+<td align="left">3.2</td>
+<td align="right">12.160</td>
+<td align="right">265.934</td>
+</tr>
+<tr class="even">
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">Linux</td>
+<td align="left">1.2.6</td>
+<td align="left">3.2</td>
+<td align="right">30.168</td>
+<td align="right">748.675</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.6</td>
+<td align="left">3.2</td>
+<td align="right">12.007</td>
+<td align="right">286.757</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.9</td>
+<td align="left">3.3</td>
+<td align="right">12.420</td>
+<td align="right">289.338</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.10</td>
+<td align="left">3.3</td>
+<td align="right">11.590</td>
+<td align="right">279.782</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="section level3">
+<h3 id="three-metabolites-1">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites-1"></a>
+</h3>
+<p>Two-component error for SFORB-SFO3-plus</p>
+<table class="table">
+<colgroup>
+<col width="58%">
+<col width="8%">
+<col width="10%">
+<col width="10%">
+<col width="12%">
+</colgroup>
+<thead><tr class="header">
+<th align="left">CPU</th>
+<th align="left">OS</th>
+<th align="left">mkin</th>
+<th align="left">saemix</th>
+<th align="right">t11</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td align="left">Ryzen 7 1700</td>
+<td align="left">Linux</td>
+<td align="left">1.2.0</td>
+<td align="left">3.2</td>
+<td align="right">1289.198</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 7 1700</td>
+<td align="left">Linux</td>
+<td align="left">1.2.2</td>
+<td align="left">3.2</td>
+<td align="right">1312.445</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.1</td>
+<td align="left">3.2</td>
+<td align="right">489.939</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.2</td>
+<td align="left">3.2</td>
+<td align="right">482.970</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.3</td>
+<td align="left">3.2</td>
+<td align="right">392.364</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.3</td>
+<td align="left">3.2</td>
+<td align="right">483.027</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.4</td>
+<td align="left">3.2</td>
+<td align="right">456.252</td>
+</tr>
+<tr class="even">
+<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td>
+<td align="left">Linux</td>
+<td align="left">1.2.6</td>
+<td align="left">3.2</td>
+<td align="right">1235.028</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.6</td>
+<td align="left">3.2</td>
+<td align="right">480.577</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.9</td>
+<td align="left">3.3</td>
+<td align="right">485.836</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.10</td>
+<td align="left">3.3</td>
+<td align="right">469.036</td>
+</tr>
+</tbody>
+</table>
+</div>
+</div>
+ </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+ </nav></aside>
+</div>
+
+
+
+ <footer><div class="pkgdown-footer-left">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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