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diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html deleted file mode 100644 index 66740a11..00000000 --- a/docs/dev/articles/web_only/saem_benchmarks.html +++ /dev/null @@ -1,639 +0,0 @@ -<!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"> -<head> -<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> -<meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Benchmark timings for saem.mmkin • mkin</title> -<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"> -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../../bootstrap-toc.css"> -<script src="../../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"> -<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../../pkgdown.css" rel="stylesheet"> -<script src="../../pkgdown.js"></script><meta property="og:title" content="Benchmark timings for saem.mmkin"> -<meta property="og:description" content="mkin"> -<meta name="robots" content="noindex"> -<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> -</head> -<body data-spy="scroll" data-target="#toc"> - 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Articles - - <span class="caret"></span> - </a> - <ul class="dropdown-menu" role="menu"> -<li> - <a href="../../articles/mkin.html">Introduction to mkin</a> - </li> - <li class="divider"> - </li> -<li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> - <li> - <a href="../../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> - </li> - <li> - <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> - </li> - <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - </li> - <li class="divider"> - </li> -<li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> - <li> - <a href="../../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> - 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</li> - <li> - <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> - </li> - </ul> -</li> -<li> - <a href="../../news/index.html">News</a> -</li> - </ul> -<ul class="nav navbar-nav navbar-right"> -<li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> - - </a> -</li> - </ul> -</div> -<!--/.nav-collapse --> - </div> -<!--/.container --> -</div> -<!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Benchmark timings for saem.mmkin</h1> - <h4 data-toc-skip class="author">Johannes -Ranke</h4> - - <h4 data-toc-skip class="date">Last change 17 February 2023 -(rebuilt 2023-04-16)</h4> - - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small> - <div class="hidden name"><code>saem_benchmarks.rmd</code></div> - - </div> - - - -<p>Each system is characterized by operating system type, CPU type, mkin -version, saemix version and R version. A compiler was available, so if -no analytical solution was available, compiled ODE models are used.</p> -<p>Every fit is only performed once, so the accuracy of the benchmarks -is limited.</p> -<p>For the initial mmkin fits, we use all available cores.</p> -<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="va">n_cores</span> <span class="op"><-</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> -<div class="section level2"> -<h2 id="test-data">Test data<a class="anchor" aria-label="anchor" href="#test-data"></a> -</h2> -<p>Please refer to the vignette <code>dimethenamid_2018</code> for an -explanation of the following preprocessing.</p> -<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="va">dmta_ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span> -<span> <span class="va">ds_i</span> <span class="op"><-</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> -<span> <span class="va">ds_i</span><span class="op">[</span><span class="va">ds_i</span><span class="op">$</span><span class="va">name</span> <span class="op">==</span> <span class="st">"DMTAP"</span>, <span class="st">"name"</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"DMTA"</span></span> -<span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">*</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">f_time_norm</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span> -<span> <span class="va">ds_i</span></span> -<span><span class="op">}</span><span class="op">)</span></span> -<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span> -<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span> -<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span> -<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span></code></pre></div> -</div> -<div class="section level2"> -<h2 id="test-cases">Test cases<a class="anchor" aria-label="anchor" href="#test-cases"></a> -</h2> -<div class="section level3"> -<h3 id="parent-only">Parent only<a class="anchor" aria-label="anchor" href="#parent-only"></a> -</h3> -<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="va">parent_mods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span>, <span class="st">"SFORB"</span>, <span class="st">"HS"</span><span class="op">)</span></span> -<span><span class="va">parent_sep_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">parent_mods</span>, <span class="va">dmta_ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span></span> -<span><span class="va">parent_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">parent_sep_const</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> -<span></span> -<span><span class="va">t1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sfo_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> -<span><span class="va">t2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> -<span><span class="va">t3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> -<span><span class="va">t4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hs_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> -<span><span class="va">t5</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> -<span><span class="va">t6</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> -<span><span class="va">t7</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> -<span><span class="va">t8</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hs_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> -<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span></span> -<span> <span class="va">sfo_const</span>, <span class="va">dfop_const</span>, <span class="va">sforb_const</span>, <span class="va">hs_const</span>,</span> -<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> -<table class="table"> -<thead><tr class="header"> -<th align="left"></th> -<th align="right">npar</th> -<th align="right">AIC</th> -<th align="right">BIC</th> -<th align="right">Lik</th> -</tr></thead> -<tbody> -<tr class="odd"> -<td align="left">sfo_const</td> -<td align="right">5</td> -<td align="right">796.3</td> -<td align="right">795.3</td> -<td align="right">-393.2</td> -</tr> -<tr class="even"> -<td align="left">sfo_tc</td> -<td align="right">6</td> -<td align="right">798.3</td> -<td align="right">797.1</td> -<td align="right">-393.2</td> -</tr> -<tr class="odd"> -<td align="left">dfop_const</td> -<td align="right">9</td> -<td align="right">709.4</td> -<td align="right">707.5</td> -<td align="right">-345.7</td> -</tr> -<tr class="even"> -<td align="left">sforb_const</td> -<td align="right">9</td> -<td align="right">710.0</td> -<td align="right">708.1</td> -<td align="right">-346.0</td> -</tr> -<tr class="odd"> -<td align="left">hs_const</td> -<td align="right">9</td> -<td align="right">713.7</td> -<td align="right">711.8</td> -<td align="right">-347.8</td> -</tr> -<tr class="even"> -<td align="left">dfop_tc</td> -<td align="right">10</td> -<td align="right">669.8</td> -<td align="right">667.7</td> -<td align="right">-324.9</td> -</tr> -<tr class="odd"> -<td align="left">sforb_tc</td> -<td align="right">10</td> -<td align="right">662.8</td> -<td align="right">660.7</td> -<td align="right">-321.4</td> -</tr> -<tr class="even"> -<td align="left">hs_tc</td> -<td align="right">10</td> -<td align="right">667.3</td> -<td align="right">665.2</td> -<td align="right">-323.6</td> -</tr> -</tbody> -</table> -<p>The above model comparison suggests to use the SFORB model with -two-component error. For comparison, we keep the DFOP model with -two-component error, as it competes with SFORB for biphasic curves.</p> -<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_tc</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## [1] "sd(log_k2)"</span></span></code></pre> -<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_tc</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## [1] "sd(log_k_DMTA_bound_free)"</span></span></code></pre> -<p>For these two models, random effects for the transformed parameters -<code>k2</code> and <code>k_DMTA_bound_free</code> could not be -quantified.</p> -</div> -<div class="section level3"> -<h3 id="one-metabolite">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite"></a> -</h3> -<p>We remove parameters that were found to be ill-defined in the parent -only fits.</p> -<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="va">one_met_mods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span> -<span> DFOP_SFO <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"M23"</span><span class="op">)</span>,</span> -<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>,</span> -<span> SFORB_SFO <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"M23"</span><span class="op">)</span>,</span> -<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> -<span></span> -<span><span class="va">one_met_sep_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">one_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"const"</span>,</span> -<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span><span class="va">one_met_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">one_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> -<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span></span> -<span><span class="va">t9</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">one_met_sep_tc</span><span class="op">[</span><span class="st">"DFOP_SFO"</span>, <span class="op">]</span>,</span> -<span> no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> -<span><span class="va">t10</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">one_met_sep_tc</span><span class="op">[</span><span class="st">"SFORB_SFO"</span>, <span class="op">]</span>,</span> -<span> no_random_effect <span class="op">=</span> <span class="st">"log_k_DMTA_bound_free"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> -</div> -<div class="section level3"> -<h3 id="three-metabolites">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites"></a> -</h3> -<p>For the case of three metabolites, we only keep the SFORB model in -order to limit the time for compiling this vignette, and as fitting in -parallel may disturb the benchmark. Again, we do not include random -effects that were ill-defined in previous fits of subsets of the -degradation model.</p> -<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_sfo_tc</span><span class="op">)</span></span></code></pre></div> -<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="va">three_met_mods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span> -<span> SFORB_SFO3_plus <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M23"</span>, <span class="st">"M27"</span>, <span class="st">"M31"</span><span class="op">)</span><span class="op">)</span>,</span> -<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span> M27 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span> M31 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M27"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> -<span></span> -<span><span class="va">three_met_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">three_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> -<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span></span> -<span><span class="va">t11</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_sfo3_plus_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">three_met_sep_tc</span><span class="op">[</span><span class="st">"SFORB_SFO3_plus"</span>, <span class="op">]</span>,</span> -<span> no_random_effect <span class="op">=</span> <span class="st">"log_k_DMTA_bound_free"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> -</div> -</div> -<div class="section level2"> -<h2 id="results">Results<a class="anchor" aria-label="anchor" href="#results"></a> -</h2> -<p>Benchmarks for all available error models are shown. They are -intended for improving mkin, not for comparing CPUs or operating -systems. All trademarks belong to their respective owners.</p> -<div class="section level3"> -<h3 id="parent-only-1">Parent only<a class="anchor" aria-label="anchor" href="#parent-only-1"></a> -</h3> -<p>Constant variance for SFO, DFOP, SFORB and HS.</p> -<table class="table"> -<thead><tr class="header"> -<th align="left">CPU</th> -<th align="left">OS</th> -<th align="left">mkin</th> -<th align="left">saemix</th> -<th align="right">t1</th> -<th align="right">t2</th> -<th align="right">t3</th> -<th align="right">t4</th> -</tr></thead> -<tbody> -<tr class="odd"> -<td align="left">Ryzen 7 1700</td> -<td align="left">Linux</td> -<td align="left">1.2.0</td> -<td align="left">3.2</td> -<td align="right">2.140</td> -<td align="right">4.626</td> -<td align="right">4.328</td> -<td align="right">4.998</td> -</tr> -<tr class="even"> -<td align="left">Ryzen 7 1700</td> -<td align="left">Linux</td> -<td align="left">1.2.2</td> -<td align="left">3.2</td> -<td align="right">2.427</td> -<td align="right">4.550</td> -<td align="right">4.217</td> -<td align="right">4.851</td> -</tr> -<tr class="odd"> -<td align="left">Ryzen 9 7950X</td> -<td align="left">Linux</td> -<td align="left">1.2.1</td> -<td align="left">3.2</td> -<td align="right">1.352</td> -<td align="right">2.813</td> -<td align="right">2.401</td> -<td align="right">2.074</td> -</tr> -<tr class="even"> -<td align="left">Ryzen 9 7950X</td> -<td align="left">Linux</td> -<td align="left">1.2.2</td> -<td align="left">3.2</td> -<td align="right">1.328</td> -<td align="right">2.738</td> -<td align="right">2.336</td> -<td align="right">2.023</td> -</tr> -<tr class="odd"> -<td align="left">Ryzen 9 7950X</td> -<td align="left">Linux</td> -<td align="left">1.2.3</td> -<td align="left">3.2</td> -<td align="right">1.118</td> -<td align="right">2.036</td> -<td align="right">2.010</td> -<td align="right">2.088</td> -</tr> -<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">1.389</td> -<td align="right">2.300</td> -<td align="right">1.880</td> -<td align="right">2.355</td> -</tr> -</tbody> -</table> -<p>Two-component error fits for SFO, DFOP, SFORB and HS.</p> -<table class="table"> -<thead><tr class="header"> -<th align="left">CPU</th> -<th align="left">OS</th> -<th align="left">mkin</th> -<th align="left">saemix</th> -<th align="right">t5</th> -<th align="right">t6</th> -<th align="right">t7</th> -<th align="right">t8</th> -</tr></thead> -<tbody> -<tr class="odd"> -<td align="left">Ryzen 7 1700</td> -<td align="left">Linux</td> -<td align="left">1.2.0</td> -<td align="left">3.2</td> -<td align="right">5.678</td> -<td align="right">7.441</td> -<td align="right">8.000</td> -<td align="right">7.980</td> -</tr> -<tr class="even"> -<td align="left">Ryzen 7 1700</td> -<td align="left">Linux</td> -<td align="left">1.2.2</td> -<td align="left">3.2</td> -<td align="right">5.352</td> -<td align="right">7.201</td> -<td align="right">8.174</td> -<td align="right">8.401</td> -</tr> -<tr class="odd"> -<td align="left">Ryzen 9 7950X</td> -<td align="left">Linux</td> -<td align="left">1.2.1</td> -<td align="left">3.2</td> -<td align="right">2.388</td> -<td align="right">3.033</td> -<td align="right">3.532</td> -<td align="right">3.310</td> -</tr> -<tr class="even"> -<td align="left">Ryzen 9 7950X</td> -<td align="left">Linux</td> -<td align="left">1.2.2</td> -<td align="left">3.2</td> -<td align="right">2.341</td> -<td align="right">2.968</td> -<td align="right">3.465</td> -<td align="right">3.341</td> -</tr> -<tr class="odd"> -<td align="left">Ryzen 9 7950X</td> -<td align="left">Linux</td> -<td align="left">1.2.3</td> -<td align="left">3.2</td> -<td align="right">2.159</td> -<td align="right">3.584</td> -<td align="right">3.307</td> -<td align="right">3.460</td> -</tr> -<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">2.300</td> -<td align="right">3.075</td> -<td align="right">3.206</td> -<td align="right">3.471</td> -</tr> -</tbody> -</table> -</div> -<div class="section level3"> -<h3 id="one-metabolite-1">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite-1"></a> -</h3> -<p>Two-component error for DFOP-SFO and SFORB-SFO.</p> -<table class="table"> -<thead><tr class="header"> -<th align="left">CPU</th> -<th align="left">OS</th> -<th align="left">mkin</th> -<th align="left">saemix</th> -<th align="right">t9</th> -<th align="right">t10</th> -</tr></thead> -<tbody> -<tr class="odd"> -<td align="left">Ryzen 7 1700</td> -<td align="left">Linux</td> -<td align="left">1.2.0</td> -<td align="left">3.2</td> -<td align="right">24.465</td> -<td align="right">800.266</td> -</tr> -<tr class="even"> -<td align="left">Ryzen 7 1700</td> -<td align="left">Linux</td> -<td align="left">1.2.2</td> -<td align="left">3.2</td> -<td align="right">25.193</td> -<td align="right">798.580</td> -</tr> -<tr class="odd"> -<td align="left">Ryzen 9 7950X</td> -<td align="left">Linux</td> -<td align="left">1.2.1</td> -<td align="left">3.2</td> -<td align="right">11.247</td> -<td align="right">285.216</td> -</tr> -<tr class="even"> -<td align="left">Ryzen 9 7950X</td> -<td align="left">Linux</td> -<td align="left">1.2.2</td> -<td align="left">3.2</td> -<td align="right">11.242</td> -<td align="right">284.258</td> -</tr> -<tr class="odd"> -<td align="left">Ryzen 9 7950X</td> -<td align="left">Linux</td> -<td align="left">1.2.3</td> -<td align="left">3.2</td> -<td align="right">11.796</td> -<td align="right">216.012</td> -</tr> -<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">12.951</td> -<td align="right">294.082</td> -</tr> -</tbody> -</table> -</div> -<div class="section level3"> -<h3 id="three-metabolites-1">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites-1"></a> -</h3> -<p>Two-component error for SFORB-SFO3-plus</p> -<table class="table"> -<thead><tr class="header"> -<th align="left">CPU</th> -<th align="left">OS</th> -<th align="left">mkin</th> -<th align="left">saemix</th> -<th align="right">t11</th> -</tr></thead> -<tbody> -<tr class="odd"> -<td align="left">Ryzen 7 1700</td> -<td align="left">Linux</td> -<td align="left">1.2.0</td> -<td align="left">3.2</td> -<td align="right">1289.198</td> -</tr> -<tr class="even"> -<td align="left">Ryzen 7 1700</td> -<td align="left">Linux</td> -<td align="left">1.2.2</td> -<td align="left">3.2</td> -<td align="right">1312.445</td> -</tr> -<tr class="odd"> -<td align="left">Ryzen 9 7950X</td> -<td align="left">Linux</td> -<td align="left">1.2.1</td> -<td align="left">3.2</td> -<td align="right">489.939</td> -</tr> -<tr class="even"> -<td align="left">Ryzen 9 7950X</td> -<td align="left">Linux</td> -<td align="left">1.2.2</td> -<td align="left">3.2</td> -<td align="right">482.970</td> -</tr> -<tr class="odd"> -<td align="left">Ryzen 9 7950X</td> -<td align="left">Linux</td> -<td align="left">1.2.3</td> -<td align="left">3.2</td> -<td align="right">392.364</td> -</tr> -<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">477.297</td> -</tr> -</tbody> -</table> -</div> -</div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - -</div> - - - - <footer><div class="copyright"> - <p></p> -<p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> -</div> - - </footer> -</div> - - - - - - - </body> -</html> |