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diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index 64c68ea0..3e73bd12 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -33,14 +33,14 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> - <a href="../../reference/index.html">Functions and data</a> + <a href="../../reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> @@ -52,6 +52,9 @@ <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> @@ -59,22 +62,31 @@ <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + <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/web_only/multistart.html">Short demo of the multistart method</a> + <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/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> - <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> </li> <li> - <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> + </li> + <li class="divider"> + </li> +<li class="dropdown-header">Performance</li> + <li> + <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> @@ -82,6 +94,15 @@ <li> <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> + <li class="divider"> + </li> +<li class="dropdown-header">Miscellaneous</li> + <li> + <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + <li> + <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> </ul> </li> <li> @@ -105,13 +126,15 @@ - </header><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Benchmark timings for mkin</h1> - <h4 data-toc-skip class="author">Johannes Ranke</h4> + <h4 data-toc-skip class="author">Johannes +Ranke</h4> - <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-17)</h4> + <h4 data-toc-skip class="date">Last change 17 February 2023 +(rebuilt 2023-04-20)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> @@ -120,9 +143,15 @@ -<p>Each system is characterized by the operating system type, the CPU type, the mkin version, and, as in June 2022 the current R version lead to worse performance, the R version. A compiler was available, so if no analytical solution was available, compiled ODE models are used.</p> -<p>Every fit is only performed once, so the accuracy of the benchmarks is limited.</p> -<p>The following wrapper function for <code>mmkin</code> is used because the way the error model is specified was changed in mkin version 0.9.49.1.</p> +<p>Each system is characterized by the operating system type, the CPU +type, the mkin version, and, as in June 2022 the current R version lead +to worse performance, the R version. A compiler was available, so if no +analytical solution was available, compiled ODE models are used.</p> +<p>Every fit is only performed once, so the accuracy of the benchmarks +is limited.</p> +<p>The following wrapper function for <code>mmkin</code> is used because +the way the error model is specified was changed in mkin version +0.9.49.1.</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/packageDescription.html" class="external-link">packageVersion</a></span><span class="op">(</span><span class="st">"mkin"</span><span class="op">)</span> <span class="op">></span> <span class="st">"0.9.48.1"</span><span class="op">)</span> <span class="op">{</span></span> <span> <span class="va">mmkin_bench</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, <span class="va">error_model</span> <span class="op">=</span> <span class="st">"const"</span><span class="op">)</span> <span class="op">{</span></span> @@ -194,11 +223,14 @@ <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> +<p>Benchmarks for all available error models are shown. They are +intended for improving mkin, not for comparing CPUs or operating +systems. All trademarks belong to their respective owners.</p> <div class="section level3"> <h3 id="parent-only">Parent only<a class="anchor" aria-label="anchor" href="#parent-only"></a> </h3> -<p>Constant variance (t1) and two-component error model (t2) for four models fitted to two datasets, i.e. eight fits for each test.</p> +<p>Constant variance (t1) and two-component error model (t2) for four +models fitted to two datasets, i.e. eight fits for each test.</p> <table class="table"> <thead><tr class="header"> <th align="left">OS</th> @@ -353,13 +385,55 @@ <td align="right">2.140</td> <td align="right">3.774</td> </tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">2.187</td> +<td align="right">3.851</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">1.288</td> +<td align="right">1.794</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">1.276</td> +<td align="right">1.804</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.3</td> +<td align="right">1.370</td> +<td align="right">1.883</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.3</td> +<td align="left">1.2.3</td> +<td align="right">1.406</td> +<td align="right">1.948</td> +</tr> </tbody> </table> </div> <div class="section level3"> <h3 id="one-metabolite">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite"></a> </h3> -<p>Constant variance (t3), two-component error model (t4), and variance by variable (t5) for three models fitted to one dataset, i.e. three fits for each test.</p> +<p>Constant variance (t3), two-component error model (t4), and variance +by variable (t5) for three models fitted to one dataset, i.e. three fits +for each test.</p> <table class="table"> <thead><tr class="header"> <th align="left">OS</th> @@ -533,14 +607,73 @@ <td align="right">6.193</td> <td align="right">2.843</td> </tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">1.585</td> +<td align="right">6.335</td> +<td align="right">3.003</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">0.792</td> +<td align="right">2.378</td> +<td align="right">1.245</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">0.784</td> +<td align="right">2.355</td> +<td align="right">1.233</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.3</td> +<td align="right">0.770</td> +<td align="right">2.011</td> +<td align="right">1.123</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.3</td> +<td align="left">1.2.3</td> +<td align="right">0.793</td> +<td align="right">2.109</td> +<td align="right">1.178</td> +</tr> </tbody> </table> </div> <div class="section level3"> <h3 id="two-metabolites">Two metabolites<a class="anchor" aria-label="anchor" href="#two-metabolites"></a> </h3> -<p>Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.</p> +<p>Constant variance (t6 and t7), two-component error model (t8 and t9), +and variance by variable (t10 and t11) for one model fitted to one +dataset, i.e. one fit for each test.</p> <table class="table"> +<colgroup> +<col width="8%"> +<col width="19%"> +<col width="8%"> +<col width="12%"> +<col width="8%"> +<col width="8%"> +<col width="8%"> +<col width="9%"> +<col width="8%"> +<col width="9%"> +</colgroup> <thead><tr class="header"> <th align="left">OS</th> <th align="left">CPU</th> @@ -770,6 +903,66 @@ <td align="right">1.987</td> <td align="right">2.802</td> </tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">0.935</td> +<td align="right">1.381</td> +<td align="right">1.551</td> +<td align="right">3.209</td> +<td align="right">1.976</td> +<td align="right">3.013</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">0.445</td> +<td align="right">0.591</td> +<td align="right">0.660</td> +<td align="right">1.190</td> +<td align="right">0.814</td> +<td align="right">1.100</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">0.443</td> +<td align="right">0.586</td> +<td align="right">0.661</td> +<td align="right">1.176</td> +<td align="right">0.803</td> +<td align="right">1.097</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.3</td> +<td align="right">0.418</td> +<td align="right">0.530</td> +<td align="right">0.591</td> +<td align="right">1.006</td> +<td align="right">0.716</td> +<td align="right">0.949</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.3</td> +<td align="left">1.2.3</td> +<td align="right">0.432</td> +<td align="right">0.549</td> +<td align="right">0.609</td> +<td align="right">1.052</td> +<td align="right">0.743</td> +<td align="right">0.989</td> +</tr> </tbody> </table> </div> @@ -793,7 +986,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> </footer> |