diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-06-04 15:09:28 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-06-04 15:09:28 +0200 |
| commit | 95178837d3f91e84837628446b5fd468179af2b9 (patch) | |
| tree | 8b162d5a22b28b59ca9c6bb27bf8f9dfbeaefbae /docs/articles/web_only/benchmarks.html | |
| parent | 9a96391589fef9f80f9c6c4881cc48a509cb75f2 (diff) | |
Additional algorithm "d_c", more tests, docs
The new algorithm tries direct optimization of the likelihood, as well
as a three step procedure. In this way, we consistently get the
model with the highest likelihood for SFO, DFOP and HS for all 12
new test datasets.
Diffstat (limited to 'docs/articles/web_only/benchmarks.html')
| -rw-r--r-- | docs/articles/web_only/benchmarks.html | 140 |
1 files changed, 77 insertions, 63 deletions
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index a53f1927..43f8d238 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -30,7 +30,7 @@ </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">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Benchmark timings for mkin on various systems</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-05-08</h4> + <h4 class="date">2019-06-04</h4> <div class="hidden name"><code>benchmarks.Rmd</code></div> @@ -115,32 +115,32 @@ <a class="sourceLine" id="cb1-12" title="12">}</a></code></pre></div> <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="co"># Parent only</span></a> <a class="sourceLine" id="cb2-2" title="2">t1 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">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="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a> -<a class="sourceLine" id="cb2-3" title="3">t2 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">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="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a> -<a class="sourceLine" id="cb2-4" title="4"></a> -<a class="sourceLine" id="cb2-5" title="5"><span class="co"># One metabolite</span></a> -<a class="sourceLine" id="cb2-6" title="6">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb2-7" title="7"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a> -<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<a class="sourceLine" id="cb2-3" title="3">t2 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">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="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: +## iteration limit reached without convergence (10)</code></pre> +<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="co"># One metabolite</span></a> +<a class="sourceLine" id="cb4-2" title="2">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb4-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a> +<a class="sourceLine" id="cb4-4" title="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb4-2" title="2"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> -<a class="sourceLine" id="cb4-3" title="3"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">DFOP_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> <a class="sourceLine" id="cb6-2" title="2"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> <a class="sourceLine" id="cb6-3" title="3"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">t3 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">DFOP_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb8-2" title="2"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> +<a class="sourceLine" id="cb8-3" title="3"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">t3 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): +## Observations with value of zero were removed from the data</code></pre> <pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data - -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): ## Observations with value of zero were removed from the data ## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): ## Observations with value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">t4 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/subset">subset</a></span>(FOCUS_<span class="dv">2006</span>_D, value <span class="op">!=</span><span class="st"> </span><span class="dv">0</span>)), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a> -<a class="sourceLine" id="cb10-2" title="2">t5 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">t4 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/subset">subset</a></span>(FOCUS_<span class="dv">2006</span>_D, value <span class="op">!=</span><span class="st"> </span><span class="dv">0</span>)), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a> +<a class="sourceLine" id="cb13-2" title="2">t5 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> <pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): ## Observations with value of zero were removed from the data @@ -149,117 +149,131 @@ ## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): ## Observations with value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="co"># Two metabolites, synthetic data</span></a> -<a class="sourceLine" id="cb12-2" title="2">m_synth_SFO_lin <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a> -<a class="sourceLine" id="cb12-3" title="3"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a> -<a class="sourceLine" id="cb12-4" title="4"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb12-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb12-6" title="6"></a> -<a class="sourceLine" id="cb12-7" title="7">m_synth_DFOP_par <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"DFOP"</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"M1"</span>, <span class="st">"M2"</span>)),</a> -<a class="sourceLine" id="cb12-8" title="8"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb12-9" title="9"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb12-10" title="10"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb12-11" title="11"></a> -<a class="sourceLine" id="cb12-12" title="12">SFO_lin_a <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">1</span>]]<span class="op">$</span>data</a> -<a class="sourceLine" id="cb12-13" title="13"></a> -<a class="sourceLine" id="cb12-14" title="14">DFOP_par_c <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">12</span>]]<span class="op">$</span>data</a> -<a class="sourceLine" id="cb12-15" title="15"></a> -<a class="sourceLine" id="cb12-16" title="16">t6 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a)))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-17" title="17">t7 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c)))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-18" title="18"></a> -<a class="sourceLine" id="cb12-19" title="19">t8 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-20" title="20">t9 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-21" title="21"></a> -<a class="sourceLine" id="cb12-22" title="22">t10 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-23" title="23">t11 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-24" title="24"></a> -<a class="sourceLine" id="cb12-25" title="25">mkin_benchmarks[system_string, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste0</a></span>(<span class="st">"t"</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">11</span>)] <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)</a> -<a class="sourceLine" id="cb12-26" title="26">mkin_benchmarks</a></code></pre></div> +<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1"><span class="co"># Two metabolites, synthetic data</span></a> +<a class="sourceLine" id="cb15-2" title="2">m_synth_SFO_lin <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a> +<a class="sourceLine" id="cb15-3" title="3"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a> +<a class="sourceLine" id="cb15-4" title="4"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb15-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb15-6" title="6"></a> +<a class="sourceLine" id="cb15-7" title="7">m_synth_DFOP_par <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"DFOP"</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"M1"</span>, <span class="st">"M2"</span>)),</a> +<a class="sourceLine" id="cb15-8" title="8"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb15-9" title="9"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb15-10" title="10"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb15-11" title="11"></a> +<a class="sourceLine" id="cb15-12" title="12">SFO_lin_a <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">1</span>]]<span class="op">$</span>data</a> +<a class="sourceLine" id="cb15-13" title="13"></a> +<a class="sourceLine" id="cb15-14" title="14">DFOP_par_c <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">12</span>]]<span class="op">$</span>data</a> +<a class="sourceLine" id="cb15-15" title="15"></a> +<a class="sourceLine" id="cb15-16" title="16">t6 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a)))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-17" title="17">t7 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c)))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-18" title="18"></a> +<a class="sourceLine" id="cb15-19" title="19">t8 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-20" title="20">t9 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-21" title="21"></a> +<a class="sourceLine" id="cb15-22" title="22">t10 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-23" title="23">t11 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-24" title="24"></a> +<a class="sourceLine" id="cb15-25" title="25">mkin_benchmarks[system_string, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste0</a></span>(<span class="st">"t"</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">11</span>)] <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)</a> +<a class="sourceLine" id="cb15-26" title="26">mkin_benchmarks</a></code></pre></div> <pre><code>## CPU ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 AMD Ryzen 7 1700 Eight-Core Processor ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 AMD Ryzen 7 1700 Eight-Core Processor ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 AMD Ryzen 7 1700 Eight-Core Processor ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 AMD Ryzen 7 1700 Eight-Core Processor ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 AMD Ryzen 7 1700 Eight-Core Processor +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 AMD Ryzen 7 1700 Eight-Core Processor ## OS ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 Linux ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 Linux ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 Linux ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 Linux ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 Linux +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 Linux ## mkin ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 0.9.48.1 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 0.9.49.1 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 0.9.49.2 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 0.9.49.3 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 0.9.49.4 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 0.9.49.5 ## t1 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.610 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.792 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.805 ## t2 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 17.398 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.748 ## t3 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.427 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.403 ## t4 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 16.104 -## t5 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.527 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.613 +## t5 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.309 ## t6 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.541 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.546 ## t7 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.308 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.214 ## t8 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.775 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.871 ## t9 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 11.116 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.763 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.738 ## t10 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.063 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.763 ## t11 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.784</code></pre> -<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div> +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.527</code></pre> +<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div> </div> </div> @@ -281,7 +295,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> |