Remove outdated comment in FOCUS L vignette, update docs

This also adds the first benchmark results obtained on my laptop system

1 files changed, 92 insertions, 53 deletions

diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 2eea3cb2..058d43fa 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -43,7 +43,7 @@
   <a href="../../reference/index.html">Functions and data</a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     Articles
      
     <span class="caret"></span>
@@ -105,7 +105,7 @@
       <h1 data-toc-skip>Benchmark timings for mkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 13 May 2020 (rebuilt 2022-03-02)</h4>
+            <h4 data-toc-skip class="date">Last change 13 May 2020 (rebuilt 2022-05-18)</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>
@@ -121,7 +121,7 @@
 <p>Parent only:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span class="va">FOCUS_C</span> <span class="op">&lt;-</span> <span class="va">FOCUS_2006_C</span>
-<span class="va">FOCUS_D</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>
+<span class="va">FOCUS_D</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>
 <span class="va">parent_datasets</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 class="va">FOCUS_C</span>, <span class="va">FOCUS_D</span><span class="op">)</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="fu">mmkin_bench</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">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span><span class="op">)</span>, <span class="va">parent_datasets</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>
@@ -179,74 +179,83 @@
 <div class="section level2">
 <h2 id="results">Results<a class="anchor" aria-label="anchor" href="#results"></a>
 </h2>
-<p>Currently, we only have benchmark information on one system, therefore only the mkin version is shown with the results below. Timings are in seconds, shorter is better. All results were obtained by serial, i.e. not using multiple computing cores.</p>
 <p>Benchmarks for all available error models are shown.</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>
-<table class="table">
+<table style="width:100%;" class="table">
+<colgroup>
+<col width="84%">
+<col width="7%">
+<col width="8%">
+</colgroup>
 <thead><tr class="header">
-<th align="left">mkin version</th>
-<th align="right">t1 [s]</th>
-<th align="right">t2 [s]</th>
+<th align="left"></th>
+<th align="right">t1</th>
+<th align="right">t2</th>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">0.9.48.1</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1</td>
 <td align="right">3.610</td>
 <td align="right">11.019</td>
 </tr>
 <tr class="even">
-<td align="left">0.9.49.1</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1</td>
 <td align="right">8.184</td>
 <td align="right">22.889</td>
 </tr>
 <tr class="odd">
-<td align="left">0.9.49.2</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2</td>
 <td align="right">7.064</td>
 <td align="right">12.558</td>
 </tr>
 <tr class="even">
-<td align="left">0.9.49.3</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3</td>
 <td align="right">7.296</td>
 <td align="right">21.239</td>
 </tr>
 <tr class="odd">
-<td align="left">0.9.49.4</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4</td>
 <td align="right">5.936</td>
 <td align="right">20.545</td>
 </tr>
 <tr class="even">
-<td align="left">0.9.50.2</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2</td>
 <td align="right">1.714</td>
 <td align="right">3.971</td>
 </tr>
 <tr class="odd">
-<td align="left">0.9.50.3</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.3</td>
 <td align="right">1.752</td>
 <td align="right">4.156</td>
 </tr>
 <tr class="even">
-<td align="left">0.9.50.4</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.4</td>
 <td align="right">1.786</td>
 <td align="right">3.729</td>
 </tr>
 <tr class="odd">
-<td align="left">1.0.3</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.3</td>
 <td align="right">1.881</td>
 <td align="right">3.504</td>
 </tr>
 <tr class="even">
-<td align="left">1.0.4</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.4</td>
 <td align="right">1.867</td>
 <td align="right">3.450</td>
 </tr>
 <tr class="odd">
-<td align="left">1.1.0</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.1.0</td>
 <td align="right">1.938</td>
 <td align="right">3.517</td>
 </tr>
+<tr class="even">
+<td align="left">Linux, Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz, mkin version 1.1.0</td>
+<td align="right">1.621</td>
+<td align="right">3.123</td>
+</tr>
 </tbody>
 </table>
 </div>
@@ -255,79 +264,91 @@
 </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>
 <table class="table">
+<colgroup>
+<col width="78%">
+<col width="6%">
+<col width="7%">
+<col width="6%">
+</colgroup>
 <thead><tr class="header">
-<th align="left">mkin version</th>
-<th align="right">t3 [s]</th>
-<th align="right">t4 [s]</th>
-<th align="right">t5 [s]</th>
+<th align="left"></th>
+<th align="right">t3</th>
+<th align="right">t4</th>
+<th align="right">t5</th>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">0.9.48.1</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1</td>
 <td align="right">3.764</td>
 <td align="right">14.347</td>
 <td align="right">9.495</td>
 </tr>
 <tr class="even">
-<td align="left">0.9.49.1</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1</td>
 <td align="right">4.649</td>
 <td align="right">13.789</td>
 <td align="right">6.395</td>
 </tr>
 <tr class="odd">
-<td align="left">0.9.49.2</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2</td>
 <td align="right">4.786</td>
 <td align="right">8.461</td>
 <td align="right">5.675</td>
 </tr>
 <tr class="even">
-<td align="left">0.9.49.3</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3</td>
 <td align="right">4.510</td>
 <td align="right">13.805</td>
 <td align="right">7.386</td>
 </tr>
 <tr class="odd">
-<td align="left">0.9.49.4</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4</td>
 <td align="right">4.446</td>
 <td align="right">15.335</td>
 <td align="right">6.002</td>
 </tr>
 <tr class="even">
-<td align="left">0.9.50.2</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2</td>
 <td align="right">1.402</td>
 <td align="right">6.174</td>
 <td align="right">2.764</td>
 </tr>
 <tr class="odd">
-<td align="left">0.9.50.3</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.3</td>
 <td align="right">1.430</td>
 <td align="right">6.615</td>
 <td align="right">2.878</td>
 </tr>
 <tr class="even">
-<td align="left">0.9.50.4</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.4</td>
 <td align="right">1.397</td>
 <td align="right">7.251</td>
 <td align="right">2.810</td>
 </tr>
 <tr class="odd">
-<td align="left">1.0.3</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.3</td>
 <td align="right">1.430</td>
 <td align="right">6.344</td>
 <td align="right">2.798</td>
 </tr>
 <tr class="even">
-<td align="left">1.0.4</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.4</td>
 <td align="right">1.415</td>
 <td align="right">6.364</td>
 <td align="right">2.820</td>
 </tr>
 <tr class="odd">
-<td align="left">1.1.0</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.1.0</td>
 <td align="right">1.470</td>
 <td align="right">6.508</td>
 <td align="right">2.894</td>
 </tr>
+<tr class="even">
+<td align="left">Linux, Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz, mkin version 1.1.0</td>
+<td align="right">3.319</td>
+<td align="right">18.209</td>
+<td align="right">7.773</td>
+</tr>
 </tbody>
 </table>
 </div>
@@ -336,18 +357,27 @@
 </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>
 <table class="table">
+<colgroup>
+<col width="64%">
+<col width="5%">
+<col width="5%">
+<col width="5%">
+<col width="6%">
+<col width="5%">
+<col width="6%">
+</colgroup>
 <thead><tr class="header">
-<th align="left">mkin version</th>
-<th align="right">t6 [s]</th>
-<th align="right">t7 [s]</th>
-<th align="right">t8 [s]</th>
-<th align="right">t9 [s]</th>
-<th align="right">t10 [s]</th>
-<th align="right">t11 [s]</th>
+<th align="left"></th>
+<th align="right">t6</th>
+<th align="right">t7</th>
+<th align="right">t8</th>
+<th align="right">t9</th>
+<th align="right">t10</th>
+<th align="right">t11</th>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">0.9.48.1</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1</td>
 <td align="right">2.623</td>
 <td align="right">4.587</td>
 <td align="right">7.525</td>
@@ -356,7 +386,7 @@
 <td align="right">31.267</td>
 </tr>
 <tr class="even">
-<td align="left">0.9.49.1</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1</td>
 <td align="right">2.542</td>
 <td align="right">4.128</td>
 <td align="right">4.632</td>
@@ -365,7 +395,7 @@
 <td align="right">5.636</td>
 </tr>
 <tr class="odd">
-<td align="left">0.9.49.2</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2</td>
 <td align="right">2.723</td>
 <td align="right">4.478</td>
 <td align="right">4.862</td>
@@ -374,7 +404,7 @@
 <td align="right">5.574</td>
 </tr>
 <tr class="even">
-<td align="left">0.9.49.3</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3</td>
 <td align="right">2.643</td>
 <td align="right">4.374</td>
 <td align="right">7.020</td>
@@ -383,7 +413,7 @@
 <td align="right">7.365</td>
 </tr>
 <tr class="odd">
-<td align="left">0.9.49.4</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4</td>
 <td align="right">2.635</td>
 <td align="right">4.259</td>
 <td align="right">4.737</td>
@@ -392,7 +422,7 @@
 <td align="right">5.626</td>
 </tr>
 <tr class="even">
-<td align="left">0.9.50.2</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2</td>
 <td align="right">0.777</td>
 <td align="right">1.236</td>
 <td align="right">1.332</td>
@@ -401,7 +431,7 @@
 <td align="right">2.987</td>
 </tr>
 <tr class="odd">
-<td align="left">0.9.50.3</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.3</td>
 <td align="right">0.858</td>
 <td align="right">1.264</td>
 <td align="right">1.333</td>
@@ -410,7 +440,7 @@
 <td align="right">3.073</td>
 </tr>
 <tr class="even">
-<td align="left">0.9.50.4</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.4</td>
 <td align="right">0.783</td>
 <td align="right">1.282</td>
 <td align="right">1.486</td>
@@ -419,7 +449,7 @@
 <td align="right">3.105</td>
 </tr>
 <tr class="odd">
-<td align="left">1.0.3</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.3</td>
 <td align="right">0.763</td>
 <td align="right">1.244</td>
 <td align="right">1.457</td>
@@ -428,7 +458,7 @@
 <td align="right">2.839</td>
 </tr>
 <tr class="even">
-<td align="left">1.0.4</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.4</td>
 <td align="right">0.785</td>
 <td align="right">1.252</td>
 <td align="right">1.466</td>
@@ -437,7 +467,7 @@
 <td align="right">2.826</td>
 </tr>
 <tr class="odd">
-<td align="left">1.1.0</td>
+<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.1.0</td>
 <td align="right">0.810</td>
 <td align="right">1.264</td>
 <td align="right">1.503</td>
@@ -445,6 +475,15 @@
 <td align="right">1.984</td>
 <td align="right">2.847</td>
 </tr>
+<tr class="even">
+<td align="left">Linux, Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz, mkin version 1.1.0</td>
+<td align="right">2.348</td>
+<td align="right">3.579</td>
+<td align="right">4.254</td>
+<td align="right">11.315</td>
+<td align="right">5.981</td>
+<td align="right">8.368</td>
+</tr>
 </tbody>
 </table>
 </div>
@@ -468,7 +507,7 @@
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
 </div>
 
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