Update pkgdown

1 files changed, 165 insertions, 30 deletions

diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index b47df46f..b0bb5196 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -68,6 +68,9 @@
     <li>
       <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
+    <li>
+      <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+    </li>
   </ul>
 </li>
 <li>
@@ -168,18 +171,18 @@
 
 <span class="no">DFOP_par_c</span> <span class="kw">&lt;-</span> <span class="no">synthetic_data_for_UBA_2014</span><span class="kw">[[</span><span class="fl">12</span>]]$<span class="no">data</span>
 
-<span class="no">t6</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>)))[<span class="st">"elapsed"</span>]
-<span class="no">t7</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>)))[<span class="st">"elapsed"</span>]
+<span class="no">t6</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
+<span class="no">t7</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
 
 <span class="no">t8</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>),
-    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]
+    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
 <span class="no">t9</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>),
-    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]
+    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
 
 <span class="no">t10</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>),
-    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]
+    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]
 <span class="no">t11</span> <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>),
-    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</pre></body></html></div>
+    <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]</pre></body></html></div>
 <div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="no">mkin_benchmarks</span>[<span class="no">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"t"</span>, <span class="fl">1</span>:<span class="fl">11</span>)] <span class="kw">&lt;-</span>
   <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">t1</span>, <span class="no">t2</span>, <span class="no">t3</span>, <span class="no">t4</span>, <span class="no">t5</span>, <span class="no">t6</span>, <span class="no">t7</span>, <span class="no">t8</span>, <span class="no">t9</span>, <span class="no">t10</span>, <span class="no">t11</span>)
 <span class="fu"><a href="https://rdrr.io/r/base/save.html">save</a></span>(<span class="no">mkin_benchmarks</span>, <span class="kw">file</span> <span class="kw">=</span> <span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span>)</pre></body></html></div>
@@ -188,45 +191,177 @@
 <h2 class="hasAnchor">
 <a href="#results" class="anchor"></a>Results</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.</p>
+<div class="sourceCode" id="cb12"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/colnames.html">rownames</a></span>(<span class="no">mkin_benchmarks</span>) <span class="kw">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html">as.character</a></span>(<span class="no">mkin_benchmarks</span>$<span class="no">mkin</span>)</pre></body></html></div>
 <p>Benchmarks for all available error models are shown.</p>
 <div id="parent-only" class="section level3">
 <h3 class="hasAnchor">
 <a href="#parent-only" class="anchor"></a>Parent only</h3>
 <p>Constant variance and two-component error model:</p>
-<div class="sourceCode" id="cb12"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">mkin_benchmarks</span>[, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"mkin"</span>, <span class="st">"t1"</span>, <span class="st">"t2"</span>)], <span class="kw">row.names</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
-<pre><code>##      mkin    t1     t2
-##  0.9.48.1 3.610 11.019
-##  0.9.49.1 8.184 22.889
-##  0.9.49.2 7.064 12.558
-##  0.9.49.3 7.296 21.239
-##  0.9.49.4 5.936 20.545
-##  0.9.50.2 1.697  3.895</code></pre>
+<div class="sourceCode" id="cb13"><html><body><pre class="r"><span class="fu">kable</span>(<span class="no">mkin_benchmarks</span>[, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"t1"</span>, <span class="st">"t2"</span>)])</pre></body></html></div>
+<table class="table">
+<thead><tr class="header">
+<th></th>
+<th align="right">t1</th>
+<th align="right">t2</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td>0.9.48.1</td>
+<td align="right">3.610</td>
+<td align="right">11.019</td>
+</tr>
+<tr class="even">
+<td>0.9.49.1</td>
+<td align="right">8.184</td>
+<td align="right">22.889</td>
+</tr>
+<tr class="odd">
+<td>0.9.49.2</td>
+<td align="right">7.064</td>
+<td align="right">12.558</td>
+</tr>
+<tr class="even">
+<td>0.9.49.3</td>
+<td align="right">7.296</td>
+<td align="right">21.239</td>
+</tr>
+<tr class="odd">
+<td>0.9.49.4</td>
+<td align="right">5.936</td>
+<td align="right">20.545</td>
+</tr>
+<tr class="even">
+<td>0.9.50.2</td>
+<td align="right">1.659</td>
+<td align="right">3.900</td>
+</tr>
+</tbody>
+</table>
 </div>
 <div id="one-metabolite" class="section level3">
 <h3 class="hasAnchor">
 <a href="#one-metabolite" class="anchor"></a>One metabolite</h3>
 <p>Constant variance, variance by variable and two-component error model:</p>
-<div class="sourceCode" id="cb14"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">mkin_benchmarks</span>[, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"mkin"</span>, <span class="st">"t3"</span>, <span class="st">"t4"</span>, <span class="st">"t5"</span>)], <span class="kw">row.names</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
-<pre><code>##      mkin    t3     t4    t5
-##  0.9.48.1 3.764 14.347 9.495
-##  0.9.49.1 4.649 13.789 6.395
-##  0.9.49.2 4.786  8.461 5.675
-##  0.9.49.3 4.510 13.805 7.386
-##  0.9.49.4 4.446 15.335 6.002
-##  0.9.50.2 1.365  6.105 2.727</code></pre>
+<div class="sourceCode" id="cb14"><html><body><pre class="r"><span class="fu">kable</span>(<span class="no">mkin_benchmarks</span>[, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"t3"</span>, <span class="st">"t4"</span>, <span class="st">"t5"</span>)])</pre></body></html></div>
+<table class="table">
+<thead><tr class="header">
+<th></th>
+<th align="right">t3</th>
+<th align="right">t4</th>
+<th align="right">t5</th>
+</tr></thead>
+<tbody>
+<tr class="odd">
+<td>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>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>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>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>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>0.9.50.2</td>
+<td align="right">1.389</td>
+<td align="right">6.106</td>
+<td align="right">2.716</td>
+</tr>
+</tbody>
+</table>
 </div>
 <div id="two-metabolites" class="section level3">
 <h3 class="hasAnchor">
 <a href="#two-metabolites" class="anchor"></a>Two metabolites</h3>
 <p>Two different datasets, for each constant variance, variance by variable and two-component error model are shown:</p>
-<div class="sourceCode" id="cb16"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">mkin_benchmarks</span>[, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"mkin"</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"t"</span>, <span class="fl">6</span>:<span class="fl">11</span>))], <span class="kw">row.names</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div>
-<pre><code>##      mkin    t6    t7    t8     t9   t10    t11
-##  0.9.48.1 2.623 4.587 7.525 16.621 8.576 31.267
-##  0.9.49.1 2.542 4.128 4.632  8.171 3.676  5.636
-##  0.9.49.2 2.723 4.478 4.862  7.618 3.579  5.574
-##  0.9.49.3 2.643 4.374  7.02 11.124 5.388  7.365
-##  0.9.49.4 2.635 4.259 4.737  7.763 3.427  5.626
-##  0.9.50.2 0.752 1.218 1.273  2.851 2.038  2.968</code></pre>
+<div class="sourceCode" id="cb15"><html><body><pre class="r"><span class="fu">kable</span>(<span class="no">mkin_benchmarks</span>[, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"t"</span>, <span class="fl">6</span>:<span class="fl">11</span>)])</pre></body></html></div>
+<table class="table">
+<thead><tr class="header">
+<th></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>0.9.48.1</td>
+<td align="right">2.623</td>
+<td align="right">4.587</td>
+<td align="right">7.525</td>
+<td align="right">16.621</td>
+<td align="right">8.576</td>
+<td align="right">31.267</td>
+</tr>
+<tr class="even">
+<td>0.9.49.1</td>
+<td align="right">2.542</td>
+<td align="right">4.128</td>
+<td align="right">4.632</td>
+<td align="right">8.171</td>
+<td align="right">3.676</td>
+<td align="right">5.636</td>
+</tr>
+<tr class="odd">
+<td>0.9.49.2</td>
+<td align="right">2.723</td>
+<td align="right">4.478</td>
+<td align="right">4.862</td>
+<td align="right">7.618</td>
+<td align="right">3.579</td>
+<td align="right">5.574</td>
+</tr>
+<tr class="even">
+<td>0.9.49.3</td>
+<td align="right">2.643</td>
+<td align="right">4.374</td>
+<td align="right">7.020</td>
+<td align="right">11.124</td>
+<td align="right">5.388</td>
+<td align="right">7.365</td>
+</tr>
+<tr class="odd">
+<td>0.9.49.4</td>
+<td align="right">2.635</td>
+<td align="right">4.259</td>
+<td align="right">4.737</td>
+<td align="right">7.763</td>
+<td align="right">3.427</td>
+<td align="right">5.626</td>
+</tr>
+<tr class="even">
+<td>0.9.50.2</td>
+<td align="right">0.751</td>
+<td align="right">1.209</td>
+<td align="right">1.270</td>
+<td align="right">2.859</td>
+<td align="right">2.026</td>
+<td align="right">2.963</td>
+</tr>
+</tbody>
+</table>
 </div>
 </div>
   </div>