Fix and rebuild documentation, see NEWS

I had to fix the two pathway vignettes, as they did not work with
the released version any more. So they and the multistart vignette
which got some small fixes as well were rebuilt.

Complete rebuild of the online docs with the released version. The
documentation of the 'hierarchial_kinetics' format had to be fixed
as well.

1 files changed, 212 insertions, 19 deletions

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">&gt;</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">&lt;-</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>