Update online docs, fix bug that surfaced

2 files changed, 245 insertions, 68 deletions

diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html
index b37ac926..a2d9f7e8 100644
--- a/docs/dev/articles/web_only/benchmarks.html
+++ b/docs/dev/articles/web_only/benchmarks.html
@@ -34,14 +34,14 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development 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">
@@ -53,6 +53,9 @@
 <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>
@@ -60,22 +63,31 @@
       <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>
@@ -83,6 +95,15 @@
     <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>
@@ -106,13 +127,15 @@
 
       
 
-      </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 2022-11-24)</h4>
+            <h4 data-toc-skip class="date">Last change 17 February 2023
+(rebuilt 2023-02-17)</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>
@@ -121,9 +144,15 @@
 
     
     
-<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>
@@ -195,11 +224,14 @@
 <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>
@@ -362,13 +394,39 @@
 <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>
 </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>
@@ -551,14 +609,55 @@
 <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>
 </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>
@@ -800,6 +899,42 @@
 <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>
 </tbody>
 </table>
 </div>
@@ -823,7 +958,7 @@
 
 <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>
diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html
index 4fe648c6..551b34d4 100644
--- a/docs/dev/articles/web_only/saem_benchmarks.html
+++ b/docs/dev/articles/web_only/saem_benchmarks.html
@@ -34,7 +34,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span>
       </span>
     </div>
 
@@ -134,8 +134,8 @@
                         <h4 data-toc-skip class="author">Johannes
 Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 14 November 2022
-(rebuilt 2023-01-28)</h4>
+            <h4 data-toc-skip class="date">Last change 17 February 2023
+(rebuilt 2023-02-17)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small>
       <div class="hidden name"><code>saem_benchmarks.rmd</code></div>
@@ -191,7 +191,7 @@ explanation of the following preprocessing.</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span></span>
 <span>  <span class="va">sfo_const</span>, <span class="va">dfop_const</span>, <span class="va">sforb_const</span>, <span class="va">hs_const</span>,</span>
-<span>  <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu">kable</span><span class="op">(</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div>
+<span>  <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</span><span class="op">)</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr class="header">
 <th align="left"></th>
@@ -331,17 +331,7 @@ systems. All trademarks belong to their respective owners.</p>
 <h3 id="parent-only-1">Parent only<a class="anchor" aria-label="anchor" href="#parent-only-1"></a>
 </h3>
 <p>Constant variance for SFO, DFOP, SFORB and HS.</p>
-<table style="width:100%;" class="table">
-<colgroup>
-<col width="42%">
-<col width="8%">
-<col width="8%">
-<col width="9%">
-<col width="8%">
-<col width="8%">
-<col width="8%">
-<col width="8%">
-</colgroup>
+<table class="table">
 <thead><tr class="header">
 <th align="left">CPU</th>
 <th align="left">OS</th>
@@ -374,29 +364,39 @@ systems. All trademarks belong to their respective owners.</p>
 <td align="right">4.851</td>
 </tr>
 <tr class="odd">
-<td align="left">Ryzen 9 7950X 16-Core Processor</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.1</td>
+<td align="left">3.2</td>
+<td align="right">1.352</td>
+<td align="right">2.813</td>
+<td align="right">2.401</td>
+<td align="right">2.074</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
 <td align="left">Linux</td>
 <td align="left">1.2.2</td>
 <td align="left">3.2</td>
-<td align="right">1.470</td>
-<td align="right">2.263</td>
-<td align="right">1.840</td>
-<td align="right">2.299</td>
+<td align="right">1.328</td>
+<td align="right">2.738</td>
+<td align="right">2.336</td>
+<td align="right">2.023</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.3</td>
+<td align="left">3.2</td>
+<td align="right">1.118</td>
+<td align="right">2.036</td>
+<td align="right">2.010</td>
+<td align="right">2.088</td>
 </tr>
 </tbody>
 </table>
 <p>Two-component error fits for SFO, DFOP, SFORB and HS.</p>
-<table style="width:100%;" class="table">
-<colgroup>
-<col width="42%">
-<col width="8%">
-<col width="8%">
-<col width="9%">
-<col width="8%">
-<col width="8%">
-<col width="8%">
-<col width="8%">
-</colgroup>
+<table class="table">
 <thead><tr class="header">
 <th align="left">CPU</th>
 <th align="left">OS</th>
@@ -429,14 +429,34 @@ systems. All trademarks belong to their respective owners.</p>
 <td align="right">8.401</td>
 </tr>
 <tr class="odd">
-<td align="left">Ryzen 9 7950X 16-Core Processor</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.1</td>
+<td align="left">3.2</td>
+<td align="right">2.388</td>
+<td align="right">3.033</td>
+<td align="right">3.532</td>
+<td align="right">3.310</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
 <td align="left">Linux</td>
 <td align="left">1.2.2</td>
 <td align="left">3.2</td>
-<td align="right">2.118</td>
-<td align="right">3.528</td>
-<td align="right">3.295</td>
-<td align="right">3.157</td>
+<td align="right">2.341</td>
+<td align="right">2.968</td>
+<td align="right">3.465</td>
+<td align="right">3.341</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.3</td>
+<td align="left">3.2</td>
+<td align="right">2.159</td>
+<td align="right">3.584</td>
+<td align="right">3.307</td>
+<td align="right">3.460</td>
 </tr>
 </tbody>
 </table>
@@ -446,14 +466,6 @@ systems. All trademarks belong to their respective owners.</p>
 </h3>
 <p>Two-component error for DFOP-SFO and SFORB-SFO.</p>
 <table class="table">
-<colgroup>
-<col width="48%">
-<col width="9%">
-<col width="9%">
-<col width="10%">
-<col width="10%">
-<col width="12%">
-</colgroup>
 <thead><tr class="header">
 <th align="left">CPU</th>
 <th align="left">OS</th>
@@ -480,12 +492,28 @@ systems. All trademarks belong to their respective owners.</p>
 <td align="right">798.580</td>
 </tr>
 <tr class="odd">
-<td align="left">Ryzen 9 7950X 16-Core Processor</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.1</td>
+<td align="left">3.2</td>
+<td align="right">11.247</td>
+<td align="right">285.216</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
 <td align="left">Linux</td>
 <td align="left">1.2.2</td>
 <td align="left">3.2</td>
-<td align="right">12.336</td>
-<td align="right">277.666</td>
+<td align="right">11.242</td>
+<td align="right">284.258</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.3</td>
+<td align="left">3.2</td>
+<td align="right">11.796</td>
+<td align="right">216.012</td>
 </tr>
 </tbody>
 </table>
@@ -518,11 +546,25 @@ systems. All trademarks belong to their respective owners.</p>
 <td align="right">1312.445</td>
 </tr>
 <tr class="odd">
-<td align="left">Ryzen 9 7950X 16-Core Processor</td>
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.1</td>
+<td align="left">3.2</td>
+<td align="right">489.939</td>
+</tr>
+<tr class="even">
+<td align="left">Ryzen 9 7950X</td>
 <td align="left">Linux</td>
 <td align="left">1.2.2</td>
 <td align="left">3.2</td>
-<td align="right">459.051</td>
+<td align="right">482.970</td>
+</tr>
+<tr class="odd">
+<td align="left">Ryzen 9 7950X</td>
+<td align="left">Linux</td>
+<td align="left">1.2.3</td>
+<td align="left">3.2</td>
+<td align="right">392.364</td>
 </tr>
 </tbody>
 </table>