Improve docs of multistart method

17 files changed, 56 insertions, 128 deletions

diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html
index a82eb999..2aacc53a 100644
--- a/docs/dev/articles/index.html
+++ b/docs/dev/articles/index.html
@@ -81,11 +81,6 @@
     <li>
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
-    <li class="divider">
-    <li class="dropdown-header">Code coverage report</li>
-    <li>
-      <a href="../coverage/coverage.html"></a>
-    </li>
   </ul></li>
 <li>
   <a href="../news/index.html">News</a>
diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html
index d3d9d76d..b5635df2 100644
--- a/docs/dev/articles/web_only/multistart.html
+++ b/docs/dev/articles/web_only/multistart.html
@@ -127,15 +127,13 @@
 
       
 
-      </header><div class="row">
+      </header><script src="multistart_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Short demo of the multistart method</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 26 September 2022
-(rebuilt 2023-04-16)</h4>
+            <h4 data-toc-skip class="date">Last change 17 April 2023 (rebuilt 2023-04-17)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small>
       <div class="hidden name"><code>multistart.rmd</code></div>
@@ -144,8 +142,7 @@ Ranke</h4>
 
     
     
-<p>The dimethenamid data from 2018 from seven soils is used as example
-data in this vignette.</p>
+<p>The dimethenamid data from 2018 from seven soils is used as example data in this vignette.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span>
 <span><span class="va">dmta_ds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span>
@@ -157,54 +154,41 @@ data in this vignette.</p>
 <span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span>
 <span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span>
 <span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="cn">NULL</span></span></code></pre></div>
-<p>First, we check the DFOP model with the two-component error model and
-random effects for all degradation parameters.</p>
+<p>First, we check the DFOP model with the two-component error model and random effects for all degradation parameters.</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">f_mmkin</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">7</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span><span class="va">f_saem_full</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_full</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## [1] "sd(log_k2)"</span></span></code></pre>
-<p>We see that not all variability parameters are identifiable. The
-<code>illparms</code> function tells us that the confidence interval for
-the standard deviation of ‘log_k2’ includes zero. We check this
-assessment using multiple runs with different starting values.</p>
+<p>We see that not all variability parameters are identifiable. The <code>illparms</code> function tells us that the confidence interval for the standard deviation of ‘log_k2’ includes zero. We check this assessment using multiple runs with different starting values.</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">f_saem_full_multi</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_full</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span>
-<span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="va">f_saem_full_multi</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_full</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></span>
+<span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span><span class="op">)</span></span></code></pre></div>
 <p><img src="multistart_files/figure-html/unnamed-chunk-3-1.png" width="700"></p>
-<p>This confirms that the variance of k2 is the most problematic
-parameter, so we reduce the parameter distribution model by removing the
-intersoil variability for k2.</p>
+<p>This confirms that the variance of k2 is the most problematic parameter, so we reduce the parameter distribution model by removing the intersoil variability for k2.</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">f_saem_reduced</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span>
 <span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span>
-<span><span class="va">f_saem_reduced_multi</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span>
-<span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span><span class="op">)</span></span></code></pre></div>
+<span><span class="va">f_saem_reduced_multi</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">8</span><span class="op">)</span></span>
+<span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span>, ylim <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="fl">0.5</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <p><img src="multistart_files/figure-html/unnamed-chunk-4-1.png" width="700"></p>
-<p>The results confirm that all remaining parameters can be determined
-with sufficient certainty.</p>
-<p>We can also analyse the log-likelihoods obtained in the multiple
-runs:</p>
+<p>The results confirm that all remaining parameters can be determined with sufficient certainty.</p>
+<p>We can also analyse the log-likelihoods obtained in the multiple runs:</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../../reference/llhist.html">llhist</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span></span></code></pre></div>
 <p><img src="multistart_files/figure-html/unnamed-chunk-5-1.png" width="700"></p>
-<p>The parameter histograms can be further improved by excluding the
-result with the low likelihood.</p>
+<p>We can use the <code>anova</code> method to compare the models.</p>
 <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span>, llmin <span class="op">=</span> <span class="op">-</span><span class="fl">326</span>, ylim <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="fl">0.5</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
-<p><img src="multistart_files/figure-html/unnamed-chunk-6-1.png" width="700"></p>
-<p>We can use the <code>anova</code> method to compare the models,
-including a likelihood ratio test if the models are nested.</p>
-<div class="sourceCode" id="cb8"><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 class="va">f_saem_full</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+<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 class="va">f_saem_full</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span><span class="op">)</span>,</span>
+<span>  <span class="va">f_saem_reduced</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
 <pre><code><span><span class="co">## Data: 155 observations of 1 variable(s) grouped in 6 datasets</span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">##                            npar    AIC    BIC     Lik Chisq Df Pr(&gt;Chisq)</span></span>
-<span><span class="co">## best(f_saem_reduced_multi)    9 663.69 661.82 -322.85                    </span></span>
-<span><span class="co">## f_saem_full                  10 669.77 667.69 -324.89     0  1          1</span></span></code></pre>
-<p>While AIC and BIC are lower for the reduced model, the likelihood
-ratio test does not indicate a significant difference between the
-fits.</p>
+<span><span class="co">##                            npar    AIC    BIC     Lik  Chisq Df Pr(&gt;Chisq)</span></span>
+<span><span class="co">## f_saem_reduced                9 663.74 661.87 -322.87                     </span></span>
+<span><span class="co">## best(f_saem_reduced_multi)    9 663.60 661.72 -322.80 0.1476  0           </span></span>
+<span><span class="co">## f_saem_full                  10 670.35 668.26 -325.17 0.0000  1          1</span></span>
+<span><span class="co">## best(f_saem_full_multi)      10 665.61 663.53 -322.80 4.7372  0</span></span></code></pre>
+<p>The reduced model results in lower AIC and BIC values, so it is clearly preferable. Using multiple starting values gives a large improvement in case of the full model, because it is less well-defined, which impedes convergence. For the reduced model, using multiple starting values only results in a small improvement of the model fit.</p>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
index 8f514227..7ad9fa28 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
+++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png
diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
index 8135d270..f36995ae 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
+++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png
diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
index f0270537..152554f5 100644
--- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
+++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/dev/authors.html b/docs/dev/authors.html
index 7c11d186..3c95e7e0 100644
--- a/docs/dev/authors.html
+++ b/docs/dev/authors.html
@@ -81,11 +81,6 @@
     <li>
       <a href="articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
-    <li class="divider">
-    <li class="dropdown-header">Code coverage report</li>
-    <li>
-      <a href="coverage/coverage.html"></a>
-    </li>
   </ul></li>
 <li>
   <a href="news/index.html">News</a>
diff --git a/docs/dev/index.html b/docs/dev/index.html
index 317e3380..f892841f 100644
--- a/docs/dev/index.html
+++ b/docs/dev/index.html
@@ -115,12 +115,6 @@
     <li>
       <a href="articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
-    <li class="divider">
-    </li>
-<li class="dropdown-header">Code coverage report</li>
-    <li>
-      <a href="coverage/coverage.html"></a>
-    </li>
   </ul>
 </li>
 <li>
@@ -251,21 +245,12 @@
 <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
 </h2>
 <table class="table">
-<tr>
-<td>
-Ranke J, Wöltjen J, Schmidt J, and Comets E (2021) Taking kinetic evaluations of degradation data to the next level with nonlinear mixed-effects models. <i>Environments</i> <b>8</b> (8) 71 <a href="https://doi.org/10.3390/environments8080071" class="external-link">doi:10.3390/environments8080071</a>
-</td>
-</tr>
-<tr>
-<td>
-Ranke J, Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data <i>Environments</i> <b>6</b> (12) 124 <a href="https://doi.org/10.3390/environments6120124" class="external-link">doi:10.3390/environments6120124</a>
-</td>
-</tr>
-<tr>
-<td>
-Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic evaluation of chemical degradation data <i>Environmental Sciences Europe</i> <b>30</b> 17 <a href="https://doi.org/10.1186/s12302-018-0145-1" class="external-link">doi:10.1186/s12302-018-0145-1</a>
-</td>
-</tr>
+<tr><td>Ranke J, Wöltjen J, Schmidt J, and Comets E (2021) Taking kinetic evaluations of degradation data to the next level with nonlinear mixed-effects models. <i>Environments</i> <b>8</b> (8) 71 <a href="https://doi.org/10.3390/environments8080071" class="external-link">doi:10.3390/environments8080071</a>
+</td></tr>
+<tr><td>Ranke J, Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data <i>Environments</i> <b>6</b> (12) 124 <a href="https://doi.org/10.3390/environments6120124" class="external-link">doi:10.3390/environments6120124</a>
+</td></tr>
+<tr><td>Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic evaluation of chemical degradation data <i>Environmental Sciences Europe</i> <b>30</b> 17 <a href="https://doi.org/10.1186/s12302-018-0145-1" class="external-link">doi:10.1186/s12302-018-0145-1</a>
+</td></tr>
 </table>
 </div>
 <div class="section level2">
diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 2c169609..70eeeed6 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -81,11 +81,6 @@
     <li>
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
-    <li class="divider">
-    <li class="dropdown-header">Code coverage report</li>
-    <li>
-      <a href="../coverage/coverage.html"></a>
-    </li>
   </ul></li>
 <li>
   <a href="../news/index.html">News</a>
@@ -176,8 +171,7 @@
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.0.5" id="mkin-105-2021-09-15">mkin 1.0.5 (2021-09-15)<a class="anchor" aria-label="anchor" href="#mkin-105-2021-09-15"></a></h2>
-<ul><li>‘dimethenamid_2018’: Correct the data for the Borstel soil. The five observations from Staudenmaier (2013) that were previously stored as “Borstel 2” are actually just a subset of the 16 observations in “Borstel 1” which is now simply “Borstel”</li>
-</ul></div>
+<ul><li>‘dimethenamid_2018’: Correct the data for the Borstel soil. The five observations from Staudenmaier (2013) that were previously stored as “Borstel 2” are actually just a subset of the 16 observations in “Borstel 1” which is now simply “Borstel”</li></ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.0.4" id="mkin-104-2021-04-20">mkin 1.0.4 (2021-04-20)<a class="anchor" aria-label="anchor" href="#mkin-104-2021-04-20"></a></h2>
 <ul><li><p>All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters</p></li>
@@ -186,12 +180,10 @@
 </ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.0.3" id="mkin-103-2021-02-15">mkin 1.0.3 (2021-02-15)<a class="anchor" aria-label="anchor" href="#mkin-103-2021-02-15"></a></h2>
-<ul><li>Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages</li>
-</ul></div>
+<ul><li>Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages</li></ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.0.2" id="mkin-102-unreleased">mkin 1.0.2 (Unreleased)<a class="anchor" aria-label="anchor" href="#mkin-102-unreleased"></a></h2>
-<ul><li>‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’</li>
-</ul></div>
+<ul><li>‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’</li></ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="1.0.1" id="mkin-101-2021-02-10">mkin 1.0.1 (2021-02-10)<a class="anchor" aria-label="anchor" href="#mkin-101-2021-02-10"></a></h2>
 <ul><li><p>‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults</p></li>
@@ -246,8 +238,7 @@
 </ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9.49.11" id="mkin-094911-2020-04-20">mkin 0.9.49.11 (2020-04-20)<a class="anchor" aria-label="anchor" href="#mkin-094911-2020-04-20"></a></h2>
-<ul><li>Increase a test tolerance to make it pass on all CRAN check machines</li>
-</ul></div>
+<ul><li>Increase a test tolerance to make it pass on all CRAN check machines</li></ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9.49.10" id="mkin-094910-2020-04-18">mkin 0.9.49.10 (2020-04-18)<a class="anchor" aria-label="anchor" href="#mkin-094910-2020-04-18"></a></h2>
 <ul><li><p>‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods</p></li>
@@ -362,8 +353,7 @@
 </ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9.46" id="mkin-0946-2017-07-24">mkin 0.9.46 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-0946-2017-07-24"></a></h2>
-<ul><li>Remove <code>test_FOMC_ill-defined.R</code> as it is too platform dependent</li>
-</ul></div>
+<ul><li>Remove <code>test_FOMC_ill-defined.R</code> as it is too platform dependent</li></ul></div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9.45.2" id="mkin-09452-2017-07-24">mkin 0.9.45.2 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-09452-2017-07-24"></a></h2>
 <ul><li><p>Rename <code>twa</code> to <code>max_twa_parent</code> to avoid conflict with <code>twa</code> from my <code>pfm</code> package</p></li>
@@ -375,8 +365,7 @@
 <h2 class="page-header" data-toc-text="0.9.45.1" id="mkin-09451-2016-12-20">mkin 0.9.45.1 (2016-12-20)<a class="anchor" aria-label="anchor" href="#mkin-09451-2016-12-20"></a></h2>
 <div class="section level3">
 <h3 id="new-features-0-9-45-1">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-45-1"></a></h3>
-<ul><li>A <code>twa</code> function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).</li>
-</ul></div>
+<ul><li>A <code>twa</code> function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).</li></ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9.45" id="mkin-0945-2016-12-08">mkin 0.9.45 (2016-12-08)<a class="anchor" aria-label="anchor" href="#mkin-0945-2016-12-08"></a></h2>
@@ -391,8 +380,7 @@
 <h2 class="page-header" data-toc-text="0.9.44" id="mkin-0944-2016-06-29">mkin 0.9.44 (2016-06-29)<a class="anchor" aria-label="anchor" href="#mkin-0944-2016-06-29"></a></h2>
 <div class="section level3">
 <h3 id="bug-fixes-0-9-44">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-44"></a></h3>
-<ul><li>The test <code>test_FOMC_ill-defined</code> failed on several architectures, so the test is now skipped</li>
-</ul></div>
+<ul><li>The test <code>test_FOMC_ill-defined</code> failed on several architectures, so the test is now skipped</li></ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9.43" id="mkin-0943-2016-06-28">mkin 0.9.43 (2016-06-28)<a class="anchor" aria-label="anchor" href="#mkin-0943-2016-06-28"></a></h2>
@@ -426,8 +414,7 @@
 <h2 class="page-header" data-toc-text="0.9.42" id="mkin-0942-2016-03-25">mkin 0.9.42 (2016-03-25)<a class="anchor" aria-label="anchor" href="#mkin-0942-2016-03-25"></a></h2>
 <div class="section level3">
 <h3 id="major-changes-0-9-42">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-42"></a></h3>
-<ul><li>Add the argument <code>from_max_mean</code> to <code>mkinfit</code>, for fitting only the decline from the maximum observed value for models with a single observed variable</li>
-</ul></div>
+<ul><li>Add the argument <code>from_max_mean</code> to <code>mkinfit</code>, for fitting only the decline from the maximum observed value for models with a single observed variable</li></ul></div>
 <div class="section level3">
 <h3 id="minor-changes-0-9-42">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-9-42"></a></h3>
 <ul><li><p>Add plots to <code>compiled_models</code> vignette</p></li>
@@ -447,21 +434,18 @@
 <div class="section level3">
 <h3 id="bug-fixes-0-9-41">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-41"></a></h3>
 <ul><li>
-<code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36</li>
-</ul></div>
+<code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36</li></ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9-40" id="mkin-09-40-2015-07-21">mkin 0.9-40 (2015-07-21)<a class="anchor" aria-label="anchor" href="#mkin-09-40-2015-07-21"></a></h2>
 <div class="section level3">
 <h3 id="bug-fixes-0-9-40">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-40"></a></h3>
 <ul><li>
-<code><a href="../reference/endpoints.html">endpoints()</a></code>: For DFOP and SFORB models, where <code><a href="https://rdrr.io/r/stats/optimize.html" class="external-link">optimize()</a></code> is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as <code><a href="https://rdrr.io/r/stats/optimize.html" class="external-link">optimize()</a></code> sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient.</li>
-</ul></div>
+<code><a href="../reference/endpoints.html">endpoints()</a></code>: For DFOP and SFORB models, where <code><a href="https://rdrr.io/r/stats/optimize.html" class="external-link">optimize()</a></code> is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as <code><a href="https://rdrr.io/r/stats/optimize.html" class="external-link">optimize()</a></code> sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient.</li></ul></div>
 <div class="section level3">
 <h3 id="internal-changes-0-9-40">Internal changes<a class="anchor" aria-label="anchor" href="#internal-changes-0-9-40"></a></h3>
 <ul><li>
-<code>DESCRIPTION</code>, <code>NAMESPACE</code>, <code>R/*.R</code>: Import (from) stats, graphics and methods packages, and qualify some function calls for non-base packages installed with R to avoid NOTES made by R CMD check –as-cran with upcoming R versions.</li>
-</ul></div>
+<code>DESCRIPTION</code>, <code>NAMESPACE</code>, <code>R/*.R</code>: Import (from) stats, graphics and methods packages, and qualify some function calls for non-base packages installed with R to avoid NOTES made by R CMD check –as-cran with upcoming R versions.</li></ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9-39" id="mkin-09-39-2015-06-26">mkin 0.9-39 (2015-06-26)<a class="anchor" aria-label="anchor" href="#mkin-09-39-2015-06-26"></a></h2>
@@ -473,8 +457,7 @@
 <div class="section level3">
 <h3 id="bug-fixes-0-9-39">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-39"></a></h3>
 <ul><li>
-<code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Fix the x axis scaling for rate constants and formation fractions that got confused by the introduction of the t-values of transformed parameters.</li>
-</ul></div>
+<code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Fix the x axis scaling for rate constants and formation fractions that got confused by the introduction of the t-values of transformed parameters.</li></ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9-38" id="mkin-09-38-2015-06-24">mkin 0.9-38 (2015-06-24)<a class="anchor" aria-label="anchor" href="#mkin-09-38-2015-06-24"></a></h2>
@@ -486,8 +469,7 @@
 <div class="section level3">
 <h3 id="bug-fixes-0-9-38">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-38"></a></h3>
 <ul><li>
-<code><a href="../reference/mkinmod.html">mkinmod()</a></code>: When generating the C code for the derivatives, only declare the time variable when it is needed and remove the ‘-W-no-unused-variable’ compiler flag as the C compiler used in the CRAN checks on Solaris does not know it.</li>
-</ul></div>
+<code><a href="../reference/mkinmod.html">mkinmod()</a></code>: When generating the C code for the derivatives, only declare the time variable when it is needed and remove the ‘-W-no-unused-variable’ compiler flag as the C compiler used in the CRAN checks on Solaris does not know it.</li></ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9-36" id="mkin-09-36-2015-06-21">mkin 0.9-36 (2015-06-21)<a class="anchor" aria-label="anchor" href="#mkin-09-36-2015-06-21"></a></h2>
@@ -500,15 +482,13 @@
 </ul></div>
 <div class="section level3">
 <h3 id="minor-changes-0-9-36">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-9-36"></a></h3>
-<ul><li>Added a simple showcase vignette with an evaluation of FOCUS example dataset D</li>
-</ul></div>
+<ul><li>Added a simple showcase vignette with an evaluation of FOCUS example dataset D</li></ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9-35" id="mkin-09-35-2015-05-15">mkin 0.9-35 (2015-05-15)<a class="anchor" aria-label="anchor" href="#mkin-09-35-2015-05-15"></a></h2>
 <div class="section level3">
 <h3 id="major-changes-0-9-35">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-35"></a></h3>
-<ul><li>Switch from RUnit to testthat for testing</li>
-</ul></div>
+<ul><li>Switch from RUnit to testthat for testing</li></ul></div>
 <div class="section level3">
 <h3 id="bug-fixes-0-9-35">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-35"></a></h3>
 <ul><li><p><code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit</p></li>
@@ -590,15 +570,13 @@
 <h2 class="page-header" data-toc-text="0.9-31" id="mkin-09-31-2014-07-14">mkin 0.9-31 (2014-07-14)<a class="anchor" aria-label="anchor" href="#mkin-09-31-2014-07-14"></a></h2>
 <div class="section level3">
 <h3 id="bug-fixes-0-9-31">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-31"></a></h3>
-<ul><li>The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in <code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code> used by the summary function.</li>
-</ul></div>
+<ul><li>The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in <code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code> used by the summary function.</li></ul></div>
 </div>
     <div class="section level2">
 <h2 class="page-header" data-toc-text="0.9-30" id="mkin-09-30-2014-07-11">mkin 0.9-30 (2014-07-11)<a class="anchor" aria-label="anchor" href="#mkin-09-30-2014-07-11"></a></h2>
 <div class="section level3">
 <h3 id="new-features-0-9-30">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-30"></a></h3>
-<ul><li>It is now possible to use formation fractions in combination with turning off the sink in <code><a href="../reference/mkinmod.html">mkinmod()</a></code>.</li>
-</ul></div>
+<ul><li>It is now possible to use formation fractions in combination with turning off the sink in <code><a href="../reference/mkinmod.html">mkinmod()</a></code>.</li></ul></div>
 <div class="section level3">
 <h3 id="major-changes-0-9-30">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-30"></a></h3>
 <ul><li><p>The original and the transformed parameters now have different names (e.g. <code>k_parent</code> and <code>log_k_parent</code>. They also differ in how many they are when we have formation fractions but no pathway to sink.</p></li>
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index b7825ae1..a9ab0c60 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 2.17.1.1
+pandoc: 2.9.2.1
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
@@ -16,7 +16,7 @@ articles:
   dimethenamid_2018: web_only/dimethenamid_2018.html
   multistart: web_only/multistart.html
   saem_benchmarks: web_only/saem_benchmarks.html
-last_built: 2023-04-16T08:48Z
+last_built: 2023-04-17T17:35Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index 5de2bdc7..278fd2e2 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png
index 556ca0a7..4b646f22 100644
--- a/docs/dev/reference/Rplot002.png
+++ b/docs/dev/reference/Rplot002.png
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index 84bbbdc4..85dc7c6e 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -81,11 +81,6 @@
     <li>
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
-    <li class="divider">
-    <li class="dropdown-header">Code coverage report</li>
-    <li>
-      <a href="../coverage/coverage.html"></a>
-    </li>
   </ul></li>
 <li>
   <a href="../news/index.html">News</a>
diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html
index 01c15a19..7d8e7c26 100644
--- a/docs/dev/reference/mkinpredict.html
+++ b/docs/dev/reference/mkinpredict.html
@@ -394,11 +394,12 @@ as these always return mapped output.</p></dd>
 <span class="r-in"><span>      <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>      solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: rbenchmark</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>               test relative elapsed</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled      1.0   0.002</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4       analytical      1.0   0.002</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1            eigen      4.0   0.008</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3          deSolve     30.5   0.061</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled     1.00   0.004</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1            eigen     4.00   0.016</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4       analytical     4.25   0.017</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3          deSolve    40.75   0.163</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
 <span class="r-in"><span>  <span class="co"># Predict from a fitted model</span></span></span>
diff --git a/docs/dev/reference/multistart-1.png b/docs/dev/reference/multistart-1.png
index c7937d67..ee0306d6 100644
--- a/docs/dev/reference/multistart-1.png
+++ b/docs/dev/reference/multistart-1.png
diff --git a/docs/dev/reference/multistart-2.png b/docs/dev/reference/multistart-2.png
index e1983f12..69a178e3 100644
--- a/docs/dev/reference/multistart-2.png
+++ b/docs/dev/reference/multistart-2.png
diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html
index 3cdede7b..36767560 100644
--- a/docs/dev/reference/multistart.html
+++ b/docs/dev/reference/multistart.html
@@ -222,15 +222,13 @@ doi: 10.1186/s12859-021-04373-4.</p>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">f_saem_reduced</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="co"># On Windows, we need to create a cluster first. When working with</span></span></span>
-<span class="r-in"><span><span class="co"># such a cluster, we need to export the mmkin object to the cluster</span></span></span>
-<span class="r-in"><span><span class="co"># nodes, as it is referred to when updating the saem object on the nodes.</span></span></span>
+<span class="r-in"><span><span class="co"># On Windows, we need to create a PSOCK cluster first and refer to it</span></span></span>
+<span class="r-in"><span><span class="co"># in the call to multistart()</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">parallel</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">cl</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">f_saem_reduced_multi</span> <span class="op">&lt;-</span> <span class="fu">multistart</span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cluster <span class="op">=</span> <span class="va">cl</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in checkForRemoteErrors(val):</span> 16 nodes produced errors; first error: unused argument (mc.preschedule = FALSE)</span>
-<span class="r-in"><span><span class="fu"><a href="parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span><span class="op">)</span></span></span>
-<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in parplot(f_saem_reduced_multi, lpos = "topright"):</span> object 'f_saem_reduced_multi' not found</span>
+<span class="r-in"><span><span class="fu"><a href="parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span>, ylim <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="fl">0.5</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="multistart-2.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml
index b70dc782..b3542d0b 100644
--- a/docs/dev/sitemap.xml
+++ b/docs/dev/sitemap.xml
@@ -55,9 +55,6 @@
     <loc>https://pkgdown.jrwb.de/mkin/authors.html</loc>
   </url>
   <url>
-    <loc>https://pkgdown.jrwb.de/mkin/coverage/coverage.html</loc>
-  </url>
-  <url>
     <loc>https://pkgdown.jrwb.de/mkin/index.html</loc>
   </url>
   <url>