Update online docs

7 files changed, 183 insertions, 127 deletions

diff --git a/docs/dev/articles/mkin.html b/docs/dev/articles/mkin.html
index 6bfb63bc..27e532af 100644
--- a/docs/dev/articles/mkin.html
+++ b/docs/dev/articles/mkin.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">1.1.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span>
       </span>
     </div>
 
@@ -44,7 +44,7 @@
   <a href="../reference/index.html">Functions and data</a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     Articles
      
     <span class="caret"></span>
@@ -60,19 +60,28 @@
       <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </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>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul>
 </li>
@@ -103,7 +112,7 @@
       <h1 data-toc-skip>Introduction to mkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 15 February 2021 (rebuilt 2022-02-28)</h4>
+            <h4 data-toc-skip class="date">Last change 15 February 2021 (rebuilt 2022-11-16)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/mkin.rmd" class="external-link"><code>vignettes/mkin.rmd</code></a></small>
       <div class="hidden name"><code>mkin.rmd</code></div>
@@ -118,34 +127,34 @@
 </h2>
 <p>In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance has been developed, based on nonlinear optimisation. The <code>R</code> add-on package <code>mkin</code> implements fitting some of the models recommended in this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st"><a href="https://pkgdown.jrwb.de/mkin/">"mkin"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
-<span class="co"># Define the kinetic model</span>
-<span class="va">m_SFO_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,
-                         M1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,
-                         M2 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,
-                         use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
-
-
-<span class="co"># Produce model predictions using some arbitrary parameters</span>
-<span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span>
-<span class="va">d_SFO_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>,
-  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.03</span>,
-    f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>, k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">100</span>,
-    f_M1_to_M2 <span class="op">=</span> <span class="fl">0.9</span>, k_M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">50</span><span class="op">)</span>,
-  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,
-  <span class="va">sampling_times</span><span class="op">)</span>
-
-<span class="co"># Generate a dataset by adding normally distributed errors with</span>
-<span class="co"># standard deviation 3, for two replicates at each sampling time</span>
-<span class="va">d_SFO_SFO_SFO_err</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_SFO_SFO</span>, reps <span class="op">=</span> <span class="fl">2</span>,
-                             sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">3</span>,
-                             n <span class="op">=</span> <span class="fl">1</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span>
-
-<span class="co"># Fit the model to the dataset</span>
-<span class="va">f_SFO_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>, <span class="va">d_SFO_SFO_SFO_err</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
-
-<span class="co"># Plot the results separately for parent and metabolites</span>
-<span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_SFO_SFO_SFO</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></code></pre></div>
+<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="st"><a href="https://pkgdown.jrwb.de/mkin/">"mkin"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span><span class="co"># Define the kinetic model</span></span>
+<span><span class="va">m_SFO_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span>
+<span>                         M1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span>
+<span>                         M2 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span>
+<span>                         use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span></span>
+<span></span>
+<span><span class="co"># Produce model predictions using some arbitrary parameters</span></span>
+<span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span>
+<span><span class="va">d_SFO_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>,</span>
+<span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.03</span>,</span>
+<span>    f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>, k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">100</span>,</span>
+<span>    f_M1_to_M2 <span class="op">=</span> <span class="fl">0.9</span>, k_M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">50</span><span class="op">)</span>,</span>
+<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>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span>
+<span>  <span class="va">sampling_times</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># Generate a dataset by adding normally distributed errors with</span></span>
+<span><span class="co"># standard deviation 3, for two replicates at each sampling time</span></span>
+<span><span class="va">d_SFO_SFO_SFO_err</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_SFO_SFO</span>, reps <span class="op">=</span> <span class="fl">2</span>,</span>
+<span>                             sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">3</span>,</span>
+<span>                             n <span class="op">=</span> <span class="fl">1</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span></span>
+<span></span>
+<span><span class="co"># Fit the model to the dataset</span></span>
+<span><span class="va">f_SFO_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_SFO_SFO_SFO</span>, <span class="va">d_SFO_SFO_SFO_err</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># Plot the results separately for parent and metabolites</span></span>
+<span><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_SFO_SFO_SFO</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p>
 </div>
 <div class="section level2">
@@ -224,10 +233,10 @@
 <p>Ranke, J. 2021. <em>‘mkin‘: Kinetic Evaluation of Chemical Degradation Data</em>. <a href="https://CRAN.R-project.org/package=mkin" class="external-link">https://CRAN.R-project.org/package=mkin</a>.</p>
 </div>
 <div id="ref-ranke2012">
-<p>Ranke, J., and R. Lehmann. 2012. “Parameter Reliability in Kinetic Evaluation of Environmental Metabolism Data - Assessment and the Influence of Model Specification.” In <em>SETAC World 20-24 May</em>. Berlin.</p>
+<p>Ranke, J., and R. Lehmann. 2012. “Parameter Reliability in Kinetic Evaluation of Environmental Metabolism Data - Assessment and the Influence of Model Specification.” In <em>SETAC World 20-24 May</em>. Berlin. <a href="https://jrwb.de/posters/Poster_SETAC_2012_Kinetic_parameter_uncertainty_model_parameterization_Lehmann_Ranke.pdf" class="external-link">https://jrwb.de/posters/Poster_SETAC_2012_Kinetic_parameter_uncertainty_model_parameterization_Lehmann_Ranke.pdf</a>.</p>
 </div>
 <div id="ref-ranke2015">
-<p>———. 2015. “To T-Test or Not to T-Test, That Is the Question.” In <em>XV Symposium on Pesticide Chemistry 2-4 September 2015</em>. Piacenza. <a href="http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf" class="external-link">http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</a>.</p>
+<p>———. 2015. “To T-Test or Not to T-Test, That Is the Question.” In <em>XV Symposium on Pesticide Chemistry 2-4 September 2015</em>. Piacenza. <a href="https://jrwb.de/posters/piacenza_2015.pdf" class="external-link">https://jrwb.de/posters/piacenza_2015.pdf</a>.</p>
 </div>
 <div id="ref-ranke2019">
 <p>Ranke, Johannes, and Stefan Meinecke. 2019. “Error Models for the Kinetic Evaluation of Chemical Degradation Data.” <em>Environments</em> 6 (12). <a href="https://doi.org/10.3390/environments6120124" class="external-link">https://doi.org/10.3390/environments6120124</a>.</p>
@@ -262,7 +271,7 @@
 
 <div class="pkgdown">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer>
diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html
index e54bc38c..afff038f 100644
--- a/docs/dev/articles/web_only/saem_benchmarks.html
+++ b/docs/dev/articles/web_only/saem_benchmarks.html
@@ -112,7 +112,7 @@
       <h1 data-toc-skip>Benchmark timings for saem.mmkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-15)</h4>
+            <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-16)</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>
@@ -309,10 +309,10 @@
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">2.11</td>
-<td align="right">4.632</td>
-<td align="right">4.264</td>
-<td align="right">4.93</td>
+<td align="right">2.156</td>
+<td align="right">4.647</td>
+<td align="right">4.296</td>
+<td align="right">4.951</td>
 </tr></tbody>
 </table>
 <p>Two-component error fits for SFO, DFOP, SFORB and HS.</p>
@@ -332,10 +332,10 @@
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">5.602</td>
-<td align="right">7.373</td>
-<td align="right">7.815</td>
-<td align="right">7.831</td>
+<td align="right">5.645</td>
+<td align="right">7.415</td>
+<td align="right">7.848</td>
+<td align="right">7.967</td>
 </tr></tbody>
 </table>
 </div>
@@ -357,8 +357,8 @@
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">24.014</td>
-<td align="right">749.699</td>
+<td align="right">24.182</td>
+<td align="right">783.932</td>
 </tr></tbody>
 </table>
 </div>
@@ -379,7 +379,7 @@
 <td align="left">Linux</td>
 <td align="left">1.2.0</td>
 <td align="left">3.2</td>
-<td align="right">1249.834</td>
+<td align="right">1322.5</td>
 </tr></tbody>
 </table>
 </div>
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index e0c11a84..85be66c4 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -13,7 +13,7 @@ articles:
   dimethenamid_2018: web_only/dimethenamid_2018.html
   multistart: web_only/multistart.html
   saem_benchmarks: web_only/saem_benchmarks.html
-last_built: 2022-11-14T23:45Z
+last_built: 2022-11-16T09:48Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index 5d362f76..d0e192e7 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -21,7 +21,7 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src="
       </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">1.1.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span>
       </span>
     </div>
 
@@ -30,7 +30,7 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src="
   <a href="../reference/index.html">Functions and data</a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     Articles
      
     <span class="caret"></span>
@@ -45,19 +45,28 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src="
       <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </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>
     <li>
-      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul></li>
 <li>
@@ -92,22 +101,22 @@ components.</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinmod</span><span class="op">(</span>
-  <span class="va">...</span>,
-  use_of_ff <span class="op">=</span> <span class="st">"max"</span>,
-  name <span class="op">=</span> <span class="cn">NULL</span>,
-  speclist <span class="op">=</span> <span class="cn">NULL</span>,
-  quiet <span class="op">=</span> <span class="cn">FALSE</span>,
-  verbose <span class="op">=</span> <span class="cn">FALSE</span>,
-  dll_dir <span class="op">=</span> <span class="cn">NULL</span>,
-  unload <span class="op">=</span> <span class="cn">FALSE</span>,
-  overwrite <span class="op">=</span> <span class="cn">FALSE</span>
-<span class="op">)</span>
-
-<span class="co"># S3 method for mkinmod</span>
-<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="fu">mkinsub</span><span class="op">(</span><span class="va">submodel</span>, to <span class="op">=</span> <span class="cn">NULL</span>, sink <span class="op">=</span> <span class="cn">TRUE</span>, full_name <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinmod</span><span class="op">(</span></span>
+<span>  <span class="va">...</span>,</span>
+<span>  use_of_ff <span class="op">=</span> <span class="st">"max"</span>,</span>
+<span>  name <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  speclist <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  dll_dir <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  unload <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  overwrite <span class="op">=</span> <span class="cn">FALSE</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mkinmod</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mkinsub</span><span class="op">(</span><span class="va">submodel</span>, to <span class="op">=</span> <span class="cn">NULL</span>, sink <span class="op">=</span> <span class="cn">TRUE</span>, full_name <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -127,72 +136,108 @@ If the argument <code>use_of_ff</code> is set to "min"
 additional <code>mkinsub()</code> argument can be <code>sink = FALSE</code>, effectively
 fixing the flux to sink to zero.
 In print.mkinmod, this argument is currently not used.</p></dd>
+
+
 <dt>use_of_ff</dt>
 <dd><p>Specification of the use of formation fractions in the
 model equations and, if applicable, the coefficient matrix.  If "max",
 formation fractions are always used (default).  If "min", a minimum use of
 formation fractions is made, i.e. each first-order pathway to a metabolite
 has its own rate constant.</p></dd>
+
+
 <dt>name</dt>
 <dd><p>A name for the model. Should be a valid R object name.</p></dd>
+
+
 <dt>speclist</dt>
 <dd><p>The specification of the observed variables and their
 submodel types and pathways can be given as a single list using this
 argument. Default is NULL.</p></dd>
+
+
 <dt>quiet</dt>
 <dd><p>Should messages be suppressed?</p></dd>
+
+
 <dt>verbose</dt>
 <dd><p>If <code>TRUE</code>, passed to <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code> if
 applicable to give detailed information about the C function being built.</p></dd>
+
+
 <dt>dll_dir</dt>
 <dd><p>Directory where an DLL object, if generated internally by
 <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code>, should be saved.  The DLL will only be stored in a
 permanent location for use in future sessions, if 'dll_dir' and 'name'
 are specified.</p></dd>
+
+
 <dt>unload</dt>
 <dd><p>If a DLL from the target location in 'dll_dir' is already
 loaded, should that be unloaded first?</p></dd>
+
+
 <dt>overwrite</dt>
 <dd><p>If a file exists at the target DLL location in 'dll_dir',
 should this be overwritten?</p></dd>
+
+
 <dt>x</dt>
 <dd><p>An <code>mkinmod</code> object.</p></dd>
+
+
 <dt>submodel</dt>
 <dd><p>Character vector of length one to specify the submodel type.
 See <code>mkinmod</code> for the list of allowed submodel names.</p></dd>
+
+
 <dt>to</dt>
 <dd><p>Vector of the names of the state variable to which a
 transformation shall be included in the model.</p></dd>
+
+
 <dt>sink</dt>
 <dd><p>Should a pathway to sink be included in the model in addition to
 the pathways to other state variables?</p></dd>
+
+
 <dt>full_name</dt>
 <dd><p>An optional name to be used e.g. for plotting fits
 performed with the model.  You can use non-ASCII characters here, but then
 your R code will not be portable, <em>i.e.</em> may produce unintended plot
 results on other operating systems or system configurations.</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>A list of class <code>mkinmod</code> for use with <code><a href="mkinfit.html">mkinfit()</a></code>,
+    
+
+<p>A list of class <code>mkinmod</code> for use with <code><a href="mkinfit.html">mkinfit()</a></code>,
 containing, among others,</p>
 <dl><dt>diffs</dt>
 <dd><p>A vector of string representations of differential equations, one for
 each modelling variable.</p></dd>
+
 <dt>map</dt>
 <dd><p>A list containing named character vectors for each observed variable,
 specifying the modelling variables by which it is represented.</p></dd>
+
 <dt>use_of_ff</dt>
 <dd><p>The content of <code>use_of_ff</code> is passed on in this list component.</p></dd>
+
 <dt>deg_func</dt>
 <dd><p>If generated, a function containing the solution of the degradation
 model.</p></dd>
+
 <dt>coefmat</dt>
 <dd><p>The coefficient matrix, if the system of differential equations can be
 represented by one.</p></dd>
+
 <dt>cf</dt>
 <dd><p>If generated, a compiled function calculating the derivatives as
 returned by cfunction.</p></dd>
+
+
 </dl><p>A list for use with <code>mkinmod</code>.</p>
     </div>
     <div id="details">
@@ -230,16 +275,16 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 
     <div id="ref-examples">
     <h2>Examples</h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span>
-<span class="r-in"><span class="co"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span></span>
-<span class="r-in"><span class="va">SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span>parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># One parent compound, one metabolite, both single first order</span></span>
-<span class="r-in"><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span>
-<span class="r-in">  parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span>
-<span class="r-in">  m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span></span></span>
+<span class="r-in"><span><span class="va">SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span>parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># One parent compound, one metabolite, both single first order</span></span></span>
+<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span>
+<span class="r-in"><span>  parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;mkinmod&gt; model generated with</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Use of formation fractions $use_of_ff: max </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Specification $spec:</span>
@@ -252,30 +297,32 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Differential equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - k_parent * parent</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># \dontrun{</span></span>
-<span class="r-in"> <span class="va">fit_sfo_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span>
-<span class="r-in"></span>
-<span class="r-in"> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span>
-<span class="r-in"> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span>
-<span class="r-in"> <span class="va">DLL_dir</span> <span class="op">&lt;-</span> <span class="st">"~/.local/share/mkin"</span></span>
-<span class="r-in"> <span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.exists</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.create</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span></span>
-<span class="r-in"> <span class="va">SFO_SFO.2</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span>
-<span class="r-in">   parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span>
-<span class="r-in">   m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span>
-<span class="r-in">   name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Copied DLL from /tmp/Rtmp6NiOcv/fileb89c01ace19ec.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span>
-<span class="r-in"><span class="co"># Now we can save the model and restore it in a new session</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span>
-<span class="r-in"><span class="co"># Terminate the R session here if you would like to check, and then do</span></span>
-<span class="r-in"><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 class="r-in"><span class="va">SFO_SFO.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span>
-<span class="r-in"><span class="va">fit_sfo_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.3</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># Show details of creating the C function</span></span>
-<span class="r-in"><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span>
-<span class="r-in">  parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span>
-<span class="r-in">  m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></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="va">fit_sfo_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span></span>
+<span class="r-in"><span> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span></span>
+<span class="r-in"><span> <span class="va">DLL_dir</span> <span class="op">&lt;-</span> <span class="st">"~/.local/share/mkin"</span></span></span>
+<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.exists</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/files2.html" class="external-link">dir.create</a></span><span class="op">(</span><span class="va">DLL_dir</span><span class="op">)</span></span></span>
+<span class="r-in"><span> <span class="va">SFO_SFO.2</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span>
+<span class="r-in"><span>   parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>   m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>   name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Copied DLL from /tmp/Rtmpp1dECS/file32009e039f7a.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span>
+<span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</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"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">SFO_SFO.3</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">fit_sfo_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.3</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Show details of creating the C function</span></span></span>
+<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span>
+<span class="r-in"><span>  parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Program source:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   1: #include &lt;R.h&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   2: </span>
@@ -297,10 +344,10 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  19: }</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># The symbolic solution which is available in this case is not</span></span>
-<span class="r-in"><span class="co"># made for human reading but for speed of computation</span></span>
-<span class="r-in"><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">deg_func</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># The symbolic solution which is available in this case is not</span></span></span>
+<span class="r-in"><span><span class="co"># made for human reading but for speed of computation</span></span></span>
+<span class="r-in"><span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">deg_func</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> function (observed, odeini, odeparms) </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> {</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>     predicted &lt;- numeric(0)</span>
@@ -316,21 +363,21 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span>     })</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>     return(predicted)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x55555cd83c70&gt;</span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># If we have several parallel metabolites</span></span>
-<span class="r-in"><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span>
-<span class="r-in"><span class="va">m_synth_DFOP_par</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span>
-<span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span>
-<span class="r-in"> M1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span>
-<span class="r-in"> M2 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span>
-<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="va">fit_DFOP_par_c</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span>
-<span class="r-in">  <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>,</span>
-<span class="r-in">  quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in"><span class="co"># }</span></span>
-<span class="r-in"></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x55555d516c10&gt;</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span>
+<span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span>
+<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op">&lt;-</span> <span class="fu">mkinmod</span><span class="op">(</span></span></span>
+<span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">fit_DFOP_par_c</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span></span>
+<span class="r-in"><span>  <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>,</span></span>
+<span class="r-in"><span>  quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
   </div>
@@ -345,7 +392,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
 </div>
 
       </footer></div>
diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html
index 37930912..0e645b51 100644
--- a/docs/dev/reference/mkinpredict.html
+++ b/docs/dev/reference/mkinpredict.html
@@ -377,7 +377,7 @@ as these always return mapped output.</p></dd>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2 deSolve_compiled      1.0   0.005</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1            eigen      4.2   0.021</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 4       analytical      4.2   0.021</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3          deSolve     40.8   0.204</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3          deSolve     41.0   0.205</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/saem.html b/docs/dev/reference/saem.html
index 73382cba..d2e930e1 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -432,8 +432,8 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting:      3.2 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.2.0 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.2.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Tue Nov 15 00:45:58 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Tue Nov 15 00:45:58 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Wed Nov 16 10:49:43 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed Nov 16 10:49:43 2022 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
@@ -448,7 +448,7 @@ using <a href="mmkin.html">mmkin</a>.</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 9.189 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 8.935 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 10 chains</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Constant variance </span>
diff --git a/vignettes/web_only/saem_benchmarks.rda b/vignettes/web_only/saem_benchmarks.rda
index e8b139da..55fabf1d 100644
--- a/vignettes/web_only/saem_benchmarks.rda
+++ b/vignettes/web_only/saem_benchmarks.rda