Merge branch 'main' into custom_lsoda_call

1 files changed, 45 insertions, 39 deletions

diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html
index 43ed0f69..586a6a00 100644
--- a/docs/dev/articles/FOCUS_L.html
+++ b/docs/dev/articles/FOCUS_L.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">1.1.2</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -63,19 +63,25 @@
       <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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <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>
@@ -106,7 +112,7 @@
       <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 18 May 2022 (rebuilt 2022-09-16)</h4>
+            <h4 data-toc-skip class="date">Last change 18 May 2022 (rebuilt 2022-11-24)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_L.rmd" class="external-link"><code>vignettes/FOCUS_L.rmd</code></a></small>
       <div class="hidden name"><code>FOCUS_L.rmd</code></div>
@@ -132,17 +138,17 @@
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">m.L1.SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:35 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:35 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:09 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:09 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - k_parent * parent</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 133 model solutions performed in 0.032 s</span></span>
+<span><span class="co">## Fitted using 133 model solutions performed in 0.033 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -238,17 +244,17 @@
 <pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre>
 <pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span>
 <span><span class="co">## doubtful</span></span></code></pre>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:36 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:36 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:09 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:09 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 369 model solutions performed in 0.081 s</span></span>
+<span><span class="co">## Fitted using 369 model solutions performed in 0.091 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -350,17 +356,17 @@
 <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:36 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:36 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:10 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:10 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 239 model solutions performed in 0.049 s</span></span>
+<span><span class="co">## Fitted using 239 model solutions performed in 0.048 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -431,10 +437,10 @@
 <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p>
 <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:37 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:37 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:10 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:10 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span>
@@ -443,7 +449,7 @@
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 581 model solutions performed in 0.132 s</span></span>
+<span><span class="co">## Fitted using 581 model solutions performed in 0.13 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -537,10 +543,10 @@
 <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p>
 <div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:37 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:11 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:11 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span>
@@ -549,7 +555,7 @@
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 376 model solutions performed in 0.079 s</span></span>
+<span><span class="co">## Fitted using 376 model solutions performed in 0.078 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -650,17 +656,17 @@
 <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p>
 <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:38 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:12 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:12 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - k_parent * parent</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 142 model solutions performed in 0.03 s</span></span>
+<span><span class="co">## Fitted using 142 model solutions performed in 0.029 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>
@@ -715,17 +721,17 @@
 <span><span class="co">## parent  106  352</span></span></code></pre>
 <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## mkin version used for fitting:    1.1.2 </span></span>
-<span><span class="co">## R version used for fitting:       4.2.1 </span></span>
-<span><span class="co">## Date of fit:     Fri Sep 16 10:31:38 2022 </span></span>
-<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span>
+<pre><code><span><span class="co">## mkin version used for fitting:    1.2.2 </span></span>
+<span><span class="co">## R version used for fitting:       4.2.2 </span></span>
+<span><span class="co">## Date of fit:     Thu Nov 24 08:12:12 2022 </span></span>
+<span><span class="co">## Date of summary: Thu Nov 24 08:12:12 2022 </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Equations:</span></span>
 <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Model predictions using solution type analytical </span></span>
 <span><span class="co">## </span></span>
-<span><span class="co">## Fitted using 224 model solutions performed in 0.045 s</span></span>
+<span><span class="co">## Fitted using 224 model solutions performed in 0.044 s</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## Error model: Constant variance </span></span>
 <span><span class="co">## </span></span>