Merge branch 'main' into custom_lsoda_call

1 files changed, 73 insertions, 40 deletions

diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 3dd0203b..30d0406e 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -21,7 +21,7 @@ the fit of at least one model to the same dataset is shown."><!-- mathjax --><sc
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
       </span>
     </div>
 
@@ -48,19 +48,25 @@ the fit of at least one model to the same dataset is shown."><!-- mathjax --><sc
       <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>
 <li>
@@ -94,22 +100,22 @@ the fit of at least one model to the same dataset is shown.</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mmkin</span>
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span>
-  <span class="va">x</span>,
-  main <span class="op">=</span> <span class="st">"auto"</span>,
-  legends <span class="op">=</span> <span class="fl">1</span>,
-  resplot <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">"time"</span>, <span class="st">"errmod"</span><span class="op">)</span>,
-  ylab <span class="op">=</span> <span class="st">"Residue"</span>,
-  standardized <span class="op">=</span> <span class="cn">FALSE</span>,
-  show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,
-  errmin_var <span class="op">=</span> <span class="st">"All data"</span>,
-  errmin_digits <span class="op">=</span> <span class="fl">3</span>,
-  cex <span class="op">=</span> <span class="fl">0.7</span>,
-  rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>,
-  ymax <span class="op">=</span> <span class="st">"auto"</span>,
-  <span class="va">...</span>
-<span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  main <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  legends <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>  resplot <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">"time"</span>, <span class="st">"errmod"</span><span class="op">)</span>,</span>
+<span>  ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span>
+<span>  standardized <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  errmin_var <span class="op">=</span> <span class="st">"All data"</span>,</span>
+<span>  errmin_digits <span class="op">=</span> <span class="fl">3</span>,</span>
+<span>  cex <span class="op">=</span> <span class="fl">0.7</span>,</span>
+<span>  rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>,</span>
+<span>  ymax <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -117,43 +123,70 @@ the fit of at least one model to the same dataset is shown.</p>
     <dl><dt>x</dt>
 <dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, with either one row or one
 column.</p></dd>
+
+
 <dt>main</dt>
 <dd><p>The main title placed on the outer margin of the plot.</p></dd>
+
+
 <dt>legends</dt>
 <dd><p>An index for the fits for which legends should be shown.</p></dd>
+
+
 <dt>resplot</dt>
 <dd><p>Should the residuals plotted against time, using
 <code><a href="mkinresplot.html">mkinresplot</a></code>, or as squared residuals against predicted
 values, with the error model, using <code><a href="mkinerrplot.html">mkinerrplot</a></code>.</p></dd>
+
+
 <dt>ylab</dt>
 <dd><p>Label for the y axis.</p></dd>
+
+
 <dt>standardized</dt>
 <dd><p>Should the residuals be standardized? This option
 is passed to <code><a href="mkinresplot.html">mkinresplot</a></code>, it only takes effect if
 <code>resplot = "time"</code>.</p></dd>
+
+
 <dt>show_errmin</dt>
 <dd><p>Should the chi2 error level be shown on top of the plots
 to the left?</p></dd>
+
+
 <dt>errmin_var</dt>
 <dd><p>The variable for which the FOCUS chi2 error value should
 be shown.</p></dd>
+
+
 <dt>errmin_digits</dt>
 <dd><p>The number of significant digits for rounding the FOCUS
 chi2 error percentage.</p></dd>
+
+
 <dt>cex</dt>
 <dd><p>Passed to the plot functions and <code><a href="https://rdrr.io/r/graphics/mtext.html" class="external-link">mtext</a></code>.</p></dd>
+
+
 <dt>rel.height.middle</dt>
 <dd><p>The relative height of the middle plot, if more
 than two rows of plots are shown.</p></dd>
+
+
 <dt>ymax</dt>
 <dd><p>Maximum y axis value for <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p></dd>
+
+
 <dt>...</dt>
 <dd><p>Further arguments passed to <code><a href="plot.mkinfit.html">plot.mkinfit</a></code> and
 <code><a href="mkinresplot.html">mkinresplot</a></code>.</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>The function is called for its side effect.</p>
+    
+
+<p>The function is called for its side effect.</p>
     </div>
     <div id="details">
     <h2>Details</h2>
@@ -167,32 +200,32 @@ latex is being used for the formatting of the chi2 error level.</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"># \dontrun{</span></span>
-<span class="r-in">  <span class="co"># Only use one core not to offend CRAN checks</span></span>
-<span class="r-in">  <span class="va">fits</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></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="st">"FOMC"</span>, <span class="st">"HS"</span><span class="op">)</span>,</span>
-<span class="r-in">                <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, <span class="co"># named list for titles</span></span>
-<span class="r-in">                cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</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"># \dontrun{</span></span></span>
+<span class="r-in"><span>  <span class="co"># Only use one core not to offend CRAN checks</span></span></span>
+<span class="r-in"><span>  <span class="va">fits</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></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="st">"FOMC"</span>, <span class="st">"HS"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, <span class="co"># named list for titles</span></span></span>
+<span class="r-in"><span>                cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Optimisation did not converge:</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> iteration limit reached without convergence (10)</span>
-<span class="r-in">  <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="plot.mmkin-1.png" alt="" width="700" height="433"></span>
-<span class="r-in">  <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="plot.mmkin-2.png" alt="" width="700" height="433"></span>
-<span class="r-in">  <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, show_errmin <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, show_errmin <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="plot.mmkin-3.png" alt="" width="700" height="433"></span>
-<span class="r-in"></span>
-<span class="r-in">  <span class="co"># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span></span>
-<span class="r-in">  <span class="co"># height should be smaller than the plot width (this is not possible for the html pages</span></span>
-<span class="r-in">  <span class="co"># generated by pkgdown, as far as I know).</span></span>
-<span class="r-in">  <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span> <span class="co"># same as plot(fits[1, 2])</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="co"># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span></span></span>
+<span class="r-in"><span>  <span class="co"># height should be smaller than the plot width (this is not possible for the html pages</span></span></span>
+<span class="r-in"><span>  <span class="co"># generated by pkgdown, as far as I know).</span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span> <span class="co"># same as plot(fits[1, 2])</span></span></span>
 <span class="r-plt img"><img src="plot.mmkin-4.png" alt="" width="700" height="433"></span>
-<span class="r-in"></span>
-<span class="r-in">  <span class="co"># Show the error models</span></span>
-<span class="r-in">  <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="co"># Show the error models</span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="plot.mmkin-5.png" alt="" width="700" height="433"></span>
-<span class="r-in">  <span class="co"># }</span></span>
-<span class="r-in"></span>
+<span class="r-in"><span>  <span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
   </div>
@@ -207,7 +240,7 @@ latex is being used for the formatting of the chi2 error level.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</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>