Merge branch 'main' into custom_lsoda_call

1 files changed, 36 insertions, 19 deletions

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index e00391e8..1f528615 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -17,7 +17,7 @@
       </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>
 
@@ -44,19 +44,25 @@
       <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>
 <li>
@@ -95,19 +101,30 @@
     <h2>Arguments</h2>
     <dl><dt>x</dt>
 <dd><p>An <code><a href="mmkin.html">mmkin</a> object</code></p></dd>
+
+
 <dt>i</dt>
 <dd><p>Row index selecting the fits for specific models</p></dd>
+
+
 <dt>j</dt>
 <dd><p>Column index selecting the fits to specific datasets</p></dd>
+
+
 <dt>...</dt>
 <dd><p>Not used, only there to satisfy the generic method definition</p></dd>
+
+
 <dt>drop</dt>
 <dd><p>If FALSE, the method always returns an mmkin object, otherwise
 either a list of mkinfit objects or a single mkinfit object.</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>An object of class <code><a href="mmkin.html">mmkin</a></code>.</p>
+    
+
+<p>An object of class <code><a href="mmkin.html">mmkin</a></code>.</p>
     </div>
     <div id="author">
     <h2>Author</h2>
@@ -116,11 +133,11 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd>
 
     <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"># Only use one core, to pass R CMD check --as-cran</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">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</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><span class="op">)</span></span>
-<span class="r-in">  <span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</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"># Only use one core, to pass R CMD check --as-cran</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">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</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><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;mmkin&gt; object</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Status of individual fits:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -129,7 +146,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   FOMC OK OK</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> OK: No warnings</span>
-<span class="r-in">  <span class="va">fits</span><span class="op">[</span>, <span class="st">"B"</span><span class="op">]</span></span>
+<span class="r-in"><span>  <span class="va">fits</span><span class="op">[</span>, <span class="st">"B"</span><span class="op">]</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;mmkin&gt; object</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Status of individual fits:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -139,7 +156,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   FOMC OK</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> OK: No warnings</span>
-<span class="r-in">  <span class="va">fits</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="st">"B"</span><span class="op">]</span></span>
+<span class="r-in"><span>  <span class="va">fits</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="st">"B"</span><span class="op">]</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> &lt;mmkin&gt; object</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Status of individual fits:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -148,14 +165,14 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   SFO OK</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> OK: No warnings</span>
-<span class="r-in"></span>
-<span class="r-in">  <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span></span>
-<span class="r-in">    <span class="co"># This extracts an mkinfit object with lots of components</span></span>
-<span class="r-in">    <span class="va">fits</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"B"</span><span class="op">]</span><span class="op">]</span></span>
-<span class="r-in">  <span class="op">)</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>    <span class="co"># This extracts an mkinfit object with lots of components</span></span></span>
+<span class="r-in"><span>    <span class="va">fits</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"B"</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-out co"><span class="r-pr">#&gt;</span> $par</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  parent_0 log_alpha  log_beta     sigma </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 99.666193  2.549849  5.050586  1.890202 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 99.666192  2.549850  5.050586  1.890202 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $objective</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 28.58291</span>
@@ -168,7 +185,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $evaluations</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> function gradient </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>       25       72 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>       25       78 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $message</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "both X-convergence and relative convergence (5)"</span>
@@ -187,7 +204,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd>
 </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>