Merge branch 'main' into custom_lsoda_call

1 files changed, 93 insertions, 78 deletions

diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index cbb46ab0..686c9310 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -20,7 +20,7 @@ datasets specified in its first two arguments."><!-- mathjax --><script src="htt
       </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>
 
@@ -47,19 +47,25 @@ datasets specified in its first two arguments."><!-- mathjax --><script src="htt
       <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>
@@ -92,16 +98,16 @@ datasets specified in its first two arguments.</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mmkin</span><span class="op">(</span>
-  models <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="st">"DFOP"</span><span class="op">)</span>,
-  <span class="va">datasets</span>,
-  cores <span class="op">=</span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="fl">1</span> <span class="kw">else</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>,
-  cluster <span class="op">=</span> <span class="cn">NULL</span>,
-  <span class="va">...</span>
-<span class="op">)</span>
-
-<span class="co"># S3 method for mmkin</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></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mmkin</span><span class="op">(</span></span>
+<span>  models <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="st">"DFOP"</span><span class="op">)</span>,</span>
+<span>  <span class="va">datasets</span>,</span>
+<span>  cores <span class="op">=</span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="fl">1</span> <span class="kw">else</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  cluster <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mmkin</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></code></pre></div>
     </div>
 
     <div id="arguments">
@@ -110,9 +116,13 @@ datasets specified in its first two arguments.</p>
 <dd><p>Either a character vector of shorthand names like
 <code>c("SFO", "FOMC", "DFOP", "HS", "SFORB")</code>, or an optionally named
 list of <code><a href="mkinmod.html">mkinmod</a></code> objects.</p></dd>
+
+
 <dt>datasets</dt>
 <dd><p>An optionally named list of datasets suitable as observed
 data for <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd>
+
+
 <dt>cores</dt>
 <dd><p>The number of cores to be used for multicore processing. This
 is only used when the <code>cluster</code> argument is <code>NULL</code>. On Windows
@@ -120,17 +130,29 @@ machines, cores &gt; 1 is not supported, you need to use the <code>cluster</code
 argument to use multiple logical processors. Per default, all cores
 detected by <code><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">parallel::detectCores()</a></code> are used, except on Windows where
 the default is 1.</p></dd>
+
+
 <dt>cluster</dt>
-<dd><p>A cluster as returned by <code><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makeCluster</a></code> to be used
+<dd><p>A cluster as returned by <code>makeCluster</code> to be used
 for parallel execution.</p></dd>
+
+
 <dt>...</dt>
 <dd><p>Not used.</p></dd>
+
+
 <dt>x</dt>
 <dd><p>An mmkin object.</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>A two-dimensional <code><a href="https://rdrr.io/r/base/array.html" class="external-link">array</a></code> of <code><a href="mkinfit.html">mkinfit</a></code>objects and/or try-errors that can be indexed using the model names for the
+    
+
+<p>A two-dimensional <code><a href="https://rdrr.io/r/base/array.html" class="external-link">array</a></code> of <code><a href="mkinfit.html">mkinfit</a></code></p>
+
+
+<p>objects and/or try-errors that can be indexed using the model names for the
 first index (row index) and the dataset names for the second index (column
 index).</p>
     </div>
@@ -146,33 +168,33 @@ plotting.</p></div>
 
     <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="va">m_synth_SFO_lin</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="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 class="r-in">                           M1 <span class="op">=</span> <span class="fu"><a href="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 class="r-in">                           M2 <span class="op">=</span> <span class="fu"><a href="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><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="va">m_synth_SFO_lin</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="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>
+<span class="r-in"><span>                           M1 <span class="op">=</span> <span class="fu"><a href="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>
+<span class="r-in"><span>                           M2 <span class="op">=</span> <span class="fu"><a href="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><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>
-<span class="r-in"><span class="va">m_synth_FOMC_lin</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span>
-<span class="r-in">                            M1 <span class="op">=</span> <span class="fu"><a href="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 class="r-in">                            M2 <span class="op">=</span> <span class="fu"><a href="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><span class="op">)</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">m_synth_FOMC_lin</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</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"><a href="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>
+<span class="r-in"><span>                            M2 <span class="op">=</span> <span class="fu"><a href="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><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>
-<span class="r-in"><span class="va">models</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>SFO_lin <span class="op">=</span> <span class="va">m_synth_SFO_lin</span>, FOMC_lin <span class="op">=</span> <span class="va">m_synth_FOMC_lin</span><span class="op">)</span></span>
-<span class="r-in"><span class="va">datasets</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">datasets</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="va">time_default</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">fits.0</span> <span class="op">&lt;-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
-<span class="r-in"><span class="va">time_1</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">fits.4</span> <span class="op">&lt;-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</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 class="op">)</span></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="va">time_default</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">models</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>SFO_lin <span class="op">=</span> <span class="va">m_synth_SFO_lin</span>, FOMC_lin <span class="op">=</span> <span class="va">m_synth_FOMC_lin</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">datasets</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">datasets</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">time_default</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">fits.0</span> <span class="op">&lt;-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">time_1</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">fits.4</span> <span class="op">&lt;-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</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 class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">time_default</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    user  system elapsed </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  35.152   1.185   8.439 </span>
-<span class="r-in"><span class="va">time_1</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   5.526   0.809   2.006 </span>
+<span class="r-in"><span><span class="va">time_1</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    user  system elapsed </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  14.744   0.008  14.768 </span>
-<span class="r-in"></span>
-<span class="r-in"><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   5.403   0.008   5.412 </span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $ff</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   parent_M1 parent_sink       M1_M2     M1_sink </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   0.7340481   0.2659519   0.7505683   0.2494317 </span>
@@ -180,51 +202,44 @@ plotting.</p></div>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $distimes</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>             DT50       DT90</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent  0.877769   2.915885</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> M1      2.325744   7.725955</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> M2     33.720111 112.015785</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> M1      2.325744   7.725956</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> M2     33.720100 112.015749</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># plot.mkinfit handles rows or columns of mmkin result objects</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.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span><span class="op">)</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># plot.mkinfit handles rows or columns of mmkin result objects</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.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="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.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span>, obs_var <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">"M1"</span>, <span class="st">"M2"</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.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span>, obs_var <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">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="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.0</span><span class="op">[</span>, <span class="fl">1</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.0</span><span class="op">[</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="mmkin-3.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span class="co"># Use double brackets to extract a single mkinfit object, which will be plotted</span></span>
-<span class="r-in"><span class="co"># by plot.mkinfit and can be plotted using plot_sep</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.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="co"># Use double brackets to extract a single mkinfit object, which will be plotted</span></span></span>
+<span class="r-in"><span><span class="co"># by plot.mkinfit and can be plotted using plot_sep</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.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="mmkin-4.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span>
-<span class="r-in"><span class="co"># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span></span>
-<span class="r-in"><span class="co"># allow to plot the observed variables separately</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.0</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="co"># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span></span></span>
+<span class="r-in"><span><span class="co"># allow to plot the observed variables separately</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.0</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="mmkin-5.png" alt="" width="700" height="433"></span>
-<span class="r-in"></span>
-<span class="r-in"><span class="co"># On Windows, we can use multiple cores by making a cluster using the parallel</span></span>
-<span class="r-in"><span class="co"># package, which gets loaded with mkin, and passing it to mmkin, e.g.</span></span>
-<span class="r-in"><span class="va">cl</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span>
-<span class="r-in"><span class="va">f</span> <span class="op">&lt;-</span> <span class="fu">mmkin</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="st">"DFOP"</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>A <span class="op">=</span> <span class="va">FOCUS_2006_A</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>, D <span class="op">=</span> <span class="va">FOCUS_2006_D</span><span class="op">)</span>,</span>
-<span class="r-in">  cluster <span class="op">=</span> <span class="va">cl</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></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">f</span><span class="op">)</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>
-<span class="r-out co"><span class="r-pr">#&gt;</span>       dataset</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> model  A  B  C  D </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   SFO  OK OK OK OK</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   FOMC C  OK OK OK</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   DFOP OK OK 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-out co"><span class="r-pr">#&gt;</span> C: Optimisation did not converge:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> false convergence (8)</span>
-<span class="r-in"><span class="co"># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span></span>
-<span class="r-in"><span class="co"># dataset is really SFO, and the FOMC fit is overparameterised</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span>
-<span class="r-in"><span class="co"># }</span></span>
-<span class="r-in"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># On Windows, we can use multiple cores by making a cluster using the parallel</span></span></span>
+<span class="r-in"><span><span class="co"># package, which gets loaded with mkin, and passing it to mmkin, e.g.</span></span></span>
+<span class="r-in"><span><span class="va">cl</span> <span class="op">&lt;-</span> <span class="fu">makePSOCKcluster</span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in makePSOCKcluster(12):</span> could not find function "makePSOCKcluster"</span>
+<span class="r-in"><span><span class="va">f</span> <span class="op">&lt;-</span> <span class="fu">mmkin</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="st">"DFOP"</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>A <span class="op">=</span> <span class="va">FOCUS_2006_A</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>, D <span class="op">=</span> <span class="va">FOCUS_2006_D</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  cluster <span class="op">=</span> <span class="va">cl</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in system.time({    if (is.null(cluster)) {        results &lt;- parallel::mclapply(as.list(1:n.fits), fit_function,             mc.cores = cores, mc.preschedule = FALSE)    }    else {        results &lt;- parallel::parLapply(cluster, as.list(1:n.fits),             fit_function)    }}):</span> object 'cl' not found</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Timing stopped at: 0 0 0</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">f</span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in print(f):</span> object 'f' not found</span>
+<span class="r-in"><span><span class="co"># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span></span></span>
+<span class="r-in"><span><span class="co"># dataset is really SFO, and the FOMC fit is overparameterised</span></span></span>
+<span class="r-in"><span><span class="fu">stopCluster</span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in stopCluster(cl):</span> could not find function "stopCluster"</span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
   </div>
@@ -239,7 +254,7 @@ plotting.</p></div>
 </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>
 
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