Merge branch 'main' into custom_lsoda_call

1 files changed, 42 insertions, 33 deletions

diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 327e8ae9..a76f23ab 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -18,7 +18,7 @@
       </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>
 
@@ -45,19 +45,25 @@
       <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>
@@ -89,7 +95,7 @@
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">test_data_from_UBA_2014</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">test_data_from_UBA_2014</span></span></code></pre></div>
     </div>
 
     <div id="format">
@@ -111,21 +117,23 @@
 
     <div id="ref-examples">
     <h2>Examples</h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in">  <span class="co"># \dontrun{</span></span>
-<span class="r-in">  <span class="co"># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span></span>
-<span class="r-in">  <span class="co"># guidance. Due to the strong correlation of the parameter estimates, the</span></span>
-<span class="r-in">  <span class="co"># covariance matrix is not returned. Note that level P-II evaluations are</span></span>
-<span class="r-in">  <span class="co"># generally considered deprecated due to the frequent occurrence of such</span></span>
-<span class="r-in">  <span class="co"># large parameter correlations, among other reasons (e.g. the adequacy of the</span></span>
-<span class="r-in">  <span class="co"># model).</span></span>
-<span class="r-in">  <span class="va">m_ws</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent_w <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">"parent_s"</span><span class="op">)</span>,</span>
-<span class="r-in">                  parent_s <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">"parent_w"</span><span class="op">)</span><span class="op">)</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span>  <span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span>  <span class="co"># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span></span></span>
+<span class="r-in"><span>  <span class="co"># guidance. Due to the strong correlation of the parameter estimates, the</span></span></span>
+<span class="r-in"><span>  <span class="co"># covariance matrix is not returned. Note that level P-II evaluations are</span></span></span>
+<span class="r-in"><span>  <span class="co"># generally considered deprecated due to the frequent occurrence of such</span></span></span>
+<span class="r-in"><span>  <span class="co"># large parameter correlations, among other reasons (e.g. the adequacy of the</span></span></span>
+<span class="r-in"><span>  <span class="co"># model).</span></span></span>
+<span class="r-in"><span>  <span class="va">m_ws</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent_w <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">"parent_s"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                  parent_s <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">"parent_w"</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="va">f_river</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_ws</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in">  <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span>
+<span class="r-in"><span>  <span class="va">f_river</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_ws</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</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 class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="test_data_from_UBA_2014-1.png" alt="" width="700" height="433"></span>
-<span class="r-in"></span>
-<span class="r-in">  <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">f_river</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Could not calculate correlation; no covariance matrix</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                           Estimate se_notrans t value Pr(&gt;t) Lower Upper</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent_w_0             95.91998118         NA      NA     NA    NA    NA</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_w              0.41145375         NA      NA     NA    NA    NA</span>
@@ -133,25 +141,26 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_w_to_parent_s  0.12467894         NA      NA     NA    NA    NA</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_s_to_parent_w  0.50000000         NA      NA     NA    NA    NA</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> sigma                   3.13612618         NA      NA     NA    NA    NA</span>
-<span class="r-in">  <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span>
+<span class="r-in"><span>  <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>            err.min n.optim df</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> All data 0.1090929       5  6</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent_w 0.0817436       3  3</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent_s 0.1619965       2  3</span>
-<span class="r-in"></span>
-<span class="r-in">  <span class="co"># This is the evaluation used for the validation of software packages</span></span>
-<span class="r-in">  <span class="co"># in the expertise from 2014</span></span>
-<span class="r-in">  <span class="va">m_soil</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="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"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</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="st">"M3"</span><span class="op">)</span>,</span>
-<span class="r-in">                    M3 <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>,</span>
-<span class="r-in">                    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="co"># This is the evaluation used for the validation of software packages</span></span></span>
+<span class="r-in"><span>  <span class="co"># in the expertise from 2014</span></span></span>
+<span class="r-in"><span>  <span class="va">m_soil</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="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"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</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="st">"M3"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>                    M3 <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>,</span></span>
+<span class="r-in"><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">f_soil</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_soil</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in">  <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_soil</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="va">f_soil</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_soil</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</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 class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_soil</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">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="test_data_from_UBA_2014-2.png" alt="" width="700" height="433"></span>
-<span class="r-in">  <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">f_soil</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                   Estimate  se_notrans    t value       Pr(&gt;t)        Lower</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent_0       76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> k_parent        0.12081956 0.004601918 26.2541722 1.077359e-16  0.111561575</span>
@@ -174,14 +183,14 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_M1_to_M3      0.86450775</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_M2_to_M3      0.99489895</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> sigma           1.45337221</span>
-<span class="r-in">  <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span></span>
+<span class="r-in"><span>  <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>             err.min n.optim df</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> All data 0.09649963       9 20</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent   0.04721283       2  6</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> M1       0.26551208       2  5</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> M2       0.20327575       2  5</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> M3       0.05196550       3  4</span>
-<span class="r-in">  <span class="co"># }</span></span>
+<span class="r-in"><span>  <span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
   </div>
@@ -196,7 +205,7 @@
 </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>
 
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