Merge branch 'main' into custom_lsoda_call

1 files changed, 34 insertions, 26 deletions

diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index 883c9e5d..1f49092e 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -23,7 +23,7 @@ advantage that the SFORB model can also be used for metabolites."><!-- mathjax -
       </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>
 
@@ -50,19 +50,25 @@ advantage that the SFORB model can also be used for metabolites."><!-- mathjax -
       <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>
@@ -98,24 +104,26 @@ advantage that the SFORB model can also be used for metabolites.</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
     <dl><dt>fit</dt>
-<dd><p>An object of class <a href="mkinfit.html">mkinfit</a>, <a href="nlme.mmkin.html">nlme.mmkin</a> or <a href="saem.html">saem.mmkin</a>,
-or another object that has list components
-mkinmod containing an <a href="mkinmod.html">mkinmod</a> degradation model, and two numeric vectors,
-bparms.optim and bparms.fixed, that contain parameter values
-for that model.</p></dd>
+<dd><p>An object of class <a href="mkinfit.html">mkinfit</a>, <a href="nlme.mmkin.html">nlme.mmkin</a> or <a href="saem.html">saem.mmkin</a>, or
+another object that has list components mkinmod containing an <a href="mkinmod.html">mkinmod</a>
+degradation model, and two numeric vectors, bparms.optim and bparms.fixed,
+that contain parameter values for that model.</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>A list with a matrix of dissipation times named distimes,
-and, if applicable, a vector of formation fractions named ff
-and, if the SFORB model was in use, a vector of eigenvalues
-of these SFORB models, equivalent to DFOP rate constants</p>
+    
+
+<p>A list with a matrix of dissipation times named distimes, and, if
+applicable, a vector of formation fractions named ff and, if the SFORB model
+was in use, a vector of eigenvalues of these SFORB models, equivalent to
+DFOP rate constants</p>
     </div>
     <div id="details">
     <h2>Details</h2>
@@ -134,36 +142,36 @@ HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</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="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in">  <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</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="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
 <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 DT50back</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent 1.785233 15.1479 4.559973</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-in">  <span class="co"># \dontrun{</span></span>
-<span class="r-in">    <span class="va">fit_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in">    <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span>
+<span class="r-in"><span>  <span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span>    <span class="va">fit_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span>    <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span></span>
 <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 DT50back  DT50_k1  DT50_k2</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent 1.886925 21.25106 6.397207 1.508293 38.83438</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-in">    <span class="va">fit_3</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in">    <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit_3</span><span class="op">)</span></span>
+<span class="r-in"><span>    <span class="va">fit_3</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span>    <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit_3</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_free </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>           1 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $SFORB</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_b1 parent_b2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 0.4595574 0.0178488 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_b1 parent_b2  parent_g </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0.4595574 0.0178488 0.8539454 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <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 DT50back DT50_parent_b1 DT50_parent_b2</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent 1.886925 21.25106 6.397208       1.508293       38.83438</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </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>
@@ -178,7 +186,7 @@ HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</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>
 
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