Merge branch 'main' into custom_lsoda_call

1 files changed, 35 insertions, 20 deletions

diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 0116760d..57e2e1f4 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -18,7 +18,7 @@ a concentration dependent rate constant."><!-- mathjax --><script src="https://c
       </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 concentration dependent rate constant."><!-- mathjax --><script src="https://c
       <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>
@@ -89,24 +95,33 @@ a concentration dependent rate constant.</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">IORE.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k__iore</span>, <span class="va">N</span><span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">IORE.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k__iore</span>, <span class="va">N</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
     <dl><dt>t</dt>
 <dd><p>Time.</p></dd>
+
+
 <dt>parent_0</dt>
 <dd><p>Starting value for the response variable at time zero.</p></dd>
+
+
 <dt>k__iore</dt>
 <dd><p>Rate constant. Note that this depends on the concentration
 units used.</p></dd>
+
+
 <dt>N</dt>
 <dd><p>Exponent describing the nonlinearity of the rate equation</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>The value of the response variable at time <code>t</code>.</p>
+    
+
+<p>The value of the response variable at time <code>t</code>.</p>
     </div>
     <div id="note">
     <h2>Note</h2>
@@ -133,29 +148,29 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media</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="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></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="fu">IORE.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.2</span>, <span class="fl">1.3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span>, ylim <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="fl">0</span>, <span class="fl">100</span><span class="op">)</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="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></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="fu">IORE.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.2</span>, <span class="fl">1.3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span>, ylim <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="fl">0</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="IORE.solution-1.png" alt="" width="700" height="433"></span>
-<span class="r-in">  <span class="co"># \dontrun{</span></span>
-<span class="r-in">    <span class="va">fit.fomc</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="va">fit.iore</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"IORE"</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="va">fit.iore.deS</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"IORE"</span>, <span class="va">FOCUS_2006_C</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in"></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="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span><span class="va">fit.fomc</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore.deS</span><span class="op">$</span><span class="va">par</span>, </span>
-<span class="r-in">                     row.names <span class="op">=</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">"model par"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">)</span><span class="op">)</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.fomc</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="va">fit.iore</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"IORE"</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="va">fit.iore.deS</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"IORE"</span>, <span class="va">FOCUS_2006_C</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></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="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span><span class="va">fit.fomc</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore.deS</span><span class="op">$</span><span class="va">par</span>,</span></span>
+<span class="r-in"><span>                     row.names <span class="op">=</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">"model par"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">4</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>             fit.fomc.par fit.iore.par fit.iore.deS.par</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> model par 1  85.87489063    85.874890        85.874891</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> model par 1  85.87489063    85.874890        85.874890</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> model par 2   0.05192238    -4.826631        -4.826631</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> model par 3   0.65096665     1.949403         1.949403</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> model par 4   1.85744396     1.857444         1.857444</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="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span>fomc <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.fomc</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span>, iore <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.iore</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span>, </span>
-<span class="r-in">                iore.deS <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.iore</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span>fomc <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.fomc</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span>, iore <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.iore</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span>,</span></span>
+<span class="r-in"><span>                iore.deS <span class="op">=</span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.iore</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span><span class="op">)</span><span class="op">)</span></span></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> fomc     1.785233 15.1479 4.559973</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> iore     1.785233 15.1479 4.559973</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> iore.deS 1.785233 15.1479 4.559973</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>
@@ -170,7 +185,7 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media</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>