Complete update of online docs for v1.2.0

1 files changed, 26 insertions, 15 deletions

diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index b9eda413..a41456f2 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -18,7 +18,7 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma
       </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 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma
       <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>
@@ -89,17 +95,20 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
     <dl><dt>object</dt>
 <dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>Nothing is returned by this function, as it is called for its side
+    
+
+<p>Nothing is returned by this function, as it is called for its side
 effect, namely to produce a plot.</p>
     </div>
     <div id="author">
@@ -109,18 +118,20 @@ effect, namely to produce a plot.</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="co"># \dontrun{</span></span>
-<span class="r-in"><span class="va">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
-<span class="r-in">  T245 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <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">"phenol"</span><span class="op">)</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span>
-<span class="r-in">  phenol <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <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">"anisole"</span><span class="op">)</span><span class="op">)</span>,</span>
-<span class="r-in">  anisole <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">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>  T245 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <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">"phenol"</span><span class="op">)</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  phenol <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <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">"anisole"</span><span class="op">)</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  anisole <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 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="va">model</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</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="va">model</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</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 class="fu">mkinparplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Optimisation did not converge:</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> false convergence (8)</span>
+<span class="r-in"><span><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="mkinparplot-1.png" alt="" width="700" height="433"></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>
@@ -135,7 +146,7 @@ effect, namely to produce a plot.</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>