From e5d1df9a9b1f0951d7dfbaf24eee4294470b73e2 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 17 Nov 2022 14:54:20 +0100
Subject: Complete update of online docs for v1.2.0

---
 docs/reference/mkinresplot.html | 83 ++++++++++++++++++++++++++++-------------
 1 file changed, 58 insertions(+), 25 deletions(-)

(limited to 'docs/reference/mkinresplot.html')

diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index 654b93d8..6966cd90 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -20,7 +20,7 @@ argument show_residuals = TRUE."><!-- mathjax --><script src="https://cdnjs.clou
       </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>
 
@@ -47,11 +47,14 @@ argument show_residuals = TRUE."><!-- mathjax --><script src="https://cdnjs.clou
       <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>
@@ -59,7 +62,10 @@ argument show_residuals = TRUE."><!-- mathjax --><script src="https://cdnjs.clou
       <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>
@@ -93,60 +99,87 @@ argument <code>show_residuals = TRUE</code>.</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mkinresplot</span><span class="op">(</span>
-  <span class="va">object</span>,
-  obs_vars <span class="op">=</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">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,
-  xlim <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">1.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span><span class="op">)</span>,
-  standardized <span class="op">=</span> <span class="cn">FALSE</span>,
-  xlab <span class="op">=</span> <span class="st">"Time"</span>,
-  ylab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">standardized</span>, <span class="st">"Standardized residual"</span>, <span class="st">"Residual"</span><span class="op">)</span>,
-  maxabs <span class="op">=</span> <span class="st">"auto"</span>,
-  legend <span class="op">=</span> <span class="cn">TRUE</span>,
-  lpos <span class="op">=</span> <span class="st">"topright"</span>,
-  col_obs <span class="op">=</span> <span class="st">"auto"</span>,
-  pch_obs <span class="op">=</span> <span class="st">"auto"</span>,
-  frame <span class="op">=</span> <span class="cn">TRUE</span>,
-  <span class="va">...</span>
-<span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinresplot</span><span class="op">(</span></span>
+<span>  <span class="va">object</span>,</span>
+<span>  obs_vars <span class="op">=</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">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span>
+<span>  xlim <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">1.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span><span class="op">)</span>,</span>
+<span>  standardized <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  xlab <span class="op">=</span> <span class="st">"Time"</span>,</span>
+<span>  ylab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">standardized</span>, <span class="st">"Standardized residual"</span>, <span class="st">"Residual"</span><span class="op">)</span>,</span>
+<span>  maxabs <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  legend <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  lpos <span class="op">=</span> <span class="st">"topright"</span>,</span>
+<span>  col_obs <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  pch_obs <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span>  frame <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<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>
+
+
 <dt>obs_vars</dt>
 <dd><p>A character vector of names of the observed variables for
 which residuals should be plotted. Defaults to all observed variables in
 the model</p></dd>
+
+
 <dt>xlim</dt>
 <dd><p>plot range in x direction.</p></dd>
+
+
 <dt>standardized</dt>
 <dd><p>Should the residuals be standardized by dividing by the
 standard deviation given by the error model of the fit?</p></dd>
+
+
 <dt>xlab</dt>
 <dd><p>Label for the x axis.</p></dd>
+
+
 <dt>ylab</dt>
 <dd><p>Label for the y axis.</p></dd>
+
+
 <dt>maxabs</dt>
 <dd><p>Maximum absolute value of the residuals. This is used for the
 scaling of the y axis and defaults to "auto".</p></dd>
+
+
 <dt>legend</dt>
 <dd><p>Should a legend be plotted?</p></dd>
+
+
 <dt>lpos</dt>
 <dd><p>Where should the legend be placed? Default is "topright". Will
 be passed on to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code>.</p></dd>
+
+
 <dt>col_obs</dt>
 <dd><p>Colors for the observed variables.</p></dd>
+
+
 <dt>pch_obs</dt>
 <dd><p>Symbols to be used for the observed variables.</p></dd>
+
+
 <dt>frame</dt>
 <dd><p>Should a frame be drawn around the plots?</p></dd>
+
+
 <dt>...</dt>
 <dd><p>further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</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="see-also">
@@ -162,14 +195,14 @@ combining the plot of the fit and the residual plot.</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="va">model</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>, 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="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="va">model</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>, 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="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">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="va">FOCUS_2006_D</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="va">FOCUS_2006_D</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">mkinresplot</span><span class="op">(</span><span class="va">fit</span>, <span class="st">"m1"</span><span class="op">)</span></span>
+<span class="r-in"><span><span class="fu">mkinresplot</span><span class="op">(</span><span class="va">fit</span>, <span class="st">"m1"</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="mkinresplot-1.png" alt="" width="700" height="433"></span>
-<span class="r-in"></span>
+<span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
   </div>
@@ -184,7 +217,7 @@ combining the plot of the fit and the residual plot.</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>
 
       </footer></div>
-- 
cgit v1.2.1