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diff --git a/docs/dev/reference/plot.mmkin.html b/docs/dev/reference/plot.mmkin.html
index 9ca0df94..09f311c5 100644
--- a/docs/dev/reference/plot.mmkin.html
+++ b/docs/dev/reference/plot.mmkin.html
@@ -1,71 +1,16 @@
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+of an mmkin object — plot.mmkin"><meta property="og:description" content="When x is a row selected from an mmkin object ([.mmkin), the
same model fitted for at least one dataset is shown. When it is a column,
-the fit of at least one model to the same dataset is shown." />
-
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-<meta name="robots" content="noindex">
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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-
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+the fit of at least one model to the same dataset is shown."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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-<![endif]-->
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+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+
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-
- <body data-spy="scroll" data-target="#toc">
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- <header>
- <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
@@ -76,23 +21,21 @@ the fit of at least one model to the same dataset is shown." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
- <ul class="nav navbar-nav">
- <li>
+ <ul class="nav navbar-nav"><li>
<a href="../reference/index.html">Functions and data</a>
</li>
<li class="dropdown">
- <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
- <ul class="dropdown-menu" role="menu">
- <li>
+ <ul class="dropdown-menu" role="menu"><li>
<a href="../articles/mkin.html">Introduction to mkin</a>
</li>
<li>
@@ -102,200 +45,210 @@ the fit of at least one model to the same dataset is shown." />
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
- <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <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/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>
- </ul>
-</li>
+ <li>
+ <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
+ </li>
+ </ul></li>
<li>
<a href="../news/index.html">News</a>
</li>
- </ul>
- <ul class="nav navbar-nav navbar-right">
- <li>
- <a href="https://github.com/jranke/mkin/">
+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="https://github.com/jranke/mkin/" class="external-link">
<span class="fab fa-github fa-lg"></span>
</a>
</li>
- </ul>
-
- </div><!--/.nav-collapse -->
+ </ul></div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
- </header>
-
-<div class="row">
+ </header><div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Plot model fits (observed and fitted) and the residuals for a row or column
of an mmkin object</h1>
- <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.mmkin.R'><code>R/plot.mmkin.R</code></a></small>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mmkin.R" class="external-link"><code>R/plot.mmkin.R</code></a></small>
<div class="hidden name"><code>plot.mmkin.Rd</code></div>
</div>
<div class="ref-description">
- <p>When x is a row selected from an mmkin object (<code><a href='[.mmkin.html'>[.mmkin</a></code>), the
+ <p>When x is a row selected from an mmkin object (<code><a href="Extract.mmkin.html">[.mmkin</a></code>), the
same model fitted for at least one dataset is shown. When it is a column,
the fit of at least one model to the same dataset is shown.</p>
</div>
- <pre class="usage"><span class='co'># S3 method for mmkin</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
- <span class='va'>x</span>,
- main <span class='op'>=</span> <span class='st'>"auto"</span>,
- legends <span class='op'>=</span> <span class='fl'>1</span>,
- resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"time"</span>, <span class='st'>"errmod"</span><span class='op'>)</span>,
- ylab <span class='op'>=</span> <span class='st'>"Residue"</span>,
- standardized <span class='op'>=</span> <span class='cn'>FALSE</span>,
- show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span>,
- errmin_var <span class='op'>=</span> <span class='st'>"All data"</span>,
- errmin_digits <span class='op'>=</span> <span class='fl'>3</span>,
- cex <span class='op'>=</span> <span class='fl'>0.7</span>,
- rel.height.middle <span class='op'>=</span> <span class='fl'>0.9</span>,
- ymax <span class='op'>=</span> <span class='st'>"auto"</span>,
- <span class='va'>...</span>
-<span class='op'>)</span></pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>x</th>
- <td><p>An object of class <code><a href='mmkin.html'>mmkin</a></code>, with either one row or one
-column.</p></td>
- </tr>
- <tr>
- <th>main</th>
- <td><p>The main title placed on the outer margin of the plot.</p></td>
- </tr>
- <tr>
- <th>legends</th>
- <td><p>An index for the fits for which legends should be shown.</p></td>
- </tr>
- <tr>
- <th>resplot</th>
- <td><p>Should the residuals plotted against time, using
-<code><a href='mkinresplot.html'>mkinresplot</a></code>, or as squared residuals against predicted
-values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td>
- </tr>
- <tr>
- <th>ylab</th>
- <td><p>Label for the y axis.</p></td>
- </tr>
- <tr>
- <th>standardized</th>
- <td><p>Should the residuals be standardized? This option
-is passed to <code><a href='mkinresplot.html'>mkinresplot</a></code>, it only takes effect if
-<code>resplot = "time"</code>.</p></td>
- </tr>
- <tr>
- <th>show_errmin</th>
- <td><p>Should the chi2 error level be shown on top of the plots
-to the left?</p></td>
- </tr>
- <tr>
- <th>errmin_var</th>
- <td><p>The variable for which the FOCUS chi2 error value should
-be shown.</p></td>
- </tr>
- <tr>
- <th>errmin_digits</th>
- <td><p>The number of significant digits for rounding the FOCUS
-chi2 error percentage.</p></td>
- </tr>
- <tr>
- <th>cex</th>
- <td><p>Passed to the plot functions and <code><a href='https://rdrr.io/r/graphics/mtext.html'>mtext</a></code>.</p></td>
- </tr>
- <tr>
- <th>rel.height.middle</th>
- <td><p>The relative height of the middle plot, if more
-than two rows of plots are shown.</p></td>
- </tr>
- <tr>
- <th>ymax</th>
- <td><p>Maximum y axis value for <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
-<code><a href='mkinresplot.html'>mkinresplot</a></code>.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>The function is called for its side effect.</p>
- <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
- <p>If the current plot device is a <code><a href='https://rdrr.io/pkg/tikzDevice/man/tikz.html'>tikz</a></code> device, then
-latex is being used for the formatting of the chi2 error level.</p>
- <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span>
+<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>
+<span> <span class="va">x</span>,</span>
+<span> main <span class="op">=</span> <span class="st">"auto"</span>,</span>
+<span> legends <span class="op">=</span> <span class="fl">1</span>,</span>
+<span> resplot <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">"time"</span>, <span class="st">"errmod"</span><span class="op">)</span>,</span>
+<span> ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span>
+<span> standardized <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span> show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span> errmin_var <span class="op">=</span> <span class="st">"All data"</span>,</span>
+<span> errmin_digits <span class="op">=</span> <span class="fl">3</span>,</span>
+<span> cex <span class="op">=</span> <span class="fl">0.7</span>,</span>
+<span> rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>,</span>
+<span> ymax <span class="op">=</span> <span class="st">"auto"</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>x</dt>
+<dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, with either one row or one
+column.</p></dd>
+
+
+<dt>main</dt>
+<dd><p>The main title placed on the outer margin of the plot.</p></dd>
+
+
+<dt>legends</dt>
+<dd><p>An index for the fits for which legends should be shown.</p></dd>
+
+
+<dt>resplot</dt>
+<dd><p>Should the residuals plotted against time, using
+<code><a href="mkinresplot.html">mkinresplot</a></code>, or as squared residuals against predicted
+values, with the error model, using <code><a href="mkinerrplot.html">mkinerrplot</a></code>.</p></dd>
+
+
+<dt>ylab</dt>
+<dd><p>Label for the y axis.</p></dd>
+
+
+<dt>standardized</dt>
+<dd><p>Should the residuals be standardized? This option
+is passed to <code><a href="mkinresplot.html">mkinresplot</a></code>, it only takes effect if
+<code>resplot = "time"</code>.</p></dd>
+
+
+<dt>show_errmin</dt>
+<dd><p>Should the chi2 error level be shown on top of the plots
+to the left?</p></dd>
+
+
+<dt>errmin_var</dt>
+<dd><p>The variable for which the FOCUS chi2 error value should
+be shown.</p></dd>
+
+<dt>errmin_digits</dt>
+<dd><p>The number of significant digits for rounding the FOCUS
+chi2 error percentage.</p></dd>
+
+
+<dt>cex</dt>
+<dd><p>Passed to the plot functions and <code><a href="https://rdrr.io/r/graphics/mtext.html" class="external-link">mtext</a></code>.</p></dd>
+
+
+<dt>rel.height.middle</dt>
+<dd><p>The relative height of the middle plot, if more
+than two rows of plots are shown.</p></dd>
+
+
+<dt>ymax</dt>
+<dd><p>Maximum y axis value for <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p></dd>
+
+
+<dt>...</dt>
+<dd><p>Further arguments passed to <code><a href="plot.mkinfit.html">plot.mkinfit</a></code> and
+<code><a href="mkinresplot.html">mkinresplot</a></code>.</p></dd>
+
+</dl></div>
+ <div id="value">
+ <h2>Value</h2>
+
+
+<p>The function is called for its side effect.</p>
+ </div>
+ <div id="details">
+ <h2>Details</h2>
+ <p>If the current plot device is a <code><a href="https://rdrr.io/pkg/tikzDevice/man/tikz.html" class="external-link">tikz</a></code> device, then
+latex is being used for the formatting of the chi2 error level.</p>
+ </div>
+ <div id="author">
+ <h2>Author</h2>
<p>Johannes Ranke</p>
+ </div>
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'>
- <span class='co'># \dontrun{</span>
- <span class='co'># Only use one core not to offend CRAN checks</span>
- <span class='va'>fits</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"HS"</span><span class='op'>)</span>,
- <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"FOCUS B"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, <span class='co'># named list for titles</span>
- cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
-#&gt; <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>, show_errmin <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
- <span class='co'># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span>
- <span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span>
- <span class='co'># generated by pkgdown, as far as I know).</span>
- <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># same as plot(fits[1, 2])</span>
-</div><div class='img'><img src='plot.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'>
- <span class='co'># Show the error models</span>
- <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>, resplot <span class='op'>=</span> <span class='st'>"errmod"</span><span class='op'>)</span>
-</div><div class='img'><img src='plot.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># }</span>
-
-</div></pre>
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <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="co"># Only use one core not to offend CRAN checks</span></span></span>
+<span class="r-in"><span> <span class="va">fits</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><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">"FOMC"</span>, <span class="st">"HS"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, <span class="co"># named list for titles</span></span></span>
+<span class="r-in"><span> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></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> iteration limit reached without convergence (10)</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="va">fits</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.mmkin-1.png" alt="" width="700" height="433"></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="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.mmkin-2.png" alt="" width="700" height="433"></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="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, show_errmin <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.mmkin-3.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="co"># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span></span></span>
+<span class="r-in"><span> <span class="co"># height should be smaller than the plot width (this is not possible for the html pages</span></span></span>
+<span class="r-in"><span> <span class="co"># generated by pkgdown, as far as I know).</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="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span> <span class="co"># same as plot(fits[1, 2])</span></span></span>
+<span class="r-plt img"><img src="plot.mmkin-4.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span> <span class="co"># Show the error models</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="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot.mmkin-5.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span> <span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+ </div>
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