A plot method for nlme.mmkin fits

author: Johannes Ranke <jranke@uni-bremen.de> 2020-04-15 01:27:02 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2020-04-15 01:51:55 +0200
commit: 082be7baa35d7e8131a70ca8cc061d90e08fa584 (patch)
tree: 29774198fae54ac13f2a0c2d2fb385a5fc44ab92 /docs/reference/plot.nlme.mmkin.html
parent: 26085403289e29259e500282e8e88a5ab00c07a0 (diff)
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+    <div class="page-header">
+    <h1>Plot a fitted nonlinear mixed model obtained via an mmkin row object</h1>
+    
+    <div class="hidden name"><code>plot.nlme.mmkin.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Plot a fitted nonlinear mixed model obtained via an mmkin row object</p>
+    </div>
+
+    <pre class="usage"><span class='co'># S3 method for nlme.mmkin</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(
+  <span class='no'>x</span>,
+  <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span>(<span class='no'>x</span>$<span class='no'>mmkin_orig</span>),
+  <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+  <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>,
+  <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"time"</span>, <span class='st'>"errmod"</span>),
+  <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>,
+  <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>,
+  <span class='kw'>ymax</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+  <span class='no'>...</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='nlme.mmkin.html'>nlme.mmkin</a></code></p></td>
+    </tr>
+    <tr>
+      <th>i</th>
+      <td><p>A numeric index to select datasets for which to plot the nlme fit,
+in case plots get too large</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>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
+`resplot = "time"`.</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="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='no'>ds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
+ <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)], <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>))
+<span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</span>, <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)
+<span class='co'>#plot(f) # too many panels for pkgdown</span>
+<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>)
+<span class='no'>f_nlme</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>)
+
+<span class='co'>#plot(f_nlme) # too many panels for pkgdown</span>
+<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f_nlme</span>, <span class='fl'>1</span>:<span class='fl'>2</span>)</div><div class='img'><img src='plot.nlme.mmkin-1.png' alt='' width='700' height='433' /></div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      <li><a href="#arguments">Arguments</a></li>
+      <li><a href="#value">Value</a></li>
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+    <h2>Author</h2>
+    <p>Johannes Ranke</p>
+  </div>
+</div>
+
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author	Johannes Ranke <jranke@uni-bremen.de>	2020-04-15 01:27:02 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2020-04-15 01:51:55 +0200
commit	082be7baa35d7e8131a70ca8cc061d90e08fa584 (patch)
tree	29774198fae54ac13f2a0c2d2fb385a5fc44ab92 /docs/reference/plot.nlme.mmkin.html
parent	26085403289e29259e500282e8e88a5ab00c07a0 (diff)