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authorJohannes Ranke <jranke@uni-bremen.de>2020-05-27 06:06:08 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-27 06:06:08 +0200
commita77a10ea6c607346778ba0700b3b66ac393101a2 (patch)
treee91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/mkinresplot.html
parent675a733fa2acc08daabb9b8b571c7d658f281f73 (diff)
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+<meta property="og:description" content="This function plots the residuals for the specified subset of the observed
+variables from an mkinfit object. A combined plot of the fitted model and
+the residuals can be obtained using plot.mkinfit using the
+argument show_residuals = TRUE." />
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+ <h1>Function to plot residuals stored in an mkin object</h1>
+ <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinresplot.R'><code>R/mkinresplot.R</code></a></small>
+ <div class="hidden name"><code>mkinresplot.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>This function plots the residuals for the specified subset of the observed
+variables from an mkinfit object. A combined plot of the fitted model and
+the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> using the
+argument <code>show_residuals = TRUE</code>.</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>mkinresplot</span>(
+ <span class='no'>object</span>,
+ <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>),
+ <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>time</span>)),
+ <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>,
+ <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='no'>standardized</span>, <span class='st'>"Standardized residual"</span>, <span class='st'>"Residual"</span>),
+ <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>,
+ <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+ <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</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>object</th>
+ <td><p>A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.</p></td>
+ </tr>
+ <tr>
+ <th>obs_vars</th>
+ <td><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></td>
+ </tr>
+ <tr>
+ <th>xlim</th>
+ <td><p>plot range in x direction.</p></td>
+ </tr>
+ <tr>
+ <th>standardized</th>
+ <td><p>Should the residuals be standardized by dividing by the
+standard deviation given by the error model of the fit?</p></td>
+ </tr>
+ <tr>
+ <th>xlab</th>
+ <td><p>Label for the x axis.</p></td>
+ </tr>
+ <tr>
+ <th>ylab</th>
+ <td><p>Label for the y axis.</p></td>
+ </tr>
+ <tr>
+ <th>maxabs</th>
+ <td><p>Maximum absolute value of the residuals. This is used for the
+scaling of the y axis and defaults to "auto".</p></td>
+ </tr>
+ <tr>
+ <th>legend</th>
+ <td><p>Should a legend be plotted?</p></td>
+ </tr>
+ <tr>
+ <th>lpos</th>
+ <td><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'>legend</a></code>.</p></td>
+ </tr>
+ <tr>
+ <th>col_obs</th>
+ <td><p>Colors for the observed variables.</p></td>
+ </tr>
+ <tr>
+ <th>pch_obs</th>
+ <td><p>Symbols to be used for the observed variables.</p></td>
+ </tr>
+ <tr>
+ <th>frame</th>
+ <td><p>Should a frame be drawn around the plots?</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>further arguments passed to <code><a href='https://rdrr.io/r/base/plot.html'>plot</a></code>.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>Nothing is returned by this function, as it is called for its side
+effect, namely to produce a plot.</p>
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted
+lines of the mkinfit object, and <code><a href='plot.mkinfit.html'>plot_res</a></code> for a function
+combining the plot of the fit and the residual plot.</p></div>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'>
+<span class='no'>model</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div><div class='input'>
+</div></pre>
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