Create up to date pkgdown docs in development mode

author: Johannes Ranke <jranke@uni-bremen.de> 2020-05-27 06:06:08 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2020-05-27 06:06:08 +0200
commit: a77a10ea6c607346778ba0700b3b66ac393101a2 (patch)
tree: e91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/plot.mkinfit.html
parent: 675a733fa2acc08daabb9b8b571c7d658f281f73 (diff)
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+<meta property="og:description" content="Solves the differential equations with the optimised and fixed parameters
+from a previous successful call to mkinfit and plots the
+observed data together with the solution of the fitted model." />
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+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Plot the observed data and the fitted model of an mkinfit object</h1>
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/plot.mkinfit.R'><code>R/plot.mkinfit.R</code></a></small>
+    <div class="hidden name"><code>plot.mkinfit.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Solves the differential equations with the optimised and fixed parameters
+from a previous successful call to <code><a href='mkinfit.html'>mkinfit</a></code> and plots the
+observed data together with the solution of the fitted model.</p>
+    </div>
+
+    <pre class="usage"><span class='co'># S3 method for mkinfit</span>
+<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(
+  <span class='no'>x</span>,
+  <span class='kw'>fit</span> <span class='kw'>=</span> <span class='no'>x</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'>fit</span>$<span class='no'>mkinmod</span>$<span class='no'>map</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='st'>"Observed"</span>,
+  <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='no'>fit</span>$<span class='no'>data</span>$<span class='no'>time</span>),
+  <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='st'>"default"</span>,
+  <span class='kw'>col_obs</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>),
+  <span class='kw'>pch_obs</span> <span class='kw'>=</span> <span class='no'>col_obs</span>,
+  <span class='kw'>lty_obs</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>obs_vars</span>)),
+  <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>legend</span> <span class='kw'>=</span> !<span class='no'>add</span>,
+  <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>,
+  <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>,
+  <span class='kw'>row_layout</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>,
+  <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.05</span>, <span class='fl'>0.05</span>),
+  <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>,
+  <span class='kw'>frame</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='no'>...</span>
+)
+
+<span class='fu'>plot_sep</span>(
+  <span class='no'>fit</span>,
+  <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='no'>fit</span>$<span class='no'>err_mod</span>, <span class='st'>"const"</span>), <span class='fl'>TRUE</span>, <span class='st'>"standardized"</span>),
+  <span class='no'>...</span>
+)
+
+<span class='fu'>plot_res</span>(
+  <span class='no'>fit</span>,
+  <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</span>,
+  <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span>(<span class='no'>fit</span>$<span class='no'>err_mod</span>, <span class='st'>"const"</span>), <span class='fl'>FALSE</span>, <span class='fl'>TRUE</span>),
+  <span class='no'>...</span>
+)
+
+<span class='fu'>plot_err</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='no'>sep_obs</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>Alias for fit introduced for compatibility with the generic S3
+method.</p></td>
+    </tr>
+    <tr>
+      <th>fit</th>
+      <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
+    </tr>
+    <tr>
+      <th>obs_vars</th>
+      <td><p>A character vector of names of the observed variables for
+which the data and the model should be plotted. Defauls to all observed
+variables in the model.</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>xlim</th>
+      <td><p>Plot range in x direction.</p></td>
+    </tr>
+    <tr>
+      <th>ylim</th>
+      <td><p>Plot range in y direction.</p></td>
+    </tr>
+    <tr>
+      <th>col_obs</th>
+      <td><p>Colors used for plotting the observed data and the
+corresponding model prediction lines.</p></td>
+    </tr>
+    <tr>
+      <th>pch_obs</th>
+      <td><p>Symbols to be used for plotting the data.</p></td>
+    </tr>
+    <tr>
+      <th>lty_obs</th>
+      <td><p>Line types to be used for the model predictions.</p></td>
+    </tr>
+    <tr>
+      <th>add</th>
+      <td><p>Should the plot be added to an existing plot?</p></td>
+    </tr>
+    <tr>
+      <th>legend</th>
+      <td><p>Should a legend be added to the plot?</p></td>
+    </tr>
+    <tr>
+      <th>show_residuals</th>
+      <td><p>Should residuals be shown? If only one plot of the
+fits is shown, the residual plot is in the lower third of the plot.
+Otherwise, i.e. if "sep_obs" is given, the residual plots will be located
+to the right of the plots of the fitted curves. If this is set to
+'standardized', a plot of the residuals divided by the standard deviation
+given by the fitted error model will be shown.</p></td>
+    </tr>
+    <tr>
+      <th>show_errplot</th>
+      <td><p>Should squared residuals and the error model be shown?
+If only one plot of the fits is shown, this plot is in the lower third of
+the plot.  Otherwise, i.e. if "sep_obs" is given, the residual plots will
+be located to the right of the plots of the fitted curves.</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>sep_obs</th>
+      <td><p>Should the observed variables be shown in separate subplots?
+If yes, residual plots requested by "show_residuals" will be shown next
+to, not below the plot of the fits.</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>row_layout</th>
+      <td><p>Should we use a row layout where the residual plot or the
+error model plot is shown to the right?</p></td>
+    </tr>
+    <tr>
+      <th>lpos</th>
+      <td><p>Position(s) of the legend(s). Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> as
+the first argument.  If not length one, this should be of the same length
+as the obs_var argument.</p></td>
+    </tr>
+    <tr>
+      <th>inset</th>
+      <td><p>Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> if applicable.</p></td>
+    </tr>
+    <tr>
+      <th>show_errmin</th>
+      <td><p>Should the FOCUS chi2 error value be shown in the upper
+margin of the plot?</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>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>
+    <tr>
+      <th>standardized</th>
+      <td><p>When calling 'plot_res', should the residuals be
+standardized in the residual plot?</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, if
+<code>show_errmin = TRUE</code>.</p>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'>
+<span class='co'># One parent compound, one metabolite, both single first order, path from</span>
+<span class='co'># parent to sink included</span>
+<span class='co'># \dontrun{</span>
+<span class='no'>SFO_SFO</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'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</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>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</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'>SFO_SFO</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='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_res</span>(<span class='no'>fit</span>, <span class='kw'>standardized</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot_err</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='co'># Show the observed variables separately, with residuals</span>
+<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>),
+     <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-5.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='co'># The same can be obtained with less typing, using the convenience function plot_sep</span>
+<span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-6.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='co'># Show the observed variables separately, with the error model</span>
+<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>),
+     <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-7.png' alt='' width='700' height='433' /></div><div class='input'># }
+
+</div></pre>
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author	Johannes Ranke <jranke@uni-bremen.de>	2020-05-27 06:06:08 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2020-05-27 06:06:08 +0200
commit	a77a10ea6c607346778ba0700b3b66ac393101a2 (patch)
tree	e91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/plot.mkinfit.html
parent	675a733fa2acc08daabb9b8b571c7d658f281f73 (diff)