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<title>plot.mkinfit. mkin 0.9.44.9000</title>
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Johannes Ranke
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<h1>
Plot the observed data and the fitted model of an mkinfit object
</h1>
<div class="row">
<div class="span8">
<h2>Usage</h2>
<pre><span class="comment"># S3 method for mkinfit</span>
<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="argument">fit</span> <span class="argument">=</span> <span class="symbol">x</span><span class="keyword">,</span>
<span class="argument">obs_vars</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/names'>names</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">$</span><span class="symbol">mkinmod</span><span class="keyword">$</span><span class="symbol">map</span><span class="keyword">)</span><span class="keyword">,</span>
<span class="argument">xlab</span> <span class="argument">=</span> <span class="string">"Time"</span><span class="keyword">,</span> <span class="argument">ylab</span> <span class="argument">=</span> <span class="string">"Observed"</span><span class="keyword">,</span>
<span class="argument">xlim</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/range'>range</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">$</span><span class="symbol">data</span><span class="keyword">$</span><span class="symbol">time</span><span class="keyword">)</span><span class="keyword">,</span>
<span class="argument">ylim</span> <span class="argument">=</span> <span class="string">"default"</span><span class="keyword">,</span>
<span class="argument">col_obs</span> <span class="argument">=</span> <span class="number">1</span><span class="keyword">:</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/length'>length</a></span><span class="keyword">(</span><span class="symbol">obs_vars</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">pch_obs</span> <span class="argument">=</span> <span class="symbol">col_obs</span><span class="keyword">,</span>
<span class="argument">lty_obs</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span><span class="keyword">(</span><span class="number">1</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/length'>length</a></span><span class="keyword">(</span><span class="symbol">obs_vars</span><span class="keyword">)</span><span class="keyword">)</span><span class="keyword">,</span>
<span class="argument">add</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">legend</span> <span class="argument">=</span> <span class="keyword">!</span><span class="symbol">add</span><span class="keyword">,</span>
<span class="argument">show_residuals</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">maxabs</span> <span class="argument">=</span> <span class="string">"auto"</span><span class="keyword">,</span>
<span class="argument">sep_obs</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">rel.height.middle</span> <span class="argument">=</span> <span class="number">0.9</span><span class="keyword">,</span>
<span class="argument">lpos</span> <span class="argument">=</span> <span class="string">"topright"</span><span class="keyword">,</span> <span class="argument">inset</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0.05</span><span class="keyword">,</span> <span class="number">0.05</span><span class="keyword">)</span><span class="keyword">,</span>
<span class="argument">show_errmin</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">errmin_digits</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span>
<span class="functioncall"><a href='plot.mkinfit.html'>plot_sep</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">sep_obs</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">show_residuals</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">show_errmin</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span></pre>
<h2>Arguments</h2>
<dl>
<dt>x</dt>
<dd>
Alias for fit introduced for compatibility with the generic S3 method.
</dd>
<dt>fit</dt>
<dd>
An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.
</dd>
<dt>obs_vars</dt>
<dd>
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.
</dd>
<dt>xlab</dt>
<dd>
Label for the x axis.
</dd>
<dt>ylab</dt>
<dd>
Label for the y axis.
</dd>
<dt>xlim</dt>
<dd>
Plot range in x direction.
</dd>
<dt>ylim</dt>
<dd>
Plot range in y direction.
</dd>
<dt>col_obs</dt>
<dd>
Colors used for plotting the observed data and the corresponding model prediction lines.
</dd>
<dt>pch_obs</dt>
<dd>
Symbols to be used for plotting the data.
</dd>
<dt>lty_obs</dt>
<dd>
Line types to be used for the model predictions.
</dd>
<dt>add</dt>
<dd>
Should the plot be added to an existing plot?
</dd>
<dt>legend</dt>
<dd>
Should a legend be added to the plot?
</dd>
<dt>show_residuals</dt>
<dd>
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.
</dd>
<dt>maxabs</dt>
<dd>
Maximum absolute value of the residuals. This is used for the scaling of
the y axis and defaults to "auto".
</dd>
<dt>sep_obs</dt>
<dd>
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.
</dd>
<dt>rel.height.middle</dt>
<dd>
The relative height of the middle plot, if more than two rows of plots are shown.
</dd>
<dt>lpos</dt>
<dd>
Position(s) of the legend(s). Passed to <code><a href='http://www.rdocumentation.org/packages/graphics/topics/legend'>legend</a></code> as the first argument.
If not length one, this should be of the same length as the obs_var argument.
</dd>
<dt>inset</dt>
<dd>
Passed to <code><a href='http://www.rdocumentation.org/packages/graphics/topics/legend'>legend</a></code> if applicable.
</dd>
<dt>show_errmin</dt>
<dd>
Should the FOCUS chi2 error value be shown in the upper margin of the plot?
</dd>
<dt>errmin_digits</dt>
<dd>
The number of significant digits for rounding the FOCUS chi2 error percentage.
</dd>
<dt>...</dt>
<dd>
Further arguments passed to <code><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></code>.
</dd>
</dl>
<div class="Description">
<h2>Description</h2>
<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>
<div class="Value">
<h2>Value</h2>
<p><dl>
The function is called for its side effect.
</dl></p>
</div>
<h2 id="examples">Examples</h2>
<pre class="examples"><div class='input'><span class="comment"># One parent compound, one metabolite, both single first order, path from</span>
<span class="comment"># parent to sink included, use Levenberg-Marquardt for speed</span>
<span class="symbol">SFO_SFO</span> <span class="assignement"><-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span><span class="argument">parent</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"m1"</span><span class="keyword">,</span> <span class="argument">full</span> <span class="argument">=</span> <span class="string">"Parent"</span><span class="keyword">)</span><span class="keyword">,</span>
<span class="argument">m1</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">full</span> <span class="argument">=</span> <span class="string">"Metabolite M1"</span> <span class="keyword">)</span><span class="keyword">)</span></div>
<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
<div class='input'><span class="symbol">fit</span> <span class="assignement"><-</span> <span class="functioncall"><a href='mkinfit.html'>mkinfit</a></span><span class="keyword">(</span><span class="symbol">SFO_SFO</span><span class="keyword">,</span> <span class="symbol">FOCUS_2006_D</span><span class="keyword">,</span> <span class="argument">quiet</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">method.modFit</span> <span class="argument">=</span> <span class="string">"Marq"</span><span class="keyword">)</span>
<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">)</span></div>
<p><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /></p>
<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">show_residuals</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></div>
<p><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /></p>
<div class='input'>
<span class="comment"># Show the observed variables separately</span>
<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">sep_obs</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">lpos</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"topright"</span><span class="keyword">,</span> <span class="string">"bottomright"</span><span class="keyword">)</span><span class="keyword">)</span></div>
<p><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /></p>
<div class='input'>
<span class="comment"># Show the observed variables separately, with residuals</span>
<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">sep_obs</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">show_residuals</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">lpos</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"topright"</span><span class="keyword">,</span> <span class="string">"bottomright"</span><span class="keyword">)</span><span class="keyword">,</span>
<span class="argument">show_errmin</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></div>
<p><img src='plot.mkinfit-10.png' alt='' width='540' height='400' /></p>
<div class='input'>
<span class="comment"># The same can be obtained with less typing, using the convenience function plot_sep</span>
<span class="functioncall"><a href='plot.mkinfit.html'>plot_sep</a></span><span class="keyword">(</span><span class="symbol">fit</span><span class="keyword">,</span> <span class="argument">lpos</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"topright"</span><span class="keyword">,</span> <span class="string">"bottomright"</span><span class="keyword">)</span><span class="keyword">)</span></div></pre>
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