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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.
If the current plot device is a tikz device,
then latex is being used for the formatting of the chi2 error level,
if show_errmin = TRUE." />
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<h1>Plot the observed data and the fitted model of an mkinfit object</h1>
<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>
<p>If the current plot device is a <code><a href='https://www.rdocumentation.org/packages/tikzDevice/topics/tikz'>tikz</a></code> device,
then latex is being used for the formatting of the chi2 error level,
if <code>show_errmin = TRUE</code>.</p>
</div>
<pre class="usage"># S3 method for mkinfit
plot(x, fit = x,
obs_vars = names(fit$mkinmod$map),
xlab = "Time", ylab = "Observed",
xlim = range(fit$data$time),
ylim = "default",
col_obs = 1:length(obs_vars), pch_obs = col_obs,
lty_obs = rep(1, length(obs_vars)),
add = FALSE, legend = !add,
show_residuals = FALSE, maxabs = "auto",
sep_obs = FALSE, rel.height.middle = 0.9,
lpos = "topright", inset = c(0.05, 0.05),
show_errmin = FALSE, errmin_digits = 3, …)
plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …)</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.</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>lpos</th>
<td><p>Position(s) of the legend(s). Passed to <code><a href='https://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.</p></td>
</tr>
<tr>
<th>inset</th>
<td><p>Passed to <code><a href='https://www.rdocumentation.org/packages/graphics/topics/legend'>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>…</th>
<td><p>Further arguments passed to <code><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</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='co'># One parent compound, one metabolite, both single first order, path from</span>
<span class='co'># parent to sink included, use Levenberg-Marquardt for speed</span>
<span class='no'>SFO_SFO</span> <span class='kw'><-</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'>#> <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'><-</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'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>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'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># Show the observed variables separately</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>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'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-3.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://www.rdocumentation.org/packages/graphics/topics/plot'>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://www.rdocumentation.org/packages/base/topics/c'>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-4.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://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div></pre>
</div>
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<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>
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