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<title>plot.mkinfit. mkin 0.9.44</title>
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  Johannes Ranke
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      <header>
        
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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><div>"plot"(x, fit&nbsp;=&nbsp;x, obs_vars&nbsp;=&nbsp;names(fit$mkinmod$map), xlab&nbsp;=&nbsp;"Time", ylab&nbsp;=&nbsp;"Observed",  xlim&nbsp;=&nbsp;range(fit$data$time), ylim&nbsp;=&nbsp;"default", col_obs&nbsp;=&nbsp;1:length(obs_vars), pch_obs&nbsp;=&nbsp;col_obs,  lty_obs&nbsp;=&nbsp;rep(1, length(obs_vars)), add&nbsp;=&nbsp;FALSE, legend&nbsp;=&nbsp;!add, show_residuals&nbsp;=&nbsp;FALSE, maxabs&nbsp;=&nbsp;"auto", sep_obs&nbsp;=&nbsp;FALSE, rel.height.middle&nbsp;=&nbsp;0.9, lpos&nbsp;=&nbsp;"topright", inset&nbsp;=&nbsp;c(0.05, 0.05),  show_errmin&nbsp;=&nbsp;FALSE, errmin_digits&nbsp;=&nbsp;3, ...)
plot_sep(fit, sep_obs&nbsp;=&nbsp;TRUE,  show_residuals&nbsp;=&nbsp;TRUE, show_errmin&nbsp;=&nbsp;TRUE, ...)</div></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.inside-r.org/r-doc/graphics/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.inside-r.org/r-doc/graphics/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.inside-r.org/r-doc/graphics/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'># One parent compound, one metabolite, both single first order, path from
# parent to sink included, use Levenberg-Marquardt for speed
SFO_SFO &lt;- mkinmod(parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;, full = &quot;Parent&quot;),
                   m1 = mkinsub(&quot;SFO&quot;, full = &quot;Metabolite M1&quot; ))
</div>
<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
<div class='input'>fit &lt;- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = &quot;Marq&quot;)
plot(fit)
</div>
<p><img src='plot.mkinfit-4.png' alt='' width='540' height='400' /></p>
<div class='input'>plot(fit, show_residuals = TRUE)
</div>
<p><img src='plot.mkinfit-6.png' alt='' width='540' height='400' /></p>
<div class='input'>
# Show the observed variables separately
plot(fit, sep_obs = TRUE, lpos = c(&quot;topright&quot;, &quot;bottomright&quot;))
</div>
<p><img src='plot.mkinfit-8.png' alt='' width='540' height='400' /></p>
<div class='input'>
# Show the observed variables separately, with residuals
plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c(&quot;topright&quot;, &quot;bottomright&quot;),
     show_errmin = TRUE)
</div>
<p><img src='plot.mkinfit-10.png' alt='' width='540' height='400' /></p>
<div class='input'>
# The same can be obtained with less typing, using the convenience function plot_sep
plot_sep(fit, lpos = c(&quot;topright&quot;, &quot;bottomright&quot;))
</div></pre>
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      <li>plot.mkinfit</li><li>plot_sep</li>
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    <h2>Author</h2>
    
  Johannes Ranke

    
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