path: root/docs/reference/plot.mkinfit.html



<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html>
  <head>
  <meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin</title>

<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
<!-- Bootstrap -->

<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>

<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">

<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>

<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
  
  
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>

<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->


  </head>

  <body>
    <div class="container template-reference-topic">
      <header>
      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
  <div class="container">
    <div class="navbar-header">
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </button>
      <a class="navbar-brand" href="../index.html">mkin</a>
    </div>
    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav">
        <li>
  <a href="../reference/index.html">Functions and data</a>
</li>
<li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
    Articles
     
    <span class="caret"></span>
  </a>
  <ul class="dropdown-menu" role="menu">
    <li>
      <a href="../articles/mkin.html">Introduction to mkin</a>
    </li>
    <li>
      <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
    </li>
    <li>
      <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
    </li>
    <li>
      <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
    </li>
    <li>
      <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
    </li>
    <li>
      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
    </li>
  </ul>
</li>
<li>
  <a href="../news/index.html">News</a>
</li>
      </ul>
      
      <ul class="nav navbar-nav navbar-right">
        
      </ul>
    </div><!--/.nav-collapse -->
  </div><!--/.container -->
</div><!--/.navbar -->

      
      </header>

      <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>
    </div>

    
    <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='http://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>
    

    <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, &#8230;)
plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, &#8230;)</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>legend</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>legend</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>&#8230;</th>
      <td><p>Further arguments passed to <code>plot</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'>&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>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>)
<span class='fu'>plot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'><span class='fu'>plot</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='432.632880098887' /></div><div class='input'>
<span class='co'># Show the observed variables separately</span>
<span class='fu'>plot</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'>c</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='432.632880098887' /></div><div class='input'>
<span class='co'># Show the observed variables separately, with residuals</span>
<span class='fu'>plot</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'>c</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='432.632880098887' /></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'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div></pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
    <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>
    
  Johannes Ranke

  </div>
</div>

      <footer>
      <div class="copyright">
  <p>Developed by Johannes Ranke.</p>
</div>

<div class="pkgdown">
  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>

      </footer>
   </div>

  </body>
</html>