path: root/docs/dev/reference/mkinresplot.html

               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Function to plot residuals stored in an mkin object — mkinresplot • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Function to plot residuals stored in an mkin object — mkinresplot"><meta property="og:description" content="This function plots the residuals for the specified subset of the observed
variables from an mkinfit object. A combined plot of the fitted model and
the residuals can be obtained using plot.mkinfit using the
argument show_residuals = TRUE."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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 data-spy="scroll" data-target="#toc">
    

    <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" aria-expanded="false">
        <span class="sr-only">Toggle navigation</span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">mkin</a>
        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav"><li>
  <a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" 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 class="divider">
    <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
    </li>
    <li class="divider">
    <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li>
    <li>
      <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
    </li>
    <li>
      <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
    </li>
    <li>
      <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
    </li>
    <li>
      <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
    </li>
    <li>
      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
    </li>
    <li class="divider">
    <li class="dropdown-header">Performance</li>
    <li>
      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
    </li>
    <li>
      <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
    </li>
    <li>
      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
    </li>
    <li class="divider">
    <li class="dropdown-header">Miscellaneous</li>
    <li>
      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
    </li>
    <li>
      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
    </li>
  </ul></li>
<li>
  <a href="../news/index.html">News</a>
</li>
      </ul><ul class="nav navbar-nav navbar-right"><li>
  <a href="https://github.com/jranke/mkin/" class="external-link">
    <span class="fab fa-github fa-lg"></span>
     
  </a>
</li>
      </ul></div><!--/.nav-collapse -->
  </div><!--/.container -->
</div><!--/.navbar -->

      
      </header><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Function to plot residuals stored in an mkin object</h1>
    <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinresplot.R" class="external-link"><code>R/mkinresplot.R</code></a></small>
    <div class="hidden name"><code>mkinresplot.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This function plots the residuals for the specified subset of the observed
variables from an mkinfit object. A combined plot of the fitted model and
the residuals can be obtained using <code><a href="plot.mkinfit.html">plot.mkinfit</a></code> using the
argument <code>show_residuals = TRUE</code>.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinresplot</span><span class="op">(</span></span>
<span>  <span class="va">object</span>,</span>
<span>  obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span>
<span>  xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span><span class="op">)</span>,</span>
<span>  standardized <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  xlab <span class="op">=</span> <span class="st">"Time"</span>,</span>
<span>  ylab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">standardized</span>, <span class="st">"Standardized residual"</span>, <span class="st">"Residual"</span><span class="op">)</span>,</span>
<span>  maxabs <span class="op">=</span> <span class="st">"auto"</span>,</span>
<span>  legend <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  lpos <span class="op">=</span> <span class="st">"topright"</span>,</span>
<span>  col_obs <span class="op">=</span> <span class="st">"auto"</span>,</span>
<span>  pch_obs <span class="op">=</span> <span class="st">"auto"</span>,</span>
<span>  frame <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>object</dt>
<dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd>


<dt>obs_vars</dt>
<dd><p>A character vector of names of the observed variables for
which residuals should be plotted. Defaults to all observed variables in
the model</p></dd>


<dt>xlim</dt>
<dd><p>plot range in x direction.</p></dd>


<dt>standardized</dt>
<dd><p>Should the residuals be standardized by dividing by the
standard deviation given by the error model of the fit?</p></dd>


<dt>xlab</dt>
<dd><p>Label for the x axis.</p></dd>


<dt>ylab</dt>
<dd><p>Label for the y axis.</p></dd>


<dt>maxabs</dt>
<dd><p>Maximum absolute value of the residuals. This is used for the
scaling of the y axis and defaults to "auto".</p></dd>


<dt>legend</dt>
<dd><p>Should a legend be plotted?</p></dd>


<dt>lpos</dt>
<dd><p>Where should the legend be placed? Default is "topright". Will
be passed on to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code>.</p></dd>


<dt>col_obs</dt>
<dd><p>Colors for the observed variables.</p></dd>


<dt>pch_obs</dt>
<dd><p>Symbols to be used for the observed variables.</p></dd>


<dt>frame</dt>
<dd><p>Should a frame be drawn around the plots?</p></dd>


<dt>...</dt>
<dd><p>further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>Nothing is returned by this function, as it is called for its side
effect, namely to produce a plot.</p>
    </div>
    <div id="see-also">
    <h2>See also</h2>
    <div class="dont-index"><p><code><a href="mkinplot.html">mkinplot</a></code>, for a way to plot the data and the fitted
lines of the mkinfit object, and <code><a href="plot.mkinfit.html">plot_res</a></code> for a function
combining the plot of the fit and the residual plot.</p></div>
    </div>
    <div id="author">
    <h2>Author</h2>
    <p>Johannes Ranke and Katrin Lindenberger</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"><span><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
<span class="r-in"><span><span class="fu">mkinresplot</span><span class="op">(</span><span class="va">fit</span>, <span class="st">"m1"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="mkinresplot-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
</code></pre></div>
    </div>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
    </nav></div>
</div>


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

<div class="pkgdown">
  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>

      </footer></div>

  
  </body></html>