aboutsummaryrefslogblamecommitdiff
path: root/docs/reference/mkinerrplot.html
blob: dfbd88be49da56f58770143d633843386b0fa160 (plain) (tree)
1
2
3
4
5
6
7
8
9
10








                                                                                                                 
 
               
                                                                                                                                                                                 
                  
                                                                                                                                                                                                             
 



                                                                                                                                                                                                  
                           
                                                                                                                                                                                                        
                     
                                                                                                                                                                                          
 
                    
                                                                                                                                                                                             





                                             
 
                                                                                                                                
                                                                                                                  


                                                                          

 
 








                                                                                                                                                                                                    
 
         
                                             











                                                                                                                               
                                                                                                                                        


































                                                                                                                             

                                                                               




                                       
                                              
            
                                            


                                                    





                                
 




                                                                                      
                                                                                                                                                   


                                                              
                                                                                


                                                                                                        
          












                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
 







                                                                                                     

                                                                        














                                                                            
                                           





                                                 
                                                                                                  








                                                                    



                                                               
                                                                                                                               
            
 
                                                                                   
                                                                         
                                     
                                                                                            
                                                                                                                           
                                      

                                                                                      
                                                                                            
                                             


                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
 
            
        


                                                                 

        
 




                                     
                                                                                
      
 



               
 

         
 
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
  <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>Function to plot squared residuals and the error model for an mkin object — mkinerrplot • 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 squared residuals and the error model for an mkin object — mkinerrplot" />
<meta property="og:description" content="This function plots the squared residuals for the specified subset of the
observed variables from an mkinfit object. In addition, one or more dashed
line(s) show the fitted error model.  A combined plot of the fitted model
and this error model plot can be obtained with plot.mkinfit
using the argument show_errplot = TRUE." />




<!-- 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span>
      </span>
    </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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
    </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/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>
    <li>
      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</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/">
    <span class="fab fa 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 squared residuals and the error model for an mkin object</h1>
    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinerrplot.R'><code>R/mkinerrplot.R</code></a></small>
    <div class="hidden name"><code>mkinerrplot.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This function plots the squared residuals for the specified subset of the
observed variables from an mkinfit object. In addition, one or more dashed
line(s) show the fitted error model.  A combined plot of the fitted model
and this error model plot can be obtained with <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>
using the argument <code>show_errplot = TRUE</code>.</p>
    </div>

    <pre class="usage"><span class='fu'>mkinerrplot</span><span class='op'>(</span>
  <span class='va'>object</span>,
  obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>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>,
  xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>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'>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'>predicted</span><span class='op'>)</span><span class='op'>)</span>,
  xlab <span class='op'>=</span> <span class='st'>"Predicted"</span>,
  ylab <span class='op'>=</span> <span class='st'>"Squared residual"</span>,
  maxy <span class='op'>=</span> <span class='st'>"auto"</span>,
  legend <span class='op'>=</span> <span class='cn'>TRUE</span>,
  lpos <span class='op'>=</span> <span class='st'>"topright"</span>,
  col_obs <span class='op'>=</span> <span class='st'>"auto"</span>,
  pch_obs <span class='op'>=</span> <span class='st'>"auto"</span>,
  frame <span class='op'>=</span> <span class='cn'>TRUE</span>,
  <span class='va'>...</span>
<span class='op'>)</span></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>object</th>
      <td><p>A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.</p></td>
    </tr>
    <tr>
      <th>obs_vars</th>
      <td><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></td>
    </tr>
    <tr>
      <th>xlim</th>
      <td><p>plot range in x direction.</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>maxy</th>
      <td><p>Maximum value of the residuals. This is used for the scaling of
the y axis and defaults to "auto".</p></td>
    </tr>
    <tr>
      <th>legend</th>
      <td><p>Should a legend be plotted?</p></td>
    </tr>
    <tr>
      <th>lpos</th>
      <td><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'>legend</a></code>.</p></td>
    </tr>
    <tr>
      <th>col_obs</th>
      <td><p>Colors for the observed variables.</p></td>
    </tr>
    <tr>
      <th>pch_obs</th>
      <td><p>Symbols to be used for the observed variables.</p></td>
    </tr>
    <tr>
      <th>frame</th>
      <td><p>Should a frame be drawn around the plots?</p></td>
    </tr>
    <tr>
      <th>...</th>
      <td><p>further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td>
    </tr>
    </table>

    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

    <p>Nothing is returned by this function, as it is called for its side
effect, namely to produce a plot.</p>
    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>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.</p></div>
    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>

    <p>Johannes Ranke</p>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'>
<span class='co'># \dontrun{</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='mkinsub.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='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</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='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>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinerrplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
</div><div class='img'><img src='mkinerrplot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span>

</div></pre>
  </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>Developed by Johannes Ranke.</p>
</div>

<div class="pkgdown">
  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>

      </footer>
   </div>

  


  </body>
</html>


Contact - Imprint