aboutsummaryrefslogblamecommitdiff
path: root/docs/reference/plot.mmkin.html
blob: 20f9033d2a09f867a0cc6df7b7dbc735b212b86a (plain) (tree)
1
2
3
4
5
6
7
8
                                                  
                



                                                                      

                                                                                  
               
                                                                                                                                                                                 
                  
 
                                                                                                                                                                                                             
 



                                                                                                                                                                                                  
                           
                                                                                                                                                                                                        
 
                     
                                                                                                                                                                                          
 
                    
                                                                                                                                                                                             
 

                                             

 
 



                                                                                                              

 
 
                
                                                                                                                                                                                                    



                                                                               
 
 
         
                                             
                                                    
              
                                                                            
                               
                                                                                                                               


                                      
                                                            
                                                                                                                                     
             
          
 

                                                      
                                                          
     















                                                                                                 
                                                                                                   
         
                                                                                                                             
         

                                                                                                      

                                                                                                                

                                                                               
       
     

                                       
                                              
            
                                            
                                             

      
           
      

                                
 
      
 
               
                 
                                 
                                                                                   
                                                                                                                                                 
                                                             
          
 
                                 
                                                                                                           
                                                                         
          
 
                                                                    



                                                                                                                                                                                                                            
                                                                   







                                                                          
 
                                                                                               


                                                                 
                                                                                                       








                                                                              
                      

                                                                                                     
         


                                           
                                                              
                                                                                             
                                       
         
                          
                                                                     
         
                         
                                                                     

                            
                                                                    

                  
                                                                                                                              

                                
                                                            
         


                                                                                                         
                  
                                                                                                      
            
 
                                                                                   
 
                                                      


                                                                                                                                

                                                                                      
 
                                                                                            
                                             
                                                                       






                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                 
                                                                                                                 
                                                                    
                                                                                                                                                                                                                                                                                                                                             
                                                 
                                                                                                                                                                                                                                                                                                                             
 
            
        


                                                                 

        
 
              
                             
                                     

                     
                                                                                
      
 

               
  
 
         
 
 
<!-- 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>Plot model fits (observed and fitted) and the residuals for a row or column
of an mmkin object — plot.mmkin • 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="Plot model fits (observed and fitted) and the residuals for a row or column
of an mmkin object — plot.mmkin" />
<meta property="og:description" content="When x is a row selected from an mmkin object ([.mmkin), the
same model fitted for at least one dataset is shown. When it is a column,
the fit of at least one model to the same dataset is shown." />




<!-- 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">1.0.3</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-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>Plot model fits (observed and fitted) and the residuals for a row or column
of an mmkin object</h1>
    <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.mmkin.R'><code>R/plot.mmkin.R</code></a></small>
    <div class="hidden name"><code>plot.mmkin.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>When x is a row selected from an mmkin object (<code><a href='[.mmkin.html'>[.mmkin</a></code>), the
same model fitted for at least one dataset is shown. When it is a column,
the fit of at least one model to the same dataset is shown.</p>
    </div>

    <pre class="usage"><span class='co'># S3 method for mmkin</span>
<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span>
  <span class='va'>x</span>,
  main <span class='op'>=</span> <span class='st'>"auto"</span>,
  legends <span class='op'>=</span> <span class='fl'>1</span>,
  resplot <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='st'>"time"</span>, <span class='st'>"errmod"</span><span class='op'>)</span>,
  ylab <span class='op'>=</span> <span class='st'>"Residue"</span>,
  standardized <span class='op'>=</span> <span class='cn'>FALSE</span>,
  show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span>,
  errmin_var <span class='op'>=</span> <span class='st'>"All data"</span>,
  errmin_digits <span class='op'>=</span> <span class='fl'>3</span>,
  cex <span class='op'>=</span> <span class='fl'>0.7</span>,
  rel.height.middle <span class='op'>=</span> <span class='fl'>0.9</span>,
  ymax <span class='op'>=</span> <span class='st'>"auto"</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>x</th>
      <td><p>An object of class <code><a href='mmkin.html'>mmkin</a></code>, with either one row or one
column.</p></td>
    </tr>
    <tr>
      <th>main</th>
      <td><p>The main title placed on the outer margin of the plot.</p></td>
    </tr>
    <tr>
      <th>legends</th>
      <td><p>An index for the fits for which legends should be shown.</p></td>
    </tr>
    <tr>
      <th>resplot</th>
      <td><p>Should the residuals plotted against time, using
<code><a href='mkinresplot.html'>mkinresplot</a></code>, or as squared residuals against predicted
values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td>
    </tr>
    <tr>
      <th>ylab</th>
      <td><p>Label for the y axis.</p></td>
    </tr>
    <tr>
      <th>standardized</th>
      <td><p>Should the residuals be standardized? This option
is passed to <code><a href='mkinresplot.html'>mkinresplot</a></code>, it only takes effect if
<code>resplot = "time"</code>.</p></td>
    </tr>
    <tr>
      <th>show_errmin</th>
      <td><p>Should the chi2 error level be shown on top of the plots
to the left?</p></td>
    </tr>
    <tr>
      <th>errmin_var</th>
      <td><p>The variable for which the FOCUS chi2 error value should
be shown.</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>cex</th>
      <td><p>Passed to the plot functions and <code><a href='https://rdrr.io/r/graphics/mtext.html'>mtext</a></code>.</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>ymax</th>
      <td><p>Maximum y axis value for <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p></td>
    </tr>
    <tr>
      <th>...</th>
      <td><p>Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and
<code><a href='mkinresplot.html'>mkinresplot</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="details"><a class="anchor" href="#details"></a>Details</h2>

    <p>If the current plot device is a <code><a href='https://rdrr.io/pkg/tikzDevice/man/tikz.html'>tikz</a></code> device, then
latex is being used for the formatting of the chi2 error level.</p>
    <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='co'># Only use one core not to offend CRAN checks</span>
  <span class='va'>fits</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><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='st'>"FOMC"</span>, <span class='st'>"HS"</span><span class='op'>)</span>,
                <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"FOCUS B"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, <span class='co'># named list for titles</span>
                cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
#&gt; <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span>
</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>, show_errmin <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
</div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
  <span class='co'># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span>
  <span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span>
  <span class='co'># generated by pkgdown, as far as I know).</span>
  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># same as plot(fits[1, 2])</span>
</div><div class='img'><img src='plot.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'>
  <span class='co'># Show the error models</span>
  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>, resplot <span class='op'>=</span> <span class='st'>"errmod"</span><span class='op'>)</span>
</div><div class='img'><img src='plot.mmkin-5.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