aboutsummaryrefslogblamecommitdiff
path: root/docs/reference/calplot.lm.html
blob: fb329f648f2d8f6651c766035bbfe50477e956d5 (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>Plot calibration graphs from univariate linear models — calplot • chemCal</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 calibration graphs from univariate linear models — calplot" />
<meta property="og:description" content="Produce graphics of calibration data, the fitted model as well
  as confidence, and, for unweighted regression, prediction bands." />




<!-- 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">chemCal</a>
        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.2</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
    <span class="fas fa-home fa-lg"></span>
     
  </a>
</li>
<li>
  <a href="../articles/chemCal.html">Get started</a>
</li>
<li>
  <a href="../reference/index.html">Reference</a>
</li>
<li>
  <a href="../news/index.html">Changelog</a>
</li>
      </ul>
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="http://github.com/jranke/chemCal/">
    <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 calibration graphs from univariate linear models</h1>
    
    <div class="hidden name"><code>calplot.lm.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Produce graphics of calibration data, the fitted model as well
  as confidence, and, for unweighted regression, prediction bands.</p>
    </div>

    <pre class="usage"><span class='fu'>calplot</span><span class='op'>(</span><span class='va'>object</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='st'>"auto"</span>, <span class='st'>"auto"</span><span class='op'>)</span>, ylim <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'>"auto"</span>, <span class='st'>"auto"</span><span class='op'>)</span>,
    xlab <span class='op'>=</span> <span class='st'>"Concentration"</span>, ylab <span class='op'>=</span> <span class='st'>"Response"</span>, legend_x <span class='op'>=</span> <span class='st'>"auto"</span>,
    alpha<span class='op'>=</span><span class='fl'>0.05</span>, varfunc <span class='op'>=</span> <span class='cn'>NULL</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 univariate model object of class <code><a href='https://rdrr.io/r/stats/lm.html'>lm</a></code> or 
    <code><a href='https://rdrr.io/pkg/MASS/man/rlm.html'>rlm</a></code> 
    with model formula <code>y ~ x</code> or <code>y ~ x - 1</code>.</p></td>
    </tr>
    <tr>
      <th>xlim</th>
      <td><p>The limits of the plot on the x axis.</p></td>
    </tr>
    <tr>
      <th>ylim</th>
      <td><p>The limits of the plot on the y axis.</p></td>
    </tr>
    <tr>
      <th>xlab</th>
      <td><p>The label of the x axis.</p></td>
    </tr>
    <tr>
      <th>ylab</th>
      <td><p>The label of the y axis.</p></td>
    </tr>
    <tr>
      <th>legend_x</th>
      <td><p>An optional numeric value for adjusting the x coordinate of the legend.</p></td>
    </tr>
    <tr>
      <th>alpha</th>
      <td><p>The error tolerance level for the confidence and prediction bands. Note that this 
    includes both tails of the Gaussian distribution, unlike the alpha and beta parameters
    used in <code><a href='lod.html'>lod</a></code> (see note below).</p></td>
    </tr>
    <tr>
      <th>varfunc</th>
      <td><p>The variance function for generating the weights in the model.
    Currently, this argument is ignored (see note below).</p></td>
    </tr>
    </table>

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

    <p>A plot of the calibration data, of your fitted model as well as lines showing
  the confidence limits. Prediction limits are only shown for models from
  unweighted regression.</p>
    <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>

    <p>Prediction bands for models from weighted linear regression require weights
  for the data, for which responses should be predicted. Prediction intervals
  using weights e.g. from a variance function are currently not supported by
  the internally used function <code><a href='https://rdrr.io/r/stats/predict.lm.html'>predict.lm</a></code>, therefore,
  <code>calplot</code> does not draw prediction bands for such models.</p>  
<p>It is possible to compare the <code>calplot</code> prediction bands with the
  <code><a href='lod.html'>lod</a></code> values if the <code><a href='lod.html'>lod()</a></code> alpha and beta parameters are
  half the value of the <code>calplot()</code> alpha parameter.</p>
    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>

    <p>Johannes Ranke 
  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>massart97ex3</span><span class='op'>)</span>
<span class='va'>m</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span><span class='op'>(</span><span class='va'>y</span> <span class='op'>~</span> <span class='va'>x</span>, data <span class='op'>=</span> <span class='va'>massart97ex3</span><span class='op'>)</span>
<span class='fu'>calplot</span><span class='op'>(</span><span class='va'>m</span><span class='op'>)</span>
</div><div class='img'><img src='calplot.lm-1.png' alt='' width='700' height='433' /></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