aboutsummaryrefslogblamecommitdiff
path: root/docs/reference/schaefer07_complex_case.html
blob: 979e4c29701abbedd203bc995e780a36079d06aa (plain) (tree)
1
2
3
4
5
6
7
8
9
                                                  
                



                                                                      
                                                                                                                        
 
 
               
                                                                                                                                                                                 
                  
 
                                                                                                                                                                                                             
 



                                                                                                                                                                                                  
                           
                                                                                                                                                                                                        
 
                     
                                                                                                                                                                                          
 
                    
                                                                                                                                                                                             
 

                                             

 
 
                                                                                                                                       

                                                                                                                     

 
 
                
                                                                                                                                                                                                    



                                                                               
 
 
         
                                             
                                                    
              
                                                                            
                               
                                                                                                                               


                                      
                                                            
                                                                                                                                     
             
          
 

                                                      
                                                          
     















                                                                                                 
                                                                                                   
         
                                                                                                                             
         

                                                                                                      

                                                                                                                

                                                                               
       
     

                                       
                                              
            
                                             

      
           
      

                                
 
      
 
               
                 
                                 
                                                                                 
                                                                          
          
 
                                 

                                                                                   
          
 
                                                                            
 
                                                                                      
 
                                                                                             




                                                                
                                                                                       
                                                                                                  
 
                                                                                     

                                                                                
 
                                                                                            










                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
                                                                              
                                                                              


                               


                               
                                                                                        
                                                                                                                                                                                  












                                                                                  
        


                                                                 

        
 
              
                             
                                     

                     
                                                                                
      
 

               
  
 
         
 
 
<!-- 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>Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • 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="Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case" />
<meta property="og:description" content="This dataset was used for a comparison of KinGUI and ModelMaker to check the
  software quality of KinGUI in the original publication (Schäfer et al., 2007).
  The results from the fitting are also included." />




<!-- 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>Metabolism data set used for checking the software quality of KinGUI</h1>
    
    <div class="hidden name"><code>schaefer07_complex_case.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This dataset was used for a comparison of KinGUI and ModelMaker to check the
  software quality of KinGUI in the original publication (Schäfer et al., 2007).
  The results from the fitting are also included.</p>
    </div>

    <pre class="usage"><span class='va'>schaefer07_complex_case</span></pre>


    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>

    <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl>
    <dt><code>time</code></dt><dd><p>a numeric vector</p></dd>
    <dt><code>parent</code></dt><dd><p>a numeric vector</p></dd>
    <dt><code>A1</code></dt><dd><p>a numeric vector</p></dd>
    <dt><code>B1</code></dt><dd><p>a numeric vector</p></dd>
    <dt><code>C1</code></dt><dd><p>a numeric vector</p></dd>
    <dt><code>A2</code></dt><dd><p>a numeric vector</p></dd>
  
</dl><p>The results are a data frame with 14 results for different parameter values</p>
    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>

    <p>Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic
  software tool for evaluations according to FOCUS degradation kinetics. In: Del
  Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII
  Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'><span class='va'>data</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span><span class='op'>(</span><span class='va'>schaefer07_complex_case</span>, time <span class='op'>=</span> <span class='st'>"time"</span><span class='op'>)</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='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <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'>"A1"</span>, <span class='st'>"B1"</span>, <span class='st'>"C1"</span><span class='op'>)</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>,
  A1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>,
  B1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>,
  C1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>,
  A2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'>  <span class='co'># \dontrun{</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'>data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
    <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $ff
#&gt;   parent_A1   parent_B1   parent_C1 parent_sink       A1_A2     A1_sink 
#&gt;   0.3809620   0.1954667   0.4235713   0.0000000   0.4479619   0.5520381 
#&gt; 
#&gt; $distimes
#&gt;            DT50      DT90
#&gt; parent 13.95078  46.34350
#&gt; A1     49.75342 165.27728
#&gt; B1     37.26908 123.80520
#&gt; C1     11.23131  37.30961
#&gt; A2     28.50624  94.69567
#&gt; </div><div class='input'>  <span class='co'># }</span>
 <span class='co'># Compare with the results obtained in the original publication</span>
 <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>schaefer07_complex_results</span><span class='op'>)</span>
</div><div class='output co'>#&gt;         compound          parameter  KinGUI ModelMaker deviation
#&gt; 1         parent   degradation rate  0.0496     0.0506       2.0
#&gt; 2         parent               DT50 13.9900    13.6900       2.2
#&gt; 3  metabolite A1 formation fraction  0.3803     0.3696       2.9
#&gt; 4  metabolite A1   degradation rate  0.0139     0.0136       2.2
#&gt; 5  metabolite A1               DT50 49.9600    50.8900       1.8
#&gt; 6  metabolite B1 formation fraction  0.1866     0.1818       2.6
#&gt; 7  metabolite B1   degradation rate  0.0175     0.0172       1.7
#&gt; 8  metabolite B1               DT50 39.6100    40.2400       1.6
#&gt; 9  metabolite C1 formation fraction  0.4331     0.4486       3.5
#&gt; 10 metabolite C1   degradation rate  0.0638     0.0700       8.9
#&gt; 11 metabolite C1               DT50 10.8700     9.9000       9.8
#&gt; 12 metabolite A2 formation fraction  0.4529     0.4559       0.7
#&gt; 13 metabolite A2   degradation rate  0.0245     0.0244       0.4
#&gt; 14 metabolite A2               DT50 28.2400    28.4500       0.7</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