aboutsummaryrefslogblamecommitdiff
path: root/docs/reference/schaefer07_complex_case.html
blob: b22c67fac86facbbfbdf9eadcd5e7d52cceab0ff (plain) (tree)
1
2
3
4
5
6
7
8
9







                                                                      
                                                                                                                        


                                                                                                                                                                               
                  
 
                                                                                                                                                                                                                




                                                                                                                                                                                                                      

                                                                                                                                                                                                              
 


                                                                                                                                                                                         


                                             


 





                                                                                                                                       


 
                
                                                                                                  




                                                                               

 


         
                                                    
              
                                                                            






                                                                                                         

                                                            
                                                                                                                                
             
          
 


                                                      
                                                          
     
















                                                                                                 
                                                                                                   

         
                                                                                                                             
         


                                                                                                      
       
     


                                       
           
      
                                              
        
           
      


                                
 


               
                 

                                 
                                                                                 

                                                                          
          
 
                                 




                                                                                   
          
 
                                                                            
        
                                                                                      
 







                                                                                                                   

                                                                                                  
 
                                                                                     


                                                                                
    
 
                                                                                            

                                                                                                                                                                                                                                                                                                                              



                                                                                                                                                                                                                                                                                                                                                                                                                                              















                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 














                                                                                                                                                                                     
        










                                                         



              
                             
                                     


                     
                                                                         

      


               

  

         
 
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html>
  <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://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
<!-- Bootstrap -->

<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>

<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">

<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>

<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" 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." />
<meta name="twitter:card" content="summary" />



<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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>
    <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">
        <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</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>
  </ul>
</li>
<li>
  <a href="../news/index.html">News</a>
</li>
      </ul>
      
      <ul class="nav navbar-nav navbar-right">
        
      </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='no'>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 class='dl-horizontal'>
    <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='no'>data</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>schaefer07_complex_case</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>)
<span class='no'>model</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
  <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"A1"</span>, <span class='st'>"B1"</span>, <span class='st'>"C1"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
  <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>),
  <span class='kw'>B1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
  <span class='kw'>C1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
  <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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'>  </div><div class='input'>    <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
    <span class='fu'>plot</span>(<span class='no'>fit</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='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt;   parent_A1   parent_B1   parent_C1 parent_sink       A1_A2     A1_sink 
#&gt;   0.3809621   0.1954665   0.4235714   0.0000000   0.4479674   0.5520326 
#&gt; 
#&gt; $SFORB
#&gt; logical(0)
#&gt; 
#&gt; $distimes
#&gt;            DT50      DT90
#&gt; parent 13.95078  46.34350
#&gt; A1     49.75342 165.27728
#&gt; B1     37.26913 123.80536
#&gt; C1     11.23133  37.30968
#&gt; A2     28.50591  94.69457
#&gt; </div><div class='input'>  </div><div class='input'> <span class='co'># Compare with the results obtained in the original publication</span>
 <span class='fu'>print</span>(<span class='no'>schaefer07_complex_results</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="sidebar">
    <h2>Contents</h2>
    <ul class="nav nav-pills nav-stacked">
      
      <li><a href="#format">Format</a></li>

      <li><a href="#references">References</a></li>
      
      <li><a href="#examples">Examples</a></li>
    </ul>

  </div>
</div>

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

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

      </footer>
   </div>

  

  </body>
</html>

Contact - Imprint