aboutsummaryrefslogblamecommitdiff
path: root/docs/dev/reference/schaefer07_complex_case.html
blob: 9e1eb3cfd02e86dcb9549ad247cda0b26a3d69f7 (plain) (tree)
1
2
3
4
5
6
7
8
9
               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
                                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             

                                                                               

                                                              
 
                                                    
                                                                                    









                                                                                                                               
                                                                                                                                        



                                                      
                                     
                                                 

                     
                                                                                                                           



                               
                                            

                                                              

                                                                                                   






                                                                                                 
                                                                                                   
         

                                                                                                                  
        
                                                                                                                                                                    

         
                                                                                                                                                          

         
                                                                                                                                           

         
                                                                                                                                        

         





                                                                                                                             

         
                                                                                   
         


                                                                                              







                                                                                                                
            


                                       

                                                                  
                                             


      
                                       




                           
                                












                                                                                   










                                                                                                                                           
 

                                
 







                                
 

                                                                                       


                         



                                                                                     
          
 














































                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            

                                                                 

                                                                                      


      

                                            


                     
                                                                                                             

      
                     



  
  
 
                
 
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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."><meta name="robots" content="noindex"><!-- 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav"><li>
  <a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" 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 class="divider">
    <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</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 class="divider">
    <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li>
    <li>
      <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
    </li>
    <li>
      <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
    </li>
    <li>
      <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
    </li>
    <li>
      <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
    </li>
    <li>
      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
    </li>
    <li class="divider">
    <li class="dropdown-header">Performance</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/web_only/benchmarks.html">Benchmark timings for mkin</a>
    </li>
    <li>
      <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
    </li>
    <li class="divider">
    <li class="dropdown-header">Miscellaneous</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>
  </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/" class="external-link">
    <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>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">schaefer07_complex_case</span></span></code></pre></div>
    </div>

    <div id="format">
    <h2>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>
    </div>
    <div id="references">
    <h2>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>
    </div>

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

<div class="pkgdown">
  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>

      </footer></div>

  


  

  </body></html>

Contact - Imprint