aboutsummaryrefslogblamecommitdiff
path: root/docs/reference/mccall81_245T.html
blob: a336a840f9d57a280ac111cbe89026f03de99675 (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>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin</title>

<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->

<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>

<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />

<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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="Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T" />

<meta property="og:description" content="Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding
 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether
 extracts." />
<meta name="twitter:card" content="summary" />



<!-- 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>
    <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">0.9.49.4</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>
  </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>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1>
    
    <div class="hidden name"><code>mccall81_245T.Rd</code></div>
    </div>

    <div class="ref-description">
    
    <p>Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding
 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether
 extracts.</p>
    
    </div>

    <pre class="usage"><span class='no'>mccall81_245T</span></pre>
        
    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>

    <p>A dataframe containing the following variables.</p><dl class='dl-horizontal'>
    <dt><code>name</code></dt><dd><p>the name of the compound observed. Note that T245 is used as
                       an acronym for 2,4,5-T. T245 is a legitimate object name
                       in R, which is necessary for specifying models using
                       <code><a href='mkinmod.html'>mkinmod</a></code>.</p></dd>
    <dt><code>time</code></dt><dd><p>a numeric vector containing sampling times in days after
                       treatment</p></dd>
    <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations in percent of applied radioactivity</p></dd>
    <dt><code>soil</code></dt><dd><p>a factor containing the name of the soil</p></dd>
  </dl>
    
    <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

    <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
  <a href='http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p>
    

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'>  <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'>"phenol"</span>),
                         <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'>"anisole"</span>),
                         <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</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.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>    <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt;                      Estimate   se_notrans   t value       Pr(&gt;t)        Lower
#&gt; T245_0           1.038550e+02 2.1508106806 48.286460 3.542223e-18 99.246062186
#&gt; k_T245_sink      1.636106e-02          NaN       NaN          NaN  0.012661557
#&gt; k_T245_phenol    2.700936e-02          NaN       NaN          NaN  0.024487315
#&gt; k_phenol_sink    1.054519e-10          NaN       NaN          NaN  0.000000000
#&gt; k_phenol_anisole 4.050581e-01 0.1053797258  3.843795 7.969973e-04  0.218013983
#&gt; k_anisole_sink   6.678742e-03 0.0006205825 10.762053 9.427693e-09  0.005370739
#&gt; sigma            2.514628e+00 0.3383657682  7.431685 1.054052e-06  1.706607296
#&gt;                         Upper
#&gt; T245_0           1.084640e+02
#&gt; k_T245_sink      2.114150e-02
#&gt; k_T245_phenol    2.979116e-02
#&gt; k_phenol_sink             Inf
#&gt; k_phenol_anisole 7.525759e-01
#&gt; k_anisole_sink   8.305299e-03
#&gt; sigma            3.322649e+00</div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
#&gt;      T245_sink    T245_phenol    phenol_sink phenol_anisole   anisole_sink 
#&gt;   3.772401e-01   6.227599e-01   2.603376e-10   1.000000e+00   1.000000e+00 
#&gt; 
#&gt; $SFORB
#&gt; logical(0)
#&gt; 
#&gt; $distimes
#&gt;               DT50      DT90
#&gt; T245     15.982025  53.09114
#&gt; phenol    1.711229   5.68458
#&gt; anisole 103.784092 344.76329
#&gt; </div><div class='input'>    <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span>
    <span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
                   <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
                   <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>    <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;                      Estimate   se_notrans   t value       Pr(&gt;t)        Lower
#&gt; T245_0           1.038550e+02 2.1623652988 48.028441 4.993105e-19 99.271024566
#&gt; k_T245_sink      1.636106e-02 0.0019676253  8.315129 1.673677e-07  0.012679144
#&gt; k_T245_phenol    2.700936e-02 0.0012421965 21.743225 1.314080e-13  0.024500318
#&gt; k_phenol_anisole 4.050581e-01 0.1177235385  3.440757 1.679236e-03  0.218746681
#&gt; k_anisole_sink   6.678743e-03 0.0006829745  9.778904 1.872891e-08  0.005377084
#&gt; sigma            2.514628e+00 0.3790944250  6.633250 2.875782e-06  1.710983655
#&gt;                         Upper
#&gt; T245_0           1.084390e+02
#&gt; k_T245_sink      2.111217e-02
#&gt; k_T245_phenol    2.977534e-02
#&gt; k_phenol_anisole 7.500550e-01
#&gt; k_anisole_sink   8.295501e-03
#&gt; sigma            3.318272e+00</div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
#&gt;      T245_sink    T245_phenol    phenol_sink phenol_anisole   anisole_sink 
#&gt;   3.772401e-01   6.227599e-01   2.603376e-10   1.000000e+00   1.000000e+00 
#&gt; 
#&gt; $SFORB
#&gt; logical(0)
#&gt; 
#&gt; $distimes
#&gt;               DT50      DT90
#&gt; T245     15.982025  53.09114
#&gt; phenol    1.711229   5.68458
#&gt; anisole 103.784092 344.76329
#&gt; </div><div class='input'>    <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit.2</span>)</div><div class='img'><img src='mccall81_245T-1.png' alt='' width='700' height='433' /></div><div class='input'>  </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="#source">Source</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="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
      </footer>
   </div>

  

  </body>
</html>

Contact - Imprint