<!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>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/3.4.1/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="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="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">1.2.3</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>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>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">mccall81_245T</span></span></code></pre></div>
    </div>

    <div id="format">
    <h2>Format</h2>
    <p>A dataframe containing the following variables.</p><dl><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></div>
    <div id="source">
    <h2>Source</h2>
    <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labelled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
  <a href="https://doi.org/10.1021/jf00103a026" class="external-link">doi:10.1021/jf00103a026</a></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">SFO_SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>T245 <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">"phenol"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>    phenol <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">"anisole"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>    anisole <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 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.1</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
<span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                         Estimate   se_notrans   t value       Pr(&gt;t)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> T245_0              1.038550e+02 2.1847074945 47.537272 4.472189e-18</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_T245              4.337042e-02 0.0018983965 22.845818 2.276911e-13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_phenol            4.050581e-01 0.2986993563  1.356073 9.756989e-02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_anisole           6.678742e-03 0.0008021439  8.326114 2.623177e-07</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_T245_to_phenol    6.227599e-01 0.3985340558  1.562627 6.949413e-02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_phenol_to_anisole 1.000000e+00 0.6718439825  1.488441 7.867789e-02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma               2.514628e+00 0.4907558883  5.123989 6.233157e-05</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                            Lower        Upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> T245_0              99.246061385 1.084640e+02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_T245               0.039631621 4.746194e-02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_phenol             0.218013879 7.525762e-01</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_anisole            0.005370739 8.305299e-03</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_T245_to_phenol     0.547559081 6.924813e-01</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_phenol_to_anisole  0.000000000 1.000000e+00</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma                1.706607296 3.322649e+00</span>
<span class="r-in"><span>    <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</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>    T245_phenol      T245_sink phenol_anisole    phenol_sink </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   6.227599e-01   3.772401e-01   1.000000e+00   3.773626e-10 </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> T245     15.982025  53.09114</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> phenol    1.711229   5.68458</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> anisole 103.784093 344.76329</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span>    <span class="co"># formation fraction from phenol to anisol is practically 1. As we cannot</span></span></span>
<span class="r-in"><span>    <span class="co"># fix formation fractions when using the ilr transformation, we can turn of</span></span></span>
<span class="r-in"><span>    <span class="co"># the sink in the model generation</span></span></span>
<span class="r-in"><span>    <span class="va">SFO_SFO_SFO_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>T245 <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">"phenol"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      phenol <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">"anisole"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      anisole <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 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="va">fit.2</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO_2</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
<span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                      Estimate   se_notrans   t value       Pr(&gt;t)        Lower</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> T245_0           1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_T245           4.337042e-02 0.0018343666 23.643268 3.573556e-14  0.039650976</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_phenol         4.050582e-01 0.1177237473  3.440752 1.679254e-03  0.218746587</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_anisole        6.678742e-03 0.0006829745  9.778903 1.872894e-08  0.005377083</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12  0.547975637</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma            2.514628e+00 0.3790944250  6.633250 2.875782e-06  1.710983655</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                         Upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> T245_0           108.43904074</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_T245             0.04743877</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_phenol           0.75005585</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_anisole          0.00829550</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_T245_to_phenol   0.69212308</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma              3.31827222</span>
<span class="r-in"><span>    <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</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>    T245_phenol      T245_sink phenol_anisole    phenol_sink </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   6.227599e-01   3.772401e-01   1.000000e+00   3.773626e-10 </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> T245     15.982025  53.09114</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> phenol    1.711229   5.68458</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> anisole 103.784093 344.76329</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span>    <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="mccall81_245T-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span>  <span class="co"># }</span></span></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>