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<title>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin</title>


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<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
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    <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://rdrr.io/r/base/list.html'>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://rdrr.io/r/base/list.html'>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://rdrr.io/r/base/list.html'>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'>  <span class='co'># \dontrun{</span>
    <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://rdrr.io/r/base/subset.html'>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://rdrr.io/r/base/summary.html'>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 2.1508110557 48.286452 3.542232e-18 99.246062215
#&gt; k_T245_sink      1.636106e-02          NaN       NaN          NaN  0.012661558
#&gt; k_T245_phenol    2.700936e-02          NaN       NaN          NaN  0.024487315
#&gt; k_phenol_sink    1.788604e-10          NaN       NaN          NaN  0.000000000
#&gt; k_phenol_anisole 4.050581e-01 0.1053801116  3.843781 7.970202e-04  0.218013982
#&gt; k_anisole_sink   6.678742e-03 0.0006205844 10.762020 9.428076e-09  0.005370739
#&gt; sigma            2.514628e+00 0.3383670685  7.431657 1.054101e-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   4.415672e-10   1.000000e+00   1.000000e+00 
#&gt; 
#&gt; $SFORB
#&gt; logical(0)
#&gt; 
#&gt; $distimes
#&gt;               DT50      DT90
#&gt; T245     15.982025  53.09114
#&gt; phenol    1.711229   5.68458
#&gt; anisole 103.784092 344.76329
#&gt; </div><div class='input'>    <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span>
    <span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
                   <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
                   <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>    <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)$<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 2.1623653063 48.028441 4.993105e-19 99.271025146
#&gt; k_T245_sink      1.636106e-02 0.0019676255  8.315130 1.673674e-07  0.012679148
#&gt; k_T245_phenol    2.700936e-02 0.0012421966 21.743224 1.314080e-13  0.024500319
#&gt; k_phenol_anisole 4.050581e-01 0.1177235488  3.440757 1.679237e-03  0.218746679
#&gt; k_anisole_sink   6.678742e-03 0.0006829745  9.778904 1.872892e-08  0.005377084
#&gt; sigma            2.514628e+00 0.3790944250  6.633250 2.875782e-06  1.710983655
#&gt;                         Upper
#&gt; T245_0           108.43904395
#&gt; k_T245_sink        0.02111217
#&gt; k_T245_phenol      0.02977535
#&gt; k_phenol_anisole   0.75005504
#&gt; k_anisole_sink     0.00829550
#&gt; sigma              3.31827222</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   4.415672e-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>
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