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<meta property="og:description" content="Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding
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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'><-</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'>#> <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'><-</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'>#> <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'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower
#> T245_0 1.038550e+02 2.1508110557 48.286452 3.542232e-18 99.246062215
#> k_T245_sink 1.636106e-02 NaN NaN NaN 0.012661558
#> k_T245_phenol 2.700936e-02 NaN NaN NaN 0.024487315
#> k_phenol_sink 1.788604e-10 NaN NaN NaN 0.000000000
#> k_phenol_anisole 4.050581e-01 0.1053801116 3.843781 7.970202e-04 0.218013982
#> k_anisole_sink 6.678742e-03 0.0006205844 10.762020 9.428076e-09 0.005370739
#> sigma 2.514628e+00 0.3383670685 7.431657 1.054101e-06 1.706607296
#> Upper
#> T245_0 1.084640e+02
#> k_T245_sink 2.114150e-02
#> k_T245_phenol 2.979116e-02
#> k_phenol_sink Inf
#> k_phenol_anisole 7.525759e-01
#> k_anisole_sink 8.305299e-03
#> 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'>#> $ff
#> T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink
#> 3.772401e-01 6.227599e-01 4.415672e-10 1.000000e+00 1.000000e+00
#>
#> $SFORB
#> logical(0)
#>
#> $distimes
#> DT50 DT90
#> T245 15.982025 53.09114
#> phenol 1.711229 5.68458
#> anisole 103.784092 344.76329
#> </div><div class='input'> <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span>
<span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
<span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
<span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower
#> T245_0 1.038550e+02 2.1623653063 48.028441 4.993105e-19 99.271025146
#> k_T245_sink 1.636106e-02 0.0019676255 8.315130 1.673674e-07 0.012679148
#> k_T245_phenol 2.700936e-02 0.0012421966 21.743224 1.314080e-13 0.024500319
#> k_phenol_anisole 4.050581e-01 0.1177235488 3.440757 1.679237e-03 0.218746679
#> k_anisole_sink 6.678742e-03 0.0006829745 9.778904 1.872892e-08 0.005377084
#> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655
#> Upper
#> T245_0 108.43904395
#> k_T245_sink 0.02111217
#> k_T245_phenol 0.02977535
#> k_phenol_anisole 0.75005504
#> k_anisole_sink 0.00829550
#> 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'>#> $ff
#> T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink
#> 3.772401e-01 6.227599e-01 4.415672e-10 1.000000e+00 1.000000e+00
#>
#> $SFORB
#> logical(0)
#>
#> $distimes
#> DT50 DT90
#> T245 15.982025 53.09114
#> phenol 1.711229 5.68458
#> anisole 103.784092 344.76329
#> </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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