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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='va'>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>
<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 labelled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
doi: <a href='https://doi.org/10.1021/jf00103a026'>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='va'>SFO_SFO_SFO</span> <span class='op'><-</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'>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>,
phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>,
anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>
</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='co'># \dontrun{</span>
<span class='va'>fit.1</span> <span class='op'><-</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'>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>
</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://rdrr.io/r/base/summary.html'>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>
</div><div class='output co'>#> Estimate se_notrans t value Pr(>t)
#> T245_0 1.038550e+02 2.1847074888 47.537272 4.472189e-18
#> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13
#> k_phenol 4.050581e-01 0.2986993400 1.356073 9.756988e-02
#> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623176e-07
#> f_T245_to_phenol 6.227599e-01 0.3985340295 1.562627 6.949412e-02
#> f_phenol_to_anisole 1.000000e+00 0.6718439378 1.488441 7.867787e-02
#> sigma 2.514628e+00 0.4907558750 5.123989 6.233156e-05
#> Lower Upper
#> T245_0 99.246061370 1.084640e+02
#> k_T245 0.039631621 4.746194e-02
#> k_phenol 0.218013878 7.525762e-01
#> k_anisole 0.005370739 8.305299e-03
#> f_T245_to_phenol 0.547559083 6.924813e-01
#> f_phenol_to_anisole 0.000000000 1.000000e+00
#> sigma 1.706607296 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span>
</div><div class='output co'>#> $ff
#> T245_phenol T245_sink phenol_anisole phenol_sink
#> 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11
#>
#> $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'># formation fraction from phenol to anisol is practically 1. As we cannot</span>
<span class='co'># fix formation fractions when using the ilr transformation, we can turn of</span>
<span class='co'># the sink in the model generation</span>
<span class='va'>SFO_SFO_SFO_2</span> <span class='op'><-</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'>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>,
phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>,
anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>
</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>fit.2</span> <span class='op'><-</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'>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>
</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://rdrr.io/r/base/summary.html'>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>
</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower
#> T245_0 1.038550e+02 2.1623653027 48.028439 4.993108e-19 99.271020526
#> k_T245 4.337042e-02 0.0018343666 23.643268 3.573555e-14 0.039650977
#> k_phenol 4.050582e-01 0.1177237248 3.440752 1.679252e-03 0.218746585
#> k_anisole 6.678741e-03 0.0006829745 9.778903 1.872894e-08 0.005377083
#> f_T245_to_phenol 6.227599e-01 0.0342197865 18.198825 2.039410e-12 0.547975628
#> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655
#> Upper
#> T245_0 108.43904097
#> k_T245 0.04743877
#> k_phenol 0.75005577
#> k_anisole 0.00829550
#> f_T245_to_phenol 0.69212306
#> sigma 3.31827222</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span>
</div><div class='output co'>#> $ff
#> T245_phenol T245_sink phenol_anisole phenol_sink
#> 6.227599e-01 3.772401e-01 1.000000e+00 6.894640e-11
#>
#> $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='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span>
</div><div class='img'><img src='mccall81_245T-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># }</span>
</div></pre>
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