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<img src="" class="logo" alt=""><h1>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1>
<div class="d-none name"><code>mccall81_245T.Rd</code></div>
</div>
<div class="ref-description section level2">
<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 class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">mccall81_245T</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></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 class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></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 class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <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" 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">#></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"><-</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">#></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">#></span> Estimate se_notrans t value Pr(>t)</span>
<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1847074943 47.537272 4.472189e-18</span>
<span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13</span>
<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050581e-01 0.2986993738 1.356073 9.756990e-02</span>
<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07</span>
<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.3985340721 1.562626 6.949414e-02</span>
<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 1.000000e+00 0.6718440131 1.488441 7.867790e-02</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.4907558973 5.123989 6.233159e-05</span>
<span class="r-out co"><span class="r-pr">#></span> Lower Upper</span>
<span class="r-out co"><span class="r-pr">#></span> T245_0 99.246061490 1.084640e+02</span>
<span class="r-out co"><span class="r-pr">#></span> k_T245 0.039631621 4.746194e-02</span>
<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.218013879 7.525762e-01</span>
<span class="r-out co"><span class="r-pr">#></span> k_anisole 0.005370739 8.305299e-03</span>
<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.547559080 6.924813e-01</span>
<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 0.000000000 1.000000e+00</span>
<span class="r-out co"><span class="r-pr">#></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">#></span> $ff</span>
<span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span>
<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.072478e-10 </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> $distimes</span>
<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span>
<span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span>
<span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span>
<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span>
<span class="r-out co"><span class="r-pr">#></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"><-</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">#></span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"><span> <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" 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">#></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">#></span> Estimate se_notrans t value Pr(>t) Lower</span>
<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1623653059 48.028439 4.993108e-19 99.271020328</span>
<span class="r-out co"><span class="r-pr">#></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">#></span> k_phenol 4.050582e-01 0.1177237651 3.440752 1.679255e-03 0.218746589</span>
<span class="r-out co"><span class="r-pr">#></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">#></span> f_T245_to_phenol 6.227599e-01 0.0342197873 18.198824 2.039411e-12 0.547975634</span>
<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655</span>
<span class="r-out co"><span class="r-pr">#></span> Upper</span>
<span class="r-out co"><span class="r-pr">#></span> T245_0 108.43904079</span>
<span class="r-out co"><span class="r-pr">#></span> k_T245 0.04743877</span>
<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.75005593</span>
<span class="r-out co"><span class="r-pr">#></span> k_anisole 0.00829550</span>
<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.69212307</span>
<span class="r-out co"><span class="r-pr">#></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">#></span> $ff</span>
<span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span>
<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.072478e-10 </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> $distimes</span>
<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span>
<span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span>
<span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span>
<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span>
<span class="r-out co"><span class="r-pr">#></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>
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