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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'>
+ <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
+ <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; Estimate se_notrans t value Pr(&gt;t)
+#&gt; T245_0 1.038550e+02 2.184707509 47.537272 4.472189e-18
+#&gt; k_T245 4.337042e-02 0.001898397 22.845818 2.276912e-13
+#&gt; k_phenol 4.050581e-01 0.298699410 1.356073 9.756993e-02
+#&gt; k_anisole 6.678742e-03 0.000802144 8.326114 2.623179e-07
+#&gt; f_T245_to_phenol 6.227599e-01 0.398534147 1.562626 6.949418e-02
+#&gt; f_phenol_to_anisole 1.000000e+00 0.671844135 1.488440 7.867793e-02
+#&gt; sigma 2.514628e+00 0.490755933 5.123989 6.233163e-05
+#&gt; Lower Upper
+#&gt; T245_0 99.246061427 1.084640e+02
+#&gt; k_T245 0.039631621 4.746194e-02
+#&gt; k_phenol 0.218013878 7.525762e-01
+#&gt; k_anisole 0.005370739 8.305299e-03
+#&gt; f_T245_to_phenol 0.547559082 6.924813e-01
+#&gt; f_phenol_to_anisole 0.000000000 1.000000e+00
+#&gt; sigma 1.706607296 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_phenol T245_sink phenol_anisole phenol_sink
+#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 1.005127e-10
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90
+#&gt; T245 15.982025 53.09114
+#&gt; phenol 1.711229 5.68458
+#&gt; anisole 103.784092 344.76329
+#&gt; </div><div class='input'> <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span>
+ <span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
+ <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
+ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Initial parameter(s) k_phenol_sink not used in the model</span></div><div class='output co'>#&gt; <span class='error'>Error in data.frame(value = c(state.ini.fixed, parms.fixed)): row names contain missing values</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='error'>Error in summary(fit.2): object 'fit.2' not found</span></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_phenol T245_sink phenol_anisole phenol_sink
+#&gt; 6.227599e-01 3.772401e-01 1.000000e+00 1.005127e-10
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90
+#&gt; T245 15.982025 53.09114
+#&gt; phenol 1.711229 5.68458
+#&gt; anisole 103.784092 344.76329
+#&gt; </div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit.2</span>)</div><div class='output co'>#&gt; <span class='error'>Error in identical(fit$err_mod, "const"): object 'fit.2' not found</span></div><div class='input'> # }
+</div></pre>
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