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+
+ <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>
+
+
+ <pre><span class='no'>mccall81_245T</span></pre>
+
+ <div class="Format">
+ <h2>Format</h2>
+
+ <p>A dataframe containing the following variables.
+ <dl class='dl-horizontal'>
+ <dt><code>name</code></dt><dd>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>mkinmod</code>.</dd>
+ <dt><code>time</code></dt><dd>a numeric vector containing sampling times in days after
+ treatment</dd>
+ <dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd>
+ <dt><code>soil</code></dt><dd>a factor containing the name of the soil</dd>
+ </dl></p>
+ </div>
+
+ <div class="Source">
+ <h2>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>
+ </div>
+
+ <h2 id="examples">Examples</h2>
+ <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</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'>list</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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># fit.1 &lt;- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span>
+<span class='co'># summary(fit.1, data = FALSE)</span>
+<span class='co'># </span>
+<span class='co'>## ---------------------------------------------</span>
+ <span class='co'># No covariance matrix and 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'>mkinfit</span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</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'>c</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>)
+ <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.1
+#&gt; Date of fit: Thu Oct 6 09:17:57 2016
+#&gt; Date of summary: Thu Oct 6 09:17:57 2016
+#&gt;
+#&gt; Equations:
+#&gt; d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
+#&gt; d_phenol = + k_T245_phenol * T245 - k_phenol_sink * phenol -
+#&gt; k_phenol_anisole * phenol
+#&gt; d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 246 model solutions performed in 1.508 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; T245_0 100.9000 state
+#&gt; k_T245_sink 0.1000 deparm
+#&gt; k_T245_phenol 0.1001 deparm
+#&gt; k_phenol_anisole 0.1002 deparm
+#&gt; k_anisole_sink 0.1003 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; T245_0 100.900000 -Inf Inf
+#&gt; log_k_T245_sink -2.302585 -Inf Inf
+#&gt; log_k_T245_phenol -2.301586 -Inf Inf
+#&gt; log_k_phenol_anisole -2.300587 -Inf Inf
+#&gt; log_k_anisole_sink -2.299590 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; phenol_0 0 state
+#&gt; anisole_0 0 state
+#&gt; k_phenol_sink 0 deparm
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; T245_0 103.9000 2.35200 98.930 108.8000
+#&gt; log_k_T245_sink -4.1130 0.13250 -4.390 -3.8350
+#&gt; log_k_T245_phenol -3.6120 0.05002 -3.716 -3.5070
+#&gt; log_k_phenol_anisole -0.9037 0.30580 -1.544 -0.2637
+#&gt; log_k_anisole_sink -5.0090 0.11180 -5.243 -4.7750
+#&gt;
+#&gt; Parameter correlation:
+#&gt; T245_0 log_k_T245_sink log_k_T245_phenol
+#&gt; T245_0 1.00000 0.63761 -0.1742
+#&gt; log_k_T245_sink 0.63761 1.00000 -0.3831
+#&gt; log_k_T245_phenol -0.17416 -0.38313 1.0000
+#&gt; log_k_phenol_anisole -0.05948 0.08745 -0.3047
+#&gt; log_k_anisole_sink -0.16208 -0.60469 0.5227
+#&gt; log_k_phenol_anisole log_k_anisole_sink
+#&gt; T245_0 -0.05948 -0.1621
+#&gt; log_k_T245_sink 0.08745 -0.6047
+#&gt; log_k_T245_phenol -0.30470 0.5227
+#&gt; log_k_phenol_anisole 1.00000 -0.1774
+#&gt; log_k_anisole_sink -0.17744 1.0000
+#&gt;
+#&gt; Residual standard error: 2.706 on 19 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; T245_0 1.039e+02 44.160 6.462e-21 98.930000 108.80000
+#&gt; k_T245_sink 1.636e-02 7.545 1.978e-07 0.012400 0.02159
+#&gt; k_T245_phenol 2.701e-02 19.990 1.607e-14 0.024320 0.02999
+#&gt; k_phenol_anisole 4.051e-01 3.270 2.014e-03 0.213600 0.76820
+#&gt; k_anisole_sink 6.679e-03 8.942 1.544e-08 0.005285 0.00844
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 9.831 5 17
+#&gt; T245 7.908 3 5
+#&gt; phenol 99.808 1 6
+#&gt; anisole 5.379 1 6
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; T245_sink 0.3772
+#&gt; T245_phenol 0.6228
+#&gt; phenol_anisole 1.0000
+#&gt; phenol_sink 0.0000
+#&gt; anisole_sink 1.0000
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; T245 15.982 53.091
+#&gt; phenol 1.711 5.685
+#&gt; anisole 103.784 344.763
+#&gt; </div></pre>
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