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<h1>
Datasets on aerobic soil metabolism of 2,4,5-T in six soils
</h1>
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<div class="span8">
<h2>Usage</h2>
<pre><span class="symbol">mccall81_245T</span></pre>
<div class="Description">
<h2>Description</h2>
<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="Format">
<h2>Format</h2>
<p>A dataframe containing the following variables.
<dl>
<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><a href='mkinmod.html'>mkinmod</a></code>.</dd></p>
<p><dt><code>time</code></dt><dd>a numeric vector containing sampling times in days after
treatment</dd></p>
<p><dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd></p>
<p><dt><code>soil</code></dt><dd>a factor containing the name of the soil</dd></p>
<p></dl></p>
<p></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="symbol">SFO_SFO_SFO</span> <span class="assignement"><-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span><span class="argument">T245</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">to</span> <span class="argument">=</span> <span class="string">"phenol"</span><span class="keyword">)</span><span class="keyword">,</span>
<span class="argument">phenol</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">to</span> <span class="argument">=</span> <span class="string">"anisole"</span><span class="keyword">)</span><span class="keyword">,</span>
<span class="argument">anisole</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">)</span><span class="keyword">)</span></div>
<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
<div class='input'> <span class="comment">## Not run: ------------------------------------</span>
<span class="comment"># fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span>
<span class="comment"># summary(fit.1, data = FALSE)</span>
<span class="comment"># </span>
<span class="comment">## ---------------------------------------------</span>
<span class="comment"># No covariance matrix and k_phenol_sink is really small, therefore fix it to zero</span>
<span class="symbol">fit.2</span> <span class="assignement"><-</span> <span class="functioncall"><a href='mkinfit.html'>mkinfit</a></span><span class="keyword">(</span><span class="symbol">SFO_SFO_SFO</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span><span class="keyword">(</span><span class="symbol">mccall81_245T</span><span class="keyword">,</span> <span class="symbol">soil</span> == <span class="string">"Commerce"</span><span class="keyword">)</span><span class="keyword">,</span>
<span class="argument">parms.ini</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_phenol_sink</span> <span class="argument">=</span> <span class="number">0</span><span class="keyword">)</span><span class="keyword">,</span>
<span class="argument">fixed_parms</span> <span class="argument">=</span> <span class="string">"k_phenol_sink"</span><span class="keyword">,</span> <span class="argument">quiet</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span>
<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span><span class="keyword">(</span><span class="symbol">fit.2</span><span class="keyword">,</span> <span class="argument">data</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span></div>
<div class='output'>mkin version: 0.9.44.9000
R version: 3.3.1
Date of fit: Sat Sep 10 05:53:00 2016
Date of summary: Sat Sep 10 05:53:00 2016
Equations:
d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
d_phenol = + k_T245_phenol * T245 - k_phenol_sink * phenol -
k_phenol_anisole * phenol
d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole
Model predictions using solution type deSolve
Fitted with method Port using 246 model solutions performed in 1.45 s
Weighting: none
Starting values for parameters to be optimised:
value type
T245_0 100.9000 state
k_T245_sink 0.1000 deparm
k_T245_phenol 0.1001 deparm
k_phenol_anisole 0.1002 deparm
k_anisole_sink 0.1003 deparm
Starting values for the transformed parameters actually optimised:
value lower upper
T245_0 100.900000 -Inf Inf
log_k_T245_sink -2.302585 -Inf Inf
log_k_T245_phenol -2.301586 -Inf Inf
log_k_phenol_anisole -2.300587 -Inf Inf
log_k_anisole_sink -2.299590 -Inf Inf
Fixed parameter values:
value type
phenol_0 0 state
anisole_0 0 state
k_phenol_sink 0 deparm
Optimised, transformed parameters with symmetric confidence intervals:
Estimate Std. Error Lower Upper
T245_0 103.9000 2.35200 98.930 108.8000
log_k_T245_sink -4.1130 0.13250 -4.390 -3.8350
log_k_T245_phenol -3.6120 0.05002 -3.716 -3.5070
log_k_phenol_anisole -0.9037 0.30580 -1.544 -0.2637
log_k_anisole_sink -5.0090 0.11180 -5.243 -4.7750
Parameter correlation:
T245_0 log_k_T245_sink log_k_T245_phenol
T245_0 1.00000 0.63761 -0.1742
log_k_T245_sink 0.63761 1.00000 -0.3831
log_k_T245_phenol -0.17416 -0.38313 1.0000
log_k_phenol_anisole -0.05948 0.08745 -0.3047
log_k_anisole_sink -0.16208 -0.60469 0.5227
log_k_phenol_anisole log_k_anisole_sink
T245_0 -0.05948 -0.1621
log_k_T245_sink 0.08745 -0.6047
log_k_T245_phenol -0.30470 0.5227
log_k_phenol_anisole 1.00000 -0.1774
log_k_anisole_sink -0.17744 1.0000
Residual standard error: 2.706 on 19 degrees of freedom
Backtransformed parameters:
Confidence intervals for internally transformed parameters are asymmetric.
t-test (unrealistically) based on the assumption of normal distribution
for estimators of untransformed parameters.
Estimate t value Pr(>t) Lower Upper
T245_0 1.039e+02 44.160 6.462e-21 98.930000 108.80000
k_T245_sink 1.636e-02 7.545 1.978e-07 0.012400 0.02159
k_T245_phenol 2.701e-02 19.990 1.607e-14 0.024320 0.02999
k_phenol_anisole 4.051e-01 3.270 2.014e-03 0.213600 0.76820
k_anisole_sink 6.679e-03 8.942 1.544e-08 0.005285 0.00844
Chi2 error levels in percent:
err.min n.optim df
All data 9.831 5 17
T245 7.908 3 5
phenol 99.808 1 6
anisole 5.379 1 6
Resulting formation fractions:
ff
T245_sink 0.3772
T245_phenol 0.6228
phenol_anisole 1.0000
phenol_sink 0.0000
anisole_sink 1.0000
Estimated disappearance times:
DT50 DT90
T245 15.982 53.091
phenol 1.711 5.685
anisole 103.784 344.763
</div></pre>
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