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authorJohannes Ranke <jranke@uni-bremen.de>2016-10-06 09:40:35 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-10-06 09:40:35 +0200
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-<title>mccall81_245T. mkin 0.9.44.9000</title>
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- <h1>
- Datasets on aerobic soil metabolism of 2,4,5-T in six soils
-</h1>
-
-<div class="row">
- <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">&lt;-</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 &lt;- 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">&lt;-</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(&gt;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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