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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 class='dl-horizontal'>
    <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 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>
    

    <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'>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 co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>  </div><div class='input'>    <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'>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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
    <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.47.5 
#&gt; R version used for fitting:       3.5.1 
#&gt; Date of fit:     Fri Sep 14 18:20:57 2018 
#&gt; Date of summary: Fri Sep 14 18:20:57 2018 
#&gt; 
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
#&gt; d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol -
#&gt;            k_phenol_anisole * phenol
#&gt; d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole
#&gt; 
#&gt; Model predictions using solution type deSolve 
#&gt; 
#&gt; Fitted with method Port using 574 model solutions performed in 3.418 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_sink      0.1002 deparm
#&gt; k_phenol_anisole   0.1003 deparm
#&gt; k_anisole_sink     0.1004 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_sink     -2.300587  -Inf   Inf
#&gt; log_k_phenol_anisole  -2.299590  -Inf   Inf
#&gt; log_k_anisole_sink    -2.298593  -Inf   Inf
#&gt; 
#&gt; Fixed parameter values:
#&gt;           value  type
#&gt; phenol_0      0 state
#&gt; anisole_0     0 state
#&gt; 
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
#&gt;                      Estimate Std. Error Lower Upper
#&gt; T245_0               103.9000         NA    NA    NA
#&gt; log_k_T245_sink       -4.1130         NA    NA    NA
#&gt; log_k_T245_phenol     -3.6120         NA    NA    NA
#&gt; log_k_phenol_sink    -25.0800         NA    NA    NA
#&gt; log_k_phenol_anisole  -0.9037         NA    NA    NA
#&gt; log_k_anisole_sink    -5.0090         NA    NA    NA
#&gt; 
#&gt; Parameter correlation:</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not estimate covariance matrix; singular system:</span></div><div class='output co'>#&gt; Could not estimate covariance matrix; singular system:
#&gt; 
#&gt; Residual standard error: 2.78 on 18 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 4.282e+01 7.236e-20    NA    NA
#&gt; k_T245_sink      1.636e-02 8.901e-01 1.926e-01    NA    NA
#&gt; k_T245_phenol    2.701e-02 1.504e+00 7.498e-02    NA    NA
#&gt; k_phenol_sink    1.286e-11 4.575e-11 5.000e-01    NA    NA
#&gt; k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02    NA    NA
#&gt; k_anisole_sink   6.679e-03 8.146e+00 9.469e-08    NA    NA
#&gt; 
#&gt; Chi2 error levels in percent:
#&gt;          err.min n.optim df
#&gt; All data  10.070       6 16
#&gt; T245       7.908       3  5
#&gt; phenol   106.445       2  5
#&gt; anisole    5.379       1  6
#&gt; 
#&gt; Resulting formation fractions:
#&gt;                       ff
#&gt; T245_sink      3.772e-01
#&gt; T245_phenol    6.228e-01
#&gt; phenol_sink    3.175e-11
#&gt; phenol_anisole 1.000e+00
#&gt; anisole_sink   1.000e+00
#&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</div><div class='input'>    <span class='co'># No convergence, no covariance matrix ...</span>
    <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'>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 used for fitting:    0.9.47.5 
#&gt; R version used for fitting:       3.5.1 
#&gt; Date of fit:     Fri Sep 14 18:20:59 2018 
#&gt; Date of summary: Fri Sep 14 18:20:59 2018 
#&gt; 
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
#&gt; d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol -
#&gt;            k_phenol_anisole * phenol
#&gt; d_anisole/dt = + 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 1.458 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</div><div class='input'>  </div></pre>
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