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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-03 16:41:31 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-03 18:18:19 +0100
commitf0ef23a7598e5d19648ae4edc2b74e0fba27a41c (patch)
tree03af20e730330e148acf3a7c008d82387dbe52eb /docs/reference/D24_2014.html
parent82814b17ec182467c25325d747fffa8ffbe4bb33 (diff)
Prepare for v1.0.0v1.0.0
- Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest
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+ <h1>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014</h1>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/D24_2014.R'><code>R/D24_2014.R</code></a></small>
+ <div class="hidden name"><code>D24_2014.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>The five datasets were extracted from the active substance evaluation dossier
+published by EFSA. Kinetic evaluations shown for these datasets are intended
+to illustrate and advance kinetic modelling. The fact that these data and
+some results are shown here does not imply a license to use them in the
+context of pesticide registrations, as the use of the data may be
+constrained by data protection regulations.</p>
+ </div>
+
+ <pre class="usage"><span class='va'>D24_2014</span></pre>
+
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>An <a href='mkindsg.html'>mkindsg</a> object grouping five datasets</p>
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+ <p>Hellenic Ministry of Rural Development and Agriculture (2014)
+Final addendum to the Renewal Assessment Report - public version - 2,4-D
+Volume 3 Annex B.8 Fate and behaviour in the environment
+<a href='http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-3812'>http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-3812</a></p>
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>Data for the first dataset are from p. 685. Data for the other four
+datasets were used in the preprocessed versions given in the kinetics
+section (p. 761ff.), with the exception of residues smaller than 1 for DCP
+in the soil from Site I2, where the values given on p. 694 were used.</p>
+<p>The R code used to create this data object is installed with this package
+in the 'dataset_generation' directory. In the code, page numbers are given for
+specific pieces of information in the comments.</p>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>D24_2014</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 5 mkinds objects
+#&gt; Title $title: Aerobic soil degradation data on 2,4-D from the EU assessment in 2014
+#&gt; Occurrence of observed compounds $observed_n:
+#&gt; D24 DCP DCA
+#&gt; 5 4 4
+#&gt; Time normalisation factors $f_time_norm:
+#&gt; [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124
+#&gt; Meta information $meta:
+#&gt; study usda_soil_type study_moisture_ref_type
+#&gt; Mississippi Cohen 1991 Silt loam &lt;NA&gt;
+#&gt; Fayette Liu and Adelfinskaya 2011 Silt loam pF1
+#&gt; RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1
+#&gt; Site E1 Liu and Adelfinskaya 2011 Loam pF1
+#&gt; Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1
+#&gt; rel_moisture temperature
+#&gt; Mississippi NA 25
+#&gt; Fayette 0.5 20
+#&gt; RefSol 03-G 0.5 20
+#&gt; Site E1 0.5 20
+#&gt; Site I2 0.5 20</div><div class='input'><span class='co'># \dontrun{</span>
+<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>D24_2014</span><span class='op'>$</span><span class='va'>ds</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; &lt;mkinds&gt; with $title: Mississippi
+#&gt; Observed compounds $observed: D24
+#&gt; Sampling times $sampling_times:
+#&gt; 0, 2, 4, 7, 15, 24, 35, 56, 71, 114, 183, 273, 365
+#&gt; With a maximum of 1 replicates
+#&gt; time D24
+#&gt; 1 0 96.8
+#&gt; 2 2 81.0
+#&gt; 3 4 81.7
+#&gt; 4 7 88.2
+#&gt; 5 15 66.3
+#&gt; 6 24 72.9
+#&gt; 7 35 62.6
+#&gt; 8 56 54.6
+#&gt; 9 71 35.2
+#&gt; 10 114 18.0
+#&gt; 11 183 11.3
+#&gt; 12 273 9.9
+#&gt; 13 365 6.3</div><div class='input'><span class='va'>m_D24</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>D24 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"DCP"</span><span class='op'>)</span>,
+ DCP <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"DCA"</span><span class='op'>)</span>,
+ DCA <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>m_D24</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; &lt;mkinmod&gt; model generated with
+#&gt; Use of formation fractions $use_of_ff: max
+#&gt; Specification $spec:
+#&gt; $D24
+#&gt; $type: SFO; $to: DCP; $sink: TRUE
+#&gt; $DCP
+#&gt; $type: SFO; $to: DCA; $sink: TRUE
+#&gt; $DCA
+#&gt; $type: SFO; $sink: TRUE
+#&gt; Coefficient matrix $coefmat available
+#&gt; Compiled model $cf available
+#&gt; Differential equations:
+#&gt; d_D24/dt = - k_D24 * D24
+#&gt; d_DCP/dt = + f_D24_to_DCP * k_D24 * D24 - k_DCP * DCP
+#&gt; d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA</div><div class='input'><span class='va'>m_D24_2</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>D24 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"DCP"</span><span class='op'>)</span>,
+ DCP <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"DCA"</span><span class='op'>)</span>,
+ DCA <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>m_D24_2</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; &lt;mkinmod&gt; model generated with
+#&gt; Use of formation fractions $use_of_ff: max
+#&gt; Specification $spec:
+#&gt; $D24
+#&gt; $type: DFOP; $to: DCP; $sink: TRUE
+#&gt; $DCP
+#&gt; $type: SFO; $to: DCA; $sink: TRUE
+#&gt; $DCA
+#&gt; $type: SFO; $sink: TRUE
+#&gt; Compiled model $cf available
+#&gt; Differential equations:
+#&gt; d_D24/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+#&gt; time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
+#&gt; * D24
+#&gt; d_DCP/dt = + f_D24_to_DCP * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
+#&gt; exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2
+#&gt; * time))) * D24 - k_DCP * DCP
+#&gt; d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA</div><div class='input'><span class='co'># }</span>
+</div></pre>
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