1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
|
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014 • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014"><meta property="og:description" content="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."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--></head><body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.5</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu"><li>
<a href="../articles/mkin.html">Introduction to mkin</a>
</li>
<li class="divider">
<li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li>
<li>
<a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
</li>
<li>
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
<a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
</li>
<li class="divider">
<li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li>
<li>
<a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
</li>
<li>
<a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
</li>
<li>
<a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
</li>
<li>
<a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
</li>
<li>
<a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
</li>
<li class="divider">
<li class="dropdown-header">Performance</li>
<li>
<a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
<a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
</li>
<li>
<a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
</li>
<li class="divider">
<li class="dropdown-header">Miscellaneous</li>
<li>
<a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
</li>
<li>
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
</ul></li>
<li>
<a href="../news/index.html">News</a>
</li>
</ul><ul class="nav navbar-nav navbar-right"><li>
<a href="https://github.com/jranke/mkin/" class="external-link">
<span class="fab fa-github fa-lg"></span>
</a>
</li>
</ul></div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<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/HEAD/R/D24_2014.R" class="external-link"><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>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">D24_2014</span></span></code></pre></div>
</div>
<div id="format">
<h2>Format</h2>
<p>An <a href="mkindsg.html">mkindsg</a> object grouping five datasets</p>
</div>
<div id="source">
<h2>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
https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811</p>
</div>
<div id="details">
<h2>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>
</div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> <mkindsg> holding 5 mkinds objects</span>
<span class="r-out co"><span class="r-pr">#></span> Title $title: Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 </span>
<span class="r-out co"><span class="r-pr">#></span> Occurrence of observed compounds $observed_n:</span>
<span class="r-out co"><span class="r-pr">#></span> D24 DCP DCA </span>
<span class="r-out co"><span class="r-pr">#></span> 5 4 4 </span>
<span class="r-out co"><span class="r-pr">#></span> Time normalisation factors $f_time_norm:</span>
<span class="r-out co"><span class="r-pr">#></span> [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124</span>
<span class="r-out co"><span class="r-pr">#></span> Meta information $meta:</span>
<span class="r-out co"><span class="r-pr">#></span> study usda_soil_type study_moisture_ref_type</span>
<span class="r-out co"><span class="r-pr">#></span> Mississippi Cohen 1991 Silt loam <NA></span>
<span class="r-out co"><span class="r-pr">#></span> Fayette Liu and Adelfinskaya 2011 Silt loam pF1</span>
<span class="r-out co"><span class="r-pr">#></span> RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1</span>
<span class="r-out co"><span class="r-pr">#></span> Site E1 Liu and Adelfinskaya 2011 Loam pF1</span>
<span class="r-out co"><span class="r-pr">#></span> Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1</span>
<span class="r-out co"><span class="r-pr">#></span> rel_moisture temperature</span>
<span class="r-out co"><span class="r-pr">#></span> Mississippi NA 25</span>
<span class="r-out co"><span class="r-pr">#></span> Fayette 0.5 20</span>
<span class="r-out co"><span class="r-pr">#></span> RefSol 03-G 0.5 20</span>
<span class="r-out co"><span class="r-pr">#></span> Site E1 0.5 20</span>
<span class="r-out co"><span class="r-pr">#></span> Site I2 0.5 20</span>
<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">$</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></span></span>
<span class="r-out co"><span class="r-pr">#></span> <mkinds> with $title: Mississippi </span>
<span class="r-out co"><span class="r-pr">#></span> Observed compounds $observed: D24 </span>
<span class="r-out co"><span class="r-pr">#></span> Sampling times $sampling_times:</span>
<span class="r-out co"><span class="r-pr">#></span> 0, 2, 4, 7, 15, 24, 35, 56, 71, 114, 183, 273, 365 </span>
<span class="r-out co"><span class="r-pr">#></span> With a maximum of 1 replicates</span>
<span class="r-out co"><span class="r-pr">#></span> time D24</span>
<span class="r-out co"><span class="r-pr">#></span> 1 0 96.8</span>
<span class="r-out co"><span class="r-pr">#></span> 2 2 81.0</span>
<span class="r-out co"><span class="r-pr">#></span> 3 4 81.7</span>
<span class="r-out co"><span class="r-pr">#></span> 4 7 88.2</span>
<span class="r-out co"><span class="r-pr">#></span> 5 15 66.3</span>
<span class="r-out co"><span class="r-pr">#></span> 6 24 72.9</span>
<span class="r-out co"><span class="r-pr">#></span> 7 35 62.6</span>
<span class="r-out co"><span class="r-pr">#></span> 8 56 54.6</span>
<span class="r-out co"><span class="r-pr">#></span> 9 71 35.2</span>
<span class="r-out co"><span class="r-pr">#></span> 10 114 18.0</span>
<span class="r-out co"><span class="r-pr">#></span> 11 183 11.3</span>
<span class="r-out co"><span class="r-pr">#></span> 12 273 9.9</span>
<span class="r-out co"><span class="r-pr">#></span> 13 365 6.3</span>
<span class="r-in"><span><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>,</span></span>
<span class="r-in"><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>,</span></span>
<span class="r-in"><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></span></span>
<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">m_D24</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> <mkinmod> model generated with</span>
<span class="r-out co"><span class="r-pr">#></span> Use of formation fractions $use_of_ff: max </span>
<span class="r-out co"><span class="r-pr">#></span> Specification $spec:</span>
<span class="r-out co"><span class="r-pr">#></span> $D24</span>
<span class="r-out co"><span class="r-pr">#></span> $type: SFO; $to: DCP; $sink: TRUE</span>
<span class="r-out co"><span class="r-pr">#></span> $DCP</span>
<span class="r-out co"><span class="r-pr">#></span> $type: SFO; $to: DCA; $sink: TRUE</span>
<span class="r-out co"><span class="r-pr">#></span> $DCA</span>
<span class="r-out co"><span class="r-pr">#></span> $type: SFO; $sink: TRUE</span>
<span class="r-out co"><span class="r-pr">#></span> Coefficient matrix $coefmat available</span>
<span class="r-out co"><span class="r-pr">#></span> Compiled model $cf available</span>
<span class="r-out co"><span class="r-pr">#></span> Differential equations:</span>
<span class="r-out co"><span class="r-pr">#></span> d_D24/dt = - k_D24 * D24</span>
<span class="r-out co"><span class="r-pr">#></span> d_DCP/dt = + f_D24_to_DCP * k_D24 * D24 - k_DCP * DCP</span>
<span class="r-out co"><span class="r-pr">#></span> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA</span>
<span class="r-in"><span><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>,</span></span>
<span class="r-in"><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>,</span></span>
<span class="r-in"><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></span></span>
<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">m_D24_2</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> <mkinmod> model generated with</span>
<span class="r-out co"><span class="r-pr">#></span> Use of formation fractions $use_of_ff: max </span>
<span class="r-out co"><span class="r-pr">#></span> Specification $spec:</span>
<span class="r-out co"><span class="r-pr">#></span> $D24</span>
<span class="r-out co"><span class="r-pr">#></span> $type: DFOP; $to: DCP; $sink: TRUE</span>
<span class="r-out co"><span class="r-pr">#></span> $DCP</span>
<span class="r-out co"><span class="r-pr">#></span> $type: SFO; $to: DCA; $sink: TRUE</span>
<span class="r-out co"><span class="r-pr">#></span> $DCA</span>
<span class="r-out co"><span class="r-pr">#></span> $type: SFO; $sink: TRUE</span>
<span class="r-out co"><span class="r-pr">#></span> Compiled model $cf available</span>
<span class="r-out co"><span class="r-pr">#></span> Differential equations:</span>
<span class="r-out co"><span class="r-pr">#></span> d_D24/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span>
<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span>
<span class="r-out co"><span class="r-pr">#></span> * D24</span>
<span class="r-out co"><span class="r-pr">#></span> d_DCP/dt = + f_D24_to_DCP * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *</span>
<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2</span>
<span class="r-out co"><span class="r-pr">#></span> * time))) * D24 - k_DCP * DCP</span>
<span class="r-out co"><span class="r-pr">#></span> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
</nav></div>
</div>
<footer><div class="copyright">
<p></p><p>Developed by Johannes Ranke.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
</body></html>
|
