aboutsummaryrefslogtreecommitdiff
path: root/docs/reference/experimental_data_for_UBA.html
blob: 6a02f430ebe3511905f6e2f41eaab4ecbf847a36 (plain) (blame)
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
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
<!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>Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019 • 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="Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019"><meta property="og:description" content="The 12 datasets were extracted from active substance evaluation dossiers published
 by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate
 and advance error model specifications. The fact that these data and some
 results are shown here do 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.
Preprocessing of data was performed based on the recommendations of the FOCUS
 kinetics workgroup (FOCUS, 2014) as described below.
Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox
 (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1
 was assumed. Metabolite residues reported for day zero were added to the
 parent compound residues.
Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid
 (Belgium, 2014, p. 8) and show the data for two different radiolabels. For
 dataset 4, the value given for the metabolite in the day zero sampling
 in replicate B was added to the parent compound, following the respective
 FOCUS recommendation.
Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate
 (Austria, 2015, p. 16).
Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate
 (Germany, 2013, pages 8, 28, 50, 51). For the initial sampling,
 the residues given for the metabolite were added to the parent
 value, following the recommendation of the FOCUS kinetics workgroup.
Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D
 (Hellas, 2013, p. 644). Values reported as zero were set to NA, with
 the exception of the day three sampling of metabolite A2, which was set
 to one half of the LOD reported to be 1% AR.
Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
 (United Kingdom, 2014, p. 81)."><!-- 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">1.2.6</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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</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>Experimental datasets used for development and testing of error models</h1>
    
    <div class="hidden name"><code>experimental_data_for_UBA.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>The 12 datasets were extracted from active substance evaluation dossiers published
 by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate
 and advance error model specifications. The fact that these data and some
 results are shown here do 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>
<p>Preprocessing of data was performed based on the recommendations of the FOCUS
 kinetics workgroup (FOCUS, 2014) as described below.</p>
<p>Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox
 (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1
 was assumed. Metabolite residues reported for day zero were added to the
 parent compound residues.</p>
<p>Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid
 (Belgium, 2014, p. 8) and show the data for two different radiolabels. For
 dataset 4, the value given for the metabolite in the day zero sampling
 in replicate B was added to the parent compound, following the respective
 FOCUS recommendation.</p>
<p>Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate
 (Austria, 2015, p. 16).</p>
<p>Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate
 (Germany, 2013, pages 8, 28, 50, 51). For the initial sampling,
 the residues given for the metabolite were added to the parent
 value, following the recommendation of the FOCUS kinetics workgroup.</p>
<p>Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D
 (Hellas, 2013, p. 644). Values reported as zero were set to NA, with
 the exception of the day three sampling of metabolite A2, which was set
 to one half of the LOD reported to be 1% AR.</p>
<p>Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
 (United Kingdom, 2014, p. 81).</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">experimental_data_for_UBA_2019</span></span></code></pre></div>
    </div>

    <div id="format">
    <h2>Format</h2>
    <p>A list containing twelve datasets as an R6 class defined by <code><a href="mkinds.html">mkinds</a></code>,
  each containing, among others, the following components</p><dl><dt><code>title</code></dt>
<dd><p>The name of the dataset, e.g. <code>Soil 1</code></p></dd>

    <dt><code>data</code></dt>
<dd><p>A data frame with the data in the form expected by <code><a href="mkinfit.html">mkinfit</a></code></p></dd>

  
</dl></div>
    <div id="source">
    <h2>Source</h2>
    

<p>Austria (2015). Ethofumesate Renewal Assessment Report Volume 3 Annex B.8 (AS)</p>
<p>Belgium (2014). Isofetamid (IKF-5411) Draft Assessment Report Volume 3 Annex B.8 (AS)</p>
<p>France (2015). Imazamox Draft Renewal Assessment Report Volume 3 Annex B.8 (AS)</p>
<p>FOCUS (2014) “Generic guidance for Estimating Persistence and
  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
  Registration” Report of the FOCUS Work Group on Degradation Kinetics,
  Version 1.1, 18 December 2014
  <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<p>Germany (2013). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate
  and Behaviour</p>
<p>Hellas (2013). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the
  environment</p>
<p>Ranke (2019) Documentation of results obtained for the error model expertise
  written for the German Umweltbundesamt.</p>
<p>United Kingdom (2014). Thifensulfuron-methyl - Annex B.8 (Volume 3) to the Report and Proposed
  Decision of the United Kingdom made to the European Commission under Regulation (EC) No.
  1141/2010 for renewal of an active substance</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Model definitions</span></span></span>
<span class="r-in"><span><span class="va">sfo_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span>
<span class="r-in"><span>  parent <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">"A1"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>  A1 <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></span>
<span class="r-in"><span>  use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">dfop_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span>
<span class="r-in"><span>  parent <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">"A1"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>  A1 <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></span>
<span class="r-in"><span>  use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">sfo_sfo_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span>
<span class="r-in"><span>  parent <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">"A1"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>  A1 <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">"A2"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>  A2 <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></span>
<span class="r-in"><span>  use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">dfop_sfo_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span>
<span class="r-in"><span>  parent <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">"A1"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>  A1 <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">"A2"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>  A2 <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></span>
<span class="r-in"><span>  use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"><span><span class="va">d_1_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">d_1_2</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Soil"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">f_1_2_tc</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo_sfo</span><span class="op">)</span>, <span class="va">d_1_2</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_1_2_tc</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="experimental_data_for_UBA-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></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>

Contact - Imprint