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
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
|
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
<head>
<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>Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm</title>
<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
<meta property="og:title" content="Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus" />
<meta property="og:description" content="This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
authored by Michael Klein, in R. Note that results for multiple
applications should be compared to the corresponding results for a
single application. At current, this is not done automatically in
this implementation. Only Step 1 PECs are calculated. However,
input files are generated that are suitable as input also for Step 2
to be used with the FOCUS calculator." />
<meta name="twitter:card" content="summary" />
<!-- 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>
<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">pfm</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.5</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">
<span class="fa fa-home fa-lg"></span>
</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/pfm">
<span class="fa 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>Calculate PEC surface water at FOCUS Step 1</h1>
<small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PEC_sw_focus.R'><code>R/PEC_sw_focus.R</code></a></small>
<div class="hidden name"><code>PEC_sw_focus.Rd</code></div>
</div>
<div class="ref-description">
<p>This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
authored by Michael Klein, in R. Note that results for multiple
applications should be compared to the corresponding results for a
single application. At current, this is not done automatically in
this implementation. Only Step 1 PECs are calculated. However,
input files are generated that are suitable as input also for Step 2
to be used with the FOCUS calculator.</p>
</div>
<pre class="usage"><span class='fu'>PEC_sw_focus</span>(<span class='no'>parent</span>, <span class='no'>rate</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>f_rd</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span>,
<span class='kw'>region</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"n"</span>, <span class='st'>"s"</span>), <span class='kw'>season</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"of"</span>, <span class='st'>"mm"</span>, <span class='st'>"js"</span>),
<span class='kw'>interception</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"no interception"</span>, <span class='st'>"minimal crop cover"</span>,
<span class='st'>"average crop cover"</span>, <span class='st'>"full canopy"</span>), <span class='kw'>met_form_water</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>txt_file</span> <span class='kw'>=</span> <span class='st'>"pesticide.txt"</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>parent</th>
<td><p>A list containing substance specific parameters, e.g.
conveniently generated by <code><a href='chent_focus_sw.html'>chent_focus_sw</a></code>.</p></td>
</tr>
<tr>
<th>rate</th>
<td><p>The application rate in g/ha. Overriden when
applications are given explicitly</p></td>
</tr>
<tr>
<th>n</th>
<td><p>The number of applications</p></td>
</tr>
<tr>
<th>i</th>
<td><p>The application interval</p></td>
</tr>
<tr>
<th>comment</th>
<td><p>A comment for the input file</p></td>
</tr>
<tr>
<th>met</th>
<td><p>A list containing metabolite specific parameters. e.g.
conveniently generated by <code><a href='chent_focus_sw.html'>chent_focus_sw</a></code>. If not NULL,
the PEC is calculated for this compound, not the parent.</p></td>
</tr>
<tr>
<th>f_drift</th>
<td><p>The fraction of the application rate reaching the waterbody
via drift. If NA, this is derived from the scenario name and the number
of applications via the drift data defined by the
<code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenarios</a></code></p></td>
</tr>
<tr>
<th>f_rd</th>
<td><p>The fraction of the amount applied reaching the waterbody via
runoff/drainage. At Step 1, it is assumed to be 10<!-- %, be it the -->
parent or a metabolite</p></td>
</tr>
<tr>
<th>scenario</th>
<td><p>The name of the scenario. Must be one of the scenario
names given in <code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenarios</a></code></p></td>
</tr>
<tr>
<th>region</th>
<td><p>'n' for Northern Europe or 's' for Southern Europe. If NA, only
Step 1 PECsw are calculated</p></td>
</tr>
<tr>
<th>season</th>
<td><p>'of' for October to February, 'mm' for March to May, and 'js'
for June to September. If NA, only step 1 PECsw are calculated</p></td>
</tr>
<tr>
<th>interception</th>
<td><p>One of 'no interception' (default), 'minimal crop cover',
'average crop cover' or 'full canopy'</p></td>
</tr>
<tr>
<th>met_form_water</th>
<td><p>Should the metabolite formation in water be taken into
account? This can be switched off to check the influence and to compare
with previous versions of the Steps 12 calculator</p></td>
</tr>
<tr>
<th>txt_file</th>
<td><p>the name, and potentially the full path to the
Steps.12 input text file to which the specification of the run(s)
should be written</p></td>
</tr>
<tr>
<th>overwrite</th>
<td><p>Should an existing file a the location specified in
<code>txt_file</code> be overwritten? Only takes effect if append is FALSE.</p></td>
</tr>
<tr>
<th>append</th>
<td><p>Should the input text file be appended?</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
<p>The formulas for input to the waterbody via runoff/drainage of the
parent and subsequent formation of the metabolite in water is not
documented in the model description coming with the calculator. As one would
expect, this appears to be (as we get the same results) calculated by
multiplying the application rate with the molar weight
correction and the formation fraction in water/sediment systems.</p>
<p>Step 2 is not implemented.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4).
FOrum for the Co-ordination of pesticde fate models and their USe.
http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic<!-- %20FOCUS_SWS_vc1.4.pdf --></p>
<p>Website of the Steps 1 and 2 calculator at the Joint Research
Center of the European Union:
http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Parent only</span>
<span class='no'>dummy_1</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"Dummy 1"</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>6000</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>344.8</span>)
<span class='fu'>PEC_sw_focus</span>(<span class='no'>dummy_1</span>, <span class='fl'>3000</span>, <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> $f_drift
#> [1] 0
#>
#> $eq_rate_drift_s
#> [1] 3000
#>
#> $eq_rate_rd_s
#> [1] 3000
#>
#> $eq_rate_rd_parent_s
#> [1] NA
#>
#> $input_drift_s
#> [1] 0
#>
#> $input_rd_s
#> [1] 300
#>
#> $f_rd_sw
#> [1] 0.6850566
#>
#> $f_rd_sed
#> [1] 0.3149434
#>
#> $PEC
#> type
#> Time PECsw TWAECsw PECsed TWAECsed
#> 0 6.850566e+02 NA 2.362075e+03 NA
#> 1 6.103161e+02 647.68635 2.104370e+03 2233.2225
#> 2 5.437298e+02 612.03420 1.874780e+03 2110.2939
#> 4 4.315586e+02 548.76030 1.488014e+03 1892.1255
#> 7 3.051580e+02 469.88375 1.052185e+03 1620.1592
#> 14 1.359325e+02 339.57370 4.686951e+02 1170.8501
#> 21 6.055102e+01 257.45458 2.087799e+02 887.7034
#> 28 2.697241e+01 203.47173 9.300089e+01 701.5705
#> 42 5.352005e+00 140.10377 1.845371e+01 483.0778
#> 50 2.123945e+00 118.24602 7.323361e+00 407.7123
#> 100 6.585062e-03 59.30629 2.270529e-02 204.4881
#>
#> $PEC_sw_max
#> [1] 685.0566
#>
#> $PEC_sed_max
#> [1] 2362.075
#> </div><div class='input'>
<span class='co'># Metabolite</span>
<span class='no'>new_dummy</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"New Dummy"</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>)
<span class='no'>M1</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"M1"</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>50</span>,
<span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
<span class='fu'>PEC_sw_focus</span>(<span class='no'>new_dummy</span>, <span class='fl'>1000</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='st'>"cereals, winter"</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='no'>M1</span>)</div><div class='output co'>#> $f_drift
#> [1] 0.02759
#>
#> $eq_rate_drift_s
#> [1] 0
#>
#> $eq_rate_rd_s
#> [1] 200
#>
#> $eq_rate_rd_parent_s
#> [1] 0
#>
#> $input_drift_s
#> [1] 0
#>
#> $input_rd_s
#> [1] 20
#>
#> $f_rd_sw
#> [1] 0.9375
#>
#> $f_rd_sed
#> [1] 0.0625
#>
#> $PEC
#> type
#> Time PECsw TWAECsw PECsed TWAECsed
#> 0 62.50000 NA 31.25000 NA
#> 1 62.06828 62.28414 31.03414 31.14207
#> 2 61.63954 62.06890 30.81977 31.03445
#> 4 60.79093 61.64158 30.39547 30.82079
#> 7 59.53987 61.00800 29.76994 30.50400
#> 14 56.71995 59.56326 28.35997 29.78163
#> 21 54.03358 58.16414 27.01679 29.08207
#> 28 51.47444 56.80902 25.73722 28.40451
#> 42 46.71404 54.22460 23.35702 27.11230
#> 50 44.19417 52.81945 22.09709 26.40973
#> 100 31.25000 45.08422 15.62500 22.54211
#>
#> $PEC_sw_max
#> [1] 62.5
#>
#> $PEC_sed_max
#> [1] 31.25
#> </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#note">Note</a></li>
<li><a href="#references">References</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Johannes Ranke.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
</footer>
</div>
</body>
</html>
|
