blob: 395b4467b6e55eef465e14f9dace0acb351190b4 (
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
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
368
369
370
371
372
373
374
375
376
377
378
379
380
|
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html>
<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>Function reference • pfm</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" 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="Function reference" />
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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-index">
<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">
<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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.4.5</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="contents col-md-9">
<div class="page-header">
<h1>Reference</h1>
</div>
<table class="ref-index">
<colgroup>
<col class="alias" />
<col class="title" />
</colgroup>
<tbody>
<tr>
<th colspan="2">
<h2 id="section-general-utility-functions" class="hasAnchor"><a href="#section-general-utility-functions" class="anchor"></a>General utility functions</h2>
<p class="section-desc"><p>Functions that are independent of specific fate modelling areas</p></p>
</th>
</tr>
<tr>
<td>
<p><code><a href="geomean.html">geomean()</a></code> </p>
</td>
<td><p>Calculate the geometric mean</p></td>
</tr><tr>
<td>
<p><code><a href="one_box.html">one_box()</a></code> </p>
</td>
<td><p>Create a time series of decline data</p></td>
</tr><tr>
<td>
<p><code><a href="plot.one_box.html">plot(<i><one_box></i>)</a></code> </p>
</td>
<td><p>Plot time series of decline data</p></td>
</tr><tr>
<td>
<p><code><a href="sawtooth.html">sawtooth()</a></code> </p>
</td>
<td><p>Create decline time series for multiple applications</p></td>
</tr><tr>
<td>
<p><code><a href="twa.html">twa()</a></code> </p>
</td>
<td><p>Calculate a time weighted average concentration</p></td>
</tr><tr>
<td>
<p><code><a href="max_twa.html">max_twa()</a></code> </p>
</td>
<td><p>The maximum time weighted average concentration for a moving window</p></td>
</tr><tr>
<td>
<p><code><a href="pfm_degradation.html">pfm_degradation()</a></code> </p>
</td>
<td><p>Calculate a time course of relative concentrations based on an mkinmod model</p></td>
</tr><tr>
<td>
<p><code><a href="SFO_actual_twa.html">SFO_actual_twa()</a></code> </p>
</td>
<td><p>Actual and maximum moving window time average concentrations for SFO kinetics</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-predicted-environmental-concentrations-in-soil" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-soil" class="anchor"></a>Predicted environmental concentrations in soil</h2>
<p class="section-desc"></p>
</th>
</tr>
<tr>
<td>
<p><code><a href="PEC_soil.html">PEC_soil()</a></code> </p>
</td>
<td><p>Calculate predicted environmental concentrations in soil</p></td>
</tr><tr>
<td>
<p><code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code> </p>
</td>
<td><p>Properties of the predefined scenarios from the EFSA guidance from 2015</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-predicted-environmental-concentrations-in-groundwater" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-groundwater" class="anchor"></a>Predicted environmental concentrations in groundwater</h2>
<p class="section-desc"></p>
</th>
</tr>
<tr>
<td>
<p><code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code> </p>
</td>
<td><p>A very small subset of the FOCUS Groundwater scenario definitions</p></td>
</tr><tr>
<td>
<p><code><a href="create_run_list.html">create_run_list()</a></code> </p>
</td>
<td><p>Create a list of runs that we can traverse</p></td>
</tr><tr>
<td>
<p><code><a href="PELMO_runs.html">PELMO_runs()</a></code> <code><a href="PELMO_runs.html">run_PELMO()</a></code> <code><a href="PELMO_runs.html">evaluate_PELMO()</a></code> </p>
</td>
<td><p>Set up runs for FOCUS PELMO</p></td>
</tr><tr>
<td>
<p><code><a href="PELMO_path.html">PELMO_path()</a></code> </p>
</td>
<td><p>Create a path of run directories as the PELMO GUI does</p></td>
</tr><tr>
<td>
<p><code><a href="FOCUS_PELMO_crop_sze_names.html">FOCUS_PELMO_crop_sze_names</a></code> </p>
</td>
<td><p>FOCUS PELMO crop acronyms used for naming sceneario files</p></td>
</tr><tr>
<td>
<p><code><a href="FOCUS_PELMO_crops.html">FOCUS_PELMO_crops</a></code> </p>
</td>
<td><p>FOCUS PELMO crop names</p></td>
</tr><tr>
<td>
<p><code><a href="FOCUS_PELMO_location_codes.html">FOCUS_PELMO_location_codes</a></code> </p>
</td>
<td><p>Location codes in FOCUS PELMO</p></td>
</tr><tr>
<td>
<p><code><a href="focus_80th.html">focus_80th()</a></code> </p>
</td>
<td><p>Calculate the 80th percentile according to FOCUS guidance</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-predicted-environmental-concentrations-in-surface-water" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-surface-water" class="anchor"></a>Predicted environmental concentrations in surface water</h2>
<p class="section-desc"></p>
</th>
</tr>
<tr>
<td>
<p><code><a href="PEC_sw_drift.html">PEC_sw_drift()</a></code> </p>
</td>
<td><p>Calculate predicted environmental concentrations in surface water due to drift</p></td>
</tr><tr>
<td>
<p><code><a href="drift_data_JKI.html">drift_data_JKI</a></code> </p>
</td>
<td><p>Deposition from spray drift expressed as percent of the applied dose as
published by the JKI</p></td>
</tr><tr>
<td>
<p><code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK()</a></code> </p>
</td>
<td><p>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</p></td>
</tr><tr>
<td>
<p><code><a href="PEC_sw_sed.html">PEC_sw_sed()</a></code> </p>
</td>
<td><p>Calculate predicted environmental concentrations in sediment from surface
water concentrations</p></td>
</tr><tr>
<td>
<p><code><a href="chent_focus_sw.html">chent_focus_sw()</a></code> </p>
</td>
<td><p>Create a chemical compound object for FOCUS Step 1 calculations</p></td>
</tr><tr>
<td>
<p><code><a href="PEC_sw_focus.html">PEC_sw_focus()</a></code> </p>
</td>
<td><p>Calculate PEC surface water at FOCUS Step 1</p></td>
</tr><tr>
<td>
<p><code><a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></code> </p>
</td>
<td><p>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</p></td>
</tr><tr>
<td>
<p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> </p>
</td>
<td><p>Runoff loss percentages as used in Exposit 3</p></td>
</tr><tr>
<td>
<p><code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> </p>
</td>
<td><p>Runoff reduction percentages as used in Exposit</p></td>
</tr><tr>
<td>
<p><code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff()</a></code> </p>
</td>
<td><p>Calculate PEC surface water due to runoff and erosion as in Exposit 3</p></td>
</tr><tr>
<td>
<p><code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code> </p>
</td>
<td><p>R6 class for holding TOXSWA cwa concentration data and associated statistics</p></td>
</tr><tr>
<td>
<p><code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa()</a></code> </p>
</td>
<td><p>Read TOXSWA surface water concentrations</p></td>
</tr><tr>
<td>
<p><code><a href="plot.TOXSWA_cwa.html">plot(<i><TOXSWA_cwa></i>)</a></code> </p>
</td>
<td><p>Plot TOXSWA surface water concentrations</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-classifications-and-indicators" class="hasAnchor"><a href="#section-classifications-and-indicators" class="anchor"></a>Classifications and indicators</h2>
<p class="section-desc"><p>Evaluating environmental fate properties</p></p>
</th>
</tr>
<tr>
<td>
<p><code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification()</a></code> </p>
</td>
<td><p>Determine the SSLRC mobility classification for a chemical substance from its Koc</p></td>
</tr><tr>
<td>
<p><code><a href="GUS.html">GUS()</a></code> <code><a href="GUS.html">print(<i><GUS_result></i>)</a></code> </p>
</td>
<td><p>Groundwater ubiquity score based on Gustafson (1989)</p></td>
</tr>
</tbody>
</table>
</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="#section-general-utility-functions">General utility functions</a></li>
<li><a href="#section-predicted-environmental-concentrations-in-soil">Predicted environmental concentrations in soil</a></li>
<li><a href="#section-predicted-environmental-concentrations-in-groundwater">Predicted environmental concentrations in groundwater</a></li>
<li><a href="#section-predicted-environmental-concentrations-in-surface-water">Predicted environmental concentrations in surface water</a></li>
<li><a href="#section-classifications-and-indicators">Classifications and indicators</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="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>
</footer>
</div>
</body>
</html>
|
