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
|
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>endpoint. pfm 0.3-7</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="author" content="">
<link href="css/bootstrap.css" rel="stylesheet">
<link href="css/bootstrap-responsive.css" rel="stylesheet">
<link href="css/highlight.css" rel="stylesheet">
<link href="css/staticdocs.css" rel="stylesheet">
<!--[if lt IE 9]>
<script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
tex2jax: {
inlineMath: [ ['$','$'], ["\\(","\\)"] ],
processEscapes: true
}
});
</script>
<script type="text/javascript"
src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>
</head>
<body>
<div class="navbar">
<div class="navbar-inner">
<div class="container">
<a class="brand" href="#">pfm 0.3-7</a>
<div class="nav">
<ul class="nav">
<li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li>
</ul>
</div>
</div>
</div>
</div>
<div class="container">
<header>
</header>
<h1>Retrieve endpoint information from the chyaml field of a chent object</h1>
<div class="row">
<div class="span8">
<h2>Usage</h2>
<pre><div>endpoint(chent, medium = "soil", type = c("degradation", "sorption"), lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic", "anaerobic"), value = c("DT50ref", "Kfoc", "N"), aggregator = geomean, raw = FALSE, signif = 3)</div>
<div>soil_DT50(chent, aggregator = geomean, signif = 3, lab_field = "laboratory", value = "DT50ref", redox = "aerobic", raw = FALSE)</div>
<div>soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)</div>
<div>soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)</div>
<div>soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), raw = FALSE)</div></pre>
<h2>Arguments</h2>
<dl>
<dt>chent</dt>
<dd>The <code><a href='http://www.inside-r.org/packages/cran/chents/docs/chent'>chent</a></code> object to get the information from</dd>
<dt>medium</dt>
<dd>The medium for which information is sought</dd>
<dt>type</dt>
<dd>The information type</dd>
<dt>lab_field</dt>
<dd>If not NA, do we want laboratory or field endpoints</dd>
<dt>redox</dt>
<dd>If not NA, are we looking for aerobic or anaerobic data</dd>
<dt>value</dt>
<dd>The name of the value we want. The list given in the
usage section is not exclusive</dd>
<dt>aggregator</dt>
<dd>The aggregator function. Can be mean,
<code><a href='geomean.html'>geomean</a></code>, or identity, for example.</dd>
<dt>raw</dt>
<dd>Should the number(s) be returned as stored in the chent
object (could be a character value) to retain original information
about precision?</dd>
<dt>signif</dt>
<dd>How many significant digits do we want</dd>
<dt>values</dt>
<dd>The values to be returned</dd>
<dt>aggregators</dt>
<dd>A named vector of aggregator functions to be used</dd>
</dl>
<div class="Value">
<h2>Value</h2>
<p><dl>
The result from applying the aggregator function to
the values converted to a numeric vector, rounded to the
given number of significant digits, or, if raw = TRUE,
the values as a character value, retaining any implicit
information on precision that may be present.
</dl></p>
</div>
<div class="Description">
<h2>Description</h2>
<p>R6 class objects of class <code><a href='http://www.inside-r.org/packages/cran/chents/docs/chent'>chent</a></code> represent chemical entities
and can hold a list of information loaded from a chemical yaml file in their
chyaml field. Such information is extracted and optionally aggregated by
this function.</p>
</div>
<div class="Details">
<h2>Details</h2>
<p>The functions <code>soil_*</code> are functions to extract soil specific endpoints.
For the Freundlich exponent, the capital letter <code>N</code> is used in order to
facilitate dealing with such data in R. In pesticide fate modelling, this
exponent is often called 1/n.</p>
</div>
</div>
<div class="span4">
<!-- <ul>
<li>endpoint</li><li>soil_DT50</li><li>soil_Kfoc</li><li>soil_N</li><li>soil_sorption</li>
</ul>
<ul>
</ul> -->
</div>
</div>
<footer>
<p class="pull-right"><a href="#">Back to top</a></p>
<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="http://twitter.github.com/bootstrap">bootstrap</a>.</p>
</footer>
</div>
</body>
</html>
|
