aboutsummaryrefslogtreecommitdiff
path: root/docs/reference/endpoint.html
blob: 5e038b114d18fa3c50080234d035d0b5ec7dd384 (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
<!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, shrink-to-fit=no"><meta name="description" content="R6 class objects of class chent 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."><title>Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Retrieve endpoint information from the chyaml field of a chent object — endpoint"><meta property="og:description" content="R6 class objects of class chent 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."><!-- 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>
    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
    

    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
    
    <a class="navbar-brand me-2" href="../index.html">pfm</a>

    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.0</small>

    
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
      <span class="navbar-toggler-icon"></span>
    </button>

    <div id="navbar" class="collapse navbar-collapse ms-3">
      <ul class="navbar-nav me-auto"><li class="active nav-item">
  <a class="nav-link" href="../reference/index.html">Reference</a>
</li>
      </ul><form class="form-inline my-2 my-lg-0" role="search">
        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>

      <ul class="navbar-nav"><li class="nav-item">
  <a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="github">
    <span class="fab fa fab fa-github fa-lg"></span>
     
  </a>
</li>
      </ul></div>

    
  </div>
</nav><div class="container template-reference-topic">
<div class="row">
  <main id="main" class="col-md-9"><div class="page-header">
      <img src="" class="logo" alt=""><h1>Retrieve endpoint information from the chyaml field of a chent object</h1>
      <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/endpoint.R" class="external-link"><code>R/endpoint.R</code></a></small>
      <div class="d-none name"><code>endpoint.Rd</code></div>
    </div>

    <div class="ref-description section level2">
    <p>R6 class objects of class chent 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="section level2">
    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">endpoint</span><span class="op">(</span></span>
<span>  <span class="va">chent</span>,</span>
<span>  medium <span class="op">=</span> <span class="st">"soil"</span>,</span>
<span>  type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"degradation"</span>, <span class="st">"sorption"</span><span class="op">)</span>,</span>
<span>  lab_field <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"laboratory"</span>, <span class="st">"field"</span><span class="op">)</span>,</span>
<span>  redox <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"aerobic"</span>, <span class="st">"anaerobic"</span><span class="op">)</span>,</span>
<span>  value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"DT50ref"</span>, <span class="st">"Kfoc"</span>, <span class="st">"N"</span><span class="op">)</span>,</span>
<span>  aggregator <span class="op">=</span> <span class="va">geomean</span>,</span>
<span>  raw <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  signif <span class="op">=</span> <span class="fl">3</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">soil_DT50</span><span class="op">(</span></span>
<span>  <span class="va">chent</span>,</span>
<span>  aggregator <span class="op">=</span> <span class="va">geomean</span>,</span>
<span>  signif <span class="op">=</span> <span class="fl">3</span>,</span>
<span>  lab_field <span class="op">=</span> <span class="st">"laboratory"</span>,</span>
<span>  value <span class="op">=</span> <span class="st">"DT50ref"</span>,</span>
<span>  redox <span class="op">=</span> <span class="st">"aerobic"</span>,</span>
<span>  raw <span class="op">=</span> <span class="cn">FALSE</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">soil_Kfoc</span><span class="op">(</span><span class="va">chent</span>, aggregator <span class="op">=</span> <span class="va">geomean</span>, signif <span class="op">=</span> <span class="fl">3</span>, value <span class="op">=</span> <span class="st">"Kfoc"</span>, raw <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">soil_N</span><span class="op">(</span><span class="va">chent</span>, aggregator <span class="op">=</span> <span class="va">mean</span>, signif <span class="op">=</span> <span class="fl">3</span>, raw <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">soil_sorption</span><span class="op">(</span></span>
<span>  <span class="va">chent</span>,</span>
<span>  values <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Kfoc"</span>, <span class="st">"N"</span><span class="op">)</span>,</span>
<span>  aggregators <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>Kfoc <span class="op">=</span> <span class="va">geomean</span>, Koc <span class="op">=</span> <span class="va">geomean</span>, N <span class="op">=</span> <span class="va">mean</span><span class="op">)</span>,</span>
<span>  signif <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>Kfoc <span class="op">=</span> <span class="fl">3</span>, N <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>,</span>
<span>  raw <span class="op">=</span> <span class="cn">FALSE</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div class="section level2">
    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
    <dl><dt>chent</dt>
<dd><p>The chent object to get the information from</p></dd>


<dt>medium</dt>
<dd><p>The medium for which information is sought</p></dd>


<dt>type</dt>
<dd><p>The information type</p></dd>


<dt>lab_field</dt>
<dd><p>If not NA, do we want laboratory or field endpoints</p></dd>


<dt>redox</dt>
<dd><p>If not NA, are we looking for aerobic or anaerobic data</p></dd>


<dt>value</dt>
<dd><p>The name of the value we want. The list given in the 
usage section is not exclusive</p></dd>


<dt>aggregator</dt>
<dd><p>The aggregator function. Can be mean, 
<code><a href="geomean.html">geomean</a></code>, or identity, for example.</p></dd>


<dt>raw</dt>
<dd><p>Should the number(s) be returned as stored in the chent
object (could be a character value) to retain original information
about precision?</p></dd>


<dt>signif</dt>
<dd><p>How many significant digits do we want</p></dd>


<dt>values</dt>
<dd><p>The values to be returned</p></dd>


<dt>aggregators</dt>
<dd><p>A named vector of aggregator functions to be used</p></dd>

</dl></div>
    <div class="section level2">
    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
    

<p>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.</p>
    </div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></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>

  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
    </nav></aside></div>


    <footer><div class="pkgdown-footer-left">
  <p></p><p>Developed by Johannes Ranke.</p>
</div>

<div class="pkgdown-footer-right">
  <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