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
|
<!-- 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>R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • 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="R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa" />
<meta property="og:description" content="An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics.
Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
<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>R6 class for holding TOXSWA water concentration data and associated statistics</h1>
<small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/TOXSWA_cwa.R'><code>R/TOXSWA_cwa.R</code></a></small>
<div class="hidden name"><code>TOXSWA_cwa.Rd</code></div>
</div>
<div class="ref-description">
<p>An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics.
Usually, an instance of this class will be generated by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p>
</div>
<pre class="usage"><span class='no'>TOXSWA_cwa</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>An <code>R6Class</code> generator object.</p>
<h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
<dl class='dl-horizontal'>
<dt><code>filename</code></dt><dd><p>Length one character vector.</p></dd>
<dt><code>basedir</code></dt><dd><p>Length one character vector.</p></dd>
<dt><code>segment</code></dt><dd><p>Length one integer, specifying for which segment the cwa data were read.</p></dd>
<dt><code>cwas</code></dt><dd><p>Dataframe holding the concentrations.</p></dd>
<dt><code>events</code></dt><dd><p>List of dataframes holding the event statistics for each threshold.</p></dd>
<dt><code>windows</code></dt><dd><p>Matrix of maximum time weighted average concentrations (TWAC_max)
and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d)
for the requested moving window sizes in days.</p></dd>
</dl>
<h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
<dl class='dl-horizontal'>
<dt><code>get_events(threshold, total = FALSE)</code></dt><dd><p>Populate a datataframe with event information for the specified threshold value
in µg/L. If <code>total = TRUE</code>, the total concentration including the amount
adsorbed to suspended matter will be used. The resulting dataframe is stored in the
<code>events</code> field of the object.</p></dd>
<dt><code>moving_windows(windows, total = FALSE)</code></dt><dd><p>Add to the <code>windows</code> field described above.
Again, if <code>total = TRUE</code>, the total concentration including the amount
adsorbed to suspended matter will be used.</p></dd>
</dl>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>H_sw_R1_stream</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>,
<span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>,
<span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.file'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>,
<span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))
<span class='no'>H_sw_R1_stream</span>$<span class='fu'>get_events</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>2</span>, <span class='fl'>10</span>))
<span class='no'>H_sw_R1_stream</span>$<span class='fu'>moving_windows</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>7</span>, <span class='fl'>21</span>))
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>H_sw_R1_stream</span>)</div><div class='output co'>#> <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20
#> datetime t t_firstjan t_rel_to_max cwa_mug_per_L
#> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0
#> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0
#> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0
#> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0
#> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0
#> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0
#> cwa_tot_mug_per_L
#> 20 0
#> 40 0
#> 60 0
#> 80 0
#> 100 0
#> 120 0
#> Moving window analysis
#> window max_TWAC max_AUC_h max_AUC_d
#> 1 7 days 2.3926551 401.9660 16.74859
#> 2 21 days 0.8369248 421.8101 17.57542
#> Event statistics for threshold 2
#> t_start cwa_max duration pre_interval AUC_h AUC_d
#> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501
#> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162
#> Event statistics for threshold 10
#> t_start cwa_max duration pre_interval AUC_h AUC_d
#> 1 55.083 40.58401 0.459 55.083 379.433 15.80971</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="#format">Format</a></li>
<li><a href="#fields">Fields</a></li>
<li><a href="#methods">Methods</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>
|
