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| author | Johannes Ranke <jranke@uni-bremen.de> | 2017-01-18 22:41:01 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2017-01-18 22:50:14 +0100 |
| commit | a76221d87485029444c8e684022ca606a0c7e68d (patch) | |
| tree | c95052ee51b35f6c5ab87bd6f27ef2877f536838 /docs/reference/TOXSWA_cwa.html | |
| parent | a1d9f93138c2cfed92a683e37e72c737d52b7ad7 (diff) | |
Update static docs using pkgdown
- Add _pkgdown.yml for a structured function/data reference
- Make seealso links active
- Make mkinfit calls quiet
- Use pkgdown branch from pull request hadley/pkgdown#229 to have topics
ordered
Diffstat (limited to 'docs/reference/TOXSWA_cwa.html')
| -rw-r--r-- | docs/reference/TOXSWA_cwa.html | 178 |
1 files changed, 178 insertions, 0 deletions
diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html new file mode 100644 index 0000000..3f9310a --- /dev/null +++ b/docs/reference/TOXSWA_cwa.html @@ -0,0 +1,178 @@ +<!-- 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>R6 class for holding TOXSWA cwa concentration data and associated statistics — TOXSWA_cwa • 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"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/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-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"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </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 cwa concentration data and associated statistics</h1> + </div> + + + <p>An R6 class for holding TOXSWA cwa concentration 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> + + + <pre><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> + + <p></p> + <p><dl class='dl-horizontal'> +<dt><code>filename</code></dt><dd>Length one character vector.</dd></p> + <p><dt><code>basedir</code></dt><dd>Length one character vector.</dd></p> + <p><dt><code>segment</code></dt><dd>Length one integer, specifying for which segment the cwa data were read.</dd></p> + <p><dt><code>cwas</code></dt><dd>Dataframe holding the concentrations.</dd></p> + <p><dt><code>events</code></dt><dd>List of dataframes holding the event statistics for each threshold.</dd></p> + <p><dt><code>windows</code></dt><dd>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.</dd> +</dl></p> + + <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> + + <p></p> + <p><dl class='dl-horizontal'> + <dt><code>get_events(threshold, total = FALSE)</code></dt><dd> + 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. + </dd> + <dt><code>moving_windows(windows, total = FALSE)</code></dt><dd> + 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. + </dd> +</dl></p> + + + <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'>system.file</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>$<span class='fu'>get_events</span>(<span class='fu'>c</span>(<span class='fl'>2</span>, <span class='fl'>10</span>)) +<span class='no'>H_sw_R1_stream</span>$<span class='fu'>moving_windows</span>(<span class='fu'>c</span>(<span class='fl'>7</span>, <span class='fl'>21</span>)) +<span class='fu'>print</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="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> |