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authorJohannes Ranke <jranke@uni-bremen.de>2017-01-18 22:41:01 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2017-01-18 22:50:14 +0100
commita76221d87485029444c8e684022ca606a0c7e68d (patch)
treec95052ee51b35f6c5ab87bd6f27ef2877f536838 /docs/reference/TOXSWA_cwa.html
parenta1d9f93138c2cfed92a683e37e72c737d52b7ad7 (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
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+ <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'>&lt;-</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'>#&gt; &lt;TOXSWA_cwa&gt; data from file 00003s_pa.cwa segment 20
+#&gt; datetime t t_firstjan t_rel_to_max cwa_mug_per_L
+#&gt; 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0
+#&gt; 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0
+#&gt; 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0
+#&gt; 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0
+#&gt; 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0
+#&gt; 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0
+#&gt; cwa_tot_mug_per_L
+#&gt; 20 0
+#&gt; 40 0
+#&gt; 60 0
+#&gt; 80 0
+#&gt; 100 0
+#&gt; 120 0
+#&gt; Moving window analysis
+#&gt; window max_TWAC max_AUC_h max_AUC_d
+#&gt; 1 7 days 2.3926551 401.9660 16.74859
+#&gt; 2 21 days 0.8369248 421.8101 17.57542
+#&gt; Event statistics for threshold 2
+#&gt; t_start cwa_max duration pre_interval AUC_h AUC_d
+#&gt; 1 44.375 4.167238 0.208 44.375 17.77202 0.740501
+#&gt; 2 55.042 40.584010 0.583 10.459 398.21189 16.592162
+#&gt; Event statistics for threshold 10
+#&gt; t_start cwa_max duration pre_interval AUC_h AUC_d
+#&gt; 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>
+
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