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and some associated statistics. like maximum moving window average
concentrations, and dataframes holding the events exceeding specified
thresholds. Usually, an instance of this class will be generated
by read.TOXSWA_cwa."><meta property="og:description" content="An R6 class for holding TOXSWA water concentration (cwa) data
and some associated statistics. like maximum moving window average
concentrations, and dataframes holding the events exceeding specified
thresholds. Usually, an instance of this class will be generated
by read.TOXSWA_cwa."></head><body>
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<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/HEAD/R/TOXSWA_cwa.R" class="external-link"><code>R/TOXSWA_cwa.R</code></a></small>
<div class="d-none name"><code>TOXSWA_cwa.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>An R6 class for holding TOXSWA water concentration (cwa) data
and some associated statistics. like maximum moving window average
concentrations, and dataframes holding the events exceeding specified
thresholds. Usually, an instance of this class will be generated
by <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code>.</p>
</div>
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>An <code><a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6Class</a></code> generator object.</p>
</div>
<div class="section level2">
<h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2>
<p></p><div class="r6-fields"><dl><dt><code>filename</code></dt>
<dd><p>Length one character vector holding the filename.</p></dd>
<dt><code>basedir</code></dt>
<dd><p>Length one character vector holding the directory where the file came from.</p></dd>
<dt><code>zipfile</code></dt>
<dd><p>If not null, giving the path to the zip file from which the file was read.</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>substance</code></dt>
<dd><p>The TOXSWA name of the substance.</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><p></p></div>
</div>
<div class="section level2">
<h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2>
<div class="section">
<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3>
<ul><li><p><a href="#method-TOXSWA_cwa-new"><code>TOXSWA_cwa$new()</code></a></p></li>
<li><p><a href="#method-TOXSWA_cwa-moving_windows"><code>TOXSWA_cwa$moving_windows()</code></a></p></li>
<li><p><a href="#method-TOXSWA_cwa-get_events"><code>TOXSWA_cwa$get_events()</code></a></p></li>
<li><p><a href="#method-TOXSWA_cwa-print"><code>TOXSWA_cwa$print()</code></a></p></li>
<li><p><a href="#method-TOXSWA_cwa-clone"><code>TOXSWA_cwa$clone()</code></a></p></li>
</ul></div><p></p><hr><a id="method-TOXSWA_cwa-new"></a><div class="section">
<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3>
<p>Create a TOXSWA_cwa object from a file</p><div class="section">
<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/TOXSWA_cwa.html">TOXSWA_cwa</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span>
<span> <span class="va">filename</span>,</span>
<span> <span class="va">basedir</span>,</span>
<span> zipfile <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> segment <span class="op">=</span> <span class="st">"last"</span>,</span>
<span> substance <span class="op">=</span> <span class="st">"parent"</span>,</span>
<span> total <span class="op">=</span> <span class="cn">FALSE</span></span>
<span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4>
<p></p><div class="arguments"><dl><dt><code>filename</code></dt>
<dd><p>The filename</p></dd>
<dt><code>basedir</code></dt>
<dd><p>The directory to look in</p></dd>
<dt><code>zipfile</code></dt>
<dd><p>Optional path to a zipfile holding the file</p></dd>
<dt><code>segment</code></dt>
<dd><p>Either "last" or the number of the segment for which to read the data</p></dd>
<dt><code>substance</code></dt>
<dd><p>The TOXSWA substance name (for TOXSWA 4 or higher)</p></dd>
<dt><code>total</code></dt>
<dd><p>Should total concentrations be read in? If FALSE, free concentrations are read</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-TOXSWA_cwa-moving_windows"></a><div class="section">
<h3 id="method-moving-windows-">Method <code>moving_windows()</code><a class="anchor" aria-label="anchor" href="#method-moving-windows-"></a></h3>
<p>Add to the <code>windows</code> field described above.</p><div class="section">
<h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">moving_windows</span><span class="op">(</span><span class="va">windows</span>, total <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4>
<p></p><div class="arguments"><dl><dt><code>windows</code></dt>
<dd><p>Window sizes in days</p></dd>
<dt><code>total</code></dt>
<dd><p>If TRUE, the total concentration including the amount adsorbed to
suspended matter will be used.</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-TOXSWA_cwa-get_events"></a><div class="section">
<h3 id="method-get-events-">Method <code>get_events()</code><a class="anchor" aria-label="anchor" href="#method-get-events-"></a></h3>
<p>Populate a datataframe with event information for the specified
threshold value. The resulting dataframe is stored in the <code>events</code>
field of the object.</p><div class="section">
<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">get_events</span><span class="op">(</span><span class="va">thresholds</span>, total <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4>
<p></p><div class="arguments"><dl><dt><code>thresholds</code></dt>
<dd><p>Threshold values in µg/L.</p></dd>
<dt><code>total</code></dt>
<dd><p>If TRUE, the total concentration including the amount adsorbed to
suspended matter will be used.</p></dd>
</dl><p></p></div>
</div>
</div><p></p><hr><a id="method-TOXSWA_cwa-print"></a><div class="section">
<h3 id="method-print-">Method <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code><a class="anchor" aria-label="anchor" href="#method-print-"></a></h3>
<p>Print a <code>TOXSWA_cwa</code> object</p><div class="section">
<h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
</div><p></p><hr><a id="method-TOXSWA_cwa-clone"></a><div class="section">
<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3>
<p>The objects of this class are cloneable with this method.</p><div class="section">
<h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4>
<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div>
</div>
<div class="section">
<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4>
<p></p><div class="arguments"><dl><dt><code>deep</code></dt>
<dd><p>Whether to make a deep clone.</p></dd>
</dl><p></p></div>
</div>
</div>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_R1_stream</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00003s_pa.cwa"</span>,</span></span>
<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span>
<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>,</span></span>
<span class="r-in"><span> package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">H_sw_R1_stream</span><span class="op">$</span><span class="fu">get_events</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">H_sw_R1_stream</span><span class="op">$</span><span class="fu">moving_windows</span><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="fl">7</span>, <span class="fl">21</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">H_sw_R1_stream</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 </span>
<span class="r-out co"><span class="r-pr">#></span> datetime t t_firstjan t_rel_to_max cwa_mug_per_L</span>
<span class="r-out co"><span class="r-pr">#></span> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0</span>
<span class="r-out co"><span class="r-pr">#></span> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0</span>
<span class="r-out co"><span class="r-pr">#></span> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0</span>
<span class="r-out co"><span class="r-pr">#></span> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0</span>
<span class="r-out co"><span class="r-pr">#></span> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0</span>
<span class="r-out co"><span class="r-pr">#></span> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0</span>
<span class="r-out co"><span class="r-pr">#></span> cwa_tot_mug_per_L</span>
<span class="r-out co"><span class="r-pr">#></span> 20 0</span>
<span class="r-out co"><span class="r-pr">#></span> 40 0</span>
<span class="r-out co"><span class="r-pr">#></span> 60 0</span>
<span class="r-out co"><span class="r-pr">#></span> 80 0</span>
<span class="r-out co"><span class="r-pr">#></span> 100 0</span>
<span class="r-out co"><span class="r-pr">#></span> 120 0</span>
<span class="r-out co"><span class="r-pr">#></span> Moving window analysis</span>
<span class="r-out co"><span class="r-pr">#></span> window max_TWAC max_AUC_h max_AUC_d</span>
<span class="r-out co"><span class="r-pr">#></span> 1 7 days 2.3926551 401.9660 16.74859</span>
<span class="r-out co"><span class="r-pr">#></span> 2 21 days 0.8369248 421.8101 17.57542</span>
<span class="r-out co"><span class="r-pr">#></span> Event statistics for threshold 2 </span>
<span class="r-out co"><span class="r-pr">#></span> t_start cwa_max duration pre_interval AUC_h AUC_d</span>
<span class="r-out co"><span class="r-pr">#></span> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501</span>
<span class="r-out co"><span class="r-pr">#></span> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162</span>
<span class="r-out co"><span class="r-pr">#></span> Event statistics for threshold 10 </span>
<span class="r-out co"><span class="r-pr">#></span> t_start cwa_max duration pre_interval AUC_h AUC_d</span>
<span class="r-out co"><span class="r-pr">#></span> 1 55.083 40.58401 0.459 55.083 379.433 15.80971</span>
</code></pre></div>
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