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Usually, an instance of this class will be generated -by read.TOXSWA_cwa."><!-- 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> +by read.TOXSWA_cwa."></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"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><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="">0.6.1</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</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 class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/pfm/" aria-label="GitHub"><span class="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>R6 class for holding TOXSWA water concentration data and associated statistics</h1> + + <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> @@ -55,13 +52,13 @@ by read.TOXSWA_cwa."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/a 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> +by <a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a>.</p> </div> <div class="section level2"> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> - <p>An <code>R6Class</code> generator object.</p> + <p>An <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6::R6Class</a> 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> @@ -69,31 +66,31 @@ by <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code>.</p> <dd><p>Length one character vector holding the filename.</p></dd> -<dt><code>basedir</code></dt> + <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> + <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> + <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> + <dt><code>substance</code></dt> <dd><p>The TOXSWA name of the substance.</p></dd> -<dt><code>cwas</code></dt> + <dt><code>cwas</code></dt> <dd><p>Dataframe holding the concentrations.</p></dd> -<dt><code>events</code></dt> + <dt><code>events</code></dt> <dd><p>List of dataframes holding the event statistics for each threshold.</p></dd> -<dt><code>windows</code></dt> + <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> @@ -103,17 +100,16 @@ for the requested moving window sizes in days.</p></dd> </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$new()</code></a></p></li> +<p></p><ul><li><p><a href="#method-TOXSWA_cwa-initialize"><code>TOXSWA_cwa$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> +</ul></div><p></p><hr><a id="method-TOXSWA_cwa-initialize"></a><div class="section"> +<h3 id="toxswa-cwa-new-"><code>TOXSWA_cwa$new()</code><a class="anchor" aria-label="anchor" href="#toxswa-cwa-new-"></a></h3> <p>Create a TOXSWA_cwa object from a file</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/TOXSWA_cwa.html">TOXSWA_cwa</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> @@ -124,51 +120,43 @@ for the requested moving window sizes in days.</p></dd> <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"> +</div><p></p><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> + <dt><code>basedir</code></dt> <dd><p>The directory to look in</p></dd> - -<dt><code>zipfile</code></dt> + <dt><code>zipfile</code></dt> <dd><p>Optional path to a zipfile holding the file</p></dd> - -<dt><code>segment</code></dt> + <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> + <dt><code>substance</code></dt> <dd><p>The TOXSWA substance name (for TOXSWA 4 or higher)</p></dd> - -<dt><code>total</code></dt> + <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> +</div> + +<p></p><hr><a id="method-TOXSWA_cwa-moving_windows"></a><div class="section"> +<h3 id="toxswa-cwa-moving-windows-"><code>TOXSWA_cwa$moving_windows()</code><a class="anchor" aria-label="anchor" href="#toxswa-cwa-moving-windows-"></a></h3> <p>Add to the <code>windows</code> field described above.</p><div class="section"> <h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</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"> +</div><p></p><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> + <dt><code>total</code></dt> <dd><p>If TRUE, the total concentration including the amount adsorbed to suspended matter will be used.</p></dd> @@ -176,22 +164,21 @@ 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> +</div> + +<p></p><hr><a id="method-TOXSWA_cwa-get_events"></a><div class="section"> +<h3 id="toxswa-cwa-get-events-"><code>TOXSWA_cwa$get_events()</code><a class="anchor" aria-label="anchor" href="#toxswa-cwa-get-events-"></a></h3> <p>Populate a datataframe with event information for the specified threshold value. The resulting dataframe is stored in the <code>events</code> field of the object.</p><div class="section"> <h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</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"> +</div><p></p><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> + <dt><code>total</code></dt> <dd><p>If TRUE, the total concentration including the amount adsorbed to suspended matter will be used.</p></dd> @@ -199,22 +186,23 @@ 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> +</div> + +<p></p><hr><a id="method-TOXSWA_cwa-print"></a><div class="section"> +<h3 id="toxswa-cwa-print-"><code>TOXSWA_cwa$print()</code><a class="anchor" aria-label="anchor" href="#toxswa-cwa-print-"></a></h3> <p>Print a <code>TOXSWA_cwa</code> object</p><div class="section"> <h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> +</div> -</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></p><hr><a id="method-TOXSWA_cwa-clone"></a><div class="section"> +<h3 id="toxswa-cwa-clone-"><code>TOXSWA_cwa$clone()</code><a class="anchor" aria-label="anchor" href="#toxswa-cwa-clone-"></a></h3> <p>The objects of this class are cloneable with this method.</p><div class="section"> <h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</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"> +</div><p></p><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> @@ -225,6 +213,7 @@ suspended matter will be used.</p></dd> </div> + </div> <div class="section level2"> @@ -264,23 +253,23 @@ suspended matter will be used.</p></dd> <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> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - <p></p><p>Developed by Johannes Ranke.</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> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> - - + + </body></html> |