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diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index f620349..48e6b44 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa"><meta name="description" content="An R6 class for holding TOXSWA water concentration (cwa) data +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa"><meta name="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 @@ -15,7 +21,7 @@ by read.TOXSWA_cwa."></head><body> <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="">0.6.3</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"> @@ -46,13 +52,13 @@ by read.TOXSWA_cwa."></head><body> 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><a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6Class</a></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> @@ -60,31 +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> @@ -97,14 +103,13 @@ for the requested moving window sizes in days.</p></dd> <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> @@ -115,51 +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> @@ -167,22 +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> @@ -190,22 +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> @@ -216,6 +213,7 @@ suspended matter will be used.</p></dd> </div> + </div> <div class="section level2"> @@ -264,7 +262,7 @@ suspended matter will be used.</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> |