From e3bc264df69f892e9ad990be22d3ec1b22041daa Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 17 Jun 2020 13:37:59 +0200
Subject: TSCF estimation equations, update docs

Briggs et al. (1982) and Dettenmaier et al. (2009)
---
 docs/reference/TOXSWA_cwa.html | 67 ++++++++++++++++++++----------------------
 1 file changed, 32 insertions(+), 35 deletions(-)

(limited to 'docs/reference/TOXSWA_cwa.html')

diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html
index cedb023..9f9e3c3 100644
--- a/docs/reference/TOXSWA_cwa.html
+++ b/docs/reference/TOXSWA_cwa.html
@@ -10,23 +10,27 @@
 
 
 <!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
 <!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -38,7 +42,6 @@
 <meta property="og:title" content="R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa" />
 <meta property="og:description" content="An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics.
 Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -56,7 +59,7 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
 
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -120,7 +123,7 @@ Usually, an instance of this class will be generated by <code><a href='read.TOXS
 
     
 
-<dl class='dl-horizontal'>
+<dl'>
   <dt><code>get_events(threshold, total = FALSE)</code></dt><dd><p>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
@@ -133,7 +136,7 @@ Usually, an instance of this class will be generated by <code><a href='read.TOXS
 
     <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
 
-    <p><div class="r6-fields"></p><dl class='dl-horizontal'>
+    <p><div class="r6-fields"></p><dl'>
 <dt><code>filename</code></dt><dd><p>Length one character vector.</p></dd>
 
 <dt><code>basedir</code></dt><dd><p>Length one character vector.</p></dd>
@@ -165,40 +168,40 @@ for the requested moving window sizes in days.</p></dd>
 <a id="method-new"></a></p><h3>Method <code>new()</code></h3>
 
 <h3>Usage</h3>
-<p><div class="r"></p><pre>TOXSWA_cwa$new(
-  filename,
-  basedir,
-  zipfile = NULL,
-  segment = "last",
-  substance = "parent",
-  total = FALSE
+<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>new</span>(
+  <span class='no'>filename</span>,
+  <span class='no'>basedir</span>,
+  <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+  <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>,
+  <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>,
+  <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
 )</pre><p></div></p>
 
 <p><hr>
 <a id="method-moving_windows"></a></p><h3>Method <code>moving_windows()</code></h3>
 
 <h3>Usage</h3>
-<p><div class="r"></p><pre>TOXSWA_cwa$moving_windows(windows, total = FALSE)</pre><p></div></p>
+<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>moving_windows</span>(<span class='no'>windows</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p>
 
 <p><hr>
 <a id="method-get_events"></a></p><h3>Method <code>get_events()</code></h3>
 
 <h3>Usage</h3>
-<p><div class="r"></p><pre>TOXSWA_cwa$get_events(thresholds, total = FALSE)</pre><p></div></p>
+<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>get_events</span>(<span class='no'>thresholds</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p>
 
 <p><hr>
 <a id="method-print"></a></p><h3>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></h3>
 
 <h3>Usage</h3>
-<p><div class="r"></p><pre>TOXSWA_cwa$print()</pre><p></div></p>
+<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>()</pre><p></div></p>
 
 <p><hr>
 <a id="method-clone"></a></p><h3>Method <code>clone()</code></h3>
 <p>The objects of this class are cloneable with this method.</p><h3>Usage</h3>
-<p><div class="r"></p><pre>TOXSWA_cwa$clone(deep = FALSE)</pre><p></div></p>
+<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>clone</span>(<span class='kw'>deep</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p>
 
 <h3>Arguments</h3>
-<p><div class="arguments"></p><dl class='dl-horizontal'>
+<p><div class="arguments"></p><dl'>
 <dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
 
 </dl><p></div></p>
@@ -239,16 +242,10 @@ for the requested moving window sizes in days.</p></dd>
 #&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="#methods">Methods</a></li>
-      <li><a href="#public-fields">Public fields</a></li>
-      <li><a href="#methods">Methods</a></li>
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
   </div>
 </div>
 
@@ -259,7 +256,7 @@ for the requested moving window sizes in days.</p></dd>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>
-- 
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