Update docs, use R6 support of roxygen

1 files changed, 53 insertions, 29 deletions

diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html
index 9f9e3c3..16dc5db 100644
--- a/docs/reference/TOXSWA_cwa.html
+++ b/docs/reference/TOXSWA_cwa.html
@@ -40,8 +40,11 @@
 
 
 <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 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." />
 
 
 
@@ -110,8 +113,11 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
     </div>
 
     <div class="ref-description">
-    <p>An R6 class for holding TOXSWA water concentration (cwa) 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>
+    <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>
 
 
@@ -119,30 +125,19 @@ Usually, an instance of this class will be generated by <code><a href='read.TOXS
     <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="methods"><a class="anchor" href="#methods"></a>Methods</h2>
-
-    
-
-<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
-        <code>events</code> field of the object.</p></dd>
-  <dt><code>moving_windows(windows, total = FALSE)</code></dt><dd><p>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.</p></dd>
-
-</dl>
-
     <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2>
 
     <p><div class="r6-fields"></p><dl'>
-<dt><code>filename</code></dt><dd><p>Length one character vector.</p></dd>
+<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.</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>
@@ -166,8 +161,7 @@ for the requested moving window sizes in days.</p></dd>
 </ul>
 <p><hr>
 <a id="method-new"></a></p><h3>Method <code>new()</code></h3>
-
-<h3>Usage</h3>
+<p>Create a TOXSWA_cwa object from a file</p><h3>Usage</h3>
 <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>,
@@ -177,22 +171,52 @@ for the requested moving window sizes in days.</p></dd>
   <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
 )</pre><p></div></p>
 
+<h3>Arguments</h3>
+<p><div class="arguments"></p><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></div></p>
 <p><hr>
 <a id="method-moving_windows"></a></p><h3>Method <code>moving_windows()</code></h3>
-
-<h3>Usage</h3>
+<p>Add to the `windows` field described above.</p><h3>Usage</h3>
 <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>
 
+<h3>Arguments</h3>
+<p><div class="arguments"></p><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></div></p>
 <p><hr>
 <a id="method-get_events"></a></p><h3>Method <code>get_events()</code></h3>
-
-<h3>Usage</h3>
+<p>Populate a datataframe with event information for the specified
+threshold value.  The resulting dataframe is stored in the `events`
+field of the object.</p><h3>Usage</h3>
 <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>
 
+<h3>Arguments</h3>
+<p><div class="arguments"></p><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></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>Print a `TOXSWA_cwa` object</p><h3>Usage</h3>
 <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>