Make na.rm = FALSE the default for geomean()

This makes more sense and is in line with mean() from base R. Adapt
tests and update docs.

1 files changed, 72 insertions, 25 deletions

diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html
index 8939850..cedb023 100644
--- a/docs/reference/TOXSWA_cwa.html
+++ b/docs/reference/TOXSWA_cwa.html
@@ -8,11 +8,13 @@
 
 <title>R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm</title>
 
+
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 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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@@ -32,14 +34,15 @@
 
 
 
-<meta property="og:title" content="R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa" />
 
+<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" />
 
 
 
+
 <!-- mathjax -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@@ -83,7 +86,6 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
@@ -105,23 +107,33 @@ 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>
-    
     </div>
 
-    <pre class="usage"><span class='no'>TOXSWA_cwa</span></pre>
-        
+
+
     <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="fields"><a class="anchor" href="#fields"></a>Fields</h2>
+    <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
 
     
 
 <dl class='dl-horizontal'>
+  <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 class='dl-horizontal'>
 <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>
@@ -136,24 +148,62 @@ Usually, an instance of this class will be generated by <code><a href='read.TOXS
 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>
-    
+</dl><p></div></p>
     <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
 
     
+<h3>Public methods</h3>
 
-<dl class='dl-horizontal'>
-  <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>
+<ul>
+<li><p><a href='#method-new'><code>TOXSWA_cwa$new()</code></a></p></li>
+<li><p><a href='#method-moving_windows'><code>TOXSWA_cwa$moving_windows()</code></a></p></li>
+<li><p><a href='#method-get_events'><code>TOXSWA_cwa$get_events()</code></a></p></li>
+<li><p><a href='#method-print'><code>TOXSWA_cwa$print()</code></a></p></li>
+<li><p><a href='#method-clone'><code>TOXSWA_cwa$clone()</code></a></p></li>
+</ul>
+<p><hr>
+<a id="method-new"></a></p><h3>Method <code>new()</code></h3>
+
+<h3>Usage</h3>
+<p><div class="r"></p><pre>TOXSWA_cwa$new(
+  filename,
+  basedir,
+  zipfile = NULL,
+  segment = "last",
+  substance = "parent",
+  total = FALSE
+)</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$moving_windows(windows, total = FALSE)</pre><p></div></p>
+
+<p><hr>
+<a id="method-get_events"></a></p><h3>Method <code>get_events()</code></h3>
+
+<h3>Usage</h3>
+<p><div class="r"></p><pre>TOXSWA_cwa$get_events(thresholds, total = FALSE)</pre><p></div></p>
+
+<p><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$print()</pre><p></div></p>
+
+<p><hr>
+<a id="method-clone"></a></p><h3>Method <code>clone()</code></h3>
+<p>The objects of this class are cloneable with this method.</p><h3>Usage</h3>
+<p><div class="r"></p><pre>TOXSWA_cwa$clone(deep = FALSE)</pre><p></div></p>
+
+<h3>Arguments</h3>
+<p><div class="arguments"></p><dl class='dl-horizontal'>
+<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
+
+</dl><p></div></p>
 
-</dl>
 
-    
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='no'>H_sw_R1_stream</span>  <span class='kw'>&lt;-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>,
@@ -192,13 +242,10 @@ for the requested moving window sizes in days.</p></dd>
   <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="#fields">Fields</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>