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, 16 insertions, 12 deletions

diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html
index df84634..9c5c2a0 100644
--- a/docs/reference/read.TOXSWA_cwa.html
+++ b/docs/reference/read.TOXSWA_cwa.html
@@ -8,11 +8,13 @@
 
 <title>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • pfm</title>
 
+
 <!-- jquery -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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" />
+
 <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
 
 <!-- Font Awesome icons -->
@@ -32,8 +34,8 @@
 
 
 
-<meta property="og:title" content="Read TOXSWA surface water concentrations — read.TOXSWA_cwa" />
 
+<meta property="og:title" content="Read TOXSWA surface water concentrations — read.TOXSWA_cwa" />
 <meta property="og:description" content="Read TOXSWA hourly concentrations of a chemical substance in a specific
 segment of a TOXSWA surface water body. Per default, the data for the last
 segment are imported. As TOXSWA 4 reports the values at the end of the hour
@@ -44,6 +46,7 @@ renamed to ConLiqWatLay in the out file." />
 
 
 
+
 <!-- 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>
@@ -87,7 +90,6 @@ renamed to ConLiqWatLay in the out file." />
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
@@ -109,20 +111,25 @@ renamed to ConLiqWatLay in the out file." />
     </div>
 
     <div class="ref-description">
-    
     <p>Read TOXSWA hourly concentrations of a chemical substance in a specific
 segment of a TOXSWA surface water body. Per default, the data for the last
 segment are imported. As TOXSWA 4 reports the values at the end of the hour
 (ConLiqWatLayCur) in its summary file, we use this value as well instead
 of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was
 renamed to ConLiqWatLay in the out file.</p>
-    
     </div>
 
-    <pre class="usage"><span class='fu'>read.TOXSWA_cwa</span>(<span class='no'>filename</span>, <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"."</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>,
-  <span class='kw'>windows</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>thresholds</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-    
+    <pre class="usage"><span class='fu'>read.TOXSWA_cwa</span>(
+  <span class='no'>filename</span>,
+  <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"."</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>,
+  <span class='kw'>windows</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+  <span class='kw'>thresholds</span> <span class='kw'>=</span> <span class='kw'>NULL</span>
+)</pre>
+
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
@@ -167,12 +174,11 @@ maximum time weighted average concentrations and areas under the curve.</p></td>
 generating event statistics.</p></td>
     </tr>
     </table>
-    
+
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>An instance of an R6 object of class
 <code><a href='TOXSWA_cwa.html'>TOXSWA_cwa</a></code>.</p>
-    
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span>  <span class='kw'>&lt;-</span> <span class='fu'>read.TOXSWA_cwa</span>(<span class='st'>"00001p_pa.cwa"</span>,
@@ -184,9 +190,7 @@ generating event statistics.</p></td>
     <h2>Contents</h2>
     <ul class="nav nav-pills nav-stacked">
       <li><a href="#arguments">Arguments</a></li>
-      
       <li><a href="#value">Value</a></li>
-      
       <li><a href="#examples">Examples</a></li>
     </ul>