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, 15 insertions, 12 deletions

diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html
index fe65d96..458eeb7 100644
--- a/docs/reference/PEC_sw_sed.html
+++ b/docs/reference/PEC_sw_sed.html
@@ -9,11 +9,13 @@
 <title>Calculate predicted environmental concentrations in sediment from surface
 water concentrations — PEC_sw_sed • 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 -->
@@ -33,15 +35,16 @@ water concentrations — PEC_sw_sed • pfm</title>
 
 
 
+
 <meta property="og:title" content="Calculate predicted environmental concentrations in sediment from surface
 water concentrations — PEC_sw_sed" />
-
 <meta property="og:description" content="The method 'percentage' is equivalent to what is used in the CRD spreadsheet
 PEC calculator" />
 <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>
 <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>
@@ -85,7 +88,6 @@ PEC calculator" />
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
@@ -108,16 +110,20 @@ water concentrations</h1>
     </div>
 
     <div class="ref-description">
-    
     <p>The method 'percentage' is equivalent to what is used in the CRD spreadsheet
 PEC calculator</p>
-    
     </div>
 
-    <pre class="usage"><span class='fu'>PEC_sw_sed</span>(<span class='no'>PEC_sw</span>, <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"percentage"</span>,
-  <span class='kw'>sediment_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>sediment_density</span> <span class='kw'>=</span> <span class='fl'>1.3</span>,
-  <span class='kw'>PEC_sed_units</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"µg/kg"</span>, <span class='st'>"mg/kg"</span>))</pre>
-    
+    <pre class="usage"><span class='fu'>PEC_sw_sed</span>(
+  <span class='no'>PEC_sw</span>,
+  <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>100</span>,
+  <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"percentage"</span>,
+  <span class='kw'>sediment_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>,
+  <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>,
+  <span class='kw'>sediment_density</span> <span class='kw'>=</span> <span class='fl'>1.3</span>,
+  <span class='kw'>PEC_sed_units</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"µg/kg"</span>, <span class='st'>"mg/kg"</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>
@@ -152,11 +158,10 @@ g/cm3)</p></td>
       <td><p>The units of the estimated sediment PEC value</p></td>
     </tr>
     </table>
-    
+
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>The predicted concentration in sediment</p>
-    
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='fu'>PEC_sw_sed</span>(<span class='fu'><a href='PEC_sw_drift.html'>PEC_sw_drift</a></span>(<span class='fl'>100</span>, <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fl'>1</span>), <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>50</span>)</div><div class='output co'>#&gt;      1 m 
@@ -166,9 +171,7 @@ g/cm3)</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>