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, 14 insertions, 10 deletions

diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html
index 7e4eab1..d2e62f6 100644
--- a/docs/reference/pfm_degradation.html
+++ b/docs/reference/pfm_degradation.html
@@ -8,11 +8,13 @@
 
 <title>Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation • 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 -->
 
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+
 <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 -->
@@ -32,13 +34,14 @@
 
 
 
-<meta property="og:title" content="Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation" />
 
+<meta property="og:title" content="Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation" />
 <meta property="og:description" content="Calculate a time course of relative concentrations based on an mkinmod model" />
 <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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@@ -82,7 +85,6 @@
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
@@ -104,15 +106,18 @@
     </div>
 
     <div class="ref-description">
-    
     <p>Calculate a time course of relative concentrations based on an mkinmod model</p>
-    
     </div>
 
-    <pre class="usage"><span class='fu'>pfm_degradation</span>(<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span>
-  <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>), <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>,
-  <span class='kw'>by</span> <span class='kw'>=</span> <span class='no'>step_days</span>))</pre>
-    
+    <pre class="usage"><span class='fu'>pfm_degradation</span>(
+  <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>,
+  <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>,
+  <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>),
+  <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>,
+  <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>,
+  <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='no'>step_days</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>
@@ -143,7 +148,7 @@ is calculated (SFO model).</p></td>
       <td><p>The output times</p></td>
     </tr>
     </table>
-    
+
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>pfm_degradation</span>(<span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>10</span>))</div><div class='output co'>#&gt;   time    parent
@@ -158,7 +163,6 @@ is calculated (SFO model).</p></td>
     <h2>Contents</h2>
     <ul class="nav nav-pills nav-stacked">
       <li><a href="#arguments">Arguments</a></li>
-            
       <li><a href="#examples">Examples</a></li>
     </ul>