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, 8 insertions, 13 deletions

diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html
index 56d60c0..cf58a58 100644
--- a/docs/reference/one_box.html
+++ b/docs/reference/one_box.html
@@ -8,11 +8,13 @@
 
 <title>Create a time series of decline data — one_box • 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 -->
@@ -32,13 +34,14 @@
 
 
 
-<meta property="og:title" content="Create a time series of decline data — one_box" />
 
+<meta property="og:title" content="Create a time series of decline data — one_box" />
 <meta property="og:description" content="Create a time series of decline data" />
 <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>
@@ -82,7 +85,6 @@
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
@@ -104,9 +106,7 @@
     </div>
 
     <div class="ref-description">
-    
     <p>Create a time series of decline data</p>
-    
     </div>
 
     <pre class="usage"><span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>ini</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
@@ -115,13 +115,11 @@
 <span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
 
 <span class='co'># S3 method for character</span>
-<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>parms</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>,
-  <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
+<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>parms</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
 
 <span class='co'># S3 method for mkinfit</span>
-<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>,
-  <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)</pre>
-    
+<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</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>
@@ -158,11 +156,10 @@ all observed variables.</p></td>
       <td><p>A named numeric vector containing the model parameters</p></td>
     </tr>
     </table>
-    
+
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
     <p>An object of class <code>one_box</code>, inheriting from <code><a href='https://rdrr.io/r/stats/ts.html'>ts</a></code>.</p>
-    
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># Only use a half-life</span>
@@ -181,9 +178,7 @@ all observed variables.</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>