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authorJohannes Ranke <jranke@uni-bremen.de>2020-04-16 18:02:18 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-04-16 18:02:18 +0200
commitd81550d0cccae824cc748de48e7fd50ea8d8033a (patch)
treecb95252ff725b5dcd0237bb8f74fdac4a3e08d15 /docs/reference/PEC_sw_focus.html
parent4bc95b3e4aae22e4052e0a4c905a9227c909e2cd (diff)
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.
Diffstat (limited to 'docs/reference/PEC_sw_focus.html')
-rw-r--r--docs/reference/PEC_sw_focus.html42
1 files changed, 25 insertions, 17 deletions
diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html
index 1647b19..8242f6a 100644
--- a/docs/reference/PEC_sw_focus.html
+++ b/docs/reference/PEC_sw_focus.html
@@ -8,11 +8,13 @@
<title>Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • 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="Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus" />
+<meta property="og:title" content="Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus" />
<meta property="og:description" content="This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
authored by Michael Klein, in R. Note that results for multiple
applications should be compared to the corresponding results for a
@@ -45,6 +47,7 @@ to be used with the FOCUS calculator." />
+
<!-- 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>
@@ -88,7 +91,6 @@ to be used with the FOCUS calculator." />
<a href="../reference/index.html">Reference</a>
</li>
</ul>
-
<ul class="nav navbar-nav navbar-right">
</ul>
@@ -110,7 +112,6 @@ to be used with the FOCUS calculator." />
</div>
<div class="ref-description">
-
<p>This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
authored by Michael Klein, in R. Note that results for multiple
applications should be compared to the corresponding results for a
@@ -118,16 +119,28 @@ single application. At current, this is not done automatically in
this implementation. Only Step 1 PECs are calculated. However,
input files are generated that are suitable as input also for Step 2
to be used with the FOCUS calculator.</p>
-
</div>
- <pre class="usage"><span class='fu'>PEC_sw_focus</span>(<span class='no'>parent</span>, <span class='no'>rate</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>f_rd</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span>,
- <span class='kw'>region</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"n"</span>, <span class='st'>"s"</span>), <span class='kw'>season</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"of"</span>, <span class='st'>"mm"</span>, <span class='st'>"js"</span>),
- <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"no interception"</span>, <span class='st'>"minimal crop cover"</span>,
- <span class='st'>"average crop cover"</span>, <span class='st'>"full canopy"</span>), <span class='kw'>met_form_water</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>txt_file</span> <span class='kw'>=</span> <span class='st'>"pesticide.txt"</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
-
+ <pre class="usage"><span class='fu'>PEC_sw_focus</span>(
+ <span class='no'>parent</span>,
+ <span class='no'>rate</span>,
+ <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>,
+ <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+ <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>""</span>,
+ <span class='kw'>met</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+ <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+ <span class='kw'>f_rd</span> <span class='kw'>=</span> <span class='fl'>0.1</span>,
+ <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span>,
+ <span class='kw'>region</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"n"</span>, <span class='st'>"s"</span>),
+ <span class='kw'>season</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"of"</span>, <span class='st'>"mm"</span>, <span class='st'>"js"</span>),
+ <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"no interception"</span>, <span class='st'>"minimal crop cover"</span>, <span class='st'>"average crop cover"</span>,
+ <span class='st'>"full canopy"</span>),
+ <span class='kw'>met_form_water</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>txt_file</span> <span class='kw'>=</span> <span class='st'>"pesticide.txt"</span>,
+ <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>TRUE</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>
@@ -214,7 +227,7 @@ should be written</p></td>
<td><p>Should the input text file be appended?</p></td>
</tr>
</table>
-
+
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
<p>The formulas for input to the waterbody via runoff/drainage of the
@@ -224,7 +237,6 @@ should be written</p></td>
multiplying the application rate with the molar weight
correction and the formation fraction in water/sediment systems.</p>
<p>Step 2 is not implemented.</p>
-
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4).
@@ -233,7 +245,6 @@ should be written</p></td>
<p>Website of the Steps 1 and 2 calculator at the Joint Research
Center of the European Union:
http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p>
-
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Parent only</span>
@@ -337,11 +348,8 @@ should be written</p></td>
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
-
<li><a href="#note">Note</a></li>
-
<li><a href="#references">References</a></li>
-
<li><a href="#examples">Examples</a></li>
</ul>

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