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| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-09-27 23:00:48 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-09-27 23:00:48 +0200 |
| commit | 12a31f4c130c551f82232d9ef7dfb608bd52c53f (patch) | |
| tree | 2525ab1ea4102a6edddbd0c2f03f4a851bf2f9c5 /docs/endpoint.html | |
| parent | 0d958ab6f84b569b5437f231c56004890c4ae23b (diff) | |
Reorganise repository using standard package layout
Diffstat (limited to 'docs/endpoint.html')
| -rw-r--r-- | docs/endpoint.html | 158 |
1 files changed, 158 insertions, 0 deletions
diff --git a/docs/endpoint.html b/docs/endpoint.html new file mode 100644 index 0000000..58696a9 --- /dev/null +++ b/docs/endpoint.html @@ -0,0 +1,158 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>endpoint. pfm 0.3-8</title> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<meta name="author" content=""> + +<link href="css/bootstrap.css" rel="stylesheet"> +<link href="css/bootstrap-responsive.css" rel="stylesheet"> +<link href="css/highlight.css" rel="stylesheet"> +<link href="css/staticdocs.css" rel="stylesheet"> + +<!--[if lt IE 9]> + <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> +<![endif]--> + +<script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + processEscapes: true + } + }); +</script> +<script type="text/javascript" + src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> +</script> + </head> + + <body> + <div class="navbar"> + <div class="navbar-inner"> + <div class="container"> + <a class="brand" href="index.html">pfm 0.3-8</a> + <div class="nav"> + <ul class="nav"> + <li><a href="index.html">Home</a></li> + <li><a href="reference.html">Reference</a></li> + </ul> + </div> + </div> + </div> +</div> + + + <div class="container"> + <header> + + </header> + + <h1>Retrieve endpoint information from the chyaml field of a chent object</h1> + +<div class="row"> + <div class="span8"> + <h2>Usage</h2> + <pre><span class="functioncall"><a href='endpoint.html'>endpoint</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">medium</span> <span class="argument">=</span> <span class="string">"soil"</span><span class="keyword">,</span> <span class="argument">type</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"degradation"</span><span class="keyword">,</span> <span class="string">"sorption"</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">lab_field</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">NA</span><span class="keyword">,</span> <span class="string">"laboratory"</span><span class="keyword">,</span> <span class="string">"field"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">redox</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">NA</span><span class="keyword">,</span> <span class="string">"aerobic"</span><span class="keyword">,</span> + <span class="string">"anaerobic"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">value</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"DT50ref"</span><span class="keyword">,</span> <span class="string">"Kfoc"</span><span class="keyword">,</span> <span class="string">"N"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">aggregator</span> <span class="argument">=</span> <span class="symbol">geomean</span><span class="keyword">,</span> + <span class="argument">raw</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">signif</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">)</span> + +<span class="functioncall"><a href='endpoint.html'>soil_DT50</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">aggregator</span> <span class="argument">=</span> <span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">signif</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">,</span> + <span class="argument">lab_field</span> <span class="argument">=</span> <span class="string">"laboratory"</span><span class="keyword">,</span> <span class="argument">value</span> <span class="argument">=</span> <span class="string">"DT50ref"</span><span class="keyword">,</span> <span class="argument">redox</span> <span class="argument">=</span> <span class="string">"aerobic"</span><span class="keyword">,</span> + <span class="argument">raw</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span> + +<span class="functioncall"><a href='endpoint.html'>soil_Kfoc</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">aggregator</span> <span class="argument">=</span> <span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">signif</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">,</span> <span class="argument">value</span> <span class="argument">=</span> <span class="string">"Kfoc"</span><span class="keyword">,</span> + <span class="argument">raw</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span> + +<span class="functioncall"><a href='endpoint.html'>soil_N</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">aggregator</span> <span class="argument">=</span> <span class="symbol">mean</span><span class="keyword">,</span> <span class="argument">signif</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">,</span> <span class="argument">raw</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span> + +<span class="functioncall"><a href='endpoint.html'>soil_sorption</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">values</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"Kfoc"</span><span class="keyword">,</span> <span class="string">"N"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">aggregators</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">Kfoc</span> <span class="argument">=</span> + <span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">Koc</span> <span class="argument">=</span> <span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">N</span> <span class="argument">=</span> <span class="symbol">mean</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">signif</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">Kfoc</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">,</span> <span class="argument">N</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">)</span><span class="keyword">,</span> + <span class="argument">raw</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span></pre> + + <h2>Arguments</h2> + <dl> + <dt>chent</dt> + <dd>The chent object to get the information from</dd> + <dt>medium</dt> + <dd>The medium for which information is sought</dd> + <dt>type</dt> + <dd>The information type</dd> + <dt>lab_field</dt> + <dd>If not NA, do we want laboratory or field endpoints</dd> + <dt>redox</dt> + <dd>If not NA, are we looking for aerobic or anaerobic data</dd> + <dt>value</dt> + <dd>The name of the value we want. The list given in the +usage section is not exclusive</dd> + <dt>aggregator</dt> + <dd>The aggregator function. Can be mean, +<code><a href='geomean.html'>geomean</a></code>, or identity, for example.</dd> + <dt>raw</dt> + <dd>Should the number(s) be returned as stored in the chent +object (could be a character value) to retain original information +about precision?</dd> + <dt>signif</dt> + <dd>How many significant digits do we want</dd> + <dt>values</dt> + <dd>The values to be returned</dd> + <dt>aggregators</dt> + <dd>A named vector of aggregator functions to be used</dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p><dl> +The result from applying the aggregator function to + the values converted to a numeric vector, rounded to the + given number of significant digits, or, if raw = TRUE, + the values as a character value, retaining any implicit + information on precision that may be present. +</dl></p> + + </div> + + <div class="Description"> + <h2>Description</h2> + + <p>R6 class objects of class chent represent chemical entities +and can hold a list of information loaded from a chemical yaml file in their +chyaml field. Such information is extracted and optionally aggregated by +this function.</p> + + </div> + + <div class="Details"> + <h2>Details</h2> + + <p>The functions <code>soil_*</code> are functions to extract soil specific endpoints. +For the Freundlich exponent, the capital letter <code>N</code> is used in order to +facilitate dealing with such data in R. In pesticide fate modelling, this +exponent is often called 1/n.</p> + + </div> + </div> + <div class="span4 sidebar"> + <!-- <ul> + <li>endpoint</li><li>soil_DT50</li><li>soil_Kfoc</li><li>soil_N</li><li>soil_sorption</li> + </ul> + <ul> + + </ul> --> + + + + + </div> +</div> + + <footer> + <p class="pull-right"><a href="#">Back to top</a></p> +<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> + </footer> + </div> + </body> +</html>
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