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diff --git a/docs/endpoint.html b/docs/endpoint.html deleted file mode 100644 index 58696a9..0000000 --- a/docs/endpoint.html +++ /dev/null @@ -1,158 +0,0 @@ -<!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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