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| author | Johannes Ranke <jranke@uni-bremen.de> | 2015-12-22 19:32:54 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2015-12-22 19:32:54 +0100 |
| commit | 3a579d87820ccbec514f1be5eb090e874fd87eec (patch) | |
| tree | fdc726d4938dc98fc741a38435372da22dc9e956 /pkg/inst/web/endpoint.html | |
| parent | 9851a97ec915ddbfc8357f1a7e2cabae56c89f7d (diff) | |
EFSA 2015 tier 1 PEC soil, clean up, add static docs
Diffstat (limited to 'pkg/inst/web/endpoint.html')
| -rw-r--r-- | pkg/inst/web/endpoint.html | 142 |
1 files changed, 142 insertions, 0 deletions
diff --git a/pkg/inst/web/endpoint.html b/pkg/inst/web/endpoint.html new file mode 100644 index 0000000..0789d95 --- /dev/null +++ b/pkg/inst/web/endpoint.html @@ -0,0 +1,142 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>endpoint. pfm 0.3-1</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="#">pfm 0.3-1</a> + <div class="nav"> + <ul class="nav"> + <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>endpoint(chent, medium = "soil", type = c("degradation", "sorption"), lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic", "anaerobic"), value = c("DT50ref", "Kfoc", "N"), aggregator = geomean, raw = FALSE, signif = 3)</div> +<div>soil_DT50(chent, aggregator = geomean, signif = 3, lab_field = "laboratory", value = "DT50ref", redox = "aerobic", raw = FALSE)</div> +<div>soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)</div> +<div>soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)</div> +<div>soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = rep(3, length(values)), raw = FALSE)</div></pre> + + <h2>Arguments</h2> + <dl> + <dt>chent</dt> + <dd>The <code><a href='http://www.inside-r.org/packages/cran/chents/docs/chent'>chent</a></code> 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 <code><a href='http://www.inside-r.org/packages/cran/chents/docs/chent'>chent</a></code> 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"> + <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> + </footer> + </div> + </body> +</html>
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