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authorJohannes Ranke <jranke@uni-bremen.de>2017-01-18 22:41:01 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2017-01-18 22:50:14 +0100
commita76221d87485029444c8e684022ca606a0c7e68d (patch)
treec95052ee51b35f6c5ab87bd6f27ef2877f536838 /docs/reference/endpoint.html
parenta1d9f93138c2cfed92a683e37e72c737d52b7ad7 (diff)
Update static docs using pkgdown
- Add _pkgdown.yml for a structured function/data reference - Make seealso links active - Make mkinfit calls quiet - Use pkgdown branch from pull request hadley/pkgdown#229 to have topics ordered
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+ <h1>Retrieve endpoint information from the chyaml field of a chent object</h1>
+ </div>
+
+
+ <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>
+
+
+ <pre><span class='fu'>endpoint</span>(<span class='no'>chent</span>, <span class='kw'>medium</span> <span class='kw'>=</span> <span class='st'>"soil"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"degradation"</span>, <span class='st'>"sorption"</span>),
+ <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='st'>"laboratory"</span>, <span class='st'>"field"</span>), <span class='kw'>redox</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='st'>"aerobic"</span>,
+ <span class='st'>"anaerobic"</span>), <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"DT50ref"</span>, <span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>,
+ <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>)
+
+<span class='fu'>soil_DT50</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>,
+ <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>, <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>,
+ <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+
+<span class='fu'>soil_Kfoc</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>,
+ <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+
+<span class='fu'>soil_N</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>mean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+
+<span class='fu'>soil_sorption</span>(<span class='no'>chent</span>, <span class='kw'>values</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), <span class='kw'>aggregators</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span>
+ <span class='no'>geomean</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='no'>mean</span>), <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='fl'>3</span>),
+ <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <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>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>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.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>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 class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <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="#details">Details</a></li>
+ </ul>
+
+ </div>
+</div>
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