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+and can hold a list of information loaded from a chemical yaml file in their
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+ <img src="" class="logo" alt=""><h1>Retrieve endpoint information from the chyaml field of a chent object</h1>
+ <small class="dont-index">Source: <a href="https://github.com/jranke/pfm/blob/HEAD/R/endpoint.R" class="external-link"><code>R/endpoint.R</code></a></small>
+ <div class="d-none name"><code>endpoint.Rd</code></div>
+ </div>
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+ <div class="ref-description section level2">
+ <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>
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+ <div class="section level2">
+ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">endpoint</span><span class="op">(</span></span>
+<span> <span class="va">chent</span>,</span>
+<span> medium <span class="op">=</span> <span class="st">"soil"</span>,</span>
+<span> type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"degradation"</span>, <span class="st">"sorption"</span><span class="op">)</span>,</span>
+<span> lab_field <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"laboratory"</span>, <span class="st">"field"</span><span class="op">)</span>,</span>
+<span> redox <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"aerobic"</span>, <span class="st">"anaerobic"</span><span class="op">)</span>,</span>
+<span> value <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"DT50ref"</span>, <span class="st">"Kfoc"</span>, <span class="st">"N"</span><span class="op">)</span>,</span>
+<span> aggregator <span class="op">=</span> <span class="va">geomean</span>,</span>
+<span> raw <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span> signif <span class="op">=</span> <span class="fl">3</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">soil_DT50</span><span class="op">(</span></span>
+<span> <span class="va">chent</span>,</span>
+<span> aggregator <span class="op">=</span> <span class="va">geomean</span>,</span>
+<span> signif <span class="op">=</span> <span class="fl">3</span>,</span>
+<span> lab_field <span class="op">=</span> <span class="st">"laboratory"</span>,</span>
+<span> value <span class="op">=</span> <span class="st">"DT50ref"</span>,</span>
+<span> redox <span class="op">=</span> <span class="st">"aerobic"</span>,</span>
+<span> raw <span class="op">=</span> <span class="cn">FALSE</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">soil_Kfoc</span><span class="op">(</span><span class="va">chent</span>, aggregator <span class="op">=</span> <span class="va">geomean</span>, signif <span class="op">=</span> <span class="fl">3</span>, value <span class="op">=</span> <span class="st">"Kfoc"</span>, raw <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">soil_N</span><span class="op">(</span><span class="va">chent</span>, aggregator <span class="op">=</span> <span class="va">mean</span>, signif <span class="op">=</span> <span class="fl">3</span>, raw <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">soil_sorption</span><span class="op">(</span></span>
+<span> <span class="va">chent</span>,</span>
+<span> values <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Kfoc"</span>, <span class="st">"N"</span><span class="op">)</span>,</span>
+<span> aggregators <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>Kfoc <span class="op">=</span> <span class="va">geomean</span>, Koc <span class="op">=</span> <span class="va">geomean</span>, N <span class="op">=</span> <span class="va">mean</span><span class="op">)</span>,</span>
+<span> signif <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>Kfoc <span class="op">=</span> <span class="fl">3</span>, N <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>,</span>
+<span> raw <span class="op">=</span> <span class="cn">FALSE</span></span>
+<span><span class="op">)</span></span></code></pre></div>
+ </div>
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
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+ <div class="section level2">
+ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+ <dl><dt>chent</dt>
+<dd><p>The chent object to get the information from</p></dd>
+<dt>medium</dt>
+<dd><p>The medium for which information is sought</p></dd>
-<meta property="og:title" content="Retrieve endpoint information from the chyaml field of a chent object — endpoint" />
-<meta property="og:description" content="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." />
-<meta name="twitter:card" content="summary" />
+<dt>type</dt>
+<dd><p>The information type</p></dd>
+<dt>lab_field</dt>
+<dd><p>If not NA, do we want laboratory or field endpoints</p></dd>
-<!-- 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>
+<dt>redox</dt>
+<dd><p>If not NA, are we looking for aerobic or anaerobic data</p></dd>
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- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span>
- </span>
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-</div><!--/.navbar -->
+<dt>value</dt>
+<dd><p>The name of the value we want. The list given in the
+usage section is not exclusive</p></dd>
-
- </header>
+<dt>aggregator</dt>
+<dd><p>The aggregator function. Can be mean,
+<code><a href="geomean.html">geomean</a></code>, or identity, for example.</p></dd>
-<div class="row">
- <div class="col-md-9 contents">
- <div class="page-header">
- <h1>Retrieve endpoint information from the chyaml field of a chent object</h1>
-
- <div class="hidden name"><code>endpoint.Rd</code></div>
- </div>
- <div class="ref-description">
- <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>
-
- <pre class="usage"><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'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"degradation"</span>, <span class='st'>"sorption"</span>),
- <span class='kw'>lab_field</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'>"laboratory"</span>, <span class='st'>"field"</span>),
- <span class='kw'>redox</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'>"aerobic"</span>, <span class='st'>"anaerobic"</span>),
- <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>),
- <span class='kw'>aggregators</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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'><a href='https://rdrr.io/r/base/c.html'>c</a></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>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>chent</th>
- <td><p>The chent object to get the information from</p></td>
- </tr>
- <tr>
- <th>medium</th>
- <td><p>The medium for which information is sought</p></td>
- </tr>
- <tr>
- <th>type</th>
- <td><p>The information type</p></td>
- </tr>
- <tr>
- <th>lab_field</th>
- <td><p>If not NA, do we want laboratory or field endpoints</p></td>
- </tr>
- <tr>
- <th>redox</th>
- <td><p>If not NA, are we looking for aerobic or anaerobic data</p></td>
- </tr>
- <tr>
- <th>value</th>
- <td><p>The name of the value we want. The list given in the
-usage section is not exclusive</p></td>
- </tr>
- <tr>
- <th>aggregator</th>
- <td><p>The aggregator function. Can be mean,
-<code><a href='geomean.html'>geomean</a></code>, or identity, for example.</p></td>
- </tr>
- <tr>
- <th>raw</th>
- <td><p>Should the number(s) be returned as stored in the chent
+<dt>raw</dt>
+<dd><p>Should the number(s) be returned as stored in the chent
object (could be a character value) to retain original information
-about precision?</p></td>
- </tr>
- <tr>
- <th>signif</th>
- <td><p>How many significant digits do we want</p></td>
- </tr>
- <tr>
- <th>values</th>
- <td><p>The values to be returned</p></td>
- </tr>
- <tr>
- <th>aggregators</th>
- <td><p>A named vector of aggregator functions to be used</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>The result from applying the aggregator function to
+about precision?</p></dd>
+
+
+<dt>signif</dt>
+<dd><p>How many significant digits do we want</p></dd>
+
+
+<dt>values</dt>
+<dd><p>The values to be returned</p></dd>
+
+
+<dt>aggregators</dt>
+<dd><p>A named vector of aggregator functions to be used</p></dd>
+
+</dl></div>
+ <div class="section level2">
+ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></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>
-
+ </div>
+ <div class="section level2">
+ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></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="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>
+ </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+ </nav></aside></div>
- </div>
-</div>
-
- <footer>
- <div class="copyright">
- <p>Developed by Johannes Ranke.</p>
+ <footer><div class="pkgdown-footer-left">
+ <p></p><p>Developed by Johannes Ranke.</p>
</div>
-<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+<div class="pkgdown-footer-right">
+ <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
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