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and can hold a list of information loaded from a chemical yaml file in their
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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."></head><body>
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<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>
<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>
<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>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt id="arg-chent">chent<a class="anchor" aria-label="anchor" href="#arg-chent"></a></dt>
<dd><p>The chent object to get the information from</p></dd>
<dt id="arg-medium">medium<a class="anchor" aria-label="anchor" href="#arg-medium"></a></dt>
<dd><p>The medium for which information is sought</p></dd>
<dt id="arg-type">type<a class="anchor" aria-label="anchor" href="#arg-type"></a></dt>
<dd><p>The information type</p></dd>
<dt id="arg-lab-field">lab_field<a class="anchor" aria-label="anchor" href="#arg-lab-field"></a></dt>
<dd><p>If not NA, do we want laboratory or field endpoints</p></dd>
<dt id="arg-redox">redox<a class="anchor" aria-label="anchor" href="#arg-redox"></a></dt>
<dd><p>If not NA, are we looking for aerobic or anaerobic data</p></dd>
<dt id="arg-value">value<a class="anchor" aria-label="anchor" href="#arg-value"></a></dt>
<dd><p>The name of the value we want. The list given in the
usage section is not exclusive</p></dd>
<dt id="arg-aggregator">aggregator<a class="anchor" aria-label="anchor" href="#arg-aggregator"></a></dt>
<dd><p>The aggregator function. Can be mean,
<code><a href="geomean.html">geomean</a></code>, or identity, for example.</p></dd>
<dt id="arg-raw">raw<a class="anchor" aria-label="anchor" href="#arg-raw"></a></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></dd>
<dt id="arg-signif">signif<a class="anchor" aria-label="anchor" href="#arg-signif"></a></dt>
<dd><p>How many significant digits do we want</p></dd>
<dt id="arg-values">values<a class="anchor" aria-label="anchor" href="#arg-values"></a></dt>
<dd><p>The values to be returned</p></dd>
<dt id="arg-aggregators">aggregators<a class="anchor" aria-label="anchor" href="#arg-aggregators"></a></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>
</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>
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