path: root/docs/reference/endpoint.html


                                                  
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html lang="en">
  <head>
  <meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">

<title>Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm</title>

<!-- jquery -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<!-- Bootstrap -->

<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>

<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />

<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>

<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>

<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>


<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" />


<!-- 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>

<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->


  </head>

  <body>
    <div class="container template-reference-topic">
      <header>
      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
  <div class="container">
    <div class="navbar-header">
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
        <span class="sr-only">Toggle navigation</span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">pfm</a>
        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.4</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
    <span class="fa fa-home fa-lg"></span>
     
  </a>
</li>
<li>
  <a href="../reference/index.html">Reference</a>
</li>
      </ul>
      
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/jranke/pfm">
    <span class="fa fa-github fa-lg"></span>
     
  </a>
</li>
      </ul>
      
    </div><!--/.nav-collapse -->
  </div><!--/.container -->
</div><!--/.navbar -->

      
      </header>

<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>
    <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/endpoint.R'><code>R/endpoint.R</code></a></small>
    <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://www.rdocumentation.org/packages/base/topics/c'>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://www.rdocumentation.org/packages/base/topics/c'>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://www.rdocumentation.org/packages/base/topics/c'>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://www.rdocumentation.org/packages/base/topics/c'>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://www.rdocumentation.org/packages/base/topics/c'>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://www.rdocumentation.org/packages/base/topics/c'>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://www.rdocumentation.org/packages/base/topics/c'>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
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
  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>

      <footer>
      <div class="copyright">
  <p>Developed by Johannes Ranke.</p>
</div>

<div class="pkgdown">
  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
</div>
      </footer>
   </div>

  
  </body>
</html>