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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/GUS.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>Groundwater ubiquity score based on Gustafson (1989)</h1>
+ </div>
+
+
+ <p>The groundwater ubiquity score GUS is calculated according to
+the following equation
+$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p>
+
+
+ <pre><span class='fu'>GUS</span>(<span class='no'>...</span>)
+
+<span class='co'># S3 method for numeric</span>
+<span class='fu'>GUS</span>(<span class='no'>DT50</span>, <span class='no'>Koc</span>, <span class='no'>...</span>)
+
+<span class='co'># S3 method for chent</span>
+<span class='fu'>GUS</span>(<span class='no'>chent</span>, <span class='kw'>degradation_value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>,
+ <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>, <span class='kw'>sorption_value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>,
+ <span class='kw'>degradation_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>sorption_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='no'>...</span>)
+
+<span class='co'># S3 method for GUS_result</span>
+<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>...</dt>
+ <dd>Included in the generic to allow for further arguments later. Therefore
+this also had to be added to the specific methods.</dd>
+ <dt>DT50</dt>
+ <dd>Half-life of the chemical in soil. Should be a field
+half-life according to Gustafson (1989). However, leaching to the sub-soil
+can not completely be excluded in field dissipation experiments and Gustafson
+did not refer to any normalisation procedure, but says the field study should
+be conducted under use conditions.</dd>
+ <dt>Koc</dt>
+ <dd>The sorption constant normalised to organic carbon. Gustafson
+does not mention the nonlinearity of the sorption constant commonly
+found and usually described by Freundlich sorption, therefore it is
+unclear at which reference concentration the Koc should be observed
+(and if the reference concentration would be in soil or in porewater).</dd>
+ <dt>chent</dt>
+ <dd>If a chent is given with appropriate information present in its
+chyaml field, this information is used, with defaults specified below.</dd>
+ <dt>degradation_value</dt>
+ <dd>Which of the available degradation values should
+be used?</dd>
+ <dt>lab_field</dt>
+ <dd>Should laboratory or field half-lives be used? This
+defaults to lab in this implementation, in order to avoid
+double-accounting for mobility. If comparability with the original GUS
+values given by Gustafson (1989) is desired, non-normalised first-order
+field half-lives obtained under actual use conditions should be used.</dd>
+ <dt>redox</dt>
+ <dd>Aerobic or anaerobic degradation data</dd>
+ <dt>sorption_value</dt>
+ <dd>Which of the available sorption values should be used?
+Defaults to Kfoc as this is what is generally available from the European
+pesticide peer review process. These values generally use a reference
+concentration of 1 mg/L in porewater, that means they would be expected to
+be Koc values at a concentration of 1 mg/L in the water phase.</dd>
+ <dt>degradation_aggregator</dt>
+ <dd>Function for aggregating half-lives</dd>
+ <dt>sorption_aggregator</dt>
+ <dd>Function for aggregation Koc values</dd>
+ <dt>x</dt>
+ <dd>An object of class GUS_result to be printed</dd>
+ <dt>digits</dt>
+ <dd>The number of digits used in the print method</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A list with the DT50 and Koc used as well as the resulting score
+ of class GUS_result</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Gustafson, David I. (1989) Groundwater ubiquity score: a simple
+method for assessing pesticide leachability. <em>Environmental
+toxicology and chemistry</em> <b>8</b>(4) 339–57.</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="#references">References</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+Johannes Ranke
+
+ </div>
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