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| author | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2024-01-31 13:16:17 +0100 |
|---|---|---|
| committer | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2024-01-31 13:27:50 +0100 |
| commit | aed160d7f0eaf5865e2bd9bf6c4b1c9d7b13d911 (patch) | |
| tree | 7ca136834857c12449f50a1e086a589cc9b79e2e /docs/reference/GUS.html | |
| parent | 64f629efbe666bae56f48a309adf33d1eb09c358 (diff) | |
Reorganise data generation
- Use inst/data_generation for R code generating data as in some of my other packages
- data/*.RData files were checked using https://github.com/jranke/dotfiles/blob/main/bin/rda_diff
contents were not changed
- Remove ChangeLog, the history is in the git logs
- Update docs and some links contained therein
- use \doi{} markup
- Move logs to log directory
Diffstat (limited to 'docs/reference/GUS.html')
| -rw-r--r-- | docs/reference/GUS.html | 287 |
1 files changed, 109 insertions, 178 deletions
diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index e371c1a..dfe3b80 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -1,66 +1,14 @@ -<!-- 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>Groundwater ubiquity score based on Gustafson (1989) — GUS • 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> - 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-<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - - -<meta property="og:title" content="Groundwater ubiquity score based on Gustafson (1989) — GUS" /> -<meta property="og:description" content="The groundwater ubiquity score GUS is calculated according to +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Groundwater ubiquity score based on Gustafson (1989) — GUS • pfm</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Groundwater ubiquity score based on Gustafson (1989) — GUS"><meta property="og:description" content="The groundwater ubiquity score GUS is calculated according to the following equation -$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> -<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]> +$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$"><!-- 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> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <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"> @@ -71,35 +19,21 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> </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">0.5.7</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.6.1</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Reference</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Groundwater ubiquity score based on Gustafson (1989)</h1> @@ -113,139 +47,136 @@ the following equation $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p> </div> - <pre class="usage"><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'><a href='https://rdrr.io/r/base/print.html'>print</a></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> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>...</th> - <td><p>Included in the generic to allow for further arguments later. Therefore -this also had to be added to the specific methods.</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>Half-life of the chemical in soil. Should be a field + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">GUS</span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for numeric</span></span> +<span><span class="fu">GUS</span><span class="op">(</span><span class="va">DT50</span>, <span class="va">Koc</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for chent</span></span> +<span><span class="fu">GUS</span><span class="op">(</span></span> +<span> <span class="va">chent</span>,</span> +<span> degradation_value <span class="op">=</span> <span class="st">"DT50ref"</span>,</span> +<span> lab_field <span class="op">=</span> <span class="st">"laboratory"</span>,</span> +<span> redox <span class="op">=</span> <span class="st">"aerobic"</span>,</span> +<span> sorption_value <span class="op">=</span> <span class="st">"Kfoc"</span>,</span> +<span> degradation_aggregator <span class="op">=</span> <span class="va">geomean</span>,</span> +<span> sorption_aggregator <span class="op">=</span> <span class="va">geomean</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for GUS_result</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>...</dt> +<dd><p>Included in the generic to allow for further arguments later. Therefore +this also had to be added to the specific methods.</p></dd> + + +<dt>DT50</dt> +<dd><p>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.</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>The sorption constant normalised to organic carbon. Gustafson +be conducted under use conditions.</p></dd> + + +<dt>Koc</dt> +<dd><p>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).</p></td> - </tr> - <tr> - <th>chent</th> - <td><p>If a chent is given with appropriate information present in its -chyaml field, this information is used, with defaults specified below.</p></td> - </tr> - <tr> - <th>degradation_value</th> - <td><p>Which of the available degradation values should -be used?</p></td> - </tr> - <tr> - <th>lab_field</th> - <td><p>Should laboratory or field half-lives be used? This +(and if the reference concentration would be in soil or in porewater).</p></dd> + + +<dt>chent</dt> +<dd><p>If a chent is given with appropriate information present in its +chyaml field, this information is used, with defaults specified below.</p></dd> + + +<dt>degradation_value</dt> +<dd><p>Which of the available degradation values should +be used?</p></dd> + + +<dt>lab_field</dt> +<dd><p>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.</p></td> - </tr> - <tr> - <th>redox</th> - <td><p>Aerobic or anaerobic degradation data</p></td> - </tr> - <tr> - <th>sorption_value</th> - <td><p>Which of the available sorption values should be used? +field half-lives obtained under actual use conditions should be used.</p></dd> + + +<dt>redox</dt> +<dd><p>Aerobic or anaerobic degradation data</p></dd> + + +<dt>sorption_value</dt> +<dd><p>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.</p></td> - </tr> - <tr> - <th>degradation_aggregator</th> - <td><p>Function for aggregating half-lives</p></td> - </tr> - <tr> - <th>sorption_aggregator</th> - <td><p>Function for aggregation Koc values</p></td> - </tr> - <tr> - <th>x</th> - <td><p>An object of class GUS_result to be printed</p></td> - </tr> - <tr> - <th>digits</th> - <td><p>The number of digits used in the print method</p></td> - </tr> - </table> - - <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> +be Koc values at a concentration of 1 mg/L in the water phase.</p></dd> + + +<dt>degradation_aggregator</dt> +<dd><p>Function for aggregating half-lives</p></dd> + + +<dt>sorption_aggregator</dt> +<dd><p>Function for aggregation Koc values</p></dd> + +<dt>x</dt> +<dd><p>An object of class GUS_result to be printed</p></dd> + + +<dt>digits</dt> +<dd><p>The number of digits used in the print method</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list with the DT50 and Koc used as well as the resulting score + of class GUS_result</p> + </div> + <div id="references"> + <h2>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> - + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <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> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> |