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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 | |
| 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')
64 files changed, 3516 insertions, 6269 deletions
diff --git a/docs/404.html b/docs/404.html index acdca31..bc1b5ff 100644 --- a/docs/404.html +++ b/docs/404.html @@ -1,66 +1,27 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> +<!-- 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>Page not found (404) • 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" /> - 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- - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-title-body"> - <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 +32,27 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="https://pkgdown.jrwb.de/pfm/index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.8</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-home fa-lg"></span> - - </a> -</li> <li> - <a href="reference/index.html">Reference</a> + <a href="https://pkgdown.jrwb.de/pfm/reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> - - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> +<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="contents col-md-9"> <div class="page-header"> <h1>Page not found (404)</h1> @@ -110,31 +63,31 @@ Content not found. Please use links in the navbar. </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 id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> </nav> - </div> +</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> 1.6.1.</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> +</div> + + </body> </html> - - diff --git a/docs/authors.html b/docs/authors.html index e4155eb..c65d25e 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,66 +1,12 @@ -<!-- 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>Authors • 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="Authors" /> - - - - -<!-- 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]> +<!-- 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>Authors and Citation • 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="Authors and Citation"><!-- 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]--> - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </head> - - <body data-spy="scroll" data-target="#toc"> - <div class="container template-authors"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container template-citation-authors"> + <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"> @@ -71,46 +17,52 @@ </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">0.5.8</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-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="contents col-md-9"> - <div class="page-header"> - <h1>Authors</h1> + <div class="section level2 authors-section"> + <div class="page-header"> + <h1>Authors</h1> + </div> + + + <ul class="list-unstyled"><li> + <p><strong>Johannes Ranke</strong>. Author, maintainer. <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> + </p> + </li> + </ul></div> + <div class="section level2 citation-section"> + <div> + <h1 id="citation">Citation</h1> + </div> + </div> + - <ul class="list-unstyled"> - <li> - <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a> - </p> - </li> - </ul> + <p>Johannes Ranke (2024). +<em>pfm: Utilities for Pesticide Fate Modelling</em>. +R package version 0.6.1, <a href="https://pkgdown.jrwb.de/pfm">https://pkgdown.jrwb.de/pfm</a>. +</p> + <pre>@Manual{, + title = {pfm: Utilities for Pesticide Fate Modelling}, + author = {{Johannes Ranke}}, + year = {2024}, + note = {R package version 0.6.1}, + url = {https://pkgdown.jrwb.de/pfm}, +}</pre> </div> @@ -118,22 +70,20 @@ - <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> 1.6.1.</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> diff --git a/docs/index.html b/docs/index.html index fd7cfd1..7658961 100644 --- a/docs/index.html +++ b/docs/index.html @@ -21,6 +21,8 @@ <![endif]--> </head> <body data-spy="scroll" data-target="#toc"> + + <div class="container template-home"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> @@ -33,19 +35,13 @@ </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">0.5.8</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-home fa-lg"></span> - - </a> -</li> -<li> <a href="reference/index.html">Reference</a> </li> </ul> @@ -61,68 +57,74 @@ </header><div class="row"> <div class="contents col-md-9"> -<div id="pfm" class="section level1"> -<div class="page-header"><h1 class="hasAnchor"> -<a href="#pfm" class="anchor"></a>pfm</h1></div> - +<div class="section level1"> +<div class="page-header"><h1 id="pfm">pfm<a class="anchor" aria-label="anchor" href="#pfm"></a> +</h1></div> +<p><a href="https://travis-ci.com/jranke/pfm" class="external-link"><img src="https://travis-ci.com/jranke/pfm.svg?branch=main" alt="Build Status"></a> <a href="https://codecov.io/github/jranke/pfm" class="external-link"><img src="https://codecov.io/github/jranke/pfm/branch/main/graphs/badge.svg" alt="codecov"></a></p> <p>The R package <strong>pfm</strong> provides some utilities for fate modelling, including dealing with FOCUS pesticide fate modelling tools, (currently only TOXSWA cwa and out files), made available under the GNU public license.</p> -<div id="installation" class="section level2"> -<h2 class="hasAnchor"> -<a href="#installation" class="anchor"></a>Installation</h2> -<p>The easiest way to install the package is probably to use <a href="https://cran.r-project.org/package=drat">drat</a>:</p> +<div class="section level2"> +<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a> +</h2> +<p>The easiest way to install the package is probably to use <a href="https://cran.r-project.org/package=drat" class="external-link">drat</a>:</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"drat"</span><span class="op">)</span> -<span class="fu">drat</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/drat/man/addRepo.html">addRepo</a></span><span class="op">(</span><span class="st">"jranke"</span><span class="op">)</span> -<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"pfm"</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"drat"</span><span class="op">)</span></span> +<span><span class="fu">drat</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/drat/man/addRepo.html" class="external-link">addRepo</a></span><span class="op">(</span><span class="st">"jranke"</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"pfm"</span><span class="op">)</span></span></code></pre></div> <p>Alternatively you can install the package using the <code>devtools</code> package. Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and vignettes.</p> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://devtools.r-lib.org/">devtools</a></span><span class="op">)</span> -<span class="fu"><a href="https://devtools.r-lib.org//reference/remote-reexports.html">install_github</a></span><span class="op">(</span><span class="st">"jranke/pfm"</span>, quick <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://devtools.r-lib.org/" class="external-link">devtools</a></span><span class="op">)</span></span> +<span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"jranke/pfm"</span>, quick <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> </div> -<div id="use" class="section level2"> -<h2 class="hasAnchor"> -<a href="#use" class="anchor"></a>Use</h2> -<p>Please refer to the <a href="http://pkgdown.jrwb.de/pfm/reference/index.html">reference</a>.</p> +<div class="section level2"> +<h2 id="use">Use<a class="anchor" aria-label="anchor" href="#use"></a> +</h2> +<p>Please refer to the <a href="http://pkgdown.jrwb.de/pfm/reference/index.html" class="external-link">reference</a>.</p> </div> -<div id="examples" class="section level2"> -<h2 class="hasAnchor"> -<a href="#examples" class="anchor"></a>Examples</h2> -<p>One recent nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown <a href="http://pkgdown.jrwb.de/pfm/reference/plot.one_box.html">here</a>.</p> +<div class="section level2"> +<h2 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a> +</h2> +<p>One recent nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown <a href="http://pkgdown.jrwb.de/pfm/reference/plot.one_box.html" class="external-link">here</a>.</p> </div> </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <div class="license"> -<h2>License</h2> +<h2 data-toc-skip>License</h2> <ul class="list-unstyled"> <li>GPL</li> </ul> </div> -<div class="developers"> -<h2>Developers</h2> + + +<div class="citation"> +<h2 data-toc-skip>Citation</h2> <ul class="list-unstyled"> -<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li> +<li><a href="authors.html#citation">Citing pfm</a></li> </ul> </div> - <div class="dev-status"> -<h2>Dev status</h2> +<div class="developers"> +<h2 data-toc-skip>Developers</h2> <ul class="list-unstyled"> -<li><a href="https://travis-ci.com/jranke/pfm"><img src="https://travis-ci.com/jranke/pfm.svg?branch=main" alt="Build Status"></a></li> -<li><a href="https://codecov.io/github/jranke/pfm"><img src="https://codecov.io/github/jranke/pfm/branch/main/graphs/badge.svg" alt="codecov"></a></li> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li> </ul> </div> -</div> + + + + </div> </div> <footer><div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <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> 1.6.1.</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> @@ -131,5 +133,7 @@ + + </body> </html> diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 1273238..80ea5b8 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -56,8 +56,10 @@ img.icon { float: right; } -img { +/* Ensure in-page images don't run outside their container */ +.contents img { max-width: 100%; + height: auto; } /* Fix bug in bootstrap (only seen in firefox) */ @@ -78,11 +80,10 @@ dd { /* Section anchors ---------------------------------*/ a.anchor { - margin-left: -30px; - display:inline-block; - width: 30px; - height: 30px; - visibility: hidden; + display: none; + margin-left: 5px; + width: 20px; + height: 20px; background-image: url(./link.svg); background-repeat: no-repeat; @@ -90,17 +91,15 @@ a.anchor { background-position: center center; } -.hasAnchor:hover a.anchor { - visibility: visible; -} - -@media (max-width: 767px) { - .hasAnchor:hover a.anchor { - visibility: hidden; - } +h1:hover .anchor, +h2:hover .anchor, +h3:hover .anchor, +h4:hover .anchor, +h5:hover .anchor, +h6:hover .anchor { + display: inline-block; } - /* Fixes for fixed navbar --------------------------*/ .contents h1, .contents h2, .contents h3, .contents h4 { @@ -264,31 +263,26 @@ table { /* Syntax highlighting ---------------------------------------------------- */ -pre { - word-wrap: normal; - word-break: normal; - border: 1px solid #eee; -} - -pre, code { +pre, code, pre code { background-color: #f8f8f8; color: #333; } +pre, pre code { + white-space: pre-wrap; + word-break: break-all; + overflow-wrap: break-word; +} -pre code { - overflow: auto; - word-wrap: normal; - white-space: pre; +pre { + border: 1px solid #eee; } -pre .img { +pre .img, pre .r-plt { margin: 5px 0; } -pre .img img { +pre .img img, pre .r-plt img { background-color: #fff; - display: block; - height: auto; } code a, pre a { @@ -305,9 +299,8 @@ a.sourceLine:hover { .kw {color: #264D66;} /* keyword */ .co {color: #888888;} /* comment */ -.message { color: black; font-weight: bolder;} -.error { color: orange; font-weight: bolder;} -.warning { color: #6A0366; font-weight: bolder;} +.error {font-weight: bolder;} +.warning {font-weight: bolder;} /* Clipboard --------------------------*/ @@ -365,3 +358,27 @@ mark { content: ""; } } + +/* Section anchors --------------------------------- + Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71 +*/ + +div.csl-bib-body { } +div.csl-entry { + clear: both; +} +.hanging-indent div.csl-entry { + margin-left:2em; + text-indent:-2em; +} +div.csl-left-margin { + min-width:2em; + float:left; +} +div.csl-right-inline { + margin-left:2em; + padding-left:1em; +} +div.csl-indent { + margin-left: 2em; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 7e7048f..6f0eee4 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -80,7 +80,7 @@ $(document).ready(function() { var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>"; - $(".examples, div.sourceCode").addClass("hasCopyButton"); + $("div.sourceCode").addClass("hasCopyButton"); // Insert copy buttons: $(copyButton).prependTo(".hasCopyButton"); @@ -91,7 +91,7 @@ // Initialize clipboard: var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { text: function(trigger) { - return trigger.parentNode.textContent; + return trigger.parentNode.textContent.replace(/\n#>[^\n]*/g, ""); } }); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index cc57584..62c4837 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,8 +1,8 @@ -pandoc: 2.9.2.1 -pkgdown: 1.6.1 +pandoc: 3.1.1 +pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2021-11-18T23:17Z +last_built: 2024-01-31T12:15Z urls: reference: https://pkgdown.jrwb.de/pfm/reference article: https://pkgdown.jrwb.de/pfm/articles diff --git a/docs/reference/EFSA_GW_interception_2014.html b/docs/reference/EFSA_GW_interception_2014.html index d7ec108..8bc0b51 100644 --- a/docs/reference/EFSA_GW_interception_2014.html +++ b/docs/reference/EFSA_GW_interception_2014.html @@ -1,67 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <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"> @@ -72,35 +17,21 @@ </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>Subset of EFSA crop interception default values for groundwater modelling</h1> @@ -112,82 +43,58 @@ <p>Subset of EFSA crop interception default values for groundwater modelling</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">EFSA_GW_interception_2014</span></span></code></pre></div> + </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A matrix containing interception values, currently only for some selected crops</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>European Food Safety Authority (2014) EFSA Guidance Document for evaluating laboratory and field dissipation studies to obtain DegT50 values of active substances of plant protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>12</b>(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to define the data</span> - <span class='no'>bbch</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='fl'>0</span>:<span class='fl'>9</span>, <span class='st'>"x"</span>) - <span class='no'>crops</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>( - <span class='st'>"Beans (field + vegetable)"</span>, - <span class='st'>"Peas"</span>, - <span class='st'>"Summer oilseed rape"</span>, <span class='st'>"Winter oilseed rape"</span>, - <span class='st'>"Tomatoes"</span>, - <span class='st'>"Spring cereals"</span>, <span class='st'>"Winter cereals"</span>) - <span class='no'>EFSA_GW_interception_2014</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>NA</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>crops</span>), <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>bbch</span>), - <span class='kw'>dimnames</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Crop</span> <span class='kw'>=</span> <span class='no'>crops</span>, <span class='kw'>BBCH</span> <span class='kw'>=</span> <span class='no'>bbch</span>)) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Beans (field + vegetable)"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.25</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.4</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.7</span>, <span class='fl'>5</span>), <span class='fl'>0.8</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Peas"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.35</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.55</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.85</span>, <span class='fl'>5</span>), <span class='fl'>0.85</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Summer oilseed rape"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.9</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Winter oilseed rape"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.9</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Tomatoes"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.5</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.7</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.5</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Spring cereals"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0</span>, <span class='fl'>0.2</span>, <span class='fl'>0.8</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.9</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fl'>0.8</span>) - <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Winter cereals"</span>, ] <span class='kw'><-</span> - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0</span>, <span class='fl'>0.2</span>, <span class='fl'>0.8</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.9</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fl'>0.8</span>) - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>EFSA_GW_interception_2014</span>, - <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"../data/EFSA_GW_interception_2014.RData"</span>) -} -<span class='no'>EFSA_GW_interception_2014</span></div><div class='output co'>#> BBCH -#> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x -#> Beans (field + vegetable) 0 0.25 0.40 0.40 0.70 0.70 0.70 0.70 0.70 0.80 -#> Peas 0 0.35 0.55 0.55 0.85 0.85 0.85 0.85 0.85 0.85 -#> Summer oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 -#> Winter oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 -#> Tomatoes 0 0.50 0.70 0.70 0.80 0.80 0.80 0.80 0.80 0.50 -#> Spring cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80 -#> Winter cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">EFSA_GW_interception_2014</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> BBCH</span> +<span class="r-out co"><span class="r-pr">#></span> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x</span> +<span class="r-out co"><span class="r-pr">#></span> Beans (field + vegetable) 0 0.25 0.40 0.40 0.70 0.70 0.70 0.70 0.70 0.80</span> +<span class="r-out co"><span class="r-pr">#></span> Peas 0 0.35 0.55 0.55 0.85 0.85 0.85 0.85 0.85 0.85</span> +<span class="r-out co"><span class="r-pr">#></span> Summer oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90</span> +<span class="r-out co"><span class="r-pr">#></span> Winter oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90</span> +<span class="r-out co"><span class="r-pr">#></span> Tomatoes 0 0.50 0.70 0.70 0.80 0.80 0.80 0.80 0.80 0.50</span> +<span class="r-out co"><span class="r-pr">#></span> Spring cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80</span> +<span class="r-out co"><span class="r-pr">#></span> Winter cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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- </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>Subset of EFSA crop washoff default values</h1> @@ -112,82 +43,58 @@ <p>Subset of EFSA crop washoff default values</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">EFSA_washoff_2017</span></span></code></pre></div> + </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A matrix containing wash-off factors, currently only for some selected crops</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>European Food Safety Authority (2017) EFSA guidance document for predicting environmental concentrations of active substances of plant protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>15</b>(10) 4982 doi:10.2903/j.efsa.2017.4982</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to define the data</span> - <span class='no'>bbch</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='fl'>0</span>:<span class='fl'>9</span>, <span class='st'>"x"</span>) - <span class='no'>crops</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>( - <span class='st'>"Beans (field + vegetable)"</span>, - <span class='st'>"Peas"</span>, - <span class='st'>"Summer oilseed rape"</span>, <span class='st'>"Winter oilseed rape"</span>, - <span class='st'>"Tomatoes"</span>, - <span class='st'>"Spring cereals"</span>, <span class='st'>"Winter cereals"</span>) - <span class='no'>EFSA_washoff_2017</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>NA</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>crops</span>), <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>bbch</span>), - <span class='kw'>dimnames</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Crop</span> <span class='kw'>=</span> <span class='no'>crops</span>, <span class='kw'>BBCH</span> <span class='kw'>=</span> <span class='no'>bbch</span>)) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Beans (field + vegetable)"</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='fl'>0.6</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.75</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.35</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Peas"</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='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.6</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.65</span>, <span class='fl'>5</span>), <span class='fl'>0.35</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Summer oilseed rape"</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='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.5</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.6</span>, <span class='fl'>5</span>), <span class='fl'>0.5</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Winter oilseed rape"</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='fl'>0.1</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.4</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.55</span>, <span class='fl'>5</span>), <span class='fl'>0.3</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Tomatoes"</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='fl'>0.55</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.75</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.7</span>, <span class='fl'>5</span>), <span class='fl'>0.35</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Spring cereals"</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='fl'>0.4</span>, <span class='fl'>0.5</span>, <span class='fl'>0.5</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.65</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.65</span>, <span class='fl'>2</span>), <span class='fl'>0.55</span>) - <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Winter cereals"</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='fl'>0.1</span>, <span class='fl'>0.4</span>, <span class='fl'>0.6</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.55</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.6</span>, <span class='fl'>2</span>), <span class='fl'>0.4</span>) - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>EFSA_washoff_2017</span>, - <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"../data/EFSA_washoff_2017.RData"</span>) -} -<span class='no'>EFSA_washoff_2017</span></div><div class='output co'>#> BBCH -#> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x -#> Beans (field + vegetable) NA 0.60 0.75 0.75 0.80 0.80 0.80 0.80 0.80 0.35 -#> Peas NA 0.40 0.60 0.60 0.65 0.65 0.65 0.65 0.65 0.35 -#> Summer oilseed rape NA 0.40 0.50 0.50 0.60 0.60 0.60 0.60 0.60 0.50 -#> Winter oilseed rape NA 0.10 0.40 0.40 0.55 0.55 0.55 0.55 0.55 0.30 -#> Tomatoes NA 0.55 0.75 0.75 0.70 0.70 0.70 0.70 0.70 0.35 -#> Spring cereals NA 0.40 0.50 0.50 0.65 0.65 0.65 0.65 0.65 0.55 -#> Winter cereals NA 0.10 0.40 0.60 0.55 0.55 0.55 0.60 0.60 0.40</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">EFSA_washoff_2017</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> BBCH</span> +<span class="r-out co"><span class="r-pr">#></span> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x</span> +<span class="r-out co"><span class="r-pr">#></span> Beans (field + vegetable) NA 0.60 0.75 0.75 0.80 0.80 0.80 0.80 0.80 0.35</span> +<span class="r-out co"><span class="r-pr">#></span> Peas NA 0.40 0.60 0.60 0.65 0.65 0.65 0.65 0.65 0.35</span> +<span class="r-out co"><span class="r-pr">#></span> Summer oilseed rape NA 0.40 0.50 0.50 0.60 0.60 0.60 0.60 0.60 0.50</span> +<span class="r-out co"><span class="r-pr">#></span> Winter oilseed rape NA 0.10 0.40 0.40 0.55 0.55 0.55 0.55 0.55 0.30</span> +<span class="r-out co"><span class="r-pr">#></span> Tomatoes NA 0.55 0.75 0.75 0.70 0.70 0.70 0.70 0.70 0.35</span> +<span class="r-out co"><span class="r-pr">#></span> Spring cereals NA 0.40 0.50 0.50 0.65 0.65 0.65 0.65 0.65 0.55</span> +<span class="r-out co"><span class="r-pr">#></span> Winter cereals NA 0.10 0.40 0.60 0.55 0.55 0.55 0.60 0.60 0.40</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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The +soil definitions are from page 46ff. from FOCUS (2012)."><!-- 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 data-spy="scroll" data-target="#toc"> <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"> @@ -73,35 +18,21 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> </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>A very small subset of the FOCUS Groundwater scenario definitions</h1> @@ -114,104 +45,107 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> soil definitions are from page 46ff. from FOCUS (2012).</p> </div> - <pre class="usage"><span class='no'>FOCUS_GW_scenarios_2012</span></pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_GW_scenarios_2012</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> <p>An object of class <code>list</code> of length 2.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div id="references"> + <h2>References</h2> <p>FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. FOrum for the Co-ordination of pesticde fate models and their USe. http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>FOCUS_GW_scenarios_2012</span></div><div class='output co'>#> $names -#> Cha Ham Jok Kre Oke -#> "Châteaudun" "Hamburg" "Jokioinen" "Kremsmünster" "Okehampton" -#> Pia Por Sev Thi -#> "Piacenza" "Porto" "Sevilla" "Thiva" -#> -#> $soils -#> location horizon number pH_H2O perc_clay perc_oc rel_deg -#> 1 Cha Ap 1 8.0 30.0 1.39 1.0 -#> 2 Cha B1 2 8.1 31.0 0.93 0.5 -#> 3 Cha B2 3 8.2 25.0 0.70 0.5 -#> 4 Cha II C1 4 8.5 26.0 0.30 0.3 -#> 5 Cha II C1 5 8.5 26.0 0.30 0.0 -#> 6 Cha II C2 6 8.5 24.0 0.27 0.0 -#> 7 Cha M 7 8.3 31.0 0.21 0.0 -#> 8 Ham Ap 1 6.4 7.2 1.50 1.0 -#> 9 Ham BvI 2 5.6 6.7 1.00 0.5 -#> 10 Ham BvII 3 5.6 0.9 0.20 0.3 -#> 11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3 -#> 12 Ham Cv 5 5.5 0.0 0.00 0.3 -#> 13 Ham Cv 6 5.5 0.0 0.00 0.0 -#> 14 Jok Ap 1 6.2 3.6 4.06 1.0 -#> 15 Jok Bs 2 5.6 1.8 0.84 0.5 -#> 16 Jok BC1 3 5.4 1.2 0.36 0.3 -#> 17 Jok BC2 4 5.4 1.7 0.29 0.3 -#> 18 Jok BC2 5 5.4 1.7 0.29 0.0 -#> 19 Jok Cg 6 5.3 1.9 0.21 0.0 -#> 20 Kre <NA> 1 7.7 14.0 3.60 1.0 -#> 21 Kre <NA> 2 7.0 25.0 1.00 0.5 -#> 22 Kre <NA> 3 7.1 27.0 0.50 0.5 -#> 23 Kre <NA> 4 7.1 27.0 0.50 0.3 -#> 24 Kre <NA> 5 7.1 27.0 0.50 0.0 -#> 25 Oke A 1 5.8 18.0 2.20 1.0 -#> 26 Oke Bw1 2 6.3 17.0 0.70 0.5 -#> 27 Oke BC 3 6.5 14.0 0.40 0.3 -#> 28 Oke C 4 6.6 9.0 0.10 0.3 -#> 29 Oke C 5 6.6 9.0 0.10 0.0 -#> 30 Pia Ap 1 7.0 15.0 1.26 1.0 -#> 31 Pia Ap 2 7.0 15.0 1.26 0.5 -#> 32 Pia Bw 3 6.3 7.0 0.47 0.5 -#> 33 Pia Bw 4 6.3 7.0 0.47 0.3 -#> 34 Pia 2C 5 6.4 0.0 0.00 0.3 -#> 35 Pia 2C 6 6.4 0.0 0.00 0.0 -#> 36 Por <NA> 1 4.9 10.0 1.42 1.0 -#> 37 Por <NA> 2 4.8 8.0 0.78 0.5 -#> 38 Por <NA> 3 4.8 8.0 0.78 0.3 -#> 39 Por <NA> 4 4.8 8.0 0.78 0.0 -#> 40 Sev <NA> 1 7.3 14.0 0.93 1.0 -#> 41 Sev <NA> 2 7.3 13.0 0.93 1.0 -#> 42 Sev <NA> 3 7.8 15.0 0.70 0.5 -#> 43 Sev <NA> 4 8.1 16.0 0.58 0.3 -#> 44 Sev <NA> 5 8.1 16.0 0.58 0.0 -#> 45 Sev <NA> 6 8.2 22.0 0.49 0.0 -#> 46 Thi Ap1 1 7.7 25.3 0.74 1.0 -#> 47 Thi Ap2 2 7.7 25.3 0.74 0.5 -#> 48 Thi Bw 3 7.8 29.6 0.57 0.5 -#> 49 Thi Bw 4 7.8 31.9 0.31 0.3 -#> 50 Thi Ck1 5 7.8 32.9 0.18 0.3 -#> 51 Thi Ck1 6 7.8 32.9 0.18 0.0 -#> </div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">FOCUS_GW_scenarios_2012</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $names</span> +<span class="r-out co"><span class="r-pr">#></span> Cha Ham Jok Kre Oke </span> +<span class="r-out co"><span class="r-pr">#></span> "Châteaudun" "Hamburg" "Jokioinen" "Kremsmünster" "Okehampton" </span> +<span class="r-out co"><span class="r-pr">#></span> Pia Por Sev Thi </span> +<span class="r-out co"><span class="r-pr">#></span> "Piacenza" "Porto" "Sevilla" "Thiva" </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $soils</span> +<span class="r-out co"><span class="r-pr">#></span> location horizon number pH_H2O perc_clay perc_oc rel_deg</span> +<span class="r-out co"><span class="r-pr">#></span> 1 Cha Ap 1 8.0 30.0 1.39 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 Cha B1 2 8.1 31.0 0.93 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 3 Cha B2 3 8.2 25.0 0.70 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 4 Cha II C1 4 8.5 26.0 0.30 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 5 Cha II C1 5 8.5 26.0 0.30 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 6 Cha II C2 6 8.5 24.0 0.27 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 7 Cha M 7 8.3 31.0 0.21 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 8 Ham Ap 1 6.4 7.2 1.50 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 9 Ham BvI 2 5.6 6.7 1.00 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 10 Ham BvII 3 5.6 0.9 0.20 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 12 Ham Cv 5 5.5 0.0 0.00 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 13 Ham Cv 6 5.5 0.0 0.00 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 14 Jok Ap 1 6.2 3.6 4.06 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 15 Jok Bs 2 5.6 1.8 0.84 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 16 Jok BC1 3 5.4 1.2 0.36 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 17 Jok BC2 4 5.4 1.7 0.29 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 18 Jok BC2 5 5.4 1.7 0.29 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 19 Jok Cg 6 5.3 1.9 0.21 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 20 Kre <NA> 1 7.7 14.0 3.60 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 21 Kre <NA> 2 7.0 25.0 1.00 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 22 Kre <NA> 3 7.1 27.0 0.50 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 23 Kre <NA> 4 7.1 27.0 0.50 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 24 Kre <NA> 5 7.1 27.0 0.50 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 25 Oke A 1 5.8 18.0 2.20 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 26 Oke Bw1 2 6.3 17.0 0.70 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 27 Oke BC 3 6.5 14.0 0.40 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 28 Oke C 4 6.6 9.0 0.10 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 29 Oke C 5 6.6 9.0 0.10 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 30 Pia Ap 1 7.0 15.0 1.26 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 31 Pia Ap 2 7.0 15.0 1.26 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 32 Pia Bw 3 6.3 7.0 0.47 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 33 Pia Bw 4 6.3 7.0 0.47 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 34 Pia 2C 5 6.4 0.0 0.00 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 35 Pia 2C 6 6.4 0.0 0.00 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 36 Por <NA> 1 4.9 10.0 1.42 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 37 Por <NA> 2 4.8 8.0 0.78 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 38 Por <NA> 3 4.8 8.0 0.78 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 39 Por <NA> 4 4.8 8.0 0.78 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 40 Sev <NA> 1 7.3 14.0 0.93 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 41 Sev <NA> 2 7.3 13.0 0.93 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 42 Sev <NA> 3 7.8 15.0 0.70 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 43 Sev <NA> 4 8.1 16.0 0.58 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 44 Sev <NA> 5 8.1 16.0 0.58 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 45 Sev <NA> 6 8.2 22.0 0.49 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 46 Thi Ap1 1 7.7 25.3 0.74 1.0</span> +<span class="r-out co"><span class="r-pr">#></span> 47 Thi Ap2 2 7.7 25.3 0.74 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 48 Thi Bw 3 7.8 29.6 0.57 0.5</span> +<span class="r-out co"><span class="r-pr">#></span> 49 Thi Bw 4 7.8 31.9 0.31 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 50 Thi Ck1 5 7.8 32.9 0.18 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> 51 Thi Ck1 6 7.8 32.9 0.18 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </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> + <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> 1.5.1.</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> diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index bbfb592..0216e4e 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not 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<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>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</h1> @@ -115,210 +46,78 @@ The text file is not included in the package as its licence is not clear.</p> </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A list containing the scenario names in a character vector called 'names', the drift percentiles in a matrix called 'drift', interception percentages in a matrix called 'interception' and the runoff/drainage percentages for Step 2 calculations in a matrix called 'rd'.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to extract the data</span> - <span class='no'>scenario_path</span> <span class='kw'><-</span> <span class='st'>"inst/extdata/FOCUS_Step_12_scenarios.txt"</span> - <span class='no'>scenarios</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/readLines.html'>readLines</a></span>(<span class='no'>scenario_path</span>)[<span class='fl'>9</span>:<span class='fl'>38</span>] - <span class='no'>FOCUS_Step_12_scenarios</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>() - <span class='no'>sce</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/utils/read.table.html'>read.table</a></span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>scenarios</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>, <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>check.names</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span> <span class='kw'>=</span> <span class='no'>sce</span>$<span class='no'>Crop</span> - <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>sce</span>) <span class='kw'><-</span> <span class='no'>sce</span>$<span class='no'>Crop</span> - <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>drift</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>3</span>:<span class='fl'>11</span>] - <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>interception</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>12</span>:<span class='fl'>15</span>] - <span class='no'>sce_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/readLines.html'>readLines</a></span>(<span class='no'>scenario_path</span>)[<span class='fl'>41</span>:<span class='fl'>46</span>] - <span class='no'>rd</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/utils/read.table.html'>read.table</a></span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>sce_2</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>)[<span class='fl'>1</span>:<span class='fl'>2</span>] - <span class='no'>rd_mat</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='no'>rd</span>$<span class='no'>V2</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - <span class='fu'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></span>(<span class='no'>rd_mat</span>) <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Oct-Feb"</span>, <span class='st'>"Mar-May"</span>, <span class='st'>"Jun-Sep"</span>), - <span class='kw'>Region</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"North"</span>, <span class='st'>"South"</span>)) - <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>rd</span> <span class='kw'>=</span> <span class='no'>rd_mat</span> - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>FOCUS_Step_12_scenarios</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/FOCUS_Step_12_scenarios.RData"</span>) -} - -<span class='co'># And this is the resulting data</span> -<span class='no'>FOCUS_Step_12_scenarios</span></div><div class='output co'>#> $names -#> [1] "cereals, spring" "cereals, winter" -#> [3] "citrus" "cotton" -#> [5] "field beans" "grass / alfalfa" -#> [7] "hops" "legumes" -#> [9] "maize" "oil seed rape, spring" -#> [11] "oil seed rape, winter" "olives" -#> [13] "pome / stone fruit, early applns" "pome / stone fruit, late applns" -#> [15] "potatoes" "soybeans" -#> [17] "sugar beets" "sunflowers" -#> [19] "tobacco" "vegetables, bulb" -#> [21] "vegetables, fruiting" "vegetables, leafy" -#> [23] "vegetables, root" "vines, early applns" -#> [25] "vines, late applns" "appln, aerial" -#> [27] "appln, hand (crop < 50 cm)" "appln, hand (crop > 50 cm)" -#> [29] "no drift (incorp or seed trtmt)" -#> -#> $drift -#> 1 2 3 4 5 6 -#> cereals, spring 2.759 2.438 2.024 1.862 1.794 1.631 -#> cereals, winter 2.759 2.438 2.024 1.862 1.794 1.631 -#> citrus 15.725 12.129 11.011 10.124 9.743 9.204 -#> cotton 2.759 2.438 2.024 1.862 1.794 1.631 -#> field beans 2.759 2.438 2.024 1.862 1.794 1.631 -#> grass / alfalfa 2.759 2.438 2.024 1.862 1.794 1.631 -#> hops 19.326 17.723 15.928 15.378 15.114 14.902 -#> legumes 2.759 2.438 2.024 1.862 1.794 1.631 -#> maize 2.759 2.438 2.024 1.862 1.794 1.631 -#> oil seed rape, spring 2.759 2.438 2.024 1.862 1.794 1.631 -#> oil seed rape, winter 2.759 2.438 2.024 1.862 1.794 1.631 -#> olives 15.725 12.129 11.011 10.124 9.743 9.204 -#> pome / stone fruit, early applns 29.197 25.531 23.960 23.603 23.116 22.760 -#> pome / stone fruit, late applns 15.725 12.129 11.011 10.124 9.743 9.204 -#> potatoes 2.759 2.438 2.024 1.862 1.794 1.631 -#> soybeans 2.759 2.438 2.024 1.862 1.794 1.631 -#> sugar beets 2.759 2.438 2.024 1.862 1.794 1.631 -#> sunflowers 2.759 2.438 2.024 1.862 1.794 1.631 -#> tobacco 2.759 2.438 2.024 1.862 1.794 1.631 -#> vegetables, bulb 2.759 2.438 2.024 1.862 1.794 1.631 -#> vegetables, fruiting 2.759 2.438 2.024 1.862 1.794 1.631 -#> vegetables, leafy 2.759 2.438 2.024 1.862 1.794 1.631 -#> vegetables, root 2.759 2.438 2.024 1.862 1.794 1.631 -#> vines, early applns 2.699 2.496 2.546 2.499 2.398 2.336 -#> vines, late applns 8.028 7.119 6.898 6.631 6.636 6.431 -#> appln, aerial 33.200 33.200 33.200 33.200 33.200 33.200 -#> appln, hand (crop < 50 cm) 2.759 2.438 2.024 1.862 1.794 1.631 -#> appln, hand (crop > 50 cm) 8.028 7.119 6.898 6.631 6.636 6.431 -#> no drift (incorp or seed trtmt) 0.000 0.000 0.000 0.000 0.000 0.000 -#> 7 8 >8 -#> cereals, spring 1.578 1.512 1.512 -#> cereals, winter 1.578 1.512 1.512 -#> citrus 9.102 8.656 8.656 -#> cotton 1.578 1.512 1.512 -#> field beans 1.578 1.512 1.512 -#> grass / alfalfa 1.578 1.512 1.512 -#> hops 14.628 13.520 13.520 -#> legumes 1.578 1.512 1.512 -#> maize 1.578 1.512 1.512 -#> oil seed rape, spring 1.578 1.512 1.512 -#> oil seed rape, winter 1.578 1.512 1.512 -#> olives 9.102 8.656 8.656 -#> pome / stone fruit, early applns 22.690 22.241 22.241 -#> pome / stone fruit, late applns 9.102 8.656 8.656 -#> potatoes 1.578 1.512 1.512 -#> soybeans 1.578 1.512 1.512 -#> sugar beets 1.578 1.512 1.512 -#> sunflowers 1.578 1.512 1.512 -#> tobacco 1.578 1.512 1.512 -#> vegetables, bulb 1.578 1.512 1.512 -#> vegetables, fruiting 1.578 1.512 1.512 -#> vegetables, leafy 1.578 1.512 1.512 -#> vegetables, root 1.578 1.512 1.512 -#> vines, early applns 2.283 2.265 2.265 -#> vines, late applns 6.227 6.173 6.173 -#> appln, aerial 33.200 33.200 33.200 -#> appln, hand (crop < 50 cm) 1.578 1.512 1.512 -#> appln, hand (crop > 50 cm) 6.227 6.173 6.173 -#> no drift (incorp or seed trtmt) 0.000 0.000 0.000 -#> -#> $interception -#> no interception minimal crop cover -#> cereals, spring 0 0.00 -#> cereals, winter 0 0.00 -#> citrus 0 0.80 -#> cotton 0 0.30 -#> field beans 0 0.25 -#> grass / alfalfa 0 0.40 -#> hops 0 0.20 -#> legumes 0 0.25 -#> maize 0 0.25 -#> oil seed rape, spring 0 0.40 -#> oil seed rape, winter 0 0.40 -#> olives 0 0.70 -#> pome / stone fruit, early applns 0 0.20 -#> pome / stone fruit, late applns 0 0.20 -#> potatoes 0 0.15 -#> soybeans 0 0.20 -#> sugar beets 0 0.20 -#> sunflowers 0 0.20 -#> tobacco 0 0.20 -#> vegetables, bulb 0 0.10 -#> vegetables, fruiting 0 0.25 -#> vegetables, leafy 0 0.25 -#> vegetables, root 0 0.25 -#> vines, early applns 0 0.40 -#> vines, late applns 0 0.40 -#> appln, aerial 0 0.20 -#> appln, hand (crop < 50 cm) 0 0.20 -#> appln, hand (crop > 50 cm) 0 0.20 -#> no drift (incorp or seed trtmt) 0 0.00 -#> average crop cover full canopy -#> cereals, spring 0.20 0.70 -#> cereals, winter 0.20 0.70 -#> citrus 0.80 0.80 -#> cotton 0.60 0.75 -#> field beans 0.40 0.70 -#> grass / alfalfa 0.60 0.75 -#> hops 0.50 0.70 -#> legumes 0.50 0.70 -#> maize 0.50 0.75 -#> oil seed rape, spring 0.70 0.75 -#> oil seed rape, winter 0.70 0.75 -#> olives 0.70 0.70 -#> pome / stone fruit, early applns 0.40 0.65 -#> pome / stone fruit, late applns 0.40 0.65 -#> potatoes 0.50 0.70 -#> soybeans 0.50 0.75 -#> sugar beets 0.70 0.75 -#> sunflowers 0.50 0.75 -#> tobacco 0.70 0.75 -#> vegetables, bulb 0.25 0.40 -#> vegetables, fruiting 0.50 0.70 -#> vegetables, leafy 0.40 0.70 -#> vegetables, root 0.50 0.70 -#> vines, early applns 0.50 0.60 -#> vines, late applns 0.50 0.60 -#> appln, aerial 0.50 0.70 -#> appln, hand (crop < 50 cm) 0.50 0.70 -#> appln, hand (crop > 50 cm) 0.50 0.70 -#> no drift (incorp or seed trtmt) 0.00 0.00 -#> -#> $rd -#> Region -#> Time North South -#> Oct-Feb 5 4 -#> Mar-May 2 4 -#> Jun-Sep 2 3 -#> </div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="co"># This is the code that was used to extract the data</span></span></span> +<span class="r-in"><span> <span class="va">scenario_path</span> <span class="op"><-</span> <span class="st">"inst/extdata/FOCUS_Step_12_scenarios.txt"</span></span></span> +<span class="r-in"><span> <span class="va">scenarios</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="va">scenario_path</span><span class="op">)</span><span class="op">[</span><span class="fl">9</span><span class="op">:</span><span class="fl">38</span><span class="op">]</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in file(con, "r"):</span> cannot open the connection</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">sce</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.table</a></span><span class="op">(</span>text <span class="op">=</span> <span class="va">scenarios</span>, sep <span class="op">=</span> <span class="st">"\t"</span>, header <span class="op">=</span> <span class="cn">TRUE</span>, check.names <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> +<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'scenarios' not found</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">names</span> <span class="op">=</span> <span class="va">sce</span><span class="op">$</span><span class="va">Crop</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span> <span class="op"><-</span> <span class="va">sce</span><span class="op">$</span><span class="va">Crop</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">drift</span> <span class="op">=</span> <span class="va">sce</span><span class="op">[</span>, <span class="fl">3</span><span class="op">:</span><span class="fl">11</span><span class="op">]</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">interception</span> <span class="op">=</span> <span class="va">sce</span><span class="op">[</span>, <span class="fl">12</span><span class="op">:</span><span class="fl">15</span><span class="op">]</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-in"><span> <span class="va">sce_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="va">scenario_path</span><span class="op">)</span><span class="op">[</span><span class="fl">41</span><span class="op">:</span><span class="fl">46</span><span class="op">]</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in file(con, "r"):</span> cannot open the connection</span> +<span class="r-in"><span> <span class="va">rd</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.table</a></span><span class="op">(</span>text <span class="op">=</span> <span class="va">sce_2</span>, sep <span class="op">=</span> <span class="st">"\t"</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce_2' not found</span> +<span class="r-in"><span> <span class="va">rd_mat</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="va">rd</span><span class="op">$</span><span class="va">V2</span>, nrow <span class="op">=</span> <span class="fl">3</span>, byrow <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'rd' not found</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/dimnames.html" class="external-link">dimnames</a></span><span class="op">(</span><span class="va">rd_mat</span><span class="op">)</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>Time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Oct-Feb"</span>, <span class="st">"Mar-May"</span>, <span class="st">"Jun-Sep"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Region <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"North"</span>, <span class="st">"South"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'rd_mat' not found</span> +<span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">rd</span> <span class="op">=</span> <span class="va">rd_mat</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'rd_mat' not found</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/save.html" class="external-link">save</a></span><span class="op">(</span><span class="va">FOCUS_Step_12_scenarios</span>, file <span class="op">=</span> <span class="st">"data/FOCUS_Step_12_scenarios.RData"</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>cannot open compressed file 'data/FOCUS_Step_12_scenarios.RData', probable reason 'No such file or directory'</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in gzfile(file, "wb"):</span> cannot open the connection</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># And this is the resulting data</span></span></span> +<span class="r-in"><span><span class="va">FOCUS_Step_12_scenarios</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> list()</span> +</code></pre></div> + </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> + <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> 1.5.1.</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> diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html index a365556..1fa9b97 100644 --- a/docs/reference/FOMC_actual_twa.html +++ b/docs/reference/FOMC_actual_twa.html @@ -1,64 +1,12 @@ -<!-- 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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>Actual and maximum moving window time average concentrations for FOMC kinetics</h1> @@ -109,79 +43,77 @@ <p>Actual and maximum moving window time average concentrations for FOMC kinetics</p> </div> - <pre class="usage"><span class='fu'>FOMC_actual_twa</span>( - <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1.0001</span>, - <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>10</span>, - <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, <span class='fl'>50</span>, <span class='fl'>100</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>alpha</th> - <td><p>Parameter of the FOMC model</p></td> - </tr> - <tr> - <th>beta</th> - <td><p>Parameter of the FOMC model</p></td> - </tr> - <tr> - <th>times</th> - <td><p>The output times, and window sizes for time weighted average concentrations</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">FOMC_actual_twa</span><span class="op">(</span></span> +<span> alpha <span class="op">=</span> <span class="fl">1.0001</span>,</span> +<span> beta <span class="op">=</span> <span class="fl">10</span>,</span> +<span> times <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="fl">0</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">21</span>, <span class="fl">28</span>, <span class="fl">42</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + <div id="source"> + <h2>Source</h2> <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 18 December 2014, p. 251</p> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>alpha</dt> +<dd><p>Parameter of the FOMC model</p></dd> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>FOMC_actual_twa</span>(<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1.0001</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>10</span>)</div><div class='output co'>#> actual twa -#> 0 1.00000000 NaN -#> 1 0.90908224 0.9530973 -#> 2 0.83331814 0.9115995 -#> 4 0.71426168 0.8411664 -#> 7 0.58820408 0.7580202 -#> 14 0.41663019 0.6253074 -#> 21 0.32254415 0.5387324 -#> 28 0.26312277 0.4767543 -#> 42 0.19227599 0.3925054 -#> 50 0.16663681 0.3583198 -#> 100 0.09088729 0.2397608</div></pre> - </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="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +<dt>beta</dt> +<dd><p>Parameter of the FOMC model</p></dd> + + +<dt>times</dt> +<dd><p>The output times, and window sizes for time weighted average concentrations</p></dd> + +</dl></div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">FOMC_actual_twa</span><span class="op">(</span>alpha <span class="op">=</span> <span class="fl">1.0001</span>, beta <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> actual twa</span> +<span class="r-out co"><span class="r-pr">#></span> 0 1.00000000 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> 1 0.90908224 0.9530973</span> +<span class="r-out co"><span class="r-pr">#></span> 2 0.83331814 0.9115995</span> +<span class="r-out co"><span class="r-pr">#></span> 4 0.71426168 0.8411664</span> +<span class="r-out co"><span class="r-pr">#></span> 7 0.58820408 0.7580202</span> +<span class="r-out co"><span class="r-pr">#></span> 14 0.41663019 0.6253074</span> +<span class="r-out co"><span class="r-pr">#></span> 21 0.32254415 0.5387324</span> +<span class="r-out co"><span class="r-pr">#></span> 28 0.26312277 0.4767543</span> +<span class="r-out co"><span class="r-pr">#></span> 42 0.19227599 0.3925054</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.16663681 0.3583198</span> +<span class="r-out co"><span class="r-pr">#></span> 100 0.09088729 0.2397608</span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 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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> - 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- - - </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"> @@ -66,36 +17,21 @@ </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>Get the relative accumulation of an FOMC model over multiples of an interval</h1> @@ -104,64 +40,55 @@ </div> <div class="ref-description"> - <p>Get the relative accumulation of an FOMC model over multiples of an interval</p> - </div> - <pre class="usage"><span class='fu'>PEC_FOMC_accu_rel</span>(<span class='no'>n</span>, <span class='no'>interval</span>, <span class='no'>FOMC</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>n</th> - <td><p>number of applications</p></td> - </tr> - <tr> - <th>interval</th> - <td><p>Time between applications</p></td> - </tr> - <tr> - <th>FOMC</th> - <td><p>Named numeric vector containing the FOMC parameters alpha and beta</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_FOMC_accu_rel</span><span class="op">(</span><span class="va">n</span>, <span class="va">interval</span>, <span class="va">FOMC</span><span class="op">)</span></span></code></pre></div> + </div> - <p>A numeric vector containing all n accumulation factors for the n applications</p> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>n</dt> +<dd><p>number of applications</p></dd> + + +<dt>interval</dt> +<dd><p>Time between applications</p></dd> + + +<dt>FOMC</dt> +<dd><p>Named numeric vector containing the FOMC parameters alpha and beta</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> - </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> - </ul> +<p>A numeric vector containing all n accumulation factors for the n applications</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> diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 3e405a5..f7e1da5 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -1,68 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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If an interval is given, an attempt is made at calculating a long term maximum concentration using the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012 -and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> -<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]> +and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)."><!-- 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"> @@ -73,35 +21,21 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> </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>Calculate predicted environmental concentrations in soil</h1> @@ -117,164 +51,167 @@ the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012 and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).</p> </div> - <pre class="usage"><span class='fu'>PEC_soil</span>( - <span class='no'>rate</span>, - <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, - <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, - <span class='kw'>mixing_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, - <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"mg/kg"</span>, - <span class='kw'>PEC_pw_units</span> <span class='kw'>=</span> <span class='st'>"mg/L"</span>, - <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>n_periods</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, - <span class='kw'>tillage_depth</span> <span class='kw'>=</span> <span class='fl'>20</span>, - <span class='kw'>leaching_depth</span> <span class='kw'>=</span> <span class='no'>tillage_depth</span>, - <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"annual"</span>, - <span class='kw'>cultivation</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>chent</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>FOMC</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='no'>Koc</span>/<span class='fl'>1.724</span>, - <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fl'>0</span>, - <span class='kw'>t_act</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"default"</span>, <span class='st'>"EFSA_2017"</span>, <span class='st'>"EFSA_2015"</span>), - <span class='kw'>leaching</span> <span class='kw'>=</span> <span class='no'>scenarios</span> <span class='kw'>==</span> <span class='st'>"EFSA_2017"</span>, - <span class='kw'>porewater</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>rate</th> - <td><p>Application rate in units specified below</p></td> - </tr> - <tr> - <th>rate_units</th> - <td><p>Defaults to g/ha</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>The fraction of the application rate that does not reach the soil</p></td> - </tr> - <tr> - <th>mixing_depth</th> - <td><p>Mixing depth in cm</p></td> - </tr> - <tr> - <th>PEC_units</th> - <td><p>Requested units for the calculated PEC. Only mg/kg currently supported</p></td> - </tr> - <tr> - <th>PEC_pw_units</th> - <td><p>Only mg/L currently supported</p></td> - </tr> - <tr> - <th>interval</th> - <td><p>Period of the deeper mixing. The default is NA, i.e. no + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_soil</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> rate_units <span class="op">=</span> <span class="st">"g/ha"</span>,</span> +<span> interception <span class="op">=</span> <span class="fl">0</span>,</span> +<span> mixing_depth <span class="op">=</span> <span class="fl">5</span>,</span> +<span> PEC_units <span class="op">=</span> <span class="st">"mg/kg"</span>,</span> +<span> PEC_pw_units <span class="op">=</span> <span class="st">"mg/L"</span>,</span> +<span> interval <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> n_periods <span class="op">=</span> <span class="cn">Inf</span>,</span> +<span> tillage_depth <span class="op">=</span> <span class="fl">20</span>,</span> +<span> leaching_depth <span class="op">=</span> <span class="va">tillage_depth</span>,</span> +<span> crop <span class="op">=</span> <span class="st">"annual"</span>,</span> +<span> cultivation <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> chent <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> DT50 <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> FOMC <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> Koc <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> Kom <span class="op">=</span> <span class="va">Koc</span><span class="op">/</span><span class="fl">1.724</span>,</span> +<span> t_avg <span class="op">=</span> <span class="fl">0</span>,</span> +<span> t_act <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> scenarios <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">"default"</span>, <span class="st">"EFSA_2017"</span>, <span class="st">"EFSA_2015"</span><span class="op">)</span>,</span> +<span> leaching <span class="op">=</span> <span class="va">scenarios</span> <span class="op">==</span> <span class="st">"EFSA_2017"</span>,</span> +<span> porewater <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>rate</dt> +<dd><p>Application rate in units specified below</p></dd> + + +<dt>rate_units</dt> +<dd><p>Defaults to g/ha</p></dd> + + +<dt>interception</dt> +<dd><p>The fraction of the application rate that does not reach the soil</p></dd> + + +<dt>mixing_depth</dt> +<dd><p>Mixing depth in cm</p></dd> + + +<dt>PEC_units</dt> +<dd><p>Requested units for the calculated PEC. Only mg/kg currently supported</p></dd> + + +<dt>PEC_pw_units</dt> +<dd><p>Only mg/L currently supported</p></dd> + + +<dt>interval</dt> +<dd><p>Period of the deeper mixing. The default is NA, i.e. no deeper mixing. For annual deeper mixing, set this to 365 when degradation -units are in days</p></td> - </tr> - <tr> - <th>n_periods</th> - <td><p>Number of periods to be considered for long term PEC calculations</p></td> - </tr> - <tr> - <th>tillage_depth</th> - <td><p>Periodic (see interval) deeper mixing in cm</p></td> - </tr> - <tr> - <th>leaching_depth</th> - <td><p>EFSA (2017) uses the mixing depth (ecotoxicological +units are in days</p></dd> + + +<dt>n_periods</dt> +<dd><p>Number of periods to be considered for long term PEC calculations</p></dd> + + +<dt>tillage_depth</dt> +<dd><p>Periodic (see interval) deeper mixing in cm</p></dd> + + +<dt>leaching_depth</dt> +<dd><p>EFSA (2017) uses the mixing depth (ecotoxicological evaluation depth) to calculate leaching for annual crops where tillage takes place. By default, losses from the layer down to the tillage -depth are taken into account in this implementation.</p></td> - </tr> - <tr> - <th>crop</th> - <td><p>Ignored for scenarios other than EFSA_2017. Only annual crops +depth are taken into account in this implementation.</p></dd> + + +<dt>crop</dt> +<dd><p>Ignored for scenarios other than EFSA_2017. Only annual crops are supported when these scenarios are used. Only crops with a single cropping -cycle per year are currently supported.</p></td> - </tr> - <tr> - <th>cultivation</th> - <td><p>Does mechanical cultivation in the sense of EFSA (2017) +cycle per year are currently supported.</p></dd> + + +<dt>cultivation</dt> +<dd><p>Does mechanical cultivation in the sense of EFSA (2017) take place, i.e. twice a year to a depth of 5 cm? Ignored for scenarios -other than EFSA_2017</p></td> - </tr> - <tr> - <th>chent</th> - <td><p>An optional chent object holding substance specific information. Can -also be a name for the substance as a character string</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>If specified, overrides soil DT50 endpoints from a chent object +other than EFSA_2017</p></dd> + + +<dt>chent</dt> +<dd><p>An optional chent object holding substance specific information. Can +also be a name for the substance as a character string</p></dd> + + +<dt>DT50</dt> +<dd><p>If specified, overrides soil DT50 endpoints from a chent object If DT50 is not specified here and not available from the chent object, zero -degradation is assumed</p></td> - </tr> - <tr> - <th>FOMC</th> - <td><p>If specified, it should be a named numeric vector containing +degradation is assumed</p></dd> + + +<dt>FOMC</dt> +<dd><p>If specified, it should be a named numeric vector containing the FOMC parameters alpha and beta. This overrides any other degradation endpoints, and the degradation during the interval and after the maximum PEC -is calculated using these parameters without temperature correction</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>If specified, overrides Koc endpoints from a chent object</p></td> - </tr> - <tr> - <th>Kom</th> - <td><p>Calculated from Koc by default, but can explicitly be specified -as Kom here</p></td> - </tr> - <tr> - <th>t_avg</th> - <td><p>Averaging times for time weighted average concentrations</p></td> - </tr> - <tr> - <th>t_act</th> - <td><p>Time series for actual concentrations</p></td> - </tr> - <tr> - <th>scenarios</th> - <td><p>If this is 'default', the DT50 will be used without correction +is calculated using these parameters without temperature correction</p></dd> + + +<dt>Koc</dt> +<dd><p>If specified, overrides Koc endpoints from a chent object</p></dd> + + +<dt>Kom</dt> +<dd><p>Calculated from Koc by default, but can explicitly be specified +as Kom here</p></dd> + + +<dt>t_avg</dt> +<dd><p>Averaging times for time weighted average concentrations</p></dd> + + +<dt>t_act</dt> +<dd><p>Time series for actual concentrations</p></dd> + + +<dt>scenarios</dt> +<dd><p>If this is 'default', the DT50 will be used without correction and soil properties as specified in the REACH guidance (R.16, Table R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when -'chents' is specified, the DegT50 with destination 'PECgw' will be used), +'chent' is specified, the DegT50 with destination 'PECgw' will be used), and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also -model and scenario adjustment factors from the EFSA guidance are used.</p></td> - </tr> - <tr> - <th>leaching</th> - <td><p>Should leaching be taken into account? The default is FALSE, -except when the EFSA_2017 scenarios are used.</p></td> - </tr> - <tr> - <th>porewater</th> - <td><p>Should equilibrium porewater concentrations be estimated +model and scenario adjustment factors from the EFSA guidance are used.</p></dd> + + +<dt>leaching</dt> +<dd><p>Should leaching be taken into account? The default is FALSE, +except when the EFSA_2017 scenarios are used.</p></dd> + + +<dt>porewater</dt> +<dd><p>Should equilibrium porewater concentrations be estimated based on Kom and the organic carbon fraction of the soil instead of total soil concentrations? Based on equation (7) given in the PPR panel opinion (EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, -p. 13).</p></td> - </tr> - </table> +p. 13).</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The predicted concentration in soil</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>The predicted concentration in soil</p> + </div> + <div id="details"> + <h2>Details</h2> <p>This assumes that the complete load to soil during the time specified by 'interval' (typically 365 days) is dosed at once. As in the PPR panel opinion cited below (EFSA PPR panel 2012), only temperature correction using the Arrhenius equation is performed.</p> <p>Total soil and porewater PEC values for the scenarios as defined in the EFSA guidance (2017, p. 14/15) can easily be calculated.</p> - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - + </div> + <div id="note"> + <h2>Note</h2> <p>While time weighted average (TWA) concentrations given in the examples from the EFSA guidance from 2015 (p. 80) are be reproduced, this is not true for the TWA concentrations given for the same example in the EFSA guidance @@ -289,8 +226,9 @@ from 2017 (p. 92).</p> e.g. in the EFSA scenarios, the DT50 for groundwater modelling (destination 'PECgw') is taken from the chent object, otherwise the DT50 with destination 'PECsoil'.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div id="references"> + <h2>References</h2> <p>EFSA Panel on Plant Protection Products and their Residues (2012) Scientific Opinion on the science behind the guidance for scenario selection and scenario parameterisation for predicting environmental @@ -306,75 +244,80 @@ from 2017 (p. 92).</p> protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 doi:10.2903/j.efsa.2015.4093</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>100</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0.25</span>)</div><div class='output co'>#> scenario -#> t_avg default -#> 0 0.1</div><div class='input'> -<span class='co'># This is example 1 starting at p. 92 of the EFSA guidance (2017)</span> -<span class='co'># Note that TWA concentrations differ from the ones given in the guidance</span> -<span class='co'># for an unknown reason (the values from EFSA (2015) can be reproduced).</span> -<span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>), - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2017"</span>)</div><div class='output co'>#> scenario -#> t_avg CTN CTC CTS -#> 0 19.76834 13.8619 10.53795 -#> 21 19.59345 13.7169 10.39882</div><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>), - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2017"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> scenario -#> t_avg CLN CLC CLS -#> 0 0.5541984 0.6779249 0.9816693 -#> 21 0.5484576 0.6693125 0.9609119</div><div class='input'> -<span class='co'># This is example 1 starting at p. 79 of the EFSA guidance (2015)</span> -<span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>), - <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>)</div><div class='output co'>#> scenario -#> t_avg CTN CTC CTS -#> 0 21.96827 11.53750 9.145259 -#> 21 21.78517 11.40701 9.017370</div><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>), - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> scenario -#> t_avg CLN CLC CLS -#> 0 0.7589401 0.6674322 0.9147861 -#> 21 0.7506036 0.6590345 0.8987279</div><div class='input'> -<span class='co'># The following is from example 4 starting at p. 85 of the EFSA guidance (2015)</span> -<span class='co'># Metabolite M2</span> -<span class='co'># Calculate total and porewater soil concentrations for tier 1 scenarios</span> -<span class='co'># Relative molar mass is 100/300, formation fraction is 0.7 * 1</span> -<span class='no'>results_pfm</span> <span class='kw'><-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>), - <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>) -<span class='no'>results_pfm_pw</span> <span class='kw'><-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>), - <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div></pre> - </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> - <li><a href="#note">Note</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">100</span>, interception <span class="op">=</span> <span class="fl">0.25</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg default</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0.1</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is example 1 starting at p. 92 of the EFSA guidance (2017)</span></span></span> +<span class="r-in"><span><span class="co"># Note that TWA concentrations differ from the ones given in the guidance</span></span></span> +<span class="r-in"><span><span class="co"># for an unknown reason (the values from EFSA (2015) can be reproduced).</span></span></span> +<span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_avg <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="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">1000</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2017"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg CTN CTC CTS</span> +<span class="r-out co"><span class="r-pr">#></span> 0 19.76834 13.8619 10.53795</span> +<span class="r-out co"><span class="r-pr">#></span> 21 19.59345 13.7169 10.39882</span> +<span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_av <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="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">1000</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2017"</span>, porewater <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg CLN CLC CLS</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0.5541984 0.6779249 0.9816693</span> +<span class="r-out co"><span class="r-pr">#></span> 21 0.5484576 0.6693125 0.9609119</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is example 1 starting at p. 79 of the EFSA guidance (2015)</span></span></span> +<span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_avg <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="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg CTN CTC CTS</span> +<span class="r-out co"><span class="r-pr">#></span> 0 21.96827 11.53750 9.145259</span> +<span class="r-out co"><span class="r-pr">#></span> 21 21.78517 11.40701 9.017370</span> +<span class="r-in"><span><span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_av <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="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">1000</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span>, porewater <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> scenario</span> +<span class="r-out co"><span class="r-pr">#></span> t_avg CLN CLC CLS</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0.7589401 0.6674322 0.9147861</span> +<span class="r-out co"><span class="r-pr">#></span> 21 0.7506036 0.6590345 0.8987279</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The following is from example 4 starting at p. 85 of the EFSA guidance (2015)</span></span></span> +<span class="r-in"><span><span class="co"># Metabolite M2</span></span></span> +<span class="r-in"><span><span class="co"># Calculate total and porewater soil concentrations for tier 1 scenarios</span></span></span> +<span class="r-in"><span><span class="co"># Relative molar mass is 100/300, formation fraction is 0.7 * 1</span></span></span> +<span class="r-in"><span><span class="va">results_pfm</span> <span class="op"><-</span> <span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">100</span><span class="op">/</span><span class="fl">300</span> <span class="op">*</span> <span class="fl">0.7</span> <span class="op">*</span> <span class="fl">1</span> <span class="op">*</span> <span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_avg <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="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">results_pfm_pw</span> <span class="op"><-</span> <span class="fu">PEC_soil</span><span class="op">(</span><span class="fl">100</span><span class="op">/</span><span class="fl">300</span> <span class="op">*</span> <span class="fl">0.7</span> <span class="op">*</span> <span class="fl">1000</span>, interval <span class="op">=</span> <span class="fl">365</span>, DT50 <span class="op">=</span> <span class="fl">250</span>, t_av <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="fl">0</span>, <span class="fl">21</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> Kom <span class="op">=</span> <span class="fl">100</span>, scenarios <span class="op">=</span> <span class="st">"EFSA_2015"</span>, porewater <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +</code></pre></div> + </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> 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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>Calculate initial and accumulation PEC soil for a set of metabolites</h1> @@ -104,68 +40,59 @@ </div> <div class="ref-description"> - <p>Calculate initial and accumulation PEC soil for a set of metabolites</p> - </div> - <pre class="usage"><span class='fu'>PEC_soil_mets</span>(<span class='no'>rate</span>, <span class='no'>mw_parent</span>, <span class='no'>mets</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='no'>...</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>rate</th> - <td><p>Application rate in units specified below</p></td> - </tr> - <tr> - <th>mw_parent</th> - <td><p>The molecular weight of the parent compound</p></td> - </tr> - <tr> - <th>mets</th> - <td><p>A dataframe with metabolite identifiers as rownames + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_soil_mets</span><span class="op">(</span><span class="va">rate</span>, <span class="va">mw_parent</span>, <span class="va">mets</span>, interval <span class="op">=</span> <span class="fl">365</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>rate</dt> +<dd><p>Application rate in units specified below</p></dd> + + +<dt>mw_parent</dt> +<dd><p>The molecular weight of the parent compound</p></dd> + + +<dt>mets</dt> +<dd><p>A dataframe with metabolite identifiers as rownames and columns "mw", "occ" and "DT50" holding their molecular weight, -maximum occurrence in soil and their soil DT50</p></td> - </tr> - <tr> - <th>interval</th> - <td><p>The interval for accumulation calculations</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments are passed to PEC_soil</p></td> - </tr> - </table> - +maximum occurrence in soil and their soil DT50</p></dd> - </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> - </ul> + +<dt>interval</dt> +<dd><p>The interval for accumulation calculations</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments are passed to PEC_soil</p></dd> + +</dl></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> diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index bdcf5af..b0be7f3 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ 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website" /> </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>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</h1> @@ -111,97 +45,97 @@ published on the CRC website" /> published on the CRC website</p> </div> - <pre class="usage"><span class='fu'>PEC_sw_drainage_UK</span>( - <span class='no'>rate</span>, - <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, - <span class='no'>Koc</span>, - <span class='kw'>latest_application</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>soil_DT50</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>model_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</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>rate</th> - <td><p>Application rate in g/ha</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>The fraction of the application rate that does not reach the soil</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>The sorption coefficient normalised to organic carbon in L/kg</p></td> - </tr> - <tr> - <th>latest_application</th> - <td><p>Latest application date, formatted as e.g. "01 July"</p></td> - </tr> - <tr> - <th>soil_DT50</th> - <td><p>Soil degradation half-life, if SFO kinetics are to be used</p></td> - </tr> - <tr> - <th>model</th> - <td><p>The soil degradation model to be used. Either one of "FOMC", -"DFOP", "HS", or "IORE", or an mkinmod object</p></td> - </tr> - <tr> - <th>model_parms</th> - <td><p>A named numeric vector containing the model parameters</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The predicted concentration in surface water in µg/L</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_drainage_UK</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> interception <span class="op">=</span> <span class="fl">0</span>,</span> +<span> <span class="va">Koc</span>,</span> +<span> latest_application <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> soil_DT50 <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> model <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> model_parms <span class="op">=</span> <span class="cn">NULL</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>rate</dt> +<dd><p>Application rate in g/ha</p></dd> + + +<dt>interception</dt> +<dd><p>The fraction of the application rate that does not reach the soil</p></dd> + + +<dt>Koc</dt> +<dd><p>The sorption coefficient normalised to organic carbon in L/kg</p></dd> + + +<dt>latest_application</dt> +<dd><p>Latest application date, formatted as e.g. "01 July"</p></dd> + + +<dt>soil_DT50</dt> +<dd><p>Soil degradation half-life, if SFO kinetics are to be used</p></dd> + + +<dt>model</dt> +<dd><p>The soil degradation model to be used. Either one of "FOMC", +"DFOP", "HS", or "IORE", or an mkinmod object</p></dd> + +<dt>model_parms</dt> +<dd><p>A named numeric vector containing the model parameters</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The predicted concentration in surface water in µg/L</p> + </div> + <div id="references"> + <h2>References</h2> <p>HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (for UK specific authorisation requests) - <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> accessed 2019-09-27</p> <p>Drainage PECs Version 1.0 (2015) Spreadsheet published at - <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> accessed 2019-09-27</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>PEC_sw_drainage_UK</span>(<span class='fl'>150</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>)</div><div class='output co'>#> [1] 8.076923</div></pre> - </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> - <li><a href="#examples">Examples</a></li> - </ul> - + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_sw_drainage_UK</span><span class="op">(</span><span class="fl">150</span>, Koc <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 8.076923</span> +</code></pre></div> + </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> diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index e2c325b..c017454 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -1,69 +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>Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift • pfm</title> - 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- - - -<!-- 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]> +with input via spray drift."><!-- 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 data-spy="scroll" data-target="#toc"> <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"> @@ -74,35 +19,21 @@ with input via spray drift." /> </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">0.5.8</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>Calculate predicted environmental concentrations in surface water due to drift</h1> @@ -116,106 +47,118 @@ concentration in surface water based on complete, instantaneous mixing with input via spray drift.</p> </div> - <pre class="usage"><span class='fu'>PEC_sw_drift</span>( - <span class='no'>rate</span>, - <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, - <span class='kw'>drift_percentages</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"JKI"</span>, <span class='st'>"RF"</span>), - <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"Ackerbau"</span>, - <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>), - <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, - <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"µg/L"</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>rate</th> - <td><p>Application rate in units specified below</p></td> - </tr> - <tr> - <th>applications</th> - <td><p>Number of applications for selection of drift percentile</p></td> - </tr> - <tr> - <th>water_depth</th> - <td><p>Depth of the water body in cm</p></td> - </tr> - <tr> - <th>drift_percentages</th> - <td><p>Percentage drift values for which to calculate PECsw. -'drift_data' and 'distances' if not NULL.</p></td> - </tr> - <tr> - <th>drift_data</th> - <td><p>Source of drift percentage data. If 'JKI', the [drift_data_JKI] + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_drift</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> applications <span class="op">=</span> <span class="fl">1</span>,</span> +<span> water_depth <span class="op">=</span> <span class="fl">30</span>,</span> +<span> drift_percentages <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> drift_data <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">"JKI"</span>, <span class="st">"RF"</span><span class="op">)</span>,</span> +<span> crop <span class="op">=</span> <span class="st">"Ackerbau"</span>,</span> +<span> distances <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="fl">1</span>, <span class="fl">5</span>, <span class="fl">10</span>, <span class="fl">20</span><span class="op">)</span>,</span> +<span> rate_units <span class="op">=</span> <span class="st">"g/ha"</span>,</span> +<span> PEC_units <span class="op">=</span> <span class="st">"µg/L"</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>rate</dt> +<dd><p>Application rate in units specified below</p></dd> + + +<dt>applications</dt> +<dd><p>Number of applications for selection of drift percentile</p></dd> + + +<dt>water_depth</dt> +<dd><p>Depth of the water body in cm</p></dd> + + +<dt>drift_percentages</dt> +<dd><p>Percentage drift values for which to calculate PECsw. +'drift_data' and 'distances' if not NULL.</p></dd> + + +<dt>drift_data</dt> +<dd><p>Source of drift percentage data. If 'JKI', the [drift_data_JKI] included in the package is used. If 'RF', the Rautmann formula is used, if -implemented for the crop type and number of applications</p></td> - </tr> - <tr> - <th>crop</th> - <td><p>Crop name (use German names for JKI data), defaults to "Ackerbau"</p></td> - </tr> - <tr> - <th>distances</th> - <td><p>The distances in m for which to get PEC values</p></td> - </tr> - <tr> - <th>rate_units</th> - <td><p>Defaults to g/ha</p></td> - </tr> - <tr> - <th>PEC_units</th> - <td><p>Requested units for the calculated PEC. Only µg/L currently supported</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The predicted concentration in surface water</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>)</div><div class='output co'>#> 1 m 5 m 10 m 20 m -#> 0.92333333 0.19000000 0.09666667 0.05000000 </div><div class='input'><span class='co'># Alternatively, we can use the formula for a single application to "Ackerbau" from the paper</span> -<span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>, <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='st'>"RF"</span>)</div><div class='output co'>#> 1 m 5 m 10 m 20 m -#> 0.92350000 0.19114149 0.09699222 0.04921742 </div><div class='input'> -<span class='co'># This makes it possible to also use different substances</span> -<span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>, <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>5</span>, <span class='fl'>6</span>, <span class='fl'>10</span>, <span class='fl'>20</span>, <span class='fl'>50</span>, <span class='fl'>100</span>), <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='st'>"RF"</span>)</div><div class='output co'>#> 1 m 3 m 5 m 6 m 10 m 20 m 50 m -#> 0.92350000 0.31512171 0.19114149 0.15990435 0.09699222 0.04921742 0.02007497 -#> 100 m -#> 0.01018678 </div><div class='input'> -<span class='co'># Using custom drift percentages is also supported</span> -<span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>, <span class='kw'>drift_percentages</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2.77</span>, <span class='fl'>0.95</span>, <span class='fl'>0.57</span>, <span class='fl'>0.48</span>, <span class='fl'>0.29</span>, <span class='fl'>0.15</span>, <span class='fl'>0.06</span>, <span class='fl'>0.03</span>))</div><div class='output co'>#> 2.77 % 0.95 % 0.57 % 0.48 % 0.29 % 0.15 % 0.06 % -#> 0.92333333 0.31666667 0.19000000 0.16000000 0.09666667 0.05000000 0.02000000 -#> 0.03 % -#> 0.01000000 </div></pre> +implemented for the crop type and number of applications</p></dd> + + +<dt>crop</dt> +<dd><p>Crop name (use German names for JKI data), defaults to "Ackerbau"</p></dd> + + +<dt>distances</dt> +<dd><p>The distances in m for which to get PEC values</p></dd> + + +<dt>rate_units</dt> +<dd><p>Defaults to g/ha</p></dd> + + +<dt>PEC_units</dt> +<dd><p>Requested units for the calculated PEC. Only µg/L currently supported</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The predicted concentration in surface water</p> + </div> + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 1 m 5 m 10 m 20 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.92333333 0.19000000 0.09666667 0.05000000 </span> +<span class="r-in"><span><span class="co"># Alternatively, we can use the formula for a single application to "Ackerbau" from the paper</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 1 m 5 m 10 m 20 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.92350000 0.19114149 0.09699222 0.04921742 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This makes it possible to also use different substances</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, distances <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="fl">1</span>, <span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">6</span>, <span class="fl">10</span>, <span class="fl">20</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 1 m 3 m 5 m 6 m 10 m 20 m 50 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.92350000 0.31512171 0.19114149 0.15990435 0.09699222 0.04921742 0.02007497 </span> +<span class="r-out co"><span class="r-pr">#></span> 100 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.01018678 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Using custom drift percentages is also supported</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, drift_percentages <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="fl">2.77</span>, <span class="fl">0.95</span>, <span class="fl">0.57</span>, <span class="fl">0.48</span>, <span class="fl">0.29</span>, <span class="fl">0.15</span>, <span class="fl">0.06</span>, <span class="fl">0.03</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.77 % 0.95 % 0.57 % 0.48 % 0.29 % 0.15 % 0.06 % </span> +<span class="r-out co"><span class="r-pr">#></span> 0.92333333 0.31666667 0.19000000 0.16000000 0.09666667 0.05000000 0.02000000 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.03 % </span> +<span class="r-out co"><span class="r-pr">#></span> 0.01000000 </span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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Although there are four groups of +compounds ("Gefährdungsgruppen"), only one distinction is made in the calculations, between compounds with low mobility (group 1) and compounds with modest to high mobility (groups 2, 3 and 4). In this implementation, the group is derived only from the Koc, if not given explicitly. For -details, see the discussion of the function arguments below." /> -<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]> +details, see the discussion of the function arguments below.'><!-- 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"> @@ -75,35 +23,21 @@ details, see the discussion of the function arguments below." /> </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>Calculate PEC surface water due to drainage as in Exposit 3</h1> @@ -121,123 +55,126 @@ the group is derived only from the Koc, if not given explicitly. For details, see the discussion of the function arguments below.</p> </div> - <pre class="usage"><span class='fu'>PEC_sw_exposit_drainage</span>( - <span class='no'>rate</span>, - <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, - <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>mobility</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'>"low"</span>, <span class='st'>"high"</span>), - <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, - <span class='kw'>t_drainage</span> <span class='kw'>=</span> <span class='fl'>3</span>, - <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>, - <span class='kw'>V_drainage</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>spring</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>autumn</span> <span class='kw'>=</span> <span class='fl'>100</span>), - <span class='kw'>dilution</span> <span class='kw'>=</span> <span class='fl'>2</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>rate</th> - <td><p>The application rate in g/ha</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>The fraction intercepted by the crop</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>The sorption coefficient to soil organic carbon used to determine the mobility. A trigger -value of 550 L/kg is used in order to decide if Koc >> 500.</p></td> - </tr> - <tr> - <th>mobility</th> - <td><p>Overrides what is determined from the Koc.</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>The soil half-life in days</p></td> - </tr> - <tr> - <th>t_drainage</th> - <td><p>The time between application and the drainage event, where degradation occurs, in days</p></td> - </tr> - <tr> - <th>V_ditch</th> - <td><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></td> - </tr> - <tr> - <th>V_drainage</th> - <td><p>The drainage volume, equivalent to 1 mm precipitation on 1 ha for spring/summer or 10 mm for -autumn/winter/early spring.</p></td> - </tr> - <tr> - <th>dilution</th> - <td><p>The dilution factor</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_exposit_drainage</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> interception <span class="op">=</span> <span class="fl">0</span>,</span> +<span> Koc <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> mobility <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">"low"</span>, <span class="st">"high"</span><span class="op">)</span>,</span> +<span> DT50 <span class="op">=</span> <span class="cn">Inf</span>,</span> +<span> t_drainage <span class="op">=</span> <span class="fl">3</span>,</span> +<span> V_ditch <span class="op">=</span> <span class="fl">30</span>,</span> +<span> V_drainage <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>spring <span class="op">=</span> <span class="fl">10</span>, autumn <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>,</span> +<span> dilution <span class="op">=</span> <span class="fl">2</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + <div id="source"> + <h2>Source</h2> <p>Excel 3.02 spreadsheet available from - <a href='https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <a href="https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html" class="external-link">https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html</a></p> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>rate</dt> +<dd><p>The application rate in g/ha</p></dd> + + +<dt>interception</dt> +<dd><p>The fraction intercepted by the crop</p></dd> + + +<dt>Koc</dt> +<dd><p>The sorption coefficient to soil organic carbon used to determine the mobility. A trigger +value of 550 L/kg is used in order to decide if Koc >> 500.</p></dd> + + +<dt>mobility</dt> +<dd><p>Overrides what is determined from the Koc.</p></dd> + + +<dt>DT50</dt> +<dd><p>The soil half-life in days</p></dd> + + +<dt>t_drainage</dt> +<dd><p>The time between application and the drainage event, where degradation occurs, in days</p></dd> + + +<dt>V_ditch</dt> +<dd><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></dd> - <p>A list containing the following components</p><dl class='dl-horizontal'> - <dt>perc_runoff</dt><dd><p>The runoff percentages for dissolved and bound substance</p></dd> - <dt>runoff</dt><dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> - <dt>PEC_sw_runoff</dt><dd><p>A matrix containing PEC values for dissolved and bound substance + +<dt>V_drainage</dt> +<dd><p>The drainage volume, equivalent to 1 mm precipitation on 1 ha for spring/summer or 10 mm for +autumn/winter/early spring.</p></dd> + + +<dt>dilution</dt> +<dd><p>The dilution factor</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list containing the following components</p> +<p></p> +<dl><dt>perc_runoff</dt> +<dd><p>The runoff percentages for dissolved and bound substance</p></dd> + + <dt>runoff</dt> +<dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> + + <dt>PEC_sw_runoff</dt> +<dd><p>A matrix containing PEC values for dissolved and bound substance for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.</p></dd> + -</dl> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p><code><a href='perc_runoff_exposit.html'>perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href='perc_runoff_reduction_exposit.html'>perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>PEC_sw_exposit_drainage</span>(<span class='fl'>500</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>150</span>)</div><div class='output co'>#> $perc_drainage_total -#> spring autumn -#> 0.2 1.0 -#> -#> $perc_peak -#> spring autumn -#> 12.5 25.0 -#> -#> $PEC_sw_drainage -#> spring autumn -#> 1.562500 4.807692 -#> </div></pre> - </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="#source">Source</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +</dl></div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p></div> + </div> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="fu">PEC_sw_exposit_drainage</span><span class="op">(</span><span class="fl">500</span>, Koc <span class="op">=</span> <span class="fl">150</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $perc_drainage_total</span> +<span class="r-out co"><span class="r-pr">#></span> spring autumn </span> +<span class="r-out co"><span class="r-pr">#></span> 0.2 1.0 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $perc_peak</span> +<span class="r-out co"><span class="r-pr">#></span> spring autumn </span> +<span class="r-out co"><span class="r-pr">#></span> 12.5 25.0 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_drainage</span> +<span class="r-out co"><span class="r-pr">#></span> spring autumn </span> +<span class="r-out co"><span class="r-pr">#></span> 1.562500 4.807692 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </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> - 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- </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>Calculate PEC surface water due to runoff and erosion as in Exposit 3</h1> @@ -111,152 +45,157 @@ in the worksheet "Konzept Runoff"." /> in the worksheet "Konzept Runoff".</p> </div> - <pre class="usage"><span class='fu'>PEC_sw_exposit_runoff</span>( - <span class='no'>rate</span>, - <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, - <span class='no'>Koc</span>, - <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, - <span class='kw'>t_runoff</span> <span class='kw'>=</span> <span class='fl'>3</span>, - <span class='kw'>exposit_reduction_version</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"3.02"</span>, <span class='st'>"3.01a"</span>, <span class='st'>"3.01a2"</span>, <span class='st'>"2.0"</span>), - <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>, - <span class='kw'>V_event</span> <span class='kw'>=</span> <span class='fl'>100</span>, - <span class='kw'>dilution</span> <span class='kw'>=</span> <span class='fl'>2</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>rate</th> - <td><p>The application rate in g/ha</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>The fraction intercepted by the crop</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>The sorption coefficient to soil organic carbon</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>The soil half-life in days</p></td> - </tr> - <tr> - <th>t_runoff</th> - <td><p>The time between application and the runoff event, where degradation occurs, in days</p></td> - </tr> - <tr> - <th>exposit_reduction_version</th> - <td><p>The version of the reduction factors to be used. "3.02" is the current + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_exposit_runoff</span><span class="op">(</span></span> +<span> <span class="va">rate</span>,</span> +<span> interception <span class="op">=</span> <span class="fl">0</span>,</span> +<span> <span class="va">Koc</span>,</span> +<span> DT50 <span class="op">=</span> <span class="cn">Inf</span>,</span> +<span> t_runoff <span class="op">=</span> <span class="fl">3</span>,</span> +<span> exposit_reduction_version <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">"3.02"</span>, <span class="st">"3.01a"</span>, <span class="st">"3.01a2"</span>, <span class="st">"2.0"</span><span class="op">)</span>,</span> +<span> V_ditch <span class="op">=</span> <span class="fl">30</span>,</span> +<span> V_event <span class="op">=</span> <span class="fl">100</span>,</span> +<span> dilution <span class="op">=</span> <span class="fl">2</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="source"> + <h2>Source</h2> + <p>Excel 3.02 spreadsheet available from + <a href="https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html" class="external-link">https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html</a></p> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>rate</dt> +<dd><p>The application rate in g/ha</p></dd> + + +<dt>interception</dt> +<dd><p>The fraction intercepted by the crop</p></dd> + + +<dt>Koc</dt> +<dd><p>The sorption coefficient to soil organic carbon</p></dd> + + +<dt>DT50</dt> +<dd><p>The soil half-life in days</p></dd> + + +<dt>t_runoff</dt> +<dd><p>The time between application and the runoff event, where degradation occurs, in days</p></dd> + + +<dt>exposit_reduction_version</dt> +<dd><p>The version of the reduction factors to be used. "3.02" is the current version used in Germany, "3.01a" is the version with additional percentages for 3 m and 6 m buffer zones used in Switzerland. "3.01a2" is a version introduced for consistency with previous calculations performed for a 3 m buffer zone in Switzerland, with the same reduction being applied to the dissolved -and the bound fraction.</p></td> - </tr> - <tr> - <th>V_ditch</th> - <td><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></td> - </tr> - <tr> - <th>V_event</th> - <td><p>The unreduced runoff volume, equivalent to 10 mm precipitation on 1 ha</p></td> - </tr> - <tr> - <th>dilution</th> - <td><p>The dilution factor</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> +and the bound fraction.</p></dd> - <p>Excel 3.02 spreadsheet available from - <a href='https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A list containing the following components</p><dl class='dl-horizontal'> - <dt>perc_runoff</dt><dd><p>The runoff percentages for dissolved and bound substance</p></dd> - <dt>runoff</dt><dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> - <dt>PEC_sw_runoff</dt><dd><p>A matrix containing PEC values for dissolved and bound substance +<dt>V_ditch</dt> +<dd><p>The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3</p></dd> + + +<dt>V_event</dt> +<dd><p>The unreduced runoff volume, equivalent to 10 mm precipitation on 1 ha</p></dd> + + +<dt>dilution</dt> +<dd><p>The dilution factor</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list containing the following components</p> +<p></p> +<dl><dt>perc_runoff</dt> +<dd><p>The runoff percentages for dissolved and bound substance</p></dd> + + <dt>runoff</dt> +<dd><p>A matrix containing dissolved and bound input for the different distances</p></dd> + + <dt>PEC_sw_runoff</dt> +<dd><p>A matrix containing PEC values for dissolved and bound substance for the different distances. If the rate was given in g/ha, the PECsw are in microg/L.</p></dd> + -</dl> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p><code><a href='perc_runoff_exposit.html'>perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href='perc_runoff_reduction_exposit.html'>perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>PEC_sw_exposit_runoff</span>(<span class='fl'>500</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>150</span>)</div><div class='output co'>#> $perc_runoff -#> dissolved bound -#> 0.248 0.001 -#> -#> $runoff -#> dissolved bound total -#> No buffer 1.240 0.00500 1.24500 -#> 5 m 0.744 0.00300 0.74700 -#> 10 m 0.496 0.00075 0.49675 -#> 20 m 0.248 0.00025 0.24825 -#> -#> $PEC_sw_runoff -#> dissolved bound total -#> No buffer 4.769231 0.019230769 4.788462 -#> 5 m 4.133333 0.016666667 4.150000 -#> 10 m 3.542857 0.005357143 3.548214 -#> 20 m 2.480000 0.002500000 2.482500 -#> </div><div class='input'> <span class='fu'>PEC_sw_exposit_runoff</span>(<span class='fl'>600</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>10000</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>195</span>, <span class='kw'>exposit</span> <span class='kw'>=</span> <span class='st'>"3.01a"</span>)</div><div class='output co'>#> $perc_runoff -#> dissolved bound -#> 0.037 0.159 -#> -#> $runoff -#> dissolved bound total -#> No buffer 0.21964521 0.94388078 1.16352600 -#> 3 m 0.16473391 0.66071655 0.82545046 -#> 5 m 0.13178713 0.56632847 0.69811560 -#> 6 m 0.12080487 0.42474635 0.54555122 -#> 10 m 0.08785809 0.14158212 0.22944020 -#> 20 m 0.04392904 0.04719404 0.09112308 -#> -#> $PEC_sw_runoff -#> dissolved bound total -#> No buffer 0.8447893 3.6303107 4.4751000 -#> 3 m 0.7844472 3.1462693 3.9307165 -#> 5 m 0.7321507 3.1462693 3.8784200 -#> 6 m 0.7106169 2.4985080 3.2091248 -#> 10 m 0.6275578 1.0113008 1.6388586 -#> 20 m 0.4392904 0.4719404 0.9112308 -#> </div></pre> - </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="#source">Source</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +</dl></div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> for runoff loss percentages and <code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> for runoff reduction percentages used</p></div> + </div> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="fu">PEC_sw_exposit_runoff</span><span class="op">(</span><span class="fl">500</span>, Koc <span class="op">=</span> <span class="fl">150</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $perc_runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound </span> +<span class="r-out co"><span class="r-pr">#></span> 0.248 0.001 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 1.240 0.00500 1.24500</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 0.744 0.00300 0.74700</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 0.496 0.00075 0.49675</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 0.248 0.00025 0.24825</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 4.769231 0.019230769 4.788462</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 4.133333 0.016666667 4.150000</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 3.542857 0.005357143 3.548214</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 2.480000 0.002500000 2.482500</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span> <span class="fu">PEC_sw_exposit_runoff</span><span class="op">(</span><span class="fl">600</span>, Koc <span class="op">=</span> <span class="fl">10000</span>, DT50 <span class="op">=</span> <span class="fl">195</span>, exposit <span class="op">=</span> <span class="st">"3.01a"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $perc_runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound </span> +<span class="r-out co"><span class="r-pr">#></span> 0.037 0.159 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0.21964521 0.94388078 1.16352600</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 0.16473391 0.66071655 0.82545046</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 0.13178713 0.56632847 0.69811560</span> +<span class="r-out co"><span class="r-pr">#></span> 6 m 0.12080487 0.42474635 0.54555122</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 0.08785809 0.14158212 0.22944020</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 0.04392904 0.04719404 0.09112308</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_runoff</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound total</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0.8447893 3.6303107 4.4751000</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 0.7844472 3.1462693 3.9307165</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 0.7321507 3.1462693 3.8784200</span> +<span class="r-out co"><span class="r-pr">#></span> 6 m 0.7106169 2.4985080 3.2091248</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 0.6275578 1.0113008 1.6388586</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 0.4392904 0.4719404 0.9112308</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </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> - 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Note that results for multiple applications should be compared to the corresponding results for a single application. At current, this is not done automatically in this implementation. Only Step 1 PECs are calculated. However, -input files are generated that are suitable as input also for Step 2 -to be used with the FOCUS calculator." /> -<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]> +input files can be generated that are suitable as input for +the FOCUS calculator."><!-- 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"> @@ -75,35 +23,21 @@ to be used with the FOCUS calculator." /> </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>Calculate PEC surface water at FOCUS Step 1</h1> @@ -117,119 +51,118 @@ authored by Michael Klein, in R. Note that results for multiple applications should be compared to the corresponding results for a single application. At current, this is not done automatically in this implementation. Only Step 1 PECs are calculated. However, -input files are generated that are suitable as input also for Step 2 -to be used with the FOCUS calculator.</p> +input files can be generated that are suitable as input for +the FOCUS calculator.</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_focus</span><span class="op">(</span></span> +<span> <span class="va">parent</span>,</span> +<span> <span class="va">rate</span>,</span> +<span> n <span class="op">=</span> <span class="fl">1</span>,</span> +<span> i <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> comment <span class="op">=</span> <span class="st">""</span>,</span> +<span> met <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> f_drift <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> f_rd <span class="op">=</span> <span class="fl">0.1</span>,</span> +<span> scenario <span class="op">=</span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">names</span>,</span> +<span> region <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">"n"</span>, <span class="st">"s"</span><span class="op">)</span>,</span> +<span> season <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">"of"</span>, <span class="st">"mm"</span>, <span class="st">"js"</span><span class="op">)</span>,</span> +<span> interception <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">"no interception"</span>, <span class="st">"minimal crop cover"</span>, <span class="st">"average crop cover"</span>,</span> +<span> <span class="st">"full canopy"</span><span class="op">)</span>,</span> +<span> met_form_water <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> txt_file <span class="op">=</span> <span class="st">"pesticide.txt"</span>,</span> +<span> overwrite <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> append <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> - <pre class="usage"><span class='fu'>PEC_sw_focus</span>( - <span class='no'>parent</span>, - <span class='no'>rate</span>, - <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>""</span>, - <span class='kw'>met</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>f_rd</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, - <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span>, - <span class='kw'>region</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"n"</span>, <span class='st'>"s"</span>), - <span class='kw'>season</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'>"of"</span>, <span class='st'>"mm"</span>, <span class='st'>"js"</span>), - <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"no interception"</span>, <span class='st'>"minimal crop cover"</span>, <span class='st'>"average crop cover"</span>, - <span class='st'>"full canopy"</span>), - <span class='kw'>met_form_water</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>txt_file</span> <span class='kw'>=</span> <span class='st'>"pesticide.txt"</span>, - <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>TRUE</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>parent</th> - <td><p>A list containing substance specific parameters, e.g. -conveniently generated by <code><a href='chent_focus_sw.html'>chent_focus_sw</a></code>.</p></td> - </tr> - <tr> - <th>rate</th> - <td><p>The application rate in g/ha. Overriden when -applications are given explicitly</p></td> - </tr> - <tr> - <th>n</th> - <td><p>The number of applications</p></td> - </tr> - <tr> - <th>i</th> - <td><p>The application interval</p></td> - </tr> - <tr> - <th>comment</th> - <td><p>A comment for the input file</p></td> - </tr> - <tr> - <th>met</th> - <td><p>A list containing metabolite specific parameters. e.g. -conveniently generated by <code><a href='chent_focus_sw.html'>chent_focus_sw</a></code>. If not NULL, -the PEC is calculated for this compound, not the parent.</p></td> - </tr> - <tr> - <th>f_drift</th> - <td><p>The fraction of the application rate reaching the waterbody + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>parent</dt> +<dd><p>A list containing substance specific parameters, e.g. +conveniently generated by [chent_focus_sw].</p></dd> + + +<dt>rate</dt> +<dd><p>The application rate in g/ha. Overriden when +applications are given explicitly</p></dd> + + +<dt>n</dt> +<dd><p>The number of applications</p></dd> + + +<dt>i</dt> +<dd><p>The application interval</p></dd> + + +<dt>comment</dt> +<dd><p>A comment for the input file</p></dd> + + +<dt>met</dt> +<dd><p>A list containing metabolite specific parameters. e.g. +conveniently generated by [chent_focus_sw]. If not NULL, +the PEC is calculated for this compound, not the parent.</p></dd> + + +<dt>f_drift</dt> +<dd><p>The fraction of the application rate reaching the waterbody via drift. If NA, this is derived from the scenario name and the number of applications via the drift data defined by the -<code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenarios</a></code></p></td> - </tr> - <tr> - <th>f_rd</th> - <td><p>The fraction of the amount applied reaching the waterbody via +[FOCUS_Step_12_scenarios]</p></dd> + + +<dt>f_rd</dt> +<dd><p>The fraction of the amount applied reaching the waterbody via runoff/drainage. At Step 1, it is assumed to be 10<!-- %, be it the --> -parent or a metabolite</p></td> - </tr> - <tr> - <th>scenario</th> - <td><p>The name of the scenario. Must be one of the scenario -names given in <code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenarios</a></code></p></td> - </tr> - <tr> - <th>region</th> - <td><p>'n' for Northern Europe or 's' for Southern Europe. If NA, only -Step 1 PECsw are calculated</p></td> - </tr> - <tr> - <th>season</th> - <td><p>'of' for October to February, 'mm' for March to May, and 'js' -for June to September. If NA, only step 1 PECsw are calculated</p></td> - </tr> - <tr> - <th>interception</th> - <td><p>One of 'no interception' (default), 'minimal crop cover', -'average crop cover' or 'full canopy'</p></td> - </tr> - <tr> - <th>met_form_water</th> - <td><p>Should the metabolite formation in water be taken into +parent or a metabolite</p></dd> + + +<dt>scenario</dt> +<dd><p>The name of the scenario. Must be one of the scenario +names given in [FOCUS_Step_12_scenarios]</p></dd> + + +<dt>region</dt> +<dd><p>'n' for Northern Europe or 's' for Southern Europe. If NA, only +Step 1 PECsw are calculated</p></dd> + + +<dt>season</dt> +<dd><p>'of' for October to February, 'mm' for March to May, and 'js' +for June to September. If NA, only step 1 PECsw are calculated</p></dd> + + +<dt>interception</dt> +<dd><p>One of 'no interception' (default), 'minimal crop cover', +'average crop cover' or 'full canopy'</p></dd> + + +<dt>met_form_water</dt> +<dd><p>Should the metabolite formation in water be taken into account? This can be switched off to check the influence and to compare -with previous versions of the Steps 12 calculator</p></td> - </tr> - <tr> - <th>txt_file</th> - <td><p>the name, and potentially the full path to the +with previous versions of the Steps 12 calculator</p></dd> + + +<dt>txt_file</dt> +<dd><p>the name, and potentially the full path to the Steps.12 input text file to which the specification of the run(s) -should be written</p></td> - </tr> - <tr> - <th>overwrite</th> - <td><p>Should an existing file a the location specified in -<code>txt_file</code> be overwritten? Only takes effect if append is FALSE.</p></td> - </tr> - <tr> - <th>append</th> - <td><p>Should the input text file be appended?</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> +should be written</p></dd> + + +<dt>overwrite</dt> +<dd><p>Should an existing file a the location specified in +<code>txt_file</code> be overwritten? Only takes effect if append is FALSE.</p></dd> + +<dt>append</dt> +<dd><p>Should the input text file be appended, if it exists?</p></dd> + +</dl></div> + <div id="note"> + <h2>Note</h2> <p>The formulas for input to the waterbody via runoff/drainage of the parent and subsequent formation of the metabolite in water is not documented in the model description coming with the calculator. As one would @@ -237,142 +170,141 @@ should be written</p></td> multiplying the application rate with the molar weight correction and the formation fraction in water/sediment systems.</p> <p>Step 2 is not implemented.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div id="references"> + <h2>References</h2> <p>FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). FOrum for the Co-ordination of pesticde fate models and their USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic<!-- %20FOCUS_SWS_vc1.4.pdf --></p> <p>Website of the Steps 1 and 2 calculator at the Joint Research Center of the European Union: http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># Parent only</span> -<span class='no'>dummy_1</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"Dummy 1"</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>6000</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>344.8</span>) -<span class='fu'>PEC_sw_focus</span>(<span class='no'>dummy_1</span>, <span class='fl'>3000</span>, <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> $f_drift -#> [1] 0 -#> -#> $eq_rate_drift_s -#> [1] 3000 -#> -#> $eq_rate_rd_s -#> [1] 3000 -#> -#> $eq_rate_rd_parent_s -#> [1] NA -#> -#> $input_drift_s -#> [1] 0 -#> -#> $input_rd_s -#> [1] 300 -#> -#> $f_rd_sw -#> [1] 0.6850566 -#> -#> $f_rd_sed -#> [1] 0.3149434 -#> -#> $PEC -#> type -#> Time PECsw TWAECsw PECsed TWAECsed -#> 0 6.850566e+02 NA 2.362075e+03 NA -#> 1 6.103161e+02 647.68635 2.104370e+03 2233.2225 -#> 2 5.437298e+02 612.03420 1.874780e+03 2110.2939 -#> 4 4.315586e+02 548.76030 1.488014e+03 1892.1255 -#> 7 3.051580e+02 469.88375 1.052185e+03 1620.1592 -#> 14 1.359325e+02 339.57370 4.686951e+02 1170.8501 -#> 21 6.055102e+01 257.45458 2.087799e+02 887.7034 -#> 28 2.697241e+01 203.47173 9.300089e+01 701.5705 -#> 42 5.352005e+00 140.10377 1.845371e+01 483.0778 -#> 50 2.123945e+00 118.24602 7.323361e+00 407.7123 -#> 100 6.585062e-03 59.30629 2.270529e-02 204.4881 -#> -#> $PEC_sw_max -#> [1] 685.0566 -#> -#> $PEC_sed_max -#> [1] 2362.075 -#> </div><div class='input'> -<span class='co'># Metabolite</span> -<span class='no'>new_dummy</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"New Dummy"</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>) -<span class='no'>M1</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"M1"</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>50</span>, - <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) -<span class='fu'>PEC_sw_focus</span>(<span class='no'>new_dummy</span>, <span class='fl'>1000</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='st'>"cereals, winter"</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='no'>M1</span>)</div><div class='output co'>#> $f_drift -#> [1] 0.02759 -#> -#> $eq_rate_drift_s -#> [1] 0 -#> -#> $eq_rate_rd_s -#> [1] 200 -#> -#> $eq_rate_rd_parent_s -#> [1] 0 -#> -#> $input_drift_s -#> [1] 0 -#> -#> $input_rd_s -#> [1] 20 -#> -#> $f_rd_sw -#> [1] 0.9375 -#> -#> $f_rd_sed -#> [1] 0.0625 -#> -#> $PEC -#> type -#> Time PECsw TWAECsw PECsed TWAECsed -#> 0 62.50000 NA 31.25000 NA -#> 1 62.06828 62.28414 31.03414 31.14207 -#> 2 61.63954 62.06890 30.81977 31.03445 -#> 4 60.79093 61.64158 30.39547 30.82079 -#> 7 59.53987 61.00800 29.76994 30.50400 -#> 14 56.71995 59.56326 28.35997 29.78163 -#> 21 54.03358 58.16414 27.01679 29.08207 -#> 28 51.47444 56.80902 25.73722 28.40451 -#> 42 46.71404 54.22460 23.35702 27.11230 -#> 50 44.19417 52.81945 22.09709 26.40973 -#> 100 31.25000 45.08422 15.62500 22.54211 -#> -#> $PEC_sw_max -#> [1] 62.5 -#> -#> $PEC_sed_max -#> [1] 31.25 -#> </div></pre> - </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="#note">Note</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Parent only</span></span></span> +<span class="r-in"><span><span class="va">dummy_1</span> <span class="op"><-</span> <span class="fu"><a href="chent_focus_sw.html">chent_focus_sw</a></span><span class="op">(</span><span class="st">"Dummy 1"</span>, cwsat <span class="op">=</span> <span class="fl">6000</span>, DT50_ws <span class="op">=</span> <span class="fl">6</span>, Koc <span class="op">=</span> <span class="fl">344.8</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_focus</span><span class="op">(</span><span class="va">dummy_1</span>, <span class="fl">3000</span>, f_drift <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $f_drift</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_drift_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 3000</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_rd_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 3000</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_rd_parent_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $input_drift_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $input_rd_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 300</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $f_rd_sw</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.6850566</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $f_rd_sed</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.3149434</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC</span> +<span class="r-out co"><span class="r-pr">#></span> type</span> +<span class="r-out co"><span class="r-pr">#></span> Time PECsw TWAECsw PECsed TWAECsed</span> +<span class="r-out co"><span class="r-pr">#></span> 0 6.850566e+02 NA 2.362075e+03 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 1 6.103161e+02 647.68635 2.104370e+03 2233.2225</span> +<span class="r-out co"><span class="r-pr">#></span> 2 5.437298e+02 612.03420 1.874780e+03 2110.2939</span> +<span class="r-out co"><span class="r-pr">#></span> 4 4.315586e+02 548.76030 1.488014e+03 1892.1255</span> +<span class="r-out co"><span class="r-pr">#></span> 7 3.051580e+02 469.88375 1.052185e+03 1620.1592</span> +<span class="r-out co"><span class="r-pr">#></span> 14 1.359325e+02 339.57370 4.686951e+02 1170.8501</span> +<span class="r-out co"><span class="r-pr">#></span> 21 6.055102e+01 257.45458 2.087799e+02 887.7034</span> +<span class="r-out co"><span class="r-pr">#></span> 28 2.697241e+01 203.47173 9.300089e+01 701.5705</span> +<span class="r-out co"><span class="r-pr">#></span> 42 5.352005e+00 140.10377 1.845371e+01 483.0778</span> +<span class="r-out co"><span class="r-pr">#></span> 50 2.123945e+00 118.24602 7.323361e+00 407.7123</span> +<span class="r-out co"><span class="r-pr">#></span> 100 6.585062e-03 59.30629 2.270529e-02 204.4881</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_max</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 685.0566</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sed_max</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 2362.075</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Metabolite</span></span></span> +<span class="r-in"><span><span class="va">new_dummy</span> <span class="op"><-</span> <span class="fu"><a href="chent_focus_sw.html">chent_focus_sw</a></span><span class="op">(</span><span class="st">"New Dummy"</span>, mw <span class="op">=</span> <span class="fl">250</span>, Koc <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">M1</span> <span class="op"><-</span> <span class="fu"><a href="chent_focus_sw.html">chent_focus_sw</a></span><span class="op">(</span><span class="st">"M1"</span>, mw <span class="op">=</span> <span class="fl">100</span>, cwsat <span class="op">=</span> <span class="fl">100</span>, DT50_ws <span class="op">=</span> <span class="fl">100</span>, Koc <span class="op">=</span> <span class="fl">50</span>,</span></span> +<span class="r-in"><span> max_ws <span class="op">=</span> <span class="fl">0</span>, max_soil <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">PEC_sw_focus</span><span class="op">(</span><span class="va">new_dummy</span>, <span class="fl">1000</span>, scenario <span class="op">=</span> <span class="st">"cereals, winter"</span>, met <span class="op">=</span> <span class="va">M1</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $f_drift</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.02759</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_drift_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_rd_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 200</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $eq_rate_rd_parent_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $input_drift_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $input_rd_s</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 20</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $f_rd_sw</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.9375</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $f_rd_sed</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC</span> +<span class="r-out co"><span class="r-pr">#></span> type</span> +<span class="r-out co"><span class="r-pr">#></span> Time PECsw TWAECsw PECsed TWAECsed</span> +<span class="r-out co"><span class="r-pr">#></span> 0 62.50000 NA 31.25000 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 1 62.06828 62.28414 31.03414 31.14207</span> +<span class="r-out co"><span class="r-pr">#></span> 2 61.63954 62.06890 30.81977 31.03445</span> +<span class="r-out co"><span class="r-pr">#></span> 4 60.79093 61.64158 30.39547 30.82079</span> +<span class="r-out co"><span class="r-pr">#></span> 7 59.53987 61.00800 29.76994 30.50400</span> +<span class="r-out co"><span class="r-pr">#></span> 14 56.71995 59.56326 28.35997 29.78163</span> +<span class="r-out co"><span class="r-pr">#></span> 21 54.03358 58.16414 27.01679 29.08207</span> +<span class="r-out co"><span class="r-pr">#></span> 28 51.47444 56.80902 25.73722 28.40451</span> +<span class="r-out co"><span class="r-pr">#></span> 42 46.71404 54.22460 23.35702 27.11230</span> +<span class="r-out co"><span class="r-pr">#></span> 50 44.19417 52.81945 22.09709 26.40973</span> +<span class="r-out co"><span class="r-pr">#></span> 100 31.25000 45.08422 15.62500 22.54211</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sw_max</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 62.5</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $PEC_sed_max</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 31.25</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </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> diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html index 458eeb7..247c8d7 100644 --- a/docs/reference/PEC_sw_sed.html +++ 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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>Calculate predicted environmental concentrations in sediment from surface @@ -114,89 +48,89 @@ water concentrations</h1> PEC calculator</p> </div> - <pre class="usage"><span class='fu'>PEC_sw_sed</span>( - <span class='no'>PEC_sw</span>, - <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>100</span>, - <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"percentage"</span>, - <span class='kw'>sediment_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, - <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, - <span class='kw'>sediment_density</span> <span class='kw'>=</span> <span class='fl'>1.3</span>, - <span class='kw'>PEC_sed_units</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"µg/kg"</span>, <span class='st'>"mg/kg"</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>PEC_sw</th> - <td><p>Numeric vector or matrix of surface water concentrations in µg/L for -which the corresponding sediment concentration is to be estimated</p></td> - </tr> - <tr> - <th>percentage</th> - <td><p>The percentage in sediment, used for the percentage method</p></td> - </tr> - <tr> - <th>method</th> - <td><p>The method used for the calculation</p></td> - </tr> - <tr> - <th>sediment_depth</th> - <td><p>Depth of the sediment layer</p></td> - </tr> - <tr> - <th>water_depth</th> - <td><p>Depth of the water body in cm</p></td> - </tr> - <tr> - <th>sediment_density</th> - <td><p>The density of the sediment in L/kg (equivalent to -g/cm3)</p></td> - </tr> - <tr> - <th>PEC_sed_units</th> - <td><p>The units of the estimated sediment PEC value</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The predicted concentration in sediment</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>PEC_sw_sed</span>(<span class='fu'><a href='PEC_sw_drift.html'>PEC_sw_drift</a></span>(<span class='fl'>100</span>, <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fl'>1</span>), <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>50</span>)</div><div class='output co'>#> 1 m -#> 2.130769 </div></pre> - </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="#examples">Examples</a></li> - </ul> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">PEC_sw_sed</span><span class="op">(</span></span> +<span> <span class="va">PEC_sw</span>,</span> +<span> percentage <span class="op">=</span> <span class="fl">100</span>,</span> +<span> method <span class="op">=</span> <span class="st">"percentage"</span>,</span> +<span> sediment_depth <span class="op">=</span> <span class="fl">5</span>,</span> +<span> water_depth <span class="op">=</span> <span class="fl">30</span>,</span> +<span> sediment_density <span class="op">=</span> <span class="fl">1.3</span>,</span> +<span> PEC_sed_units <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">"µg/kg"</span>, <span class="st">"mg/kg"</span><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>PEC_sw</dt> +<dd><p>Numeric vector or matrix of surface water concentrations in µg/L for +which the corresponding sediment concentration is to be estimated</p></dd> + + +<dt>percentage</dt> +<dd><p>The percentage in sediment, used for the percentage method</p></dd> + + +<dt>method</dt> +<dd><p>The method used for the calculation</p></dd> + + +<dt>sediment_depth</dt> +<dd><p>Depth of the sediment layer</p></dd> + + +<dt>water_depth</dt> +<dd><p>Depth of the water body in cm</p></dd> + +<dt>sediment_density</dt> +<dd><p>The density of the sediment in L/kg (equivalent to +g/cm3)</p></dd> + + +<dt>PEC_sed_units</dt> +<dd><p>The units of the estimated sediment PEC value</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The predicted concentration in sediment</p> + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">PEC_sw_sed</span><span class="op">(</span><span class="fu"><a href="PEC_sw_drift.html">PEC_sw_drift</a></span><span class="op">(</span><span class="fl">100</span>, distances <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>, percentage <span class="op">=</span> <span class="fl">50</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 1 m </span> +<span class="r-out co"><span class="r-pr">#></span> 2.130769 </span> +</code></pre></div> + </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> diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differnew file mode 100644 index 0000000..8269e66 --- /dev/null +++ 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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>Actual and maximum moving window time average concentrations for SFO kinetics</h1> @@ -109,71 +43,69 @@ <p>Actual and maximum moving window time average concentrations for SFO kinetics</p> </div> - <pre class="usage"><span class='fu'>SFO_actual_twa</span>(<span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, <span class='fl'>50</span>, <span class='fl'>100</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>DT50</th> - <td><p>The half-life.</p></td> - </tr> - <tr> - <th>times</th> - <td><p>The output times, and window sizes for time weighted average concentrations</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SFO_actual_twa</span><span class="op">(</span>DT50 <span class="op">=</span> <span class="fl">1000</span>, times <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="fl">0</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">21</span>, <span class="fl">28</span>, <span class="fl">42</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> + </div> + <div id="source"> + <h2>Source</h2> <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1, 18 December 2014, p. 251</p> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>DT50</dt> +<dd><p>The half-life.</p></dd> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>SFO_actual_twa</span>(<span class='fl'>10</span>)</div><div class='output co'>#> actual twa -#> 0 1.0000000000 NaN -#> 1 0.9330329915 0.9661297 -#> 2 0.8705505633 0.9337803 -#> 4 0.7578582833 0.8733416 -#> 7 0.6155722067 0.7923030 -#> 14 0.3789291416 0.6400113 -#> 21 0.2332582479 0.5267498 -#> 28 0.1435872944 0.4412651 -#> 42 0.0544094102 0.3248093 -#> 50 0.0312500000 0.2795222 -#> 100 0.0009765625 0.1441286</div></pre> - </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="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> - </ul> +<dt>times</dt> +<dd><p>The output times, and window sizes for time weighted average concentrations</p></dd> + +</dl></div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">SFO_actual_twa</span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> actual twa</span> +<span class="r-out co"><span class="r-pr">#></span> 0 1.0000000000 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> 1 0.9330329915 0.9661297</span> +<span class="r-out co"><span class="r-pr">#></span> 2 0.8705505633 0.9337803</span> +<span class="r-out co"><span class="r-pr">#></span> 4 0.7578582833 0.8733416</span> +<span class="r-out co"><span class="r-pr">#></span> 7 0.6155722067 0.7923030</span> +<span class="r-out co"><span class="r-pr">#></span> 14 0.3789291416 0.6400113</span> +<span class="r-out co"><span class="r-pr">#></span> 21 0.2332582479 0.5267498</span> +<span class="r-out co"><span class="r-pr">#></span> 28 0.1435872944 0.4412651</span> +<span class="r-out co"><span class="r-pr">#></span> 42 0.0544094102 0.3248093</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.0312500000 0.2795222</span> +<span class="r-out co"><span class="r-pr">#></span> 100 0.0009765625 0.1441286</span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" 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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>Determine the SSLRC mobility classification for a chemical substance from its Koc</h1> @@ -105,86 +41,81 @@ checked against the spreadsheet published on the CRC website" /> </div> <div class="ref-description"> - <p>This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website</p> - </div> - <pre class="usage"><span class='fu'>SSLRC_mobility_classification</span>(<span class='no'>Koc</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>Koc</th> - <td><p>The sorption coefficient normalised to organic carbon in L/kg</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SSLRC_mobility_classification</span><span class="op">(</span><span class="va">Koc</span><span class="op">)</span></span></code></pre></div> + </div> - <p>A list containing the classification and the percentage of the - compound transported per 10 mm drain water</p> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>Koc</dt> +<dd><p>The sorption coefficient normalised to organic carbon in L/kg</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> +<p>A list containing the classification and the percentage of the + compound transported per 10 mm drain water</p> + </div> + <div id="references"> + <h2>References</h2> <p>HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (for UK specific authorisation requests) - <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> accessed 2019-09-27</p> <p>Drainage PECs Version 1.0 (2015) Spreadsheet published at - <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> + <a href="https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx" class="external-link">https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> accessed 2019-09-27</p> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>SSLRC_mobility_classification</span>(<span class='fl'>100</span>)</div><div class='output co'>#> $`Mobility classification` -#> [1] "Moderately mobile" -#> -#> $`Percentage drained per mm of drain water` -#> [1] 0.7 -#> </div><div class='input'><span class='fu'>SSLRC_mobility_classification</span>(<span class='fl'>10000</span>)</div><div class='output co'>#> $`Mobility classification` -#> [1] "Non mobile" -#> -#> $`Percentage drained per mm of drain water` -#> [1] 0.008 -#> </div></pre> - </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> - - <li><a href="#examples">Examples</a></li> - </ul> - + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">SSLRC_mobility_classification</span><span class="op">(</span><span class="fl">100</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $`Mobility classification`</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "Moderately mobile"</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`Percentage drained per mm of drain water`</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.7</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span><span class="fu">SSLRC_mobility_classification</span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $`Mobility classification`</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "Non mobile"</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`Percentage drained per mm of drain water`</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.008</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </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/" 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Usually, an instance of this class will be generated -by read.TOXSWA_cwa." /> - - - - -<!-- 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]> +by read.TOXSWA_cwa."><!-- 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 data-spy="scroll" data-target="#toc"> <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"> @@ -76,35 +21,21 @@ by read.TOXSWA_cwa." /> </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>R6 class for holding TOXSWA water concentration data and associated statistics</h1> @@ -117,179 +48,236 @@ by read.TOXSWA_cwa." /> and some associated statistics. like maximum moving window average concentrations, and dataframes holding the events exceeding specified thresholds. Usually, an instance of this class will be generated -by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p> +by <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code>.</p> </div> + <div id="format"> + <h2>Format</h2> + <p>An <code>R6Class</code> generator object.</p> + </div> + <div id="public-fields"> + <h2>Public fields</h2> + <p></p><div class="r6-fields"><dl><dt><code>filename</code></dt> +<dd><p>Length one character vector holding the filename.</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>An <code>R6Class</code> generator object.</p> - <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> +<dt><code>basedir</code></dt> +<dd><p>Length one character vector holding the directory where the file came from.</p></dd> + - <p><div class="r6-fields"></p><dl'> -<dt><code>filename</code></dt><dd><p>Length one character vector holding the filename.</p></dd> +<dt><code>zipfile</code></dt> +<dd><p>If not null, giving the path to the zip file from which the file was read.</p></dd> -<dt><code>basedir</code></dt><dd><p>Length one character vector holding the directory where the file came from.</p></dd> -<dt><code>zipfile</code></dt><dd><p>If not null, giving the path to the zip file from which the file was read.</p></dd> +<dt><code>segment</code></dt> +<dd><p>Length one integer, specifying for which segment the cwa data were read.</p></dd> -<dt><code>segment</code></dt><dd><p>Length one integer, specifying for which segment the cwa data were read.</p></dd> -<dt><code>substance</code></dt><dd><p>The TOXSWA name of the substance.</p></dd> +<dt><code>substance</code></dt> +<dd><p>The TOXSWA name of the substance.</p></dd> -<dt><code>cwas</code></dt><dd><p>Dataframe holding the concentrations.</p></dd> -<dt><code>events</code></dt><dd><p>List of dataframes holding the event statistics for each threshold.</p></dd> +<dt><code>cwas</code></dt> +<dd><p>Dataframe holding the concentrations.</p></dd> -<dt><code>windows</code></dt><dd><p>Matrix of maximum time weighted average concentrations (TWAC_max) + +<dt><code>events</code></dt> +<dd><p>List of dataframes holding the event statistics for each threshold.</p></dd> + + +<dt><code>windows</code></dt> +<dd><p>Matrix of maximum time weighted average concentrations (TWAC_max) and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) for the requested moving window sizes in days.</p></dd> -</dl><p></div></p> - <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> +</dl><p></p></div> + </div> + <div id="methods"> + <h2>Methods</h2> -<h3>Public methods</h3> - -<ul> -<li><p><a href='#method-new'><code>TOXSWA_cwa$new()</code></a></p></li> -<li><p><a href='#method-moving_windows'><code>TOXSWA_cwa$moving_windows()</code></a></p></li> -<li><p><a href='#method-get_events'><code>TOXSWA_cwa$get_events()</code></a></p></li> -<li><p><a href='#method-print'><code>TOXSWA_cwa$print()</code></a></p></li> -<li><p><a href='#method-clone'><code>TOXSWA_cwa$clone()</code></a></p></li> -</ul> -<p><hr> -<a id="method-new"></a></p><h3>Method <code>new()</code></h3> -<p>Create a TOXSWA_cwa object from a file</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>new</span>( - <span class='no'>filename</span>, - <span class='no'>basedir</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>, - <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, - <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span> -)</pre><p></div></p> - -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> -<dt><code>filename</code></dt><dd><p>The filename</p></dd> - -<dt><code>basedir</code></dt><dd><p>The directory to look in</p></dd> - -<dt><code>zipfile</code></dt><dd><p>Optional path to a zipfile holding the file</p></dd> - -<dt><code>segment</code></dt><dd><p>Either "last" or the number of the segment for which to read the data</p></dd> - -<dt><code>substance</code></dt><dd><p>The TOXSWA substance name (for TOXSWA 4 or higher)</p></dd> - -<dt><code>total</code></dt><dd><p>Should total concentrations be read in? If FALSE, free concentrations are read</p></dd> - -</dl><p></div></p> -<p><hr> -<a id="method-moving_windows"></a></p><h3>Method <code>moving_windows()</code></h3> -<p>Add to the `windows` field described above.</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>moving_windows</span>(<span class='no'>windows</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> - -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> -<dt><code>windows</code></dt><dd><p>Window sizes in days</p></dd> - -<dt><code>total</code></dt><dd><p>If TRUE, the total concentration including the amount adsorbed to +<div class="section"> +<h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> + +<ul><li><p><a href="#method-TOXSWA_cwa-new"><code>TOXSWA_cwa$new()</code></a></p></li> +<li><p><a href="#method-TOXSWA_cwa-moving_windows"><code>TOXSWA_cwa$moving_windows()</code></a></p></li> +<li><p><a href="#method-TOXSWA_cwa-get_events"><code>TOXSWA_cwa$get_events()</code></a></p></li> +<li><p><a href="#method-TOXSWA_cwa-print"><code>TOXSWA_cwa$print()</code></a></p></li> +<li><p><a href="#method-TOXSWA_cwa-clone"><code>TOXSWA_cwa$clone()</code></a></p></li> +</ul></div><p></p><hr><a id="method-TOXSWA_cwa-new"></a><div class="section"> +<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> +<p>Create a TOXSWA_cwa object from a file</p><div class="section"> +<h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/TOXSWA_cwa.html">TOXSWA_cwa</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> +<span> <span class="va">filename</span>,</span> +<span> <span class="va">basedir</span>,</span> +<span> zipfile <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> segment <span class="op">=</span> <span class="st">"last"</span>,</span> +<span> substance <span class="op">=</span> <span class="st">"parent"</span>,</span> +<span> total <span class="op">=</span> <span class="cn">FALSE</span></span> +<span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4> +<p></p><div class="arguments"><dl><dt><code>filename</code></dt> +<dd><p>The filename</p></dd> + + +<dt><code>basedir</code></dt> +<dd><p>The directory to look in</p></dd> + + +<dt><code>zipfile</code></dt> +<dd><p>Optional path to a zipfile holding the file</p></dd> + + +<dt><code>segment</code></dt> +<dd><p>Either "last" or the number of the segment for which to read the data</p></dd> + + +<dt><code>substance</code></dt> +<dd><p>The TOXSWA substance name (for TOXSWA 4 or higher)</p></dd> + + +<dt><code>total</code></dt> +<dd><p>Should total concentrations be read in? If FALSE, free concentrations are read</p></dd> + + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-TOXSWA_cwa-moving_windows"></a><div class="section"> +<h3 id="method-moving-windows-">Method <code>moving_windows()</code><a class="anchor" aria-label="anchor" href="#method-moving-windows-"></a></h3> +<p>Add to the `windows` field described above.</p><div class="section"> +<h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">moving_windows</span><span class="op">(</span><span class="va">windows</span>, total <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4> +<p></p><div class="arguments"><dl><dt><code>windows</code></dt> +<dd><p>Window sizes in days</p></dd> + + +<dt><code>total</code></dt> +<dd><p>If TRUE, the total concentration including the amount adsorbed to suspended matter will be used.</p></dd> -</dl><p></div></p> -<p><hr> -<a id="method-get_events"></a></p><h3>Method <code>get_events()</code></h3> + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-TOXSWA_cwa-get_events"></a><div class="section"> +<h3 id="method-get-events-">Method <code>get_events()</code><a class="anchor" aria-label="anchor" href="#method-get-events-"></a></h3> <p>Populate a datataframe with event information for the specified threshold value. The resulting dataframe is stored in the `events` -field of the object.</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>get_events</span>(<span class='no'>thresholds</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> +field of the object.</p><div class="section"> +<h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">get_events</span><span class="op">(</span><span class="va">thresholds</span>, total <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4> +<p></p><div class="arguments"><dl><dt><code>thresholds</code></dt> +<dd><p>Threshold values in µg/L.</p></dd> -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> -<dt><code>thresholds</code></dt><dd><p>Threshold values in µg/L.</p></dd> -<dt><code>total</code></dt><dd><p>If TRUE, the total concentration including the amount adsorbed to +<dt><code>total</code></dt> +<dd><p>If TRUE, the total concentration including the amount adsorbed to suspended matter will be used.</p></dd> -</dl><p></div></p> -<p><hr> -<a id="method-print"></a></p><h3>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></h3> -<p>Print a `TOXSWA_cwa` object</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>()</pre><p></div></p> - -<p><hr> -<a id="method-clone"></a></p><h3>Method <code>clone()</code></h3> -<p>The objects of this class are cloneable with this method.</p><h3>Usage</h3> -<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>clone</span>(<span class='kw'>deep</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> - -<h3>Arguments</h3> -<p><div class="arguments"></p><dl'> -<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd> - -</dl><p></div></p> - - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>H_sw_R1_stream</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>, - <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/system.file.html'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>, - <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>)) -<span class='no'>H_sw_R1_stream</span>$<span class='fu'>get_events</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2</span>, <span class='fl'>10</span>)) -<span class='no'>H_sw_R1_stream</span>$<span class='fu'>moving_windows</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>7</span>, <span class='fl'>21</span>)) -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>H_sw_R1_stream</span>)</div><div class='output co'>#> <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 -#> datetime t t_firstjan t_rel_to_max cwa_mug_per_L -#> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0 -#> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0 -#> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0 -#> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0 -#> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0 -#> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0 -#> cwa_tot_mug_per_L -#> 20 0 -#> 40 0 -#> 60 0 -#> 80 0 -#> 100 0 -#> 120 0 -#> Moving window analysis -#> window max_TWAC max_AUC_h max_AUC_d -#> 1 7 days 2.3926551 401.9660 16.74859 -#> 2 21 days 0.8369248 421.8101 17.57542 -#> Event statistics for threshold 2 -#> t_start cwa_max duration pre_interval AUC_h AUC_d -#> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501 -#> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162 -#> Event statistics for threshold 10 -#> t_start cwa_max duration pre_interval AUC_h AUC_d -#> 1 55.083 40.58401 0.459 55.083 379.433 15.80971</div></pre> + +</dl><p></p></div> +</div> + +</div><p></p><hr><a id="method-TOXSWA_cwa-print"></a><div class="section"> +<h3 id="method-print-">Method <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code><a class="anchor" aria-label="anchor" href="#method-print-"></a></h3> +<p>Print a `TOXSWA_cwa` object</p><div class="section"> +<h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + + +</div><p></p><hr><a id="method-TOXSWA_cwa-clone"></a><div class="section"> +<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> +<p>The objects of this class are cloneable with this method.</p><div class="section"> +<h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4> +<p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> +</div> + +<div class="section"> +<h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4> +<p></p><div class="arguments"><dl><dt><code>deep</code></dt> +<dd><p>Whether to make a deep clone.</p></dd> + + +</dl><p></p></div> +</div> + +</div> + + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_R1_stream</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00003s_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>,</span></span> +<span class="r-in"><span> package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">H_sw_R1_stream</span><span class="op">$</span><span class="fu">get_events</span><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="fl">2</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">H_sw_R1_stream</span><span class="op">$</span><span class="fu">moving_windows</span><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="fl">7</span>, <span class="fl">21</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><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">H_sw_R1_stream</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 </span> +<span class="r-out co"><span class="r-pr">#></span> datetime t t_firstjan t_rel_to_max cwa_mug_per_L</span> +<span class="r-out co"><span class="r-pr">#></span> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0</span> +<span class="r-out co"><span class="r-pr">#></span> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0</span> +<span class="r-out co"><span class="r-pr">#></span> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0</span> +<span class="r-out co"><span class="r-pr">#></span> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0</span> +<span class="r-out co"><span class="r-pr">#></span> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0</span> +<span class="r-out co"><span class="r-pr">#></span> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0</span> +<span class="r-out co"><span class="r-pr">#></span> cwa_tot_mug_per_L</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0</span> +<span class="r-out co"><span class="r-pr">#></span> 60 0</span> +<span class="r-out co"><span class="r-pr">#></span> 80 0</span> +<span class="r-out co"><span class="r-pr">#></span> 100 0</span> +<span class="r-out co"><span class="r-pr">#></span> 120 0</span> +<span class="r-out co"><span class="r-pr">#></span> Moving window analysis</span> +<span class="r-out co"><span class="r-pr">#></span> window max_TWAC max_AUC_h max_AUC_d</span> +<span class="r-out co"><span class="r-pr">#></span> 1 7 days 2.3926551 401.9660 16.74859</span> +<span class="r-out co"><span class="r-pr">#></span> 2 21 days 0.8369248 421.8101 17.57542</span> +<span class="r-out co"><span class="r-pr">#></span> Event statistics for threshold 2 </span> +<span class="r-out co"><span class="r-pr">#></span> t_start cwa_max duration pre_interval AUC_h AUC_d</span> +<span class="r-out co"><span class="r-pr">#></span> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501</span> +<span class="r-out co"><span class="r-pr">#></span> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162</span> +<span class="r-out co"><span class="r-pr">#></span> Event statistics for threshold 10 </span> +<span class="r-out co"><span class="r-pr">#></span> t_start cwa_max duration pre_interval AUC_h AUC_d</span> +<span class="r-out co"><span class="r-pr">#></span> 1 55.083 40.58401 0.459 55.083 379.433 15.80971</span> +</code></pre></div> + </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> + <nav id="toc" data-toggle="toc" 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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="Estimation of the transpiration stream concentration factor — TSCF"><meta property="og:description" content="The FOCUS groundwater guidance (FOCUS 2014, p. 41) states that a reliable measured log Kow for neutral pH must be available in order to apply the Briggs equation. It is not clarified when it can be regarded reliable, but the equation is stated to be produced for non-ionic compounds, suggesting that the compound should not be ionogenic (weak acid/base) -or ionic." /> - - - - -<!-- 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]> +or ionic."><!-- 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 data-spy="scroll" data-target="#toc"> <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"> @@ -77,35 +22,21 @@ or ionic." /> </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>Estimation of the transpiration stream concentration factor</h1> @@ -122,60 +53,63 @@ the compound should not be ionogenic (weak acid/base) or ionic.</p> </div> - <pre class="usage"><span class='fu'>TSCF</span>(<span class='no'>log_Kow</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"briggs82"</span>, <span class='st'>"dettenmaier09"</span>))</pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">TSCF</span><span class="op">(</span><span class="va">log_Kow</span>, method <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">"briggs82"</span>, <span class="st">"dettenmaier09"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> + </div> - <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>log_Kow</th> - <td><p>The decadic logarithm of the octanol-water partition constant</p></td> - </tr> - <tr> - <th>method</th> - <td><p>Short name of the estimation method.</p></td> - </tr> - </table> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>log_Kow</dt> +<dd><p>The decadic logarithm of the octanol-water partition constant</p></dd> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - <p>The Dettenmaier equation is given to show that other views on the subject exist.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> +<dt>method</dt> +<dd><p>Short name of the estimation method.</p></dd> +</dl></div> + <div id="details"> + <h2>Details</h2> + <p>The Dettenmaier equation is given to show that other views on the subject exist.</p> + </div> + <div id="references"> + <h2>References</h2> <p>FOCUS (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessments. Version 2.2, May 2014 Dettenmaier EM, Doucette WJ and Bugbee B (2009) Chemical hydrophobicity and uptake by plant roots. Environ. Sci. Technol 43, 324 - 329</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>TSCF</span>, -<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"log Kow"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"TSCF"</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1.1</span>))</div><div class='input'><span class='no'>TSCF_2</span> <span class='kw'><-</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>TSCF</span>(<span class='no'>x</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"dettenmaier09"</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/curve.html'>curve</a></span>(<span class='no'>TSCF_2</span>, -<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></span>(<span class='st'>"topright"</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>2</span>, <span class='kw'>bty</span> <span class='kw'>=</span> <span class='st'>"n"</span>, - <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Briggs et al. (1982)"</span>, <span class='st'>"Dettenmaier et al. (2009)"</span>))</div><div class='img'><img src='TSCF-1.png' alt='' width='700' height='433' /></div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">TSCF</span>, <span class="op">-</span><span class="fl">1</span>, <span class="fl">5</span>, xlab <span class="op">=</span> <span class="st">"log Kow"</span>, ylab <span class="op">=</span> <span class="st">"TSCF"</span>, ylim <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="fl">0</span>, <span class="fl">1.1</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">TSCF_2</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">TSCF</span><span class="op">(</span><span class="va">x</span>, method <span class="op">=</span> <span class="st">"dettenmaier09"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/curve.html" class="external-link">curve</a></span><span class="op">(</span><span class="va">TSCF_2</span>, <span class="op">-</span><span class="fl">1</span>, <span class="fl">5</span>, add <span class="op">=</span> <span class="cn">TRUE</span>, lty <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></span><span class="op">(</span><span class="st">"topright"</span>, lty <span class="op">=</span> <span class="fl">1</span><span class="op">:</span><span class="fl">2</span>, bty <span class="op">=</span> <span class="st">"n"</span>,</span></span> +<span class="r-in"><span> legend <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">"Briggs et al. (1982)"</span>, <span class="st">"Dettenmaier et al. (2009)"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="TSCF-1.png" alt="" width="700" height="433"></span> +</code></pre></div> + </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> + <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> 1.5.1.</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> diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html index 70fd16d..13129b8 100644 --- a/docs/reference/chent_focus_sw.html +++ b/docs/reference/chent_focus_sw.html @@ -1,64 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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- - - </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"> @@ -69,35 +17,21 @@ </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>Create a chemical compound object for FOCUS Step 1 calculations</h1> @@ -109,98 +43,93 @@ <p>Create a chemical compound object for FOCUS Step 1 calculations</p> </div> - <pre class="usage"><span class='fu'>chent_focus_sw</span>( - <span class='no'>name</span>, - <span class='no'>Koc</span>, - <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>DT50_soil</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>DT50_water</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>DT50_sediment</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>1000</span>, - <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>max_ws</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>name</th> - <td><p>Length one character vector containing the name</p></td> - </tr> - <tr> - <th>Koc</th> - <td><p>Partition coefficient between organic carbon and water -in L/kg.</p></td> - </tr> - <tr> - <th>DT50_ws</th> - <td><p>Half-life in water/sediment systems in days</p></td> - </tr> - <tr> - <th>DT50_soil</th> - <td><p>Half-life in soil in days</p></td> - </tr> - <tr> - <th>DT50_water</th> - <td><p>Half-life in water in days (Step 2)</p></td> - </tr> - <tr> - <th>DT50_sediment</th> - <td><p>Half-life in sediment in days (Step 2)</p></td> - </tr> - <tr> - <th>cwsat</th> - <td><p>Water solubility in mg/L</p></td> - </tr> - <tr> - <th>mw</th> - <td><p>Molar weight in g/mol.</p></td> - </tr> - <tr> - <th>max_soil</th> - <td><p>Maximum observed fraction (dimensionless) in soil</p></td> - </tr> - <tr> - <th>max_ws</th> - <td><p>Maximum observed fraction (dimensionless) in water/sediment -systems</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A list with the substance specific properties</p> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">chent_focus_sw</span><span class="op">(</span></span> +<span> <span class="va">name</span>,</span> +<span> <span class="va">Koc</span>,</span> +<span> DT50_ws <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> DT50_soil <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> DT50_water <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> DT50_sediment <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> cwsat <span class="op">=</span> <span class="fl">1000</span>,</span> +<span> mw <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> max_soil <span class="op">=</span> <span class="fl">1</span>,</span> +<span> max_ws <span class="op">=</span> <span class="fl">1</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>name</dt> +<dd><p>Length one character vector containing the name</p></dd> + + +<dt>Koc</dt> +<dd><p>Partition coefficient between organic carbon and water +in L/kg.</p></dd> + + +<dt>DT50_ws</dt> +<dd><p>Half-life in water/sediment systems in days</p></dd> + + +<dt>DT50_soil</dt> +<dd><p>Half-life in soil in days</p></dd> + + +<dt>DT50_water</dt> +<dd><p>Half-life in water in days (Step 2)</p></dd> + + +<dt>DT50_sediment</dt> +<dd><p>Half-life in sediment in days (Step 2)</p></dd> - </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> - </ul> + +<dt>cwsat</dt> +<dd><p>Water solubility in mg/L</p></dd> + + +<dt>mw</dt> +<dd><p>Molar weight in g/mol.</p></dd> + + +<dt>max_soil</dt> +<dd><p>Maximum observed fraction (dimensionless) in soil</p></dd> + + +<dt>max_ws</dt> +<dd><p>Maximum observed fraction (dimensionless) in water/sediment +systems</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list with the substance specific properties</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"> - 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<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>Deposition from spray drift expressed as percent of the applied dose as @@ -118,23 +49,24 @@ published by the German Julius-Kühn Institute (JKI).</p> </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A list currently containing matrices with spray drift percentage data for field crops (Ackerbau), and Pome/stone fruit, early and late (Obstbau frueh, spaet).</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved from http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html -on 2015-06-11</p> +on 2015-06-11, not present any more 2024-01-31</p> <p>Rautmann, D., Streloke, M and Winkler, R (2001) New basic drift values in the authorization procedure for plant protection products Mitt. Biol. Bundesanst. Land- Forstwirtsch. 383, 133-141</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - + </div> + <div id="details"> + <h2>Details</h2> <p>The data were extracted from the spreadsheet cited below using the R code given in the example section. The spreadsheet is not included in the package as its licence is not clear.</p> @@ -148,272 +80,226 @@ these values are used for spray applications with handheld/knapsack equipment (tragbare Spritz- und Sprühgerate).</p> <p>Values for non-professional use listed in the JKI spreadsheet were not included.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to extract the data</span> - <span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>readxl</span>) - <span class='no'>abdrift_path</span> <span class='kw'><-</span> <span class='st'>"inst/extdata/Tabelle der Abdrifteckwerte.xls"</span> - <span class='no'>JKI_crops</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Ackerbau"</span>, <span class='st'>"Obstbau frueh"</span>, <span class='st'>"Obstbau spaet"</span>, <span class='st'>"Weinbau frueh"</span>, <span class='st'>"Weinbau spaet"</span>, - <span class='st'>"Hopfenbau"</span>, <span class='st'>"Flaechenkulturen > 900 l/ha"</span>, <span class='st'>"Gleisanlagen"</span>) - <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>JKI_crops</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Field crops"</span>, <span class='st'>"Pome/stone fruit, early"</span>, <span class='st'>"Pome/stone fruit, late"</span>, - <span class='st'>"Vines early"</span>, <span class='st'>"Vines late"</span>, <span class='st'>"Hops"</span>, <span class='st'>"Areic cultures > 900 L/ha"</span>, <span class='st'>"Railroad tracks"</span>) - <span class='no'>drift_data_JKI</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>() - - <span class='kw'>for</span> (<span class='no'>n</span> <span class='kw'>in</span> <span class='fl'>1</span>:<span class='fl'>8</span>) { - <span class='no'>drift_data_raw</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/readxl/man/read_excel.html'>read_excel</a></span>(<span class='no'>abdrift_path</span>, <span class='kw'>sheet</span> <span class='kw'>=</span> <span class='no'>n</span> + <span class='fl'>1</span>, <span class='kw'>skip</span> <span class='kw'>=</span> <span class='fl'>2</span>) - <span class='no'>drift_data</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>NA</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>9</span>, <span class='kw'>ncol</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>JKI_crops</span>)) - <span class='fu'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></span>(<span class='no'>drift_data</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>distance</span> <span class='kw'>=</span> <span class='no'>drift_data_raw</span><span class='kw'>[[</span><span class='fl'>1</span>]][<span class='fl'>1</span>:<span class='fl'>9</span>], - <span class='kw'>crop</span> <span class='kw'>=</span> <span class='no'>JKI_crops</span>) - <span class='kw'>if</span> (<span class='no'>n</span> <span class='kw'>==</span> <span class='fl'>1</span>) { <span class='co'># Values for railroad tracks only present for one application</span> - <span class='no'>drift_data</span>[, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>:<span class='fl'>3</span>, <span class='fl'>5</span>:<span class='fl'>8</span>)] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>as.matrix</a></span>(<span class='no'>drift_data_raw</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2</span>:<span class='fl'>7</span>, <span class='fl'>11</span>)][<span class='fl'>1</span>:<span class='fl'>9</span>, ]) - } <span class='kw'>else</span> { - <span class='no'>drift_data</span>[, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>:<span class='fl'>3</span>, <span class='fl'>5</span>:<span class='fl'>7</span>)] <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>as.matrix</a></span>(<span class='no'>drift_data_raw</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2</span>:<span class='fl'>7</span>)][<span class='fl'>1</span>:<span class='fl'>9</span>, ]) - } - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='no'>n</span>]] <span class='kw'><-</span> <span class='no'>drift_data</span> - } - - <span class='co'># Manual data entry from the Rautmann paper</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>1</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.95</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>1</span>]][, <span class='st'>"Weinbau frueh"</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='fl'>2.7</span>, <span class='fl'>1.18</span>, <span class='fl'>0.39</span>, <span class='fl'>0.2</span>, <span class='fl'>0.13</span>, <span class='fl'>0.07</span>, <span class='fl'>0.04</span>, <span class='fl'>0.03</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>2</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.79</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>2</span>]][, <span class='st'>"Weinbau frueh"</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='fl'>2.53</span>, <span class='fl'>1.09</span>, <span class='fl'>0.35</span>, <span class='fl'>0.18</span>, <span class='fl'>0.11</span>, <span class='fl'>0.06</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>3</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.68</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>3</span>]][, <span class='st'>"Weinbau frueh"</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='fl'>2.49</span>, <span class='fl'>1.04</span>, <span class='fl'>0.32</span>, <span class='fl'>0.16</span>, <span class='fl'>0.10</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>4</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.62</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>4</span>]][, <span class='st'>"Weinbau frueh"</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='fl'>2.44</span>, <span class='fl'>1.02</span>, <span class='fl'>0.31</span>, <span class='fl'>0.16</span>, <span class='fl'>0.10</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>5</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.59</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>5</span>]][, <span class='st'>"Weinbau frueh"</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='fl'>2.37</span>, <span class='fl'>1.00</span>, <span class='fl'>0.31</span>, <span class='fl'>0.15</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>6</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.56</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>6</span>]][, <span class='st'>"Weinbau frueh"</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='fl'>2.29</span>, <span class='fl'>0.97</span>, <span class='fl'>0.30</span>, <span class='fl'>0.15</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>7</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.55</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>7</span>]][, <span class='st'>"Weinbau frueh"</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='fl'>2.24</span>, <span class='fl'>0.94</span>, <span class='fl'>0.29</span>, <span class='fl'>0.15</span>, <span class='fl'>0.09</span>, <span class='fl'>0.05</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>8</span>]][<span class='st'>"3"</span>, <span class='st'>"Ackerbau"</span>] <span class='kw'><-</span> <span class='fl'>0.52</span> - <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='fl'>8</span>]][, <span class='st'>"Weinbau frueh"</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='fl'>2.16</span>, <span class='fl'>0.91</span>, <span class='fl'>0.28</span>, <span class='fl'>0.14</span>, <span class='fl'>0.09</span>, <span class='fl'>0.04</span>, <span class='fl'>0.03</span>, <span class='fl'>0.02</span>) - - <span class='co'># Save the data</span> - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>drift_data_JKI</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/drift_data_JKI.RData"</span>) -} - -<span class='co'># And these are the resulting data</span> -<span class='no'>drift_data_JKI</span></div><div class='output co'>#> [[1]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 2.77 NA NA NA NA -#> 3 0.95 29.20 15.73 2.70 8.02 -#> 5 0.57 19.89 8.41 1.18 3.62 -#> 10 0.29 11.81 3.60 0.39 1.23 -#> 15 0.20 5.55 1.81 0.20 0.65 -#> 20 0.15 2.77 1.09 0.13 0.42 -#> 30 0.10 1.04 0.54 0.07 0.22 -#> 40 0.07 0.52 0.32 0.04 0.14 -#> 50 0.06 0.30 0.22 0.03 0.10 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 4.440 NA -#> 3 19.33 NA 0.018721696 -#> 5 11.57 0.180 0.014363896 -#> 10 5.77 0.050 0.010026007 -#> 15 3.84 0.020 0.008124366 -#> 20 1.79 0.012 0.006998158 -#> 30 0.56 0.005 0.005670811 -#> 40 0.25 0.003 NA -#> 50 0.13 0.002 0.004350831 -#> -#> [[2]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 2.38 NA NA NA NA -#> 3 0.79 25.53 12.13 2.53 7.23 -#> 5 0.47 16.87 6.81 1.09 3.22 -#> 10 0.24 9.61 3.11 0.35 1.07 -#> 15 0.16 5.61 1.58 0.18 0.56 -#> 20 0.12 2.59 0.90 0.11 0.36 -#> 30 0.08 0.87 0.40 0.06 0.19 -#> 40 0.06 0.40 0.23 0.03 0.12 -#> 50 0.05 0.22 0.15 0.02 0.08 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 3.780 NA -#> 3 17.73 NA NA -#> 5 9.60 0.160 NA -#> 10 4.18 0.040 NA -#> 15 2.57 0.020 NA -#> 20 1.21 0.011 NA -#> 30 0.38 0.005 NA -#> 40 0.17 0.003 NA -#> 50 0.09 0.002 NA -#> -#> [[3]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 2.01 NA NA NA NA -#> 3 0.68 23.96 11.01 2.49 6.90 -#> 5 0.41 15.79 6.04 1.04 3.07 -#> 10 0.20 8.96 2.67 0.32 1.02 -#> 15 0.14 4.24 1.39 0.16 0.54 -#> 20 0.10 2.01 0.80 0.10 0.34 -#> 30 0.07 0.70 0.36 0.05 0.18 -#> 40 0.05 0.33 0.21 0.03 0.11 -#> 50 0.04 0.19 0.13 0.02 0.08 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 3.420 NA -#> 3 15.93 NA NA -#> 5 8.57 0.150 NA -#> 10 3.70 0.040 NA -#> 15 2.26 0.020 NA -#> 20 1.05 0.010 NA -#> 30 0.34 0.004 NA -#> 40 0.15 0.003 NA -#> 50 0.08 0.002 NA -#> -#> [[4]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.85 NA NA NA NA -#> 3 0.62 23.61 10.12 2.44 6.71 -#> 5 0.38 15.42 5.60 1.02 2.99 -#> 10 0.19 8.66 2.50 0.31 0.99 -#> 15 0.13 4.01 1.28 0.16 0.52 -#> 20 0.10 1.89 0.75 0.10 0.33 -#> 30 0.06 0.66 0.35 0.05 0.17 -#> 40 0.05 0.31 0.20 0.03 0.11 -#> 50 0.04 0.17 0.13 0.02 0.08 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 2.290 NA -#> 3 15.38 NA NA -#> 5 8.26 0.120 NA -#> 10 3.55 0.030 NA -#> 15 2.17 0.020 NA -#> 20 0.93 0.009 NA -#> 30 0.31 0.004 NA -#> 40 0.14 0.002 NA -#> 50 0.08 0.002 NA -#> -#> [[5]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.75 NA NA NA NA -#> 3 0.59 23.12 9.74 2.37 6.59 -#> 5 0.36 15.06 5.41 1.00 2.93 -#> 10 0.18 8.42 2.43 0.31 0.98 -#> 15 0.12 3.83 1.24 0.15 0.51 -#> 20 0.09 1.81 0.72 0.09 0.33 -#> 30 0.06 0.63 0.34 0.05 0.17 -#> 40 0.05 0.30 0.20 0.03 0.11 -#> 50 0.04 0.17 0.13 0.02 0.08 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 2.120 NA -#> 3 15.12 NA NA -#> 5 7.99 0.110 NA -#> 10 3.36 0.030 NA -#> 15 2.03 0.010 NA -#> 20 0.88 0.008 NA -#> 30 0.29 0.004 NA -#> 40 0.14 0.002 NA -#> 50 0.07 0.002 NA -#> -#> [[6]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.64 NA NA NA NA -#> 3 0.56 22.76 9.21 2.29 6.41 -#> 5 0.34 14.64 5.18 0.97 2.85 -#> 10 0.17 8.04 2.38 0.30 0.95 -#> 15 0.11 3.71 1.20 0.15 0.50 -#> 20 0.09 1.75 0.68 0.09 0.32 -#> 30 0.06 0.61 0.31 0.05 0.17 -#> 40 0.04 0.29 0.17 0.03 0.11 -#> 50 0.03 0.16 0.11 0.02 0.07 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 1.980 NA -#> 3 14.90 NA NA -#> 5 7.79 0.100 NA -#> 10 3.23 0.030 NA -#> 15 1.93 0.010 NA -#> 20 0.83 0.008 NA -#> 30 0.28 0.004 NA -#> 40 0.13 0.002 NA -#> 50 0.07 0.001 NA -#> -#> [[7]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.61 NA NA NA NA -#> 3 0.55 22.69 9.10 2.24 6.33 -#> 5 0.33 14.45 5.11 0.94 2.81 -#> 10 0.17 7.83 2.33 0.29 0.94 -#> 15 0.11 3.62 1.20 0.15 0.49 -#> 20 0.08 1.71 0.67 0.09 0.31 -#> 30 0.06 0.60 0.30 0.05 0.16 -#> 40 0.04 0.28 0.17 0.03 0.10 -#> 50 0.03 0.16 0.11 0.02 0.07 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 1.930 NA -#> 3 14.63 NA NA -#> 5 7.60 0.100 NA -#> 10 3.13 0.030 NA -#> 15 1.86 0.010 NA -#> 20 0.81 0.008 NA -#> 30 0.26 0.004 NA -#> 40 0.12 0.002 NA -#> 50 0.06 0.001 NA -#> -#> [[8]] -#> crop -#> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet -#> 1 1.52 NA NA NA NA -#> 3 0.52 22.24 8.66 2.16 6.26 -#> 5 0.31 14.09 4.92 0.91 2.78 -#> 10 0.16 7.58 2.29 0.28 0.93 -#> 15 0.11 3.48 1.14 0.14 0.49 -#> 20 0.08 1.65 0.65 0.09 0.31 -#> 30 0.05 0.57 0.29 0.04 0.16 -#> 40 0.04 0.27 0.16 0.03 0.10 -#> 50 0.03 0.15 0.11 0.02 0.07 -#> crop -#> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen -#> 1 NA 1.640 NA -#> 3 13.53 NA NA -#> 5 7.15 0.090 NA -#> 10 3.01 0.020 NA -#> 15 1.82 0.010 NA -#> 20 0.78 0.007 NA -#> 30 0.25 0.003 NA -#> 40 0.12 0.002 NA -#> 50 0.06 0.001 NA -#> </div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">drift_data_JKI</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [[1]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 2.77 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.95 29.20 15.73 2.70 8.02</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.57 19.89 8.41 1.18 3.62</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.29 11.81 3.60 0.39 1.23</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.20 5.55 1.81 0.20 0.65</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.15 2.77 1.09 0.13 0.42</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.10 1.04 0.54 0.07 0.22</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.07 0.52 0.32 0.04 0.14</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.06 0.30 0.22 0.03 0.10</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 4.440 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 19.33 NA 0.018721696</span> +<span class="r-out co"><span class="r-pr">#></span> 5 11.57 0.180 0.014363896</span> +<span class="r-out co"><span class="r-pr">#></span> 10 5.77 0.050 0.010026007</span> +<span class="r-out co"><span class="r-pr">#></span> 15 3.84 0.020 0.008124366</span> +<span class="r-out co"><span class="r-pr">#></span> 20 1.79 0.012 0.006998158</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.56 0.005 0.005670811</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.25 0.003 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.13 0.002 0.004350831</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[2]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 2.38 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.79 25.53 12.13 2.53 7.23</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.47 16.87 6.81 1.09 3.22</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.24 9.61 3.11 0.35 1.07</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.16 5.61 1.58 0.18 0.56</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.12 2.59 0.90 0.11 0.36</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.08 0.87 0.40 0.06 0.19</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.06 0.40 0.23 0.03 0.12</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.05 0.22 0.15 0.02 0.08</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 3.780 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 17.73 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 9.60 0.160 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 4.18 0.040 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 2.57 0.020 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 1.21 0.011 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.38 0.005 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.17 0.003 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.09 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[3]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 2.01 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.68 23.96 11.01 2.49 6.90</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.41 15.79 6.04 1.04 3.07</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.20 8.96 2.67 0.32 1.02</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.14 4.24 1.39 0.16 0.54</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.10 2.01 0.80 0.10 0.34</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.07 0.70 0.36 0.05 0.18</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.05 0.33 0.21 0.03 0.11</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.04 0.19 0.13 0.02 0.08</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 3.420 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 15.93 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 8.57 0.150 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.70 0.040 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 2.26 0.020 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 1.05 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.34 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.15 0.003 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.08 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[4]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.85 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.62 23.61 10.12 2.44 6.71</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.38 15.42 5.60 1.02 2.99</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.19 8.66 2.50 0.31 0.99</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.13 4.01 1.28 0.16 0.52</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.10 1.89 0.75 0.10 0.33</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.06 0.66 0.35 0.05 0.17</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.05 0.31 0.20 0.03 0.11</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.04 0.17 0.13 0.02 0.08</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 2.290 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 15.38 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 8.26 0.120 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.55 0.030 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 2.17 0.020 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.93 0.009 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.31 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.14 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.08 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[5]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.75 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.59 23.12 9.74 2.37 6.59</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.36 15.06 5.41 1.00 2.93</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.18 8.42 2.43 0.31 0.98</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.12 3.83 1.24 0.15 0.51</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.09 1.81 0.72 0.09 0.33</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.06 0.63 0.34 0.05 0.17</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.05 0.30 0.20 0.03 0.11</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.04 0.17 0.13 0.02 0.08</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 2.120 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 15.12 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 7.99 0.110 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.36 0.030 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 2.03 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.88 0.008 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.29 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.14 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.07 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[6]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.64 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.56 22.76 9.21 2.29 6.41</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.34 14.64 5.18 0.97 2.85</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.17 8.04 2.38 0.30 0.95</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.11 3.71 1.20 0.15 0.50</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.09 1.75 0.68 0.09 0.32</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.06 0.61 0.31 0.05 0.17</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.04 0.29 0.17 0.03 0.11</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.03 0.16 0.11 0.02 0.07</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 1.980 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 14.90 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 7.79 0.100 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.23 0.030 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 1.93 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.83 0.008 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.28 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.13 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.07 0.001 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[7]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.61 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.55 22.69 9.10 2.24 6.33</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.33 14.45 5.11 0.94 2.81</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.17 7.83 2.33 0.29 0.94</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.11 3.62 1.20 0.15 0.49</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.08 1.71 0.67 0.09 0.31</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.06 0.60 0.30 0.05 0.16</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.04 0.28 0.17 0.03 0.10</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.03 0.16 0.11 0.02 0.07</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 1.930 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 14.63 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 7.60 0.100 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.13 0.030 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 1.86 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.81 0.008 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.26 0.004 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.12 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.06 0.001 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> [[8]]</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1.52 NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.52 22.24 8.66 2.16 6.26</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.31 14.09 4.92 0.91 2.78</span> +<span class="r-out co"><span class="r-pr">#></span> 10 0.16 7.58 2.29 0.28 0.93</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.11 3.48 1.14 0.14 0.49</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.08 1.65 0.65 0.09 0.31</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.05 0.57 0.29 0.04 0.16</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.04 0.27 0.16 0.03 0.10</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.03 0.15 0.11 0.02 0.07</span> +<span class="r-out co"><span class="r-pr">#></span> crop</span> +<span class="r-out co"><span class="r-pr">#></span> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA 1.640 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 13.53 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 7.15 0.090 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 10 3.01 0.020 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 15 1.82 0.010 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 20 0.78 0.007 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 30 0.25 0.003 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 40 0.12 0.002 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 50 0.06 0.001 NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 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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]> +this function."><!-- 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"> @@ -72,35 +20,21 @@ this function." /> </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>Retrieve endpoint information from the chyaml field of a chent object</h1> @@ -115,136 +49,131 @@ 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 + <div id="ref-usage"> + <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 id="arguments"> + <h2>Arguments</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> + + +<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> + + +<dt>redox</dt> +<dd><p>If not NA, are we looking for aerobic or anaerobic data</p></dd> + + +<dt>value</dt> +<dd><p>The name of the value we want. The list given in the +usage section is not exclusive</p></dd> + + +<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> + + +<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 id="value"> + <h2>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> - + </div> + <div id="details"> + <h2>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> - <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 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> diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index 34befc3..540b33b 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -1,68 +1,16 @@ -<!-- 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>Calculate the geometric mean — geomean • 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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" 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> - -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/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="Calculate the geometric mean — geomean" /> -<meta property="og:description" content="Based on some posts in a thread on Stackoverflow +<!-- 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>Calculate the geometric mean — geomean • 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="Calculate the geometric mean — geomean"><meta property="og:description" content="Based on some posts in a thread on Stackoverflow http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in This function returns NA if NA values are present and na.rm = FALSE (default). If negative values are present, it gives an error message. -If at least one element of the vector is 0, it returns 0." /> -<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]> +If at least one element of the vector is 0, it returns 0."><!-- 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"> @@ -73,35 +21,21 @@ If at least one element of the vector is 0, it returns 0." /> </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>Calculate the geometric mean</h1> @@ -111,64 +45,68 @@ If at least one element of the vector is 0, it returns 0." /> <div class="ref-description"> <p>Based on some posts in a thread on Stackoverflow -<a href='http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in'>http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in</a> +<a href="http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in" class="external-link">http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in</a> This function returns NA if NA values are present and na.rm = FALSE (default). If negative values are present, it gives an error message. If at least one element of the vector is 0, it returns 0.</p> </div> - <pre class="usage"><span class='fu'>geomean</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">geomean</span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> + </div> - <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>x</th> - <td><p>Vector of numbers</p></td> - </tr> - <tr> - <th>na.rm</th> - <td><p>Should NA values be omitted?</p></td> - </tr> - </table> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>Vector of numbers</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>The geometric mean</p> +<dt>na.rm</dt> +<dd><p>Should NA values be omitted?</p></dd> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] 3</div><div class='input'><span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>NA</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] NA</div><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>geomean</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, -<span class='fl'>3</span>, <span class='fl'>9</span>)) <span class='co'># returns an error</span></div></pre> - </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="#examples">Examples</a></li> - </ul> +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>The geometric mean</p> + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">geomean</span><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="fl">1</span>, <span class="fl">3</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 3</span> +<span class="r-in"><span><span class="fu">geomean</span><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="fl">1</span>, <span class="fl">3</span>, <span class="cn">NA</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] NA</span> +<span class="r-in"><span><span class="fu">geomean</span><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="fl">1</span>, <span class="op">-</span><span class="fl">3</span>, <span class="fl">9</span><span class="op">)</span><span class="op">)</span> <span class="co"># returns an error</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in geomean(c(1, -3, 9)):</span> Only defined for positive numbers</span> +</code></pre></div> + </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> diff --git a/docs/reference/get_vertex.html b/docs/reference/get_vertex.html index 3d0bc2d..c6dc00c 100644 --- a/docs/reference/get_vertex.html +++ b/docs/reference/get_vertex.html @@ -1,62 +1,13 @@ -<!-- 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>Fit a parabola through three points — get_vertex • 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 --> - 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- </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>Fit a parabola through three points</h1> @@ -105,55 +41,46 @@ https://stackoverflow.com/a/717791" /> </div> <div class="ref-description"> - <p>This was inspired by an answer on stackoverflow https://stackoverflow.com/a/717791</p> - </div> - <pre class="usage"><span class='fu'>get_vertex</span>(<span class='no'>x</span>, <span class='no'>y</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>x</th> - <td><p>Three x coordinates</p></td> - </tr> - <tr> - <th>y</th> - <td><p>Three y coordinates</p></td> - </tr> - </table> - + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_vertex</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></code></pre></div> + </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> - </ul> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>Three x coordinates</p></dd> + + +<dt>y</dt> +<dd><p>Three y coordinates</p></dd> + +</dl></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"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-index"> - <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"> @@ -71,391 +17,226 @@ </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">0.5.8</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-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="contents col-md-9"> <div class="page-header"> <h1>Reference</h1> </div> - <table class="ref-index"> - - <colgroup> - - <col class="alias" /> - <col class="title" /> - </colgroup> - - <tbody> - <tr> - <th colspan="2"> - <h2 id="section-general-utility-functions" class="hasAnchor"><a href="#section-general-utility-functions" class="anchor"></a>General utility functions</h2> - <p class="section-desc"><p>Functions that are independent of specific fate modelling areas</p></p> + <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2"> + <h2 id="general-utility-functions">General utility functions <a href="#general-utility-functions" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p><p>Functions that are independent of specific fate modelling areas</p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="geomean.html">geomean()</a></code> </p> </td> <td><p>Calculate the geometric mean</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="one_box.html">one_box()</a></code> </p> </td> <td><p>Create a time series of decline data</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="plot.one_box.html">plot(<i><one_box></i>)</a></code> </p> </td> <td><p>Plot time series of decline data</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="sawtooth.html">sawtooth()</a></code> </p> </td> <td><p>Create decline time series for multiple applications</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="twa.html">twa()</a></code> </p> </td> <td><p>Calculate a time weighted average concentration</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="max_twa.html">max_twa()</a></code> </p> </td> <td><p>The maximum time weighted average concentration for a moving window</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="pfm_degradation.html">pfm_degradation()</a></code> </p> </td> <td><p>Calculate a time course of relative concentrations based on an mkinmod model</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="SFO_actual_twa.html">SFO_actual_twa()</a></code> </p> </td> <td><p>Actual and maximum moving window time average concentrations for SFO kinetics</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="FOMC_actual_twa.html">FOMC_actual_twa()</a></code> </p> </td> <td><p>Actual and maximum moving window time average concentrations for FOMC kinetics</p></td> - </tr><tr> - - <td> - <p><code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> </p> - </td> - <td><p>Set non-detects and unquantified values in residue series without replicates</p></td> - </tr><tr> - - <td> + </tr><tr><td> + <p><code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">set_nd_nq</a></code> <code><a href="reexports.html">set_nd_nq_focus</a></code> </p> + </td> + <td><p>Objects exported from other packages</p></td> + </tr><tr><td> <p><code><a href="TSCF.html">TSCF()</a></code> </p> </td> <td><p>Estimation of the transpiration stream concentration factor</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-predicted-environmental-concentrations-in-soil" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-soil" class="anchor"></a>Predicted environmental concentrations in soil</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="predicted-environmental-concentrations-in-soil">Predicted environmental concentrations in soil <a href="#predicted-environmental-concentrations-in-soil" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="PEC_soil.html">PEC_soil()</a></code> </p> </td> <td><p>Calculate predicted environmental concentrations in soil</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_soil_mets.html">PEC_soil_mets()</a></code> </p> </td> <td><p>Calculate initial and accumulation PEC soil for a set of metabolites</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code> </p> </td> <td><p>Properties of the predefined scenarios from the EFSA guidance from 2015</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="soil_scenario_data_EFSA_2017.html">soil_scenario_data_EFSA_2017</a></code> </p> </td> <td><p>Properties of the predefined scenarios from the EFSA guidance from 2017</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_FOMC_accu_rel.html">PEC_FOMC_accu_rel()</a></code> </p> </td> <td><p>Get the relative accumulation of an FOMC model over multiples of an interval</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="EFSA_washoff_2017.html">EFSA_washoff_2017</a></code> </p> </td> <td><p>Subset of EFSA crop washoff default values</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-predicted-environmental-concentrations-in-groundwater" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-groundwater" class="anchor"></a>Predicted environmental concentrations in groundwater</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="predicted-environmental-concentrations-in-groundwater">Predicted environmental concentrations in groundwater <a href="#predicted-environmental-concentrations-in-groundwater" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code> </p> </td> <td><p>A very small subset of the FOCUS Groundwater scenario definitions</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="EFSA_GW_interception_2014.html">EFSA_GW_interception_2014</a></code> </p> </td> <td><p>Subset of EFSA crop interception default values for groundwater modelling</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-predicted-environmental-concentrations-in-surface-water" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-surface-water" class="anchor"></a>Predicted environmental concentrations in surface water</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="predicted-environmental-concentrations-in-surface-water">Predicted environmental concentrations in surface water <a href="#predicted-environmental-concentrations-in-surface-water" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="PEC_sw_drift.html">PEC_sw_drift()</a></code> </p> </td> <td><p>Calculate predicted environmental concentrations in surface water due to drift</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="drift_data_JKI.html">drift_data_JKI</a></code> </p> </td> <td><p>Deposition from spray drift expressed as percent of the applied dose as published by the JKI</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK()</a></code> </p> </td> <td><p>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_sed.html">PEC_sw_sed()</a></code> </p> </td> <td><p>Calculate predicted environmental concentrations in sediment from surface water concentrations</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_focus.html">PEC_sw_focus()</a></code> </p> </td> <td><p>Calculate PEC surface water at FOCUS Step 1</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="chent_focus_sw.html">chent_focus_sw()</a></code> </p> </td> <td><p>Create a chemical compound object for FOCUS Step 1 calculations</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></code> </p> </td> <td><p>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_exposit_drainage.html">PEC_sw_exposit_drainage()</a></code> </p> </td> <td><p>Calculate PEC surface water due to drainage as in Exposit 3</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff()</a></code> </p> </td> <td><p>Calculate PEC surface water due to runoff and erosion as in Exposit 3</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> </p> </td> <td><p>Runoff loss percentages as used in Exposit 3</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> </p> </td> <td><p>Runoff reduction percentages as used in Exposit</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code> </p> </td> <td><p>R6 class for holding TOXSWA water concentration data and associated statistics</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa()</a></code> </p> </td> <td><p>Read TOXSWA surface water concentrations</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="plot.TOXSWA_cwa.html">plot(<i><TOXSWA_cwa></i>)</a></code> </p> </td> <td><p>Plot TOXSWA surface water concentrations</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-classifications-and-indicators" class="hasAnchor"><a href="#section-classifications-and-indicators" class="anchor"></a>Classifications and indicators</h2> - <p class="section-desc"><p>Evaluating environmental fate properties</p></p> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="classifications-and-indicators">Classifications and indicators <a href="#classifications-and-indicators" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p><p>Evaluating environmental fate properties</p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification()</a></code> </p> </td> <td><p>Determine the SSLRC mobility classification for a chemical substance from its Koc</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="GUS.html">GUS()</a></code> <code><a href="GUS.html">print(<i><GUS_result></i>)</a></code> </p> </td> <td><p>Groundwater ubiquity score based on Gustafson (1989)</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-work-with-chent-objects-containing-relevant-information" class="hasAnchor"><a href="#section-work-with-chent-objects-containing-relevant-information" class="anchor"></a>Work with chent objects containing relevant information</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="work-with-chent-objects-containing-relevant-information">Work with chent objects containing relevant information <a href="#work-with-chent-objects-containing-relevant-information" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="endpoint.html">endpoint()</a></code> <code><a href="endpoint.html">soil_DT50()</a></code> <code><a href="endpoint.html">soil_Kfoc()</a></code> <code><a href="endpoint.html">soil_N()</a></code> <code><a href="endpoint.html">soil_sorption()</a></code> </p> </td> <td><p>Retrieve endpoint information from the chyaml field of a chent object</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-utilities" class="hasAnchor"><a href="#section-utilities" class="anchor"></a>Utilities</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="utilities">Utilities <a href="#utilities" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - - - </tbody><tbody> - - - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="get_vertex.html">get_vertex()</a></code> </p> </td> <td><p>Fit a parabola through three points</p></td> - </tr> - </tbody> - 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It is therefore recommended to check this using plot.one_box using the window size for the argument -max_twa." /> -<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]> +max_twa."><!-- 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"> @@ -70,36 +21,21 @@ max_twa." /> </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>The maximum time weighted average concentration for a moving window</h1> @@ -108,101 +44,90 @@ max_twa." /> </div> <div class="ref-description"> - - <p>If you generate your time series using <code><a href='sawtooth.html'>sawtooth</a></code>, + <p>If you generate your time series using <code><a href="sawtooth.html">sawtooth</a></code>, you need to make sure that the length of the time series allows for finding the maximum. It is therefore recommended to check this using -<code><a href='plot.one_box.html'>plot.one_box</a></code> using the window size for the argument +<code><a href="plot.one_box.html">plot.one_box</a></code> using the window size for the argument <code>max_twa</code>.</p> - </div> - <pre class="usage"><span class='fu'>max_twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</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>x</th> - <td><p>An object of type <code><a href='one_box.html'>one_box</a></code></p></td> - </tr> - <tr> - <th>window</th> - <td><p>The size of the moving window</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">max_twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>An object of type <code><a href="one_box.html">one_box</a></code></p></dd> + +<dt>window</dt> +<dd><p>The size of the moving window</p></dd> + +</dl></div> + <div id="details"> + <h2>Details</h2> <p>The method working directly on fitted <code>mkinfit</code> objects uses the equations given in the PEC soil section of the FOCUS guidance and is restricted SFO, FOMC and DFOP models and to the parent compound</p> - - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + </div> + <div id="references"> + <h2>References</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p><code><a href='twa.html'>twa</a></code></p></div> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>pred</span> <span class='kw'><-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>), - <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>1</span>))) -<span class='fu'>max_twa</span>(<span class='no'>pred</span>)</div><div class='output co'>#> $max -#> parent -#> 0.9537545 -#> -#> $window_start -#> parent -#> 0 -#> -#> $window_end -#> parent -#> 21 -#> </div><div class='input'><span class='no'>pred_FOMC</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>max_twa</span>(<span class='no'>pred_FOMC</span>)</div><div class='output co'>#> 21 -#> 18.22124 </div></pre> - </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="#details">Details</a></li> - - <li><a href="#references">References</a></li> - - <li><a href="#see-also">See also</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="twa.html">twa</a></code></p></div> + </div> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">pred</span> <span class="op"><-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> applications <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <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="fl">0</span>, <span class="fl">7</span><span class="op">)</span>, amount <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="fl">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">max_twa</span><span class="op">(</span><span class="va">pred</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $max</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 0.9537545 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_start</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 0 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_end</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 21 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span><span class="va">pred_FOMC</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">max_twa</span><span class="op">(</span><span class="va">pred_FOMC</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 21 </span> +<span class="r-out co"><span class="r-pr">#></span> 18.22124 </span> +</code></pre></div> + </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> - 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- - - </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"> @@ -69,35 +17,21 @@ </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>Create a time series of decline data</h1> @@ -109,99 +43,105 @@ <p>Create a time series of decline data</p> </div> - <pre class="usage"><span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='no'>ini</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>) - -<span class='co'># S3 method for numeric</span> -<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>) - -<span class='co'># S3 method for character</span> -<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='no'>parms</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>) - -<span class='co'># S3 method for mkinfit</span> -<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)</pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, <span class="va">ini</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for numeric</span></span> +<span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="fl">1</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for character</span></span> +<span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="fl">1</span>, <span class="va">parms</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="st">"model"</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span></code></pre></div> + </div> - <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>x</th> - <td><p>When numeric, this is the half-life to be used for an exponential + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>When numeric, this is the half-life to be used for an exponential decline. When a character string specifying a parent decline model is given e.g. <code>FOMC</code>, <code>parms</code> must contain the corresponding parameters. -If x is an <code>mkinfit</code> object, the decline is calculated from this -object.</p></td> - </tr> - <tr> - <th>ini</th> - <td><p>The initial amount. If x is an <code>mkinfit</code> object, and +If x is an <code><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></code> object, the decline is calculated from this +object.</p></dd> + + +<dt>ini</dt> +<dd><p>The initial amount. If x is an <code><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></code> object, and ini is 'model', the fitted initial concentrations are used. Otherwise, ini must be numeric. If it has length one, it is used for the parent and initial values of metabolites are zero, otherwise, it must give values for -all observed variables.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to methods</p></td> - </tr> - <tr> - <th>t_end</th> - <td><p>End of the time series</p></td> - </tr> - <tr> - <th>res</th> - <td><p>Resolution of the time series</p></td> - </tr> - <tr> - <th>parms</th> - <td><p>A named numeric vector containing the model parameters</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>An object of class <code>one_box</code>, inheriting from <code><a href='https://rdrr.io/r/stats/ts.html'>ts</a></code>.</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># Only use a half-life</span> -<span class='no'>pred_0</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='fl'>10</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>pred_0</span>)</div><div class='img'><img src='one_box-1.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># Use a fitted mkinfit model</span> -<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>mkin</span>) -<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='https://pkgdown.jrwb.de/mkin/reference/mkinfit.html'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='no'>pred_1</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='no'>fit</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>pred_1</span>)</div><div class='img'><img src='one_box-2.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># Use a model with more than one observed variable</span> -<span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://pkgdown.jrwb.de/mkin/reference/mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://pkgdown.jrwb.de/mkin/reference/mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://pkgdown.jrwb.de/mkin/reference/mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://pkgdown.jrwb.de/mkin/reference/mkinfit.html'>mkinfit</a></span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>pred_2</span>)</div><div class='img'><img src='one_box-3.png' alt='' width='700' height='433' /></div></pre> - </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="#examples">Examples</a></li> - </ul> +all observed variables.</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments passed to methods</p></dd> + +<dt>t_end</dt> +<dd><p>End of the time series</p></dd> + + +<dt>res</dt> +<dd><p>Resolution of the time series</p></dd> + + +<dt>parms</dt> +<dd><p>A named numeric vector containing the model parameters</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>An object of class <code>one_box</code>, inheriting from <code><a href="https://rdrr.io/r/stats/ts.html" class="external-link">ts</a></code>.</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Only use a half-life</span></span></span> +<span class="r-in"><span><span class="va">pred_0</span> <span class="op"><-</span> <span class="fu">one_box</span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_0</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="one_box-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Use a fitted mkinfit model</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/" class="external-link">mkin</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred_1</span> <span class="op"><-</span> <span class="fu">one_box</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_1</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="one_box-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Use a model with more than one observed variable</span></span></span> +<span class="r-in"><span><span class="va">m_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="va">m_2</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="va">pred_2</span> <span class="op"><-</span> <span class="fu">one_box</span><span class="op">(</span><span class="va">fit_2</span>, ini <span class="op">=</span> <span class="st">"model"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="one_box-3.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> </div> + <div class="col-md-3 hidden-xs hidden-sm" 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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>Runoff loss percentages as used in Exposit 3</h1> @@ -112,64 +43,71 @@ <p>A table of the loss percentages used in Exposit 3 for the twelve different Koc classes</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">perc_runoff_exposit</span></span></code></pre></div> + </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A data frame with percentage values for the dissolved fraction and the fraction - bound to eroding particles, with Koc classes used as row names</p><dl'> - <dt>Koc_lower_bound</dt><dd><p>The lower bound of the Koc class</p></dd> - <dt>dissolved</dt><dd><p>The percentage of the applied substance transferred to an + bound to eroding particles, with Koc classes used as row names</p><dl><dt>Koc_lower_bound</dt> +<dd><p>The lower bound of the Koc class</p></dd> + + <dt>dissolved</dt> +<dd><p>The percentage of the applied substance transferred to an adjacent water body in the dissolved phase</p></dd> - <dt>bound</dt><dd><p>The percentage of the applied substance transferred to an - adjacent water body bound to eroding particles</p></dd> - -</dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt>bound</dt> +<dd><p>The percentage of the applied substance transferred to an + adjacent water body bound to eroding particles</p></dd> + +</dl></div> + <div id="source"> + <h2>Source</h2> <p>Excel 3.02 spreadsheet available from - <a href='https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html'>https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>perc_runoff_exposit</span>)</div><div class='output co'>#> Koc_lower_bound dissolved bound -#> 0-20 0 0.110 0.000 -#> >20-50 20 0.151 0.000 -#> >50-100 50 0.197 0.000 -#> >100-200 100 0.248 0.001 -#> >200-500 200 0.224 0.004 -#> >500-1000 500 0.184 0.020 -#> >1000-2000 1000 0.133 0.042 -#> >2000-5000 2000 0.084 0.091 -#> >5000-10000 5000 0.037 0.159 -#> >10000-20000 10000 0.031 0.192 -#> >20000-50000 20000 0.014 0.291 -#> >50000 50000 0.001 0.451</div></pre> + <a href="https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html" class="external-link">https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><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">perc_runoff_exposit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Koc_lower_bound dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> 0-20 0 0.110 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> >20-50 20 0.151 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> >50-100 50 0.197 0.000</span> +<span class="r-out co"><span class="r-pr">#></span> >100-200 100 0.248 0.001</span> +<span class="r-out co"><span class="r-pr">#></span> >200-500 200 0.224 0.004</span> +<span class="r-out co"><span class="r-pr">#></span> >500-1000 500 0.184 0.020</span> +<span class="r-out co"><span class="r-pr">#></span> >1000-2000 1000 0.133 0.042</span> +<span class="r-out co"><span class="r-pr">#></span> >2000-5000 2000 0.084 0.091</span> +<span class="r-out co"><span class="r-pr">#></span> >5000-10000 5000 0.037 0.159</span> +<span class="r-out co"><span class="r-pr">#></span> >10000-20000 10000 0.031 0.192</span> +<span class="r-out co"><span class="r-pr">#></span> >20000-50000 20000 0.014 0.291</span> +<span class="r-out co"><span class="r-pr">#></span> >50000 50000 0.001 0.451</span> +</code></pre></div> + </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> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + 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</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>Runoff reduction percentages as used in Exposit</h1> @@ -112,80 +43,83 @@ <p>A table of the runoff reduction percentages used in Exposit 3 for different vegetated buffer widths</p> </div> - <pre class="usage"><span class='va'>perc_runoff_reduction_exposit</span></pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">perc_runoff_reduction_exposit</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> <p>A named list of data frames with reduction percentage values for the dissolved fraction and the fraction bound to eroding particles, with vegetated buffer widths as row names. The names of the list items are the Exposit versions -from which the values were taken.</p><dl> - <dt>dissolved</dt><dd><p>The reduction percentage for the dissolved phase</p></dd> - <dt>bound</dt><dd><p>The reduction percentage for the particulate phase</p></dd> - -</dl> +from which the values were taken.</p><dl><dt>dissolved</dt> +<dd><p>The reduction percentage for the dissolved phase</p></dd> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt>bound</dt> +<dd><p>The reduction percentage for the particulate phase</p></dd> + +</dl></div> + <div id="source"> + <h2>Source</h2> <p>Excel 3.02 spreadsheet available from - <a href='https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html'>https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html</a></p> + <a href="https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html" class="external-link">https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html</a></p> <p>Agroscope version 3.01a with additional runoff factors for 3 m and 6 m buffer zones received from Muris Korkaric (not published). The variant 3.01a2 was introduced for consistency with previous calculations performed by Agroscope for a 3 m buffer zone.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>perc_runoff_reduction_exposit</span><span class='op'>)</span> -</div><div class='output co'>#> $`3.02` -#> dissolved bound -#> No buffer 0 0 -#> 5 m 40 40 -#> 10 m 60 85 -#> 20 m 80 95 -#> -#> $`3.01a` -#> dissolved bound -#> No buffer 0 0 -#> 3 m 25 30 -#> 5 m 40 40 -#> 6 m 45 55 -#> 10 m 60 85 -#> 20 m 80 95 -#> -#> $`3.01a2` -#> dissolved bound -#> No buffer 0 0 -#> 3 m 25 25 -#> -#> $`2.0` -#> dissolved bound -#> No buffer 0.0 0.0 -#> 20 m 97.5 97.5 -#> </div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><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">perc_runoff_reduction_exposit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $`3.02`</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 40 40</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 60 85</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 80 95</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`3.01a`</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 25 30</span> +<span class="r-out co"><span class="r-pr">#></span> 5 m 40 40</span> +<span class="r-out co"><span class="r-pr">#></span> 6 m 45 55</span> +<span class="r-out co"><span class="r-pr">#></span> 10 m 60 85</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 80 95</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`3.01a2`</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 3 m 25 25</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $`2.0`</span> +<span class="r-out co"><span class="r-pr">#></span> dissolved bound</span> +<span class="r-out co"><span class="r-pr">#></span> No buffer 0.0 0.0</span> +<span class="r-out co"><span class="r-pr">#></span> 20 m 97.5 97.5</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </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> + <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> 1.6.1.</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> diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt deleted file mode 100644 index 4618e8b..0000000 --- a/docs/reference/pesticide.txt +++ /dev/null @@ -1,3 +0,0 @@ -Active Substance Compound Comment Mol mass a.i. Mol mass met. Water solubility KOC assessed compound KOC parent compound DT50 Max. in Water Max. in Soil asessed compound App. Rate Number of App. Time between app. App. Type DT50 soil parent compound DT50 soil DT50 water DT50 sediment Region / Season Interception class -Dummy 1 cereals, spring n NA Dummy 1 cereals, spring n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 -M1 cereals, winter n NA M1 cereals, winter n NA 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html index 8d06107..724a1aa 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -1,67 +1,12 @@ -<!-- 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"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <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"> @@ -72,35 +17,21 @@ </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>Calculate a time course of relative concentrations based on an mkinmod model</h1> @@ -112,80 +43,83 @@ <p>Calculate a time course of relative concentrations based on an mkinmod model</p> </div> - <pre class="usage"><span class='fu'>pfm_degradation</span>( - <span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, - <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, - <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>), - <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='no'>step_days</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>model</th> - <td><p>The degradation model to be used. Either a parent only model like -'SFO' or 'FOMC', or an mkinmod object</p></td> - </tr> - <tr> - <th>DT50</th> - <td><p>The half-life. This is only used when simple exponential decline -is calculated (SFO model).</p></td> - </tr> - <tr> - <th>parms</th> - <td><p>The parameters used for the degradation model</p></td> - </tr> - <tr> - <th>years</th> - <td><p>For how many years should the degradation be predicted?</p></td> - </tr> - <tr> - <th>step_days</th> - <td><p>What step size in days should the output have?</p></td> - </tr> - <tr> - <th>times</th> - <td><p>The output times</p></td> - </tr> - </table> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>(<span class='fu'>pfm_degradation</span>(<span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>10</span>))</div><div class='output co'>#> time parent -#> 0 0 1.0000000 -#> 1 1 0.9330330 -#> 2 2 0.8705506 -#> 3 3 0.8122524 -#> 4 4 0.7578583 -#> 5 5 0.7071068</div></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">pfm_degradation</span><span class="op">(</span></span> +<span> model <span class="op">=</span> <span class="st">"SFO"</span>,</span> +<span> DT50 <span class="op">=</span> <span class="fl">1000</span>,</span> +<span> parms <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>k_parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="va">DT50</span><span class="op">)</span>,</span> +<span> years <span class="op">=</span> <span class="fl">1</span>,</span> +<span> step_days <span class="op">=</span> <span class="fl">1</span>,</span> +<span> times <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="va">years</span> <span class="op">*</span> <span class="fl">365</span>, by <span class="op">=</span> <span class="va">step_days</span><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>model</dt> +<dd><p>The degradation model to be used. Either a parent only model like +'SFO' or 'FOMC', or an mkinmod object</p></dd> + + +<dt>DT50</dt> +<dd><p>The half-life. This is only used when simple exponential decline +is calculated (SFO model).</p></dd> + + +<dt>parms</dt> +<dd><p>The parameters used for the degradation model</p></dd> + + +<dt>years</dt> +<dd><p>For how many years should the degradation be predicted?</p></dd> + + +<dt>step_days</dt> +<dd><p>What step size in days should the output have?</p></dd> + + +<dt>times</dt> +<dd><p>The output times</p></dd> + +</dl></div> + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu">pfm_degradation</span><span class="op">(</span><span class="st">"SFO"</span>, DT50 <span class="op">=</span> <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> time parent</span> +<span class="r-out co"><span class="r-pr">#></span> 0 0 1.0000000</span> +<span class="r-out co"><span class="r-pr">#></span> 1 1 0.9330330</span> +<span class="r-out co"><span class="r-pr">#></span> 2 2 0.8705506</span> +<span class="r-out co"><span class="r-pr">#></span> 3 3 0.8122524</span> +<span class="r-out co"><span class="r-pr">#></span> 4 4 0.7578583</span> +<span class="r-out co"><span class="r-pr">#></span> 5 5 0.7071068</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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- - - </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"> @@ -70,35 +18,21 @@ segment of a TOXSWA surface water body." /> </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>Plot TOXSWA surface water concentrations</h1> @@ -111,106 +45,112 @@ segment of a TOXSWA surface water body." /> segment of a TOXSWA surface water body.</p> </div> - <pre class="usage"><span class='co'># S3 method for TOXSWA_cwa</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( - <span class='no'>x</span>, - <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"datetime"</span>, <span class='st'>"t"</span>, <span class='st'>"t_firstjan"</span>, <span class='st'>"t_rel_to_max"</span>), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, - <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, - <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>threshold_factor</span> <span class='kw'>=</span> <span class='fl'>1000</span>, - <span class='kw'>thin_low</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>LC_TIME</span> <span class='kw'>=</span> <span class='st'>"C"</span>, - <span class='no'>...</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>x</th> - <td><p>The TOXSWA_cwa object to be plotted.</p></td> - </tr> - <tr> - <th>time_column</th> - <td><p>What should be used for the time axis. If "t_firstjan" is chosen, -the time is given in days relative to the first of January in the first year.</p></td> - </tr> - <tr> - <th>xlab, ylab</th> - <td><p>Labels for x and y axis.</p></td> - </tr> - <tr> - <th>add</th> - <td><p>Should we add to an existing plot?</p></td> - </tr> - <tr> - <th>threshold_factor</th> - <td><p>The factor by which the data have to be lower than the maximum -in order to get thinned for plotting (see next argument).</p></td> - </tr> - <tr> - <th>thin_low</th> - <td><p>If an integer greater than 1, the data close to zero (smaller than + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for TOXSWA_cwa</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> time_column <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">"datetime"</span>, <span class="st">"t"</span>, <span class="st">"t_firstjan"</span>, <span class="st">"t_rel_to_max"</span><span class="op">)</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"default"</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"default"</span>,</span> +<span> add <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> threshold_factor <span class="op">=</span> <span class="fl">1000</span>,</span> +<span> thin_low <span class="op">=</span> <span class="fl">1</span>,</span> +<span> total <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> LC_TIME <span class="op">=</span> <span class="st">"C"</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>The TOXSWA_cwa object to be plotted.</p></dd> + + +<dt>time_column</dt> +<dd><p>What should be used for the time axis. If "t_firstjan" is chosen, +the time is given in days relative to the first of January in the first year.</p></dd> + + +<dt>xlab, ylab</dt> +<dd><p>Labels for x and y axis.</p></dd> + + +<dt>add</dt> +<dd><p>Should we add to an existing plot?</p></dd> + + +<dt>threshold_factor</dt> +<dd><p>The factor by which the data have to be lower than the maximum +in order to get thinned for plotting (see next argument).</p></dd> + + +<dt>thin_low</dt> +<dd><p>If an integer greater than 1, the data close to zero (smaller than 1/threshold_factor of the maximum) in the series will be thinned by this factor -in order to decrease the amount of data that is included in the plots</p></td> - </tr> - <tr> - <th>total</th> - <td><p>Should the total concentration in water be plotted, including substance sorbed -to suspended matter?</p></td> - </tr> - <tr> - <th>LC_TIME</th> - <td><p>Specification of the locale used to format dates</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</p></td> - </tr> - </table> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00001p_pa.cwa"</span>, - <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/system.file.html'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>)) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_firstjan"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-4.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='no'>H_sw_R1_stream</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>, - <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/system.file.html'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>)) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>H_sw_R1_stream</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-5.png' alt='' width='700' height='433' /></div></pre> - </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="#examples">Examples</a></li> - </ul> +in order to decrease the amount of data that is included in the plots</p></dd> + + +<dt>total</dt> +<dd><p>Should the total concentration in water be plotted, including substance sorbed +to suspended matter?</p></dd> + + +<dt>LC_TIME</dt> +<dd><p>Specification of the locale used to format dates</p></dd> + +<dt>...</dt> +<dd><p>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</p></dd> + +</dl></div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_D4_pond</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00001p_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>, package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_D4_pond</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_D4_pond</span>, time_column <span class="op">=</span> <span class="st">"t"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_D4_pond</span>, time_column <span class="op">=</span> <span class="st">"t_firstjan"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_D4_pond</span>, time_column <span class="op">=</span> <span class="st">"t_rel_to_max"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-4.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">H_sw_R1_stream</span> <span class="op"><-</span> <span class="fu"><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span><span class="op">(</span><span class="st">"00003s_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>, package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">H_sw_R1_stream</span>, time_column <span class="op">=</span> <span class="st">"t_rel_to_max"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.TOXSWA_cwa-5.png" alt="" width="700" height="433"></span> +</code></pre></div> + </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> - 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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"> @@ -69,35 +17,21 @@ </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>Plot time series of decline data</h1> @@ -109,97 +43,101 @@ <p>Plot time series of decline data</p> </div> - <pre class="usage"><span class='co'># S3 method for one_box</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( - <span class='no'>x</span>, - <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span>(<span class='fu'><a href='https://rdrr.io/r/stats/time.html'>time</a></span>(<span class='no'>x</span>)), - <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span>(<span class='no'>x</span>)), - <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, - <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>, - <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/dimnames.html'>dimnames</a></span>(<span class='no'>x</span>)<span class='kw'>[[</span><span class='fl'>2</span>]][<span class='fl'>1</span>], - <span class='no'>...</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>x</th> - <td><p>The object of type <code><a href='one_box.html'>one_box</a></code> to be plotted</p></td> - </tr> - <tr> - <th>xlim</th> - <td><p>Limits for the x axis</p></td> - </tr> - <tr> - <th>ylim</th> - <td><p>Limits for the y axis</p></td> - </tr> - <tr> - <th>xlab</th> - <td><p>Label for the x axis</p></td> - </tr> - <tr> - <th>ylab</th> - <td><p>Label for the y axis</p></td> - </tr> - <tr> - <th>max_twa</th> - <td><p>If a numeric value is given, the maximum time weighted -average concentration(s) is/are shown in the graph.</p></td> - </tr> - <tr> - <th>max_twa_var</th> - <td><p>Variable for which the maximum time weighted average should -be shown if max_twa is not NULL.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to methods</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p><code><a href='sawtooth.html'>sawtooth</a></code></p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>dfop_pred</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='st'>"DFOP"</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>)) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>dfop_pred</span>)</div><div class='img'><img src='plot.one_box-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>dfop_pred</span>, <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><div class='img'><img src='plot.one_box-2.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># Use a fitted mkinfit model</span> -<span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>) -<span class='no'>pred_2_saw</span> <span class='kw'><-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='plot.one_box-3.png' alt='' width='700' height='433' /></div></pre> - </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="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for one_box</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/range.html" class="external-link">range</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/time.html" class="external-link">time</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span> +<span> ylim <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="fl">0</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Time"</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span> +<span> max_twa <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> max_twa_var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/dimnames.html" class="external-link">dimnames</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">[[</span><span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>The object of type <code><a href="one_box.html">one_box</a></code> to be plotted</p></dd> + + +<dt>xlim</dt> +<dd><p>Limits for the x axis</p></dd> + + +<dt>ylim</dt> +<dd><p>Limits for the y axis</p></dd> + + +<dt>xlab</dt> +<dd><p>Label for the x axis</p></dd> + +<dt>ylab</dt> +<dd><p>Label for the y axis</p></dd> + + +<dt>max_twa</dt> +<dd><p>If a numeric value is given, the maximum time weighted +average concentration(s) is/are shown in the graph.</p></dd> + + +<dt>max_twa_var</dt> +<dd><p>Variable for which the maximum time weighted average should +be shown if max_twa is not NULL.</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments passed to methods</p></dd> + +</dl></div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="sawtooth.html">sawtooth</a></code></p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">dfop_pred</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="st">"DFOP"</span>, parms <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>k1 <span class="op">=</span> <span class="fl">0.2</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.7</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">dfop_pred</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.one_box-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="va">dfop_pred</span>, <span class="fl">3</span>, <span class="fl">7</span><span class="op">)</span>, max_twa <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.one_box-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Use a fitted mkinfit model</span></span></span> +<span class="r-in"><span><span class="va">m_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="va">m_2</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="va">pred_2</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="va">fit_2</span>, ini <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred_2_saw</span> <span class="op"><-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="va">pred_2</span>, <span class="fl">2</span>, <span class="fl">7</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2_saw</span>, max_twa <span class="op">=</span> <span class="fl">21</span>, max_twa_var <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.one_box-3.png" alt="" width="700" height="433"></span> +</code></pre></div> + </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> diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index 9c5c2a0..2685c21 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -1,69 +1,17 @@ -<!-- 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>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • 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" 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of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was -renamed to ConLiqWatLay in the out file." /> -<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]> +renamed to ConLiqWatLay in the out file."><!-- 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"> @@ -74,35 +22,21 @@ renamed to ConLiqWatLay in the out file." /> </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>Read TOXSWA surface water concentrations</h1> @@ -119,103 +53,102 @@ of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was renamed to ConLiqWatLay in the out file.</p> </div> - <pre class="usage"><span class='fu'>read.TOXSWA_cwa</span>( - <span class='no'>filename</span>, - <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"."</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>, - <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, - <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>windows</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>thresholds</span> <span class='kw'>=</span> <span class='kw'>NULL</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>filename</th> - <td><p>The filename of the cwa file (TOXSWA 2.x.y or similar) or the -out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.</p></td> - </tr> - <tr> - <th>basedir</th> - <td><p>The path to the directory where the cwa file resides.</p></td> - </tr> - <tr> - <th>zipfile</th> - <td><p>Optional path to a zip file containing the cwa file.</p></td> - </tr> - <tr> - <th>segment</th> - <td><p>The segment for which the data should be read. Either "last", or -the segment number.</p></td> - </tr> - <tr> - <th>substance</th> - <td><p>For .out files, the default value "parent" leads + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read.TOXSWA_cwa</span><span class="op">(</span></span> +<span> <span class="va">filename</span>,</span> +<span> basedir <span class="op">=</span> <span class="st">"."</span>,</span> +<span> zipfile <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> segment <span class="op">=</span> <span class="st">"last"</span>,</span> +<span> substance <span class="op">=</span> <span class="st">"parent"</span>,</span> +<span> total <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> windows <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> thresholds <span class="op">=</span> <span class="cn">NULL</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>filename</dt> +<dd><p>The filename of the cwa file (TOXSWA 2.x.y or similar) or the +out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.</p></dd> + + +<dt>basedir</dt> +<dd><p>The path to the directory where the cwa file resides.</p></dd> + + +<dt>zipfile</dt> +<dd><p>Optional path to a zip file containing the cwa file.</p></dd> + + +<dt>segment</dt> +<dd><p>The segment for which the data should be read. Either "last", or +the segment number.</p></dd> + + +<dt>substance</dt> +<dd><p>For .out files, the default value "parent" leads to reading concentrations of the parent compound. Alternatively, the substance -of interested can be selected by its code name.</p></td> - </tr> - <tr> - <th>total</th> - <td><p>Set this to TRUE in order to read total concentrations as well. This is +of interested can be selected by its code name.</p></dd> + + +<dt>total</dt> +<dd><p>Set this to TRUE in order to read total concentrations as well. This is only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa -files. For .cwa files, the total concentration is always read as well.</p></td> - </tr> - <tr> - <th>windows</th> - <td><p>Numeric vector of width of moving windows in days, for calculating -maximum time weighted average concentrations and areas under the curve.</p></td> - </tr> - <tr> - <th>thresholds</th> - <td><p>Numeric vector of threshold concentrations in µg/L for -generating event statistics.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>An instance of an R6 object of class -<code><a href='TOXSWA_cwa.html'>TOXSWA_cwa</a></code>.</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'><-</span> <span class='fu'>read.TOXSWA_cwa</span>(<span class='st'>"00001p_pa.cwa"</span>, - <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, - <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/system.file.html'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>, - <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))</div></pre> - </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="#examples">Examples</a></li> - </ul> +files. For .cwa files, the total concentration is always read as well.</p></dd> + + +<dt>windows</dt> +<dd><p>Numeric vector of width of moving windows in days, for calculating +maximum time weighted average concentrations and areas under the curve.</p></dd> + + +<dt>thresholds</dt> +<dd><p>Numeric vector of threshold concentrations in µg/L for +generating event statistics.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>An instance of an R6 object of class +<code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code>.</p> + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">H_sw_D4_pond</span> <span class="op"><-</span> <span class="fu">read.TOXSWA_cwa</span><span class="op">(</span><span class="st">"00001p_pa.cwa"</span>,</span></span> +<span class="r-in"><span> basedir <span class="op">=</span> <span class="st">"SwashProjects/project_H_sw/TOXSWA"</span>,</span></span> +<span class="r-in"><span> zipfile <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testdata/SwashProjects.zip"</span>,</span></span> +<span class="r-in"><span> package <span class="op">=</span> <span class="st">"pfm"</span><span class="op">)</span><span class="op">)</span></span></span> +</code></pre></div> + </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> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html new file mode 100644 index 0000000..9b8cb48 --- /dev/null +++ b/docs/reference/reexports.html @@ -0,0 +1,83 @@ +<!DOCTYPE html> +<!-- 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>Objects exported from other packages — reexports • 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="Objects exported from other packages — reexports"><meta property="og:description" content="These objects are imported from other packages. Follow the links +below to see their documentation. + + mkin +set_nd_nq, set_nd_nq_focus + + +"><!-- 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 data-spy="scroll" data-target="#toc"> + + + <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="">0.6.1</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <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 --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Objects exported from other packages</h1> + + <div class="hidden name"><code>reexports.Rd</code></div> + </div> + + <div class="ref-description"> + <p>These objects are imported from other packages. Follow the links +below to see their documentation.</p> +<dl><dt>mkin</dt> +<dd><p><code><a href="https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html" class="external-link">set_nd_nq</a></code>, <code><a href="https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html" class="external-link">set_nd_nq_focus</a></code></p></dd> + + +</dl></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></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <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> + + + + + + + </body></html> + diff --git a/docs/reference/sawtooth-1.png b/docs/reference/sawtooth-1.png Binary files differindex 2952433..062202c 100644 --- a/docs/reference/sawtooth-1.png +++ b/docs/reference/sawtooth-1.png diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png Binary files differindex 87da954..cea8b0b 100644 --- a/docs/reference/sawtooth-2.png +++ b/docs/reference/sawtooth-2.png diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index fea24d4..8e29b9c 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <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"> @@ -73,35 +18,21 @@ n and i are disregarded." /> </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>Create decline time series for multiple applications</h1> @@ -114,81 +45,88 @@ n and i are disregarded." /> <code>n</code> and <code>i</code> are disregarded.</p> </div> - <pre class="usage"><span class='fu'>sawtooth</span>( - <span class='no'>x</span>, - <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>365</span>, - <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, (<span class='no'>n</span> - <span class='fl'>1</span>) * <span class='no'>i</span>, <span class='kw'>length.out</span> <span class='kw'>=</span> <span class='no'>n</span>), <span class='kw'>amount</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>x</th> - <td><p>A <code><a href='one_box.html'>one_box</a></code> object</p></td> - </tr> - <tr> - <th>n</th> - <td><p>The number of applications. If <code>applications</code> is specified, <code>n</code> is ignored</p></td> - </tr> - <tr> - <th>i</th> - <td><p>The interval between applications. If <code>applications</code> is specified, <code>i</code> -is ignored</p></td> - </tr> - <tr> - <th>applications</th> - <td><p>A data frame holding the application times in the first column and -the corresponding amounts applied in the second column.</p></td> - </tr> - </table> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>14</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>3</span>)) -<span class='no'>pred</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>) -<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><div class='img'><img src='sawtooth-1.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>) -<span class='no'>pred_2_saw</span> <span class='kw'><-</span> <span class='fu'>sawtooth</span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>) -<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='sawtooth-2.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred_2_saw</span>)</div><div class='output co'>#> $max -#> parent m1 -#> 0.7834480 0.8617048 -#> -#> $window_start -#> parent m1 -#> 0.00 26.85 -#> -#> $window_end -#> parent m1 -#> 21.00 47.85 -#> </div></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">sawtooth</span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> n <span class="op">=</span> <span class="fl">1</span>,</span> +<span> i <span class="op">=</span> <span class="fl">365</span>,</span> +<span> applications <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="op">(</span><span class="va">n</span> <span class="op">-</span> <span class="fl">1</span><span class="op">)</span> <span class="op">*</span> <span class="va">i</span>, length.out <span class="op">=</span> <span class="va">n</span><span class="op">)</span>, amount <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>A <code><a href="one_box.html">one_box</a></code> object</p></dd> + + +<dt>n</dt> +<dd><p>The number of applications. If <code>applications</code> is specified, <code>n</code> is ignored</p></dd> + + +<dt>i</dt> +<dd><p>The interval between applications. If <code>applications</code> is specified, <code>i</code> +is ignored</p></dd> + + +<dt>applications</dt> +<dd><p>A data frame holding the application times in the first column and +the corresponding amounts applied in the second column.</p></dd> + +</dl></div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">applications</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">14</span>, by <span class="op">=</span> <span class="fl">7</span><span class="op">)</span>, amount <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="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu">sawtooth</span><span class="op">(</span><span class="va">pred</span>, applications <span class="op">=</span> <span class="va">applications</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="sawtooth-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="va">m_2</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="va">pred_2</span> <span class="op"><-</span> <span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="va">fit_2</span>, ini <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">pred_2_saw</span> <span class="op"><-</span> <span class="fu">sawtooth</span><span class="op">(</span><span class="va">pred_2</span>, <span class="fl">2</span>, <span class="fl">7</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2_saw</span>, max_twa <span class="op">=</span> <span class="fl">21</span>, max_twa_var <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="sawtooth-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="max_twa.html">max_twa</a></span><span class="op">(</span><span class="va">pred_2_saw</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $max</span> +<span class="r-out co"><span class="r-pr">#></span> parent m1 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.7834481 0.8617049 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_start</span> +<span class="r-out co"><span class="r-pr">#></span> parent m1 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.00 26.85 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_end</span> +<span class="r-out co"><span class="r-pr">#></span> parent m1 </span> +<span class="r-out co"><span class="r-pr">#></span> 21.00 47.85 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </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> + <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> 1.5.1.</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> diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index cb3cf14..abea480 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -1,69 +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>Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • pfm</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" 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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="Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015"><meta property="og:description" content="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the -scenario and model adjustment factors from p. 15 and p. 17 are included." /> - - - - -<!-- 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]> +scenario and model adjustment factors from p. 15 and p. 17 are included."><!-- 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 data-spy="scroll" data-target="#toc"> <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"> @@ -74,35 +19,21 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> </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>Properties of the predefined scenarios from the EFSA guidance from 2015</h1> @@ -116,81 +47,65 @@ concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the scenario and model adjustment factors from p. 15 and p. 17 are included.</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">soil_scenario_data_EFSA_2015</span></span></code></pre></div> + </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A data frame with one row for each scenario. Row names are the scenario codes, e.g. CTN for the Northern scenario for the total concentration in soil. Columns are mostly self-explanatory. <code>rho</code> is the dry bulk density of the top soil.</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>EFSA (European Food Safety Authority) (2015) EFSA guidance document for predicting environmental concentrations of active substances of plant protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 - doi:10.2903/j.efsa.2015.4093</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - <span class='co'># This is the code that was used to define the data</span> - <span class='no'>soil_scenario_data_EFSA_2015</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>( - <span class='kw'>Zone</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"North"</span>, <span class='st'>"Central"</span>, <span class='st'>"South"</span>), <span class='fl'>2</span>), - <span class='kw'>Country</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Estonia"</span>, <span class='st'>"Germany"</span>, <span class='st'>"France"</span>, <span class='st'>"Denmark"</span>, <span class='st'>"Czech Republik"</span>, <span class='st'>"Spain"</span>), - <span class='kw'>T_arit</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>4.7</span>, <span class='fl'>8.0</span>, <span class='fl'>11.0</span>, <span class='fl'>8.2</span>, <span class='fl'>9.1</span>, <span class='fl'>12.8</span>), - <span class='kw'>T_arr</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>7.0</span>, <span class='fl'>10.1</span>, <span class='fl'>12.3</span>, <span class='fl'>9.8</span>, <span class='fl'>11.2</span>, <span class='fl'>14.7</span>), - <span class='kw'>Texture</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"Coarse"</span>, <span class='st'>"Coarse"</span>, <span class='st'>"Medium fine"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>), - <span class='kw'>f_om</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.118</span>, <span class='fl'>0.086</span>, <span class='fl'>0.048</span>, <span class='fl'>0.023</span>, <span class='fl'>0.018</span>, <span class='fl'>0.011</span>), - <span class='kw'>theta_fc</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.244</span>, <span class='fl'>0.244</span>, <span class='fl'>0.385</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>), - <span class='kw'>rho</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.95</span>, <span class='fl'>1.05</span>, <span class='fl'>1.22</span>, <span class='fl'>1.39</span>, <span class='fl'>1.43</span>, <span class='fl'>1.51</span>), - <span class='kw'>f_sce</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>1.5</span>, <span class='fl'>1.5</span>), - <span class='kw'>f_mod</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>4</span>, <span class='fl'>4</span>), - <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, - <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"CTN"</span>, <span class='st'>"CTC"</span>, <span class='st'>"CTS"</span>, <span class='st'>"CLN"</span>, <span class='st'>"CLC"</span>, <span class='st'>"CLS"</span>) - ) - <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>soil_scenario_data_EFSA_2015</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>'../data/soil_scenario_data_EFSA_2015.RData'</span>) -} - -<span class='co'># And this is the resulting dataframe</span> -<span class='no'>soil_scenario_data_EFSA_2015</span></div><div class='output co'>#> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce -#> CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0 -#> CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0 -#> CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0 -#> CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0 -#> CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5 -#> CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5 -#> f_mod -#> CTN 2 -#> CTC 2 -#> CTS 2 -#> CLN 4 -#> CLC 4 -#> CLS 4</div></pre> + <a href="https://doi.org/10.2903/j.efsa.2015.4093" class="external-link">doi:10.2903/j.efsa.2015.4093</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">soil_scenario_data_EFSA_2015</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce</span> +<span class="r-out co"><span class="r-pr">#></span> CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0</span> +<span class="r-out co"><span class="r-pr">#></span> CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0</span> +<span class="r-out co"><span class="r-pr">#></span> CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0</span> +<span class="r-out co"><span class="r-pr">#></span> CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0</span> +<span class="r-out co"><span class="r-pr">#></span> CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5</span> +<span class="r-out co"><span class="r-pr">#></span> CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5</span> +<span class="r-out co"><span class="r-pr">#></span> f_mod</span> +<span class="r-out co"><span class="r-pr">#></span> CTN 2</span> +<span class="r-out co"><span class="r-pr">#></span> CTC 2</span> +<span class="r-out co"><span class="r-pr">#></span> CTS 2</span> +<span class="r-out co"><span class="r-pr">#></span> CLN 4</span> +<span class="r-out co"><span class="r-pr">#></span> CLC 4</span> +<span class="r-out co"><span class="r-pr">#></span> CLS 4</span> +</code></pre></div> + </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> + <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> 1.5.1.</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> diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html index 7e8044e..96cdd1b 100644 --- a/docs/reference/soil_scenario_data_EFSA_2017.html +++ b/docs/reference/soil_scenario_data_EFSA_2017.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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Also, the -scenario and model adjustment factors from p. 16 and p. 18 are included." /> - - - - -<!-- 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]> +scenario and model adjustment factors from p. 16 and p. 18 are included."><!-- 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 data-spy="scroll" data-target="#toc"> <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"> @@ -74,35 +19,21 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." /> </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>Properties of the predefined scenarios from the EFSA guidance from 2017</h1> @@ -116,61 +47,98 @@ concentration in soil as given in the EFSA guidance (2017, p. 14/15). Also, the scenario and model adjustment factors from p. 16 and p. 18 are included.</p> </div> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">soil_scenario_data_EFSA_2017</span></span></code></pre></div> + </div> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - + <div id="format"> + <h2>Format</h2> <p>A data frame with one row for each scenario. Row names are the scenario codes, e.g. CTN for the Northern scenario for the total concentration in soil. Columns are mostly self-explanatory. <code>rho</code> is the dry bulk density of the top soil.</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>EFSA (European Food Safety Authority) (2017) EFSA guidance document for predicting environmental concentrations of active substances of plant protection products and transformation products of these active substances in soil. <em>EFSA Journal</em> <b>15</b>(10) 4982 - doi:10.2903/j.efsa.2017.4982</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>soil_scenario_data_EFSA_2017</span></div><div class='output co'>#> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce f_mod -#> CTN North Estonia 5.7 7.6 Coarse 0.220 0.244 0.707 1.4 3 -#> CTC Central Poland 7.4 9.3 Coarse 0.122 0.244 0.934 1.4 3 -#> CTS South France 10.2 11.7 Medium 0.070 0.349 1.117 1.4 3 -#> CLN North Denmark 8.0 9.2 Medium 0.025 0.349 1.371 1.6 4 -#> CLC Central Austria 9.3 11.3 Medium 0.018 0.349 1.432 1.6 4 -#> CLS South Spain 15.4 16.7 Medium 0.010 0.349 1.521 1.6 4 -#> FOCUS_zone prec -#> CTN Hamburg 639 -#> CTC Hamburg 617 -#> CTS Hamburg 667 -#> CLN Hamburg 602 -#> CLC Châteaudun 589 -#> CLS Sevilla 526</div></pre> + <a href="https://doi.org/10.2903/j.efsa.2017.4982" class="external-link">doi:10.2903/j.efsa.2017.4982</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">soil_scenario_data_EFSA_2017</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce f_mod</span> +<span class="r-out co"><span class="r-pr">#></span> CTN North Estonia 5.7 7.6 Coarse 0.220 0.244 0.707 1.4 3</span> +<span class="r-out co"><span class="r-pr">#></span> CTC Central Poland 7.4 9.3 Coarse 0.122 0.244 0.934 1.4 3</span> +<span class="r-out co"><span class="r-pr">#></span> CTS South France 10.2 11.7 Medium 0.070 0.349 1.117 1.4 3</span> +<span class="r-out co"><span class="r-pr">#></span> CLN North Denmark 8.0 9.2 Medium 0.025 0.349 1.371 1.6 4</span> +<span class="r-out co"><span class="r-pr">#></span> CLC Central Austria 9.3 11.3 Medium 0.018 0.349 1.432 1.6 4</span> +<span class="r-out co"><span class="r-pr">#></span> CLS South Spain 15.4 16.7 Medium 0.010 0.349 1.521 1.6 4</span> +<span class="r-out co"><span class="r-pr">#></span> FOCUS_zone prec</span> +<span class="r-out co"><span class="r-pr">#></span> CTN Hamburg 639</span> +<span class="r-out co"><span class="r-pr">#></span> CTC Hamburg 617</span> +<span class="r-out co"><span class="r-pr">#></span> CTS Hamburg 667</span> +<span class="r-out co"><span class="r-pr">#></span> CLN Hamburg 602</span> +<span class="r-out co"><span class="r-pr">#></span> CLC Châteaudun 589</span> +<span class="r-out co"><span class="r-pr">#></span> CLS Sevilla 526</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu">waldo</span><span class="fu">::</span><span class="fu"><a href="https://waldo.r-lib.org/reference/compare.html" class="external-link">compare</a></span><span class="op">(</span><span class="va">soil_scenario_data_EFSA_2017</span>, <span class="va">soil_scenario_data_EFSA_2015</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> `old` is length 12</span> +<span class="r-out co"><span class="r-pr">#></span> `new` is length 10</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `names(old)[8:12]`: <span style="color: #555555;">"rho"</span> <span style="color: #555555;">"f_sce"</span> <span style="color: #555555;">"f_mod"</span> <span style="color: #BBBB00;">"FOCUS_zone"</span> <span style="color: #BBBB00;">"prec"</span></span> +<span class="r-out co"><span class="r-pr">#></span> `names(new)[8:10]`: <span style="color: #555555;">"rho"</span> <span style="color: #555555;">"f_sce"</span> <span style="color: #555555;">"f_mod"</span> </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$Country`: <span style="color: #555555;">"Estonia"</span> <span style="color: #00BB00;">"Poland"</span> <span style="color: #555555;">"France"</span> <span style="color: #555555;">"Denmark"</span> <span style="color: #00BB00;">"Austria"</span> <span style="color: #555555;">"Spain"</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$Country`: <span style="color: #555555;">"Estonia"</span> <span style="color: #00BB00;">"Germany"</span> <span style="color: #555555;">"France"</span> <span style="color: #555555;">"Denmark"</span> <span style="color: #00BB00;">"Czech Republik"</span> <span style="color: #555555;">"Spain"</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$T_arit`: <span style="color: #00BB00;">5.7</span> <span style="color: #00BB00;">7.4</span> <span style="color: #00BB00;">10.2</span> <span style="color: #00BB00;">8.0</span> <span style="color: #00BB00;">9.3</span> <span style="color: #00BB00;">15.4</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$T_arit`: <span style="color: #00BB00;">4.7</span> <span style="color: #00BB00;">8.0</span> <span style="color: #00BB00;">11.0</span> <span style="color: #00BB00;">8.2</span> <span style="color: #00BB00;">9.1</span> <span style="color: #00BB00;">12.8</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$T_arr`: <span style="color: #00BB00;">7.6</span> <span style="color: #00BB00;">9.3</span> <span style="color: #00BB00;">11.7</span> <span style="color: #00BB00;">9.2</span> <span style="color: #00BB00;">11.3</span> <span style="color: #00BB00;">16.7</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$T_arr`: <span style="color: #00BB00;">7.0</span> <span style="color: #00BB00;">10.1</span> <span style="color: #00BB00;">12.3</span> <span style="color: #00BB00;">9.8</span> <span style="color: #00BB00;">11.2</span> <span style="color: #00BB00;">14.7</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$Texture`: <span style="color: #555555;">"Coarse"</span> <span style="color: #555555;">"Coarse"</span> <span style="color: #00BB00;">"Medium"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$Texture`: <span style="color: #555555;">"Coarse"</span> <span style="color: #555555;">"Coarse"</span> <span style="color: #00BB00;">"Medium fine"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$f_om`: <span style="color: #00BB00;">0.220</span> <span style="color: #00BB00;">0.122</span> <span style="color: #00BB00;">0.070</span> <span style="color: #00BB00;">0.025</span> <span style="color: #555555;">0.018</span> <span style="color: #00BB00;">0.010</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$f_om`: <span style="color: #00BB00;">0.118</span> <span style="color: #00BB00;">0.086</span> <span style="color: #00BB00;">0.048</span> <span style="color: #00BB00;">0.023</span> <span style="color: #555555;">0.018</span> <span style="color: #00BB00;">0.011</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$theta_fc`: <span style="color: #555555;">0.244</span> <span style="color: #555555;">0.244</span> <span style="color: #00BB00;">0.349</span> <span style="color: #00BB00;">0.349</span> <span style="color: #00BB00;">0.349</span> <span style="color: #00BB00;">0.349</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$theta_fc`: <span style="color: #555555;">0.244</span> <span style="color: #555555;">0.244</span> <span style="color: #00BB00;">0.385</span> <span style="color: #00BB00;">0.347</span> <span style="color: #00BB00;">0.347</span> <span style="color: #00BB00;">0.347</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$rho`: <span style="color: #00BB00;">0.707</span> <span style="color: #00BB00;">0.934</span> <span style="color: #00BB00;">1.117</span> <span style="color: #00BB00;">1.371</span> <span style="color: #00BB00;">1.432</span> <span style="color: #00BB00;">1.521</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$rho`: <span style="color: #00BB00;">0.950</span> <span style="color: #00BB00;">1.050</span> <span style="color: #00BB00;">1.220</span> <span style="color: #00BB00;">1.390</span> <span style="color: #00BB00;">1.430</span> <span style="color: #00BB00;">1.510</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> `old$f_sce`: <span style="color: #00BB00;">1.4</span> <span style="color: #00BB00;">1.4</span> <span style="color: #00BB00;">1.4</span> <span style="color: #00BB00;">1.6</span> <span style="color: #00BB00;">1.6</span> <span style="color: #00BB00;">1.6</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$f_sce`: <span style="color: #00BB00;">3.0</span> <span style="color: #00BB00;">2.0</span> <span style="color: #00BB00;">2.0</span> <span style="color: #00BB00;">2.0</span> <span style="color: #00BB00;">1.5</span> <span style="color: #00BB00;">1.5</span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> And 3 more differences ...</span> +</code></pre></div> + </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> + <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> 1.5.1.</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> diff --git 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possible time for the maximum in the time series returned -is after one window has passed." /> -<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]> +is after one window has passed."><!-- 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"> @@ -68,36 +19,21 @@ is after one window has passed." /> </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>Calculate a time weighted average concentration</h1> @@ -106,82 +42,73 @@ is after one window has passed." /> </div> <div class="ref-description"> - <p>The moving average is built only using the values in the past, so the earliest possible time for the maximum in the time series returned is after one window has passed.</p> - </div> - <pre class="usage"><span class='fu'>twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>) + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for one_box</span></span> +<span><span class="fu">twa</span><span class="op">(</span><span class="va">x</span>, window <span class="op">=</span> <span class="fl">21</span><span class="op">)</span></span></code></pre></div> + </div> -<span class='co'># S3 method for one_box</span> -<span class='fu'>twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</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>x</th> - <td><p>An object of type <code><a href='one_box.html'>one_box</a></code></p></td> - </tr> - <tr> - <th>window</th> - <td><p>The size of the moving window</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>An object of type <code><a href="one_box.html">one_box</a></code></p></dd> - <div class='dont-index'><p><code><a href='max_twa.html'>max_twa</a></code></p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>pred</span> <span class='kw'><-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>), - <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>1</span>))) -<span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred</span>)</div><div class='output co'>#> $max -#> parent -#> 0.9537545 -#> -#> $window_start -#> parent -#> 0 -#> -#> $window_end -#> parent -#> 21 -#> </div></pre> - </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="#see-also">See also</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> +<dt>window</dt> +<dd><p>The size of the moving window</p></dd> +</dl></div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="max_twa.html">max_twa</a></code></p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">pred</span> <span class="op"><-</span> <span class="fu"><a href="sawtooth.html">sawtooth</a></span><span class="op">(</span><span class="fu"><a href="one_box.html">one_box</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> applications <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <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="fl">0</span>, <span class="fl">7</span><span class="op">)</span>, amount <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="fl">1</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="max_twa.html">max_twa</a></span><span class="op">(</span><span class="va">pred</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $max</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 0.9537545 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_start</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 0 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $window_end</span> +<span class="r-out co"><span class="r-pr">#></span> parent </span> +<span class="r-out co"><span class="r-pr">#></span> 21 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </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> diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 0c507b6..6ba511d 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,6 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9"> <url> + <loc>https://pkgdown.jrwb.de/pfm/404.html</loc> + </url> + <url> + <loc>https://pkgdown.jrwb.de/pfm/authors.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/pfm/index.html</loc> </url> <url> @@ -76,6 +82,9 @@ <loc>https://pkgdown.jrwb.de/pfm/reference/get_vertex.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/pfm/reference/index.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/pfm/reference/max_twa.html</loc> </url> <url> @@ -100,6 +109,9 @@ <loc>https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/pfm/reference/reexports.html</loc> + </url> + <url> 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