diff options
39 files changed, 1008 insertions, 383 deletions
@@ -1,3 +1,12 @@ +commit d81550d0cccae824cc748de48e7fd50ea8d8033a +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2020-04-16 18:02:18 +0200 + + Make na.rm = FALSE the default for geomean() + + This makes more sense and is in line with mean() from base R. Adapt + tests and update docs. + commit 4bc95b3e4aae22e4052e0a4c905a9227c909e2cd Author: Johannes Ranke <jranke@uni-bremen.de> Date: 2020-02-19 07:49:08 +0100 diff --git a/DESCRIPTION b/DESCRIPTION index 4d471dc..d125af4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,4 +32,4 @@ LazyLoad: yes LazyData: yes Encoding: UTF-8 URL: https://pkdown.jrwb.de/pfm -RoxygenNote: 7.0.2 +RoxygenNote: 7.1.0 @@ -26,6 +26,7 @@ export(PEC_sw_sed) export(SFO_actual_twa) export(SSLRC_mobility_classification) export(TOXSWA_cwa) +export(TSCF) export(chent_focus_sw) export(endpoint) export(geomean) diff --git a/R/TSCF.R b/R/TSCF.R new file mode 100644 index 0000000..bfb4c42 --- /dev/null +++ b/R/TSCF.R @@ -0,0 +1,31 @@ +#' Estimation of the transpiration stream concentration factor +#' +#' 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. +#' +#' The Dettenmaier equation is given to show that other views on the subject exist. +#' @references 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 +#' @param log_Kow The decadic logarithm of the octanol-water partition constant +#' @param method Short name of the estimation method. +#' @export +#' @examples +#' plot(TSCF, -1, 5, xlab = "log Kow", ylab = "TSCF", ylim = c(0, 1.1)) +#' TSCF_2 <- function(x) TSCF(x, method = "dettenmaier09") +#' curve(TSCF_2, -1, 5, add = TRUE, lty = 2) +#' legend("topright", lty = 1:2, bty = "n", +#' legend = c("Briggs et al. (1982)", "Dettenmaier et al. (2009)")) +TSCF <- function(log_Kow, method = c("briggs82", "dettenmaier09")) { + method <- match.arg(method) + TSCF <- switch(method, + briggs82 = 0.784 * exp(- (log_Kow - 1.78)^2 / 2.44), + dettenmaier09 = 11 /( 11 + 2.6^log_Kow) + ) + return(TSCF) +} diff --git a/_pkgdown.yml b/_pkgdown.yml index b40e223..71f3c65 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -19,6 +19,7 @@ reference: - SFO_actual_twa - FOMC_actual_twa - set_nd_nq + - TSCF - title: Predicted environmental concentrations in soil contents: - PEC_soil diff --git a/docs/404.html b/docs/404.html index f42956b..37f381e 100644 --- a/docs/404.html +++ b/docs/404.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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="https://pkgdown.jrwb.de/pfm/bootstrap-toc.css"> +<script src="https://pkgdown.jrwb.de/pfm/bootstrap-toc.js"></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" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/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> +<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="https://pkgdown.jrwb.de/pfm/pkgdown.css" rel="stylesheet"> @@ -53,7 +57,7 @@ </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-title-body"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -105,6 +109,12 @@ 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> + </div> + </div> @@ -115,7 +125,7 @@ Content not found. 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Author, maintainer, copyright holder. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID'></a> + <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> @@ -120,7 +124,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css new file mode 100644 index 0000000..5a85941 --- /dev/null +++ b/docs/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ + +/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */ + +/* All levels of nav */ +nav[data-toggle='toc'] .nav > li > a { + display: block; + padding: 4px 20px; + font-size: 13px; + font-weight: 500; + color: #767676; +} +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 19px; + color: #563d7c; + text-decoration: none; + background-color: transparent; + border-left: 1px solid #563d7c; +} +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 18px; + font-weight: bold; + color: #563d7c; + background-color: transparent; + border-left: 2px solid #563d7c; +} + +/* Nav: second level (shown on .active) */ +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} +nav[data-toggle='toc'] .nav .nav > li > a { + padding-top: 1px; + padding-bottom: 1px; + padding-left: 30px; + font-size: 12px; + font-weight: normal; +} +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 29px; +} +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 28px; + font-weight: 500; +} + +/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */ +nav[data-toggle='toc'] .nav > .active > ul { + display: block; +} diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js new file mode 100644 index 0000000..1cdd573 --- /dev/null +++ b/docs/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ +(function() { + 'use strict'; + + window.Toc = { + helpers: { + // return all matching elements in the set, or their descendants + findOrFilter: function($el, selector) { + // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/ + // http://stackoverflow.com/a/12731439/358804 + var $descendants = $el.find(selector); + return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])'); + }, + + generateUniqueIdBase: function(el) { + var text = $(el).text(); + var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-'); + return anchor || el.tagName.toLowerCase(); + }, + + generateUniqueId: function(el) { + var anchorBase = this.generateUniqueIdBase(el); + for (var i = 0; ; i++) { + var anchor = anchorBase; + if (i > 0) { + // add suffix + anchor += '-' + i; + } + // check if ID already exists + if (!document.getElementById(anchor)) { + return anchor; + } + } + }, + + generateAnchor: function(el) { + if (el.id) { + return el.id; + } else { + var anchor = this.generateUniqueId(el); + el.id = anchor; + return anchor; + } + }, + + createNavList: function() { + return $('<ul class="nav"></ul>'); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $('<a></a>'); + $a.attr('href', '#' + anchor); + $a.text(text); + var $li = $('<li></li>'); + $li.append($a); + return $li; + }, + + generateNavItem: function(headingEl) { + var anchor = this.generateAnchor(headingEl); + var $heading = $(headingEl); + var text = $heading.data('toc-text') || $heading.text(); + return this.generateNavEl(anchor, text); + }, + + // Find the first heading level (`<h1>`, then `<h2>`, etc.) that has more than one element. 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($prevNav && $context === $topContext) { + // create a new level of the tree and switch to it + $context = helpers.createChildNavList($prevNav); + } // else use the current $context + + $context.append($newNav); + + $prevNav = $newNav; + }); + }, + + parseOps: function(arg) { + var opts; + if (arg.jquery) { + opts = { + $nav: arg + }; + } else { + opts = arg; + } + opts.$scope = opts.$scope || $(document.body); + return opts; + } + }, + + // accepts a jQuery object, or an options object + init: function(opts) { + opts = this.helpers.parseOps(opts); + + // ensure that the data attribute is in place for styling + opts.$nav.attr('data-toggle', 'toc'); + + var $topContext = this.helpers.createChildNavList(opts.$nav); + var topLevel = this.helpers.getTopLevel(opts.$scope); + var $headings = this.helpers.getHeadings(opts.$scope, topLevel); + this.helpers.populateNav($topContext, topLevel, $headings); + } + }; + + $(function() { + $('nav[data-toggle="toc"]').each(function(i, el) { + var $nav = $(el); + Toc.init($nav); + }); + }); +})(); diff --git a/docs/index.html b/docs/index.html index 2e42649..6ffb312 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,21 +6,21 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Utilities for Pesticide Fate Modelling • 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 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property="og:title" content="Utilities for Pesticide Fate Modelling"> <meta property="og:description" content="Utilities for simple calculations of predicted environmental concentrations (PEC values) and for dealing with data from some FOCUS pesticide fate modelling software packages."> -<meta name="twitter:card" content="summary"> <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> </head> -<body> +<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"> @@ -70,12 +70,12 @@ <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="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"drat"</span>)</a> -<a class="sourceLine" id="cb1-2" title="2">drat<span class="op">::</span><span class="kw"><a href="https://rdrr.io/pkg/drat/man/addRepo.html">addRepo</a></span>(<span class="st">"jranke"</span>)</a> -<a class="sourceLine" id="cb1-3" title="3"><span class="kw"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"pfm"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb1"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"drat"</span>) +<span class="kw pkg">drat</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/drat/man/addRepo.html">addRepo</a></span>(<span class="st">"jranke"</span>) +<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"pfm"</span>)</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="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(devtools)</a> -<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://devtools.r-lib.org//reference/remote-reexports.html">install_github</a></span>(<span class="st">"jranke/pfm"</span>, <span class="dt">quick =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb2"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">devtools</span>) +<span class="fu"><a href="https://devtools.r-lib.org//reference/remote-reexports.html">install_github</a></span>(<span class="st">"jranke/pfm"</span>, <span class="kw">quick</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></div> </div> <div id="use" class="section level2"> <h2 class="hasAnchor"> @@ -90,7 +90,7 @@ </div> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <div class="license"> <h2>License</h2> <ul class="list-unstyled"> @@ -100,7 +100,7 @@ <div class="developers"> <h2>Developers</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"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID"></a> </li> +<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> </ul> </div> @@ -120,7 +120,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 9145958..c01e592 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -17,6 +17,10 @@ html, body { height: 100%; } +body { + position: relative; +} + body > .container { display: flex; height: 100%; @@ -67,6 +71,10 @@ summary { margin-top: calc(-60px + 1em); } +dd { + margin-left: 3em; +} + /* Section anchors ---------------------------------*/ a.anchor { @@ -100,29 +108,132 @@ a.anchor { margin-top: -40px; } +/* Navbar submenu --------------------------*/ + +.dropdown-submenu { + position: relative; +} + +.dropdown-submenu>.dropdown-menu { + top: 0; + left: 100%; + margin-top: -6px; + margin-left: -1px; + border-radius: 0 6px 6px 6px; +} + +.dropdown-submenu:hover>.dropdown-menu { + display: block; +} + +.dropdown-submenu>a:after { + 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.active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 15px; + font-weight: 500; + font-size: 1.35rem; +} + +/* orcid ------------------------------------------------------------------- */ + .orcid { - height: 16px; + font-size: 16px; + color: #A6CE39; /* margins are required by official ORCID trademark and display guidelines */ margin-left:4px; margin-right:4px; diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 087a762..7e7048f 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -9,11 +9,6 @@ $('body').css('padding-top', $('.navbar').height() + 10); }); - $('body').scrollspy({ - target: '#sidebar', - offset: 60 - }); - $('[data-toggle="tooltip"]').tooltip(); var cur_path = paths(location.pathname); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index a975312..077f218 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,7 +1,8 @@ pandoc: 2.2.1 -pkgdown: 1.4.1 +pkgdown: 1.5.1 pkgdown_sha: ~ articles: [] +last_built: 2020-06-17T11:36Z 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 c8d08fd..d7ec108 100644 --- a/docs/reference/EFSA_GW_interception_2014.html +++ b/docs/reference/EFSA_GW_interception_2014.html @@ -8,23 +8,29 @@ <title>Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014 • 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> +<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" 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rel="stylesheet"> @@ -32,10 +38,10 @@ -<meta property="og:title" content="Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014" /> +<meta property="og:title" content="Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014" /> <meta property="og:description" content="Subset of EFSA crop interception default values for groundwater modelling" /> -<meta name="twitter:card" content="summary" /> + @@ -52,7 +58,7 @@ </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -82,7 +88,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -104,16 +109,14 @@ </div> <div class="ref-description"> - <p>Subset of EFSA crop interception default values for groundwater modelling</p> - </div> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>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> <p>European Food Safety Authority (2014) EFSA Guidance Document for @@ -121,7 +124,6 @@ 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> - <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>) { @@ -162,17 +164,10 @@ products of these active substances in soil. <em>EFSA Journal</em> #> 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> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - - <li><a href="#format">Format</a></li> - - <li><a href="#source">Source</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - + <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> @@ -183,7 +178,7 @@ products of these active substances in soil. <em>EFSA Journal</em> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/EFSA_washoff_2017.html b/docs/reference/EFSA_washoff_2017.html index 1f7bce7..abe0b24 100644 --- a/docs/reference/EFSA_washoff_2017.html +++ b/docs/reference/EFSA_washoff_2017.html @@ -8,23 +8,29 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integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -32,10 +38,10 @@ -<meta property="og:title" content="Subset of EFSA crop washoff default values — EFSA_washoff_2017" /> +<meta property="og:title" content="Subset of EFSA crop washoff default values — EFSA_washoff_2017" /> <meta property="og:description" content="Subset of EFSA crop washoff default values" /> -<meta name="twitter:card" content="summary" /> + @@ -52,7 +58,7 @@ </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -82,7 +88,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -104,16 +109,14 @@ </div> <div class="ref-description"> - <p>Subset of EFSA crop washoff default values</p> - </div> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>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> <p>European Food Safety Authority (2017) EFSA guidance document for @@ -121,7 +124,6 @@ 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='kw'>if</span> (<span class='fl'>FALSE</span>) { @@ -162,17 +164,10 @@ #> 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> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - - <li><a href="#format">Format</a></li> - - <li><a href="#source">Source</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - + <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> @@ -183,7 +178,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html 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href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/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> +<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"> @@ -32,11 +38,11 @@ -<meta property="og:title" content="A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012" /> +<meta property="og:title" content="A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012" /> <meta property="og:description" content="Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The soil definitions are from page 46ff. from FOCUS (2012)." /> -<meta name="twitter:card" content="summary" /> + @@ -53,7 +59,7 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -83,7 +89,6 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -105,24 +110,21 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> </div> <div class="ref-description"> - <p>Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The 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> <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> <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> - <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 @@ -186,17 +188,10 @@ soil definitions are from page 46ff. from FOCUS (2012).</p> #> 51 Thi Ck1 6 7.8 32.9 0.18 0.0 #> </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="#format">Format</a></li> - - <li><a href="#references">References</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - + <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> @@ -207,7 +202,7 @@ soil definitions are from page 46ff. from FOCUS (2012).</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index 77045f1..bbfb592 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/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" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/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> +<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"> @@ -38,7 +42,6 @@ <meta property="og:title" content="Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios" /> <meta property="og:description" content="The data were extracted from the scenario.txt file using the R code shown below. The text file is not included in the package as its licence is not clear." /> -<meta name="twitter:card" content="summary" /> @@ -56,7 +59,7 @@ The text file is not included in the package as its licence is not clear." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -292,13 +295,10 @@ The text file is not included in the package as its licence is not clear.</p> #> Jun-Sep 2 3 #> </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="#format">Format</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + <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> @@ -309,7 +309,7 @@ The text file is not included in the package as its licence is not clear.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index cedb023..9f9e3c3 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/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" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/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> +<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"> @@ -38,7 +42,6 @@ <meta property="og:title" content="R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa" /> <meta property="og:description" content="An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> -<meta name="twitter:card" content="summary" /> @@ -56,7 +59,7 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -120,7 +123,7 @@ Usually, an instance of this class will be generated by <code><a href='read.TOXS -<dl class='dl-horizontal'> +<dl'> <dt><code>get_events(threshold, total = FALSE)</code></dt><dd><p>Populate a datataframe with event information for the specified threshold value in µg/L. If <code>total = TRUE</code>, the total concentration including the amount adsorbed to suspended matter will be used. The resulting dataframe is stored in the @@ -133,7 +136,7 @@ Usually, an instance of this class will be generated by <code><a href='read.TOXS <h2 class="hasAnchor" id="public-fields"><a class="anchor" href="#public-fields"></a>Public fields</h2> - <p><div class="r6-fields"></p><dl class='dl-horizontal'> + <p><div class="r6-fields"></p><dl'> <dt><code>filename</code></dt><dd><p>Length one character vector.</p></dd> <dt><code>basedir</code></dt><dd><p>Length one character vector.</p></dd> @@ -165,40 +168,40 @@ for the requested moving window sizes in days.</p></dd> <a id="method-new"></a></p><h3>Method <code>new()</code></h3> <h3>Usage</h3> -<p><div class="r"></p><pre>TOXSWA_cwa$new( - filename, - basedir, - zipfile = NULL, - segment = "last", - substance = "parent", - total = FALSE +<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>new</span>( + <span class='no'>filename</span>, + <span class='no'>basedir</span>, + <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>, + <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, + <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span> )</pre><p></div></p> <p><hr> <a id="method-moving_windows"></a></p><h3>Method <code>moving_windows()</code></h3> <h3>Usage</h3> -<p><div class="r"></p><pre>TOXSWA_cwa$moving_windows(windows, total = FALSE)</pre><p></div></p> +<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>moving_windows</span>(<span class='no'>windows</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> <p><hr> <a id="method-get_events"></a></p><h3>Method <code>get_events()</code></h3> <h3>Usage</h3> -<p><div class="r"></p><pre>TOXSWA_cwa$get_events(thresholds, total = FALSE)</pre><p></div></p> +<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'>get_events</span>(<span class='no'>thresholds</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre><p></div></p> <p><hr> <a id="method-print"></a></p><h3>Method <code><a href='https://rdrr.io/r/base/print.html'>print()</a></code></h3> <h3>Usage</h3> -<p><div class="r"></p><pre>TOXSWA_cwa$print()</pre><p></div></p> +<p><div class="r"></p><pre><span class='no'>TOXSWA_cwa</span>$<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>()</pre><p></div></p> <p><hr> <a id="method-clone"></a></p><h3>Method <code>clone()</code></h3> <p>The objects of this class are cloneable with this method.</p><h3>Usage</h3> -<p><div class="r"></p><pre>TOXSWA_cwa$clone(deep = FALSE)</pre><p></div></p> +<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 class='dl-horizontal'> +<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> @@ -239,16 +242,10 @@ for the requested moving window sizes in days.</p></dd> #> 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> </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="#format">Format</a></li> - <li><a href="#methods">Methods</a></li> - <li><a href="#public-fields">Public fields</a></li> - <li><a href="#methods">Methods</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + <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> @@ -259,7 +256,7 @@ for the requested moving window sizes in days.</p></dd> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/TSCF-1.png b/docs/reference/TSCF-1.png Binary files differnew file mode 100644 index 0000000..efa9e0a --- /dev/null +++ b/docs/reference/TSCF-1.png diff --git a/docs/reference/TSCF.html b/docs/reference/TSCF.html new file mode 100644 index 0000000..b635ba2 --- /dev/null +++ b/docs/reference/TSCF.html @@ -0,0 +1,181 @@ +<!-- 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>Estimation of the transpiration stream concentration factor — TSCF • 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="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]> +<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="Released version">0.5.7</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> + <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>Estimation of the transpiration stream concentration factor</h1> + + <div class="hidden name"><code>TSCF.Rd</code></div> + </div> + + <div class="ref-description"> + <p>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.</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> + + <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> + + <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> + + <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> + + <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> + <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> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html index 08d8399..dd78451 100644 --- a/docs/reference/drift_data_JKI.html +++ b/docs/reference/drift_data_JKI.html @@ -9,23 +9,29 @@ <title>Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI • 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> +<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/3.3.7/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> +<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/5.7.1/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" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/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> +<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"> @@ -33,12 +39,12 @@ published by the JKI — drift_data_JKI • pfm</title> + <meta property="og:title" content="Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI" /> - <meta property="og:description" content="Deposition from spray drift expressed as percent of the applied dose as published by the German Julius-Kühn Institute (JKI)." /> -<meta name="twitter:card" content="summary" /> + @@ -55,7 +61,7 @@ published by the German Julius-Kühn Institute (JKI)." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -85,7 +91,6 @@ published by the German Julius-Kühn Institute (JKI)." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -108,19 +113,17 @@ published by the JKI</h1> </div> <div class="ref-description"> - <p>Deposition from spray drift expressed as percent of the applied dose as published by the German Julius-Kühn Institute (JKI).</p> - </div> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>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> <p>JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved @@ -130,7 +133,6 @@ on 2015-06-11</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> <p>The data were extracted from the spreadsheet cited below using the R code @@ -146,7 +148,6 @@ 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> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> @@ -389,19 +390,10 @@ included.</p> #> 50 0.06 0.001 NA #> </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="#format">Format</a></li> - - <li><a href="#source">Source</a></li> - - <li><a href="#details">Details</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - + <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> @@ -412,7 +404,7 @@ included.</p> </div> <div class="pkgdown"> - 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<body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-index"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -116,6 +120,11 @@ <p class="section-desc"><p>Functions that are independent of specific fate modelling areas</p></p> </th> </tr> + + + </tbody><tbody> + + <tr> <td> @@ -176,6 +185,12 @@ <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> + <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> @@ -184,6 +199,11 @@ <p class="section-desc"></p> </th> </tr> + + + </tbody><tbody> + + <tr> <td> @@ -228,6 +248,11 @@ <p class="section-desc"></p> </th> </tr> + + + </tbody><tbody> + + <tr> <td> @@ -248,6 +273,11 @@ <p class="section-desc"></p> </th> </tr> + + + </tbody><tbody> + + <tr> <td> @@ -342,6 +372,11 @@ water concentrations</p></td> <p class="section-desc"><p>Evaluating environmental fate properties</p></p> </th> </tr> + + + </tbody><tbody> + + <tr> <td> @@ -362,6 +397,11 @@ water concentrations</p></td> <p class="section-desc"></p> </th> </tr> + + + </tbody><tbody> + + <tr> <td> @@ -373,16 +413,10 @@ water concentrations</p></td> </table> </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="#section-general-utility-functions">General utility functions</a></li> - <li><a href="#section-predicted-environmental-concentrations-in-soil">Predicted environmental concentrations in soil</a></li> - <li><a href="#section-predicted-environmental-concentrations-in-groundwater">Predicted environmental concentrations in groundwater</a></li> - <li><a href="#section-predicted-environmental-concentrations-in-surface-water">Predicted environmental concentrations in surface water</a></li> - <li><a href="#section-classifications-and-indicators">Classifications and indicators</a></li> - <li><a href="#section-utilities">Utilities</a></li> - </ul> + <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> @@ -393,7 +427,7 @@ water concentrations</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html index a0f723f..38c1f70 100644 --- a/docs/reference/perc_runoff_exposit.html +++ b/docs/reference/perc_runoff_exposit.html @@ -8,23 +8,29 @@ <title>Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit • 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> +<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/3.3.7/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> +<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/5.7.1/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" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/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> +<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"> @@ -32,10 +38,10 @@ -<meta property="og:title" content="Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit" /> +<meta property="og:title" content="Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit" /> <meta property="og:description" content="A table of the loss percentages used in Exposit 3 for the twelve different Koc classes" /> -<meta name="twitter:card" content="summary" /> + @@ -52,7 +58,7 @@ </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -82,7 +88,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -104,16 +109,15 @@ </div> <div class="ref-description"> - <p>A table of the loss percentages used in Exposit 3 for the twelve different Koc classes</p> - </div> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>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 class='dl-horizontal'> + 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> @@ -121,12 +125,11 @@ adjacent water body bound to eroding particles</p></dd> </dl> - + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>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 @@ -143,17 +146,10 @@ #> >20000-50000 20000 0.014 0.291 #> >50000 50000 0.001 0.451</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="#format">Format</a></li> - - <li><a href="#source">Source</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - + <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> @@ -164,7 +160,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html index baded1c..947d4c5 100644 --- a/docs/reference/perc_runoff_reduction_exposit.html +++ b/docs/reference/perc_runoff_reduction_exposit.html @@ -8,23 +8,29 @@ <title>Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit • 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> +<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/3.3.7/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> +<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/5.7.1/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" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/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> +<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"> @@ -32,10 +38,10 @@ -<meta property="og:title" content="Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit" /> +<meta property="og:title" content="Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit" /> <meta property="og:description" content="A table of the runoff reduction percentages used in Exposit 3 for different vegetated buffer widths" /> -<meta name="twitter:card" content="summary" /> + @@ -52,7 +58,7 @@ </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -82,7 +88,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -104,31 +109,29 @@ </div> <div class="ref-description"> - <p>A table of the runoff reduction percentages used in Exposit 3 for different vegetated buffer widths</p> - </div> <pre class="usage"><span class='no'>perc_runoff_reduction_exposit</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>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 class='dl-horizontal'> +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> - + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>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> <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> - <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_reduction_exposit</span>)</div><div class='output co'>#> $`3.02` @@ -158,17 +161,10 @@ from which the values were taken.</p><dl class='dl-horizontal'> #> 20 m 97.5 97.5 #> </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="#format">Format</a></li> - - <li><a href="#source">Source</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - + <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> @@ -179,7 +175,7 @@ from which the values were taken.</p><dl class='dl-horizontal'> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index d5ef9e7..cb3cf14 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -8,23 +8,29 @@ <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/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/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> +<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/5.7.1/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" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/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> +<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"> @@ -32,12 +38,12 @@ -<meta property="og:title" content="Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015" /> +<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." /> -<meta name="twitter:card" content="summary" /> + @@ -54,7 +60,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -84,7 +90,6 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -106,20 +111,18 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> </div> <div class="ref-description"> - <p>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.</p> - </div> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>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> <p>EFSA (European Food Safety Authority) (2015) @@ -127,7 +130,6 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.</p> 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>) { @@ -165,17 +167,10 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.</p> #> CLC 4 #> CLS 4</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="#format">Format</a></li> - - <li><a href="#source">Source</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - + <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> @@ -186,7 +181,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html index f5044e7..7e8044e 100644 --- a/docs/reference/soil_scenario_data_EFSA_2017.html +++ b/docs/reference/soil_scenario_data_EFSA_2017.html @@ -8,23 +8,29 @@ <title>Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • 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> +<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/3.3.7/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> +<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/5.7.1/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" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/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> +<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"> @@ -32,12 +38,12 @@ -<meta property="og:title" content="Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017" /> +<meta property="og:title" content="Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017" /> <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 (2017, p. 14/15). Also, the scenario and model adjustment factors from p. 16 and p. 18 are included." /> -<meta name="twitter:card" content="summary" /> + @@ -54,7 +60,7 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -84,7 +90,6 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." /> <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -106,20 +111,18 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." /> </div> <div class="ref-description"> - <p>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 (2017, p. 14/15). Also, the scenario and model adjustment factors from p. 16 and p. 18 are included.</p> - </div> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>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> <p>EFSA (European Food Safety Authority) (2017) @@ -127,7 +130,6 @@ scenario and model adjustment factors from p. 16 and p. 18 are included.</p> 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 @@ -145,17 +147,10 @@ scenario and model adjustment factors from p. 16 and p. 18 are included.</p> #> CLC Châteaudun 589 #> CLS Sevilla 526</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="#format">Format</a></li> - - <li><a href="#source">Source</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - + <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> @@ -166,7 +161,7 @@ scenario and model adjustment factors from p. 16 and p. 18 are included.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/sitemap.xml b/docs/sitemap.xml index b619e4d..0c507b6 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -58,6 +58,9 @@ <loc>https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/pfm/reference/TSCF.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html</loc> </url> <url> diff --git a/man/EFSA_GW_interception_2014.Rd b/man/EFSA_GW_interception_2014.Rd index f2e8c1c..2334d7f 100644 --- a/man/EFSA_GW_interception_2014.Rd +++ b/man/EFSA_GW_interception_2014.Rd @@ -4,7 +4,9 @@ \name{EFSA_GW_interception_2014} \alias{EFSA_GW_interception_2014} \title{Subset of EFSA crop interception default values for groundwater modelling} -\format{A matrix containing interception values, currently only for some selected crops} +\format{ +A matrix containing interception values, currently only for some selected crops +} \source{ European Food Safety Authority (2014) EFSA Guidance Document for evaluating laboratory and field dissipation studies to obtain DegT50 values diff --git a/man/EFSA_washoff_2017.Rd b/man/EFSA_washoff_2017.Rd index b1ab30f..e153fbe 100644 --- a/man/EFSA_washoff_2017.Rd +++ b/man/EFSA_washoff_2017.Rd @@ -4,7 +4,9 @@ \name{EFSA_washoff_2017} \alias{EFSA_washoff_2017} \title{Subset of EFSA crop washoff default values} -\format{A matrix containing wash-off factors, currently only for some selected crops} +\format{ +A matrix containing wash-off factors, currently only for some selected crops +} \source{ European Food Safety Authority (2017) EFSA guidance document for predicting environmental concentrations of active substances of plant diff --git a/man/FOCUS_GW_scenarios_2012.Rd b/man/FOCUS_GW_scenarios_2012.Rd index 4529816..53d1d3c 100644 --- a/man/FOCUS_GW_scenarios_2012.Rd +++ b/man/FOCUS_GW_scenarios_2012.Rd @@ -4,7 +4,9 @@ \name{FOCUS_GW_scenarios_2012} \alias{FOCUS_GW_scenarios_2012} \title{A very small subset of the FOCUS Groundwater scenario definitions} -\format{An object of class \code{list} of length 2.} +\format{ +An object of class \code{list} of length 2. +} \usage{ FOCUS_GW_scenarios_2012 } diff --git a/man/FOCUS_Step_12_scenarios.Rd b/man/FOCUS_Step_12_scenarios.Rd index 0547d61..02963bf 100644 --- a/man/FOCUS_Step_12_scenarios.Rd +++ b/man/FOCUS_Step_12_scenarios.Rd @@ -4,10 +4,12 @@ \name{FOCUS_Step_12_scenarios} \alias{FOCUS_Step_12_scenarios} \title{Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator} -\format{A list containing the scenario names in a character vector called 'names', +\format{ +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'.} + calculations in a matrix called 'rd'. +} \description{ The data were extracted from the scenario.txt file using the R code shown below. The text file is not included in the package as its licence is not clear. diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd index eb3fe38..6a95a0b 100644 --- a/man/TOXSWA_cwa.Rd +++ b/man/TOXSWA_cwa.Rd @@ -4,7 +4,9 @@ \name{TOXSWA_cwa} \alias{TOXSWA_cwa} \title{R6 class for holding TOXSWA water concentration data and associated statistics} -\format{An \code{\link{R6Class}} generator object.} +\format{ +An \code{\link{R6Class}} generator object. +} \description{ An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. @@ -67,6 +69,7 @@ for the requested moving window sizes in days.} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-new"></a>}} +\if{latex}{\out{\hypertarget{method-new}{}}} \subsection{Method \code{new()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$new( @@ -82,6 +85,7 @@ for the requested moving window sizes in days.} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-moving_windows"></a>}} +\if{latex}{\out{\hypertarget{method-moving_windows}{}}} \subsection{Method \code{moving_windows()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$moving_windows(windows, total = FALSE)}\if{html}{\out{</div>}} @@ -90,6 +94,7 @@ for the requested moving window sizes in days.} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-get_events"></a>}} +\if{latex}{\out{\hypertarget{method-get_events}{}}} \subsection{Method \code{get_events()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$get_events(thresholds, total = FALSE)}\if{html}{\out{</div>}} @@ -98,6 +103,7 @@ for the requested moving window sizes in days.} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-print"></a>}} +\if{latex}{\out{\hypertarget{method-print}{}}} \subsection{Method \code{print()}}{ \subsection{Usage}{ \if{html}{\out{<div class="r">}}\preformatted{TOXSWA_cwa$print()}\if{html}{\out{</div>}} @@ -106,6 +112,7 @@ for the requested moving window sizes in days.} } \if{html}{\out{<hr>}} \if{html}{\out{<a id="method-clone"></a>}} +\if{latex}{\out{\hypertarget{method-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/TSCF.Rd b/man/TSCF.Rd new file mode 100644 index 0000000..e4cefdc --- /dev/null +++ b/man/TSCF.Rd @@ -0,0 +1,37 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/TSCF.R +\name{TSCF} +\alias{TSCF} +\title{Estimation of the transpiration stream concentration factor} +\usage{ +TSCF(log_Kow, method = c("briggs82", "dettenmaier09")) +} +\arguments{ +\item{log_Kow}{The decadic logarithm of the octanol-water partition constant} + +\item{method}{Short name of the estimation method.} +} +\description{ +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. +} +\details{ +The Dettenmaier equation is given to show that other views on the subject exist. +} +\examples{ +plot(TSCF, -1, 5, xlab = "log Kow", ylab = "TSCF", ylim = c(0, 1.1)) +TSCF_2 <- function(x) TSCF(x, method = "dettenmaier09") +curve(TSCF_2, -1, 5, add = TRUE, lty = 2) +legend("topright", lty = 1:2, bty = "n", + legend = c("Briggs et al. (1982)", "Dettenmaier et al. (2009)")) +} +\references{ +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 +} diff --git a/man/drift_data_JKI.Rd b/man/drift_data_JKI.Rd index 090910f..181eca6 100644 --- a/man/drift_data_JKI.Rd +++ b/man/drift_data_JKI.Rd @@ -5,9 +5,11 @@ \alias{drift_data_JKI} \title{Deposition from spray drift expressed as percent of the applied dose as published by the JKI} -\format{A list currently containing matrices with spray drift percentage +\format{ +A list currently containing matrices with spray drift percentage data for field crops (Ackerbau), and Pome/stone fruit, early and late -(Obstbau frueh, spaet).} +(Obstbau frueh, spaet). +} \source{ JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved from diff --git a/man/perc_runoff_exposit.Rd b/man/perc_runoff_exposit.Rd index 3f072df..0bd2827 100644 --- a/man/perc_runoff_exposit.Rd +++ b/man/perc_runoff_exposit.Rd @@ -3,7 +3,8 @@ \name{perc_runoff_exposit} \alias{perc_runoff_exposit} \title{Runoff loss percentages as used in Exposit 3} -\format{A data frame with percentage values for the dissolved fraction and the fraction +\format{ +A data frame with percentage values for the dissolved fraction and the fraction bound to eroding particles, with Koc classes used as row names \describe{ \item{Koc_lower_bound}{The lower bound of the Koc class} @@ -11,7 +12,8 @@ adjacent water body in the dissolved phase} \item{bound}{The percentage of the applied substance transferred to an adjacent water body bound to eroding particles} - }} + } +} \source{ Excel 3.02 spreadsheet available from \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html} diff --git a/man/perc_runoff_reduction_exposit.Rd b/man/perc_runoff_reduction_exposit.Rd index 016f9dd..0aa50c1 100644 --- a/man/perc_runoff_reduction_exposit.Rd +++ b/man/perc_runoff_reduction_exposit.Rd @@ -4,14 +4,16 @@ \name{perc_runoff_reduction_exposit} \alias{perc_runoff_reduction_exposit} \title{Runoff reduction percentages as used in Exposit} -\format{A named list of data frames with reduction percentage values for the +\format{ +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. \describe{ \item{dissolved}{The reduction percentage for the dissolved phase} \item{bound}{The reduction percentage for the particulate phase} - }} + } +} \source{ Excel 3.02 spreadsheet available from \url{https://www.bvl.bund.de/EN/04_PlantProtectionProducts/03_Applicants/04_AuthorisationProcedure/08_Environment/ppp_environment_node.html} diff --git a/man/soil_scenario_data_EFSA_2015.Rd b/man/soil_scenario_data_EFSA_2015.Rd index 64c00a8..dfad4aa 100644 --- a/man/soil_scenario_data_EFSA_2015.Rd +++ b/man/soil_scenario_data_EFSA_2015.Rd @@ -4,9 +4,11 @@ \name{soil_scenario_data_EFSA_2015} \alias{soil_scenario_data_EFSA_2015} \title{Properties of the predefined scenarios from the EFSA guidance from 2015} -\format{A data frame with one row for each scenario. Row names are the scenario codes, +\format{ +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} is the dry bulk density of the top soil.} + mostly self-explanatory. \code{rho} is the dry bulk density of the top soil. +} \source{ EFSA (European Food Safety Authority) (2015) EFSA guidance document for predicting environmental concentrations diff --git a/man/soil_scenario_data_EFSA_2017.Rd b/man/soil_scenario_data_EFSA_2017.Rd index aeaacac..f6de290 100644 --- a/man/soil_scenario_data_EFSA_2017.Rd +++ b/man/soil_scenario_data_EFSA_2017.Rd @@ -4,9 +4,11 @@ \name{soil_scenario_data_EFSA_2017} \alias{soil_scenario_data_EFSA_2017} \title{Properties of the predefined scenarios from the EFSA guidance from 2017} -\format{A data frame with one row for each scenario. Row names are the scenario codes, +\format{ +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} is the dry bulk density of the top soil.} + mostly self-explanatory. \code{rho} is the dry bulk density of the top soil. +} \source{ EFSA (European Food Safety Authority) (2017) EFSA guidance document for predicting environmental concentrations @@ -3,23 +3,30 @@ Loading required package: R6 Loading required package: mkin Testing pfm ✔ | OK F W S | Context -
⠏ | 0 | Exposit calculations
✔ | 7 | Exposit calculations -
⠏ | 0 | Geometric mean calculation
✔ | 6 | Geometric mean calculation -
⠏ | 0 | Check max_twa for parent mkinfit models against analytical solutions
⠋ | 1 | Check max_twa for parent mkinfit models against analytical solutions
✔ | 1 | Check max_twa for parent mkinfit models against analytical solutions [1.9 s]
⠏ | 0 | Simple PEC sediment calculations
✔ | 1 | Simple PEC sediment calculations -
⠏ | 0 | Simple PEC soil calculations
⠙ | 2 | Simple PEC soil calculations
✔ | 17 | Simple PEC soil calculations [0.2 s] +
⠏ | 0 | Simple PEC soil calculations
⠙ | 2 | Simple PEC soil calculations
✔ | 17 | Simple PEC soil calculations [0.3 s]
⠏ | 0 | Simple PEC surface water calculations with drift entry
✔ | 2 | Simple PEC surface water calculations with drift entry -
⠏ | 0 | Processing of residue series
✔ | 11 | Processing of residue series
⠏ | 0 | Actual and time weighted average concentrations for SFO kinetics
✔ | 1 | Actual and time weighted average concentrations for SFO kinetics +
⠏ | 0 | Read and analyse TOXSWA cwa files
⠋ | 1 | Read and analyse TOXSWA cwa files
⠸ | 4 | Read and analyse TOXSWA cwa files
⠼ | 5 | Read and analyse TOXSWA cwa files
⠴ | 6 | Read and analyse TOXSWA cwa files
✖ | 6 1 | Read and analyse TOXSWA cwa files [6.4 s] +──────────────────────────────────────────────────────────────────────────────────────────────────── +test_TOXSWA.R:68: failure: Getting events and moving window analysis works +H_sw_R1_stream$windows has changed from known value recorded in 'H_sw_R1_stream_windows.rds'. +Component "window": Modes: character, numeric +Component "window": Attributes: < target is NULL, current is list > +Component "window": target is character, current is factor +──────────────────────────────────────────────────────────────────────────────────────────────────── +
⠏ | 0 | UK drainage PEC calculations
✔ | 12 | UK drainage PEC calculations +
⠏ | 0 | Exposit calculations
✔ | 7 | Exposit calculations +
⠏ | 0 | Geometric mean calculation
✔ | 6 | Geometric mean calculation +
⠏ | 0 | Check max_twa for parent mkinfit models against analytical solutions
⠋ | 1 | Check max_twa for parent mkinfit models against analytical solutions
✔ | 1 | Check max_twa for parent mkinfit models against analytical solutions [2.1 s] +
⠏ | 0 | Processing of residue series
✔ | 11 | Processing of residue series
⠏ | 0 | FOCUS Step 1 calculations
⠹ | 3 | FOCUS Step 1 calculations
✔ | 9 | FOCUS Step 1 calculations [0.1 s]
⠏ | 0 | FOCUS Steps 12 input files
✔ | 8 | FOCUS Steps 12 input files -
⠏ | 0 | Read and analyse TOXSWA cwa files
⠋ | 1 | Read and analyse TOXSWA cwa files
⠸ | 4 | Read and analyse TOXSWA cwa files
⠼ | 5 | Read and analyse TOXSWA cwa files
⠴ | 6 | Read and analyse TOXSWA cwa files
✔ | 7 | Read and analyse TOXSWA cwa files [5.5 s] -
⠏ | 0 | UK drainage PEC calculations
✔ | 12 | UK drainage PEC calculations ══ Results ═════════════════════════════════════════════════════════════════════════════════════════ -Duration: 7.9 s +Duration: 9.3 s -OK: 82 -Failed: 0 +OK: 81 +Failed: 1 Warnings: 0 Skipped: 0 |
