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-rw-r--r--docs/authors.html25
-rw-r--r--docs/index.html52
-rw-r--r--docs/pkgdown.css12
-rw-r--r--docs/pkgdown.js19
-rw-r--r--docs/pkgdown.yml2
-rw-r--r--docs/reference/FOCUS_GW_scenarios_2012.html23
-rw-r--r--docs/reference/FOCUS_Step_12_scenarios.html43
-rw-r--r--docs/reference/FOMC_actual_twa.html31
-rw-r--r--docs/reference/GUS.html34
-rw-r--r--docs/reference/PEC_FOMC_accu_rel.html23
-rw-r--r--docs/reference/PEC_soil.html58
-rw-r--r--docs/reference/PEC_soil_mets.html168
-rw-r--r--docs/reference/PEC_sw_drainage_UK.html32
-rw-r--r--docs/reference/PEC_sw_drift.html30
-rw-r--r--docs/reference/PEC_sw_exposit_runoff.html25
-rw-r--r--docs/reference/PEC_sw_focus.html27
-rw-r--r--docs/reference/PEC_sw_sed.html29
-rw-r--r--docs/reference/SFO_actual_twa.html31
-rw-r--r--docs/reference/SSLRC_mobility_classification.html27
-rw-r--r--docs/reference/TOXSWA_cwa.html31
-rw-r--r--docs/reference/chent_focus_sw.html28
-rw-r--r--docs/reference/drift_data_JKI.html39
-rw-r--r--docs/reference/endpoint.html35
-rw-r--r--docs/reference/geomean.html31
-rw-r--r--docs/reference/get_vertex.html39
-rw-r--r--docs/reference/index.html92
-rw-r--r--docs/reference/max_twa.html25
-rw-r--r--docs/reference/one_box.html40
-rw-r--r--docs/reference/perc_runoff_exposit.html25
-rw-r--r--docs/reference/perc_runoff_reduction_exposit.html25
-rw-r--r--docs/reference/pesticide.txt4
-rw-r--r--docs/reference/pfm_degradation.html35
-rw-r--r--docs/reference/plot.TOXSWA_cwa.html43
-rw-r--r--docs/reference/plot.one_box.html33
-rw-r--r--docs/reference/read.TOXSWA_cwa.html35
-rw-r--r--docs/reference/sawtooth.html33
-rw-r--r--docs/reference/soil_scenario_data_EFSA_2015.html49
-rw-r--r--docs/reference/soil_scenario_data_EFSA_2017.html23
-rw-r--r--docs/reference/twa.html25
39 files changed, 782 insertions, 599 deletions
diff --git a/docs/authors.html b/docs/authors.html
index 718d419..977f810 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Authors • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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@@ -35,7 +35,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -51,14 +52,15 @@
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -99,7 +101,7 @@
<ul class="list-unstyled">
<li>
- <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' height='16'></a>
+ <p><strong>Johannes Ranke</strong>. 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' height='16'></a>
</p>
</li>
</ul>
@@ -115,9 +117,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/index.html b/docs/index.html
index a6429d3..d71ab63 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -1,20 +1,20 @@
<!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Utilities for Pesticide Fate Modelling • pfm</title>
-<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous">
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous">
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
<script src="pkgdown.js"></script><meta property="og:title" content="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://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<!-- 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]-->
@@ -24,14 +24,15 @@
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -65,32 +66,20 @@
</header><div class="row">
<div class="contents col-md-9">
- <div id="pfm" class="section level1">
+<div id="pfm" class="section level1">
<div class="page-header"><h1 class="hasAnchor">
<a href="#pfm" class="anchor"></a>pfm</h1></div>
-<p>The R package <strong>pfm</strong> provides some utilities for fate modelling, including dealing with FOCUS pesticide fate modelling tools, (currently only TOXSWA cwa and out files), made available under the GNU public license. This means:</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode R"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">This program is free software<span class="op">:</span><span class="st"> </span>you can redistribute it and<span class="op">/</span>or modify it under</a>
-<a class="sourceLine" id="cb1-2" data-line-number="2">the terms of the GNU General Public License as published by the Free Software</a>
-<a class="sourceLine" id="cb1-3" data-line-number="3">Foundation, either version <span class="dv">3</span> of the License, <span class="kw">or</span> (at your option) any later</a>
-<a class="sourceLine" id="cb1-4" data-line-number="4">version.</a>
-<a class="sourceLine" id="cb1-5" data-line-number="5"></a>
-<a class="sourceLine" id="cb1-6" data-line-number="6">This program is distributed <span class="cf">in</span> the hope that it will be useful, but WITHOUT</a>
-<a class="sourceLine" id="cb1-7" data-line-number="7">ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
-<a class="sourceLine" id="cb1-8" data-line-number="8">FOR A PARTICULAR PURPOSE. See the GNU General Public License <span class="cf">for</span> more</a>
-<a class="sourceLine" id="cb1-9" data-line-number="9">details.</a>
-<a class="sourceLine" id="cb1-10" data-line-number="10"></a>
-<a class="sourceLine" id="cb1-11" data-line-number="11">You should have received a copy of the GNU General Public License along with</a>
-<a class="sourceLine" id="cb1-12" data-line-number="12">this program. If not, see <span class="op">&lt;</span>http<span class="op">:</span><span class="er">//</span>www.gnu.org<span class="op">/</span>licenses<span class="op">/</span><span class="er">&gt;</span></a></code></pre></div>
+<p>The R package <strong>pfm</strong> provides some utilities for fate modelling, including dealing with FOCUS pesticide fate modelling tools, (currently only TOXSWA cwa and out files), made available under the GNU public license.</p>
<div id="installation" class="section level2">
<h2 class="hasAnchor">
<a href="#installation" class="anchor"></a>Installation</h2>
<p>The easiest way to install the package is probably to use <a href="https://cran.r-project.org/package=drat">drat</a>:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw">install.packages</span>(<span class="st">"drat"</span>)</a>
-<a class="sourceLine" id="cb2-2" data-line-number="2">drat<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/drat/topics/addRepo">addRepo</a></span>(<span class="st">"jranke"</span>)</a>
-<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="kw">install.packages</span>(<span class="st">"pfm"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"drat"</span>)</a>
+<a class="sourceLine" id="cb1-2" data-line-number="2">drat<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/drat/topics/addRepo">addRepo</a></span>(<span class="st">"jranke"</span>)</a>
+<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"pfm"</span>)</a></code></pre></div>
<p>Alternatively you can install the package using the <code>devtools</code> package. Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and vignettes.</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">library</span>(devtools)</a>
-<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">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="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(devtools)</a>
+<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/devtools/topics/reexports">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>
<div id="use" class="section level2">
<h2 class="hasAnchor">
@@ -101,19 +90,16 @@
<h2 class="hasAnchor">
<a href="#examples" class="anchor"></a>Examples</h2>
<p>One recent nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown <a href="http://pkgdown.jrwb.de/pfm/reference/plot.one_box.html">here</a>.</p>
-<p>Another, even more recent example shows how FOCUS PELMO can be run in parallel under Linux as shown <a href="http://pkgdown.jrwb.de/pfm/reference/PELMO_runs.html">here</a>.</p>
</div>
</div>
</div>
- <div class="col-md-3" id="sidebar">
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<div class="links">
<h2>Links</h2>
<ul class="list-unstyled">
<li>Browse source code at <br><a href="https://github.com/jranke/pfm">https://​github.com/​jranke/​pfm</a>
</li>
-<li>Report a bug at <br><a href="NA">NA</a>
-</li>
</ul>
</div>
<div class="license">
@@ -125,22 +111,20 @@
<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" height="16"></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"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
</ul>
</div>
</div>
</div>
-
<footer><div class="copyright">
<p>Developed by Johannes Ranke.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index 6ca2f37..c03fb08 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -58,9 +58,14 @@ img {
max-width: 100%;
}
+/* Fix bug in bootstrap (only seen in firefox) */
+summary {
+ display: list-item;
+}
+
/* Typographic tweaking ---------------------------------*/
-.contents h1.page-header {
+.contents .page-header {
margin-top: calc(-60px + 1em);
}
@@ -136,10 +141,9 @@ a.anchor {
.ref-index th {font-weight: normal;}
.ref-index td {vertical-align: top;}
+.ref-index .icon {width: 40px;}
.ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
-
-.ref-index .alias {width: 40%;}
+.ref-index-icons .alias {width: calc(40% - 40px);}
.ref-index .title {width: 60%;}
.ref-arguments th {text-align: right; padding-right: 10px;}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index de9bd72..eb7e83d 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -25,9 +25,13 @@
for (var i = 0; i < links.length; i++) {
if (links[i].getAttribute("href") === "#")
continue;
- var path = paths(links[i].pathname);
+ // Ignore external links
+ if (links[i].host !== location.host)
+ continue;
+
+ var nav_path = paths(links[i].pathname);
- var length = prefix_length(cur_path, path);
+ var length = prefix_length(nav_path, cur_path);
if (length > max_length) {
max_length = length;
pos = i;
@@ -52,13 +56,14 @@
return(pieces);
}
+ // Returns -1 if not found
function prefix_length(needle, haystack) {
if (needle.length > haystack.length)
- return(0);
+ return(-1);
// Special case for length-0 haystack, since for loop won't run
if (haystack.length === 0) {
- return(needle.length === 0 ? 1 : 0);
+ return(needle.length === 0 ? 0 : -1);
}
for (var i = 0; i < haystack.length; i++) {
@@ -78,9 +83,9 @@
element.setAttribute('data-original-title', tooltipOriginalTitle);
}
- if(Clipboard.isSupported()) {
+ if(ClipboardJS.isSupported()) {
$(document).ready(function() {
- var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+ var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>";
$(".examples, div.sourceCode").addClass("hasCopyButton");
@@ -91,7 +96,7 @@
$('.btn-copy-ex').tooltip({container: 'body'});
// Initialize clipboard:
- var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+ var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', {
text: function(trigger) {
return trigger.parentNode.textContent;
}
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 7908647..1dc6ec1 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
pandoc: 2.2.1
-pkgdown: 1.1.0
+pkgdown: 1.3.0
pkgdown_sha: ~
articles: []
diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html
index 65a6df2..d60f44f 100644
--- a/docs/reference/FOCUS_GW_scenarios_2012.html
+++ b/docs/reference/FOCUS_GW_scenarios_2012.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -39,7 +39,8 @@ soil definitions are from page 46ff. from FOCUS (2012)." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -55,14 +56,15 @@ soil definitions are from page 46ff. from FOCUS (2012)." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -205,9 +207,8 @@ soil definitions are from page 46ff. from FOCUS (2012).</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html
index 3b92377..2020899 100644
--- a/docs/reference/FOCUS_Step_12_scenarios.html
+++ b/docs/reference/FOCUS_Step_12_scenarios.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -39,7 +39,8 @@ The text file is not included in the package as its licence is not clear." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -55,14 +56,15 @@ The text file is not included in the package as its licence is not clear." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -124,21 +126,21 @@ The text file is not included in the package as its licence is not clear.</p>
</div><span class='co'># NOT RUN {</span>
<span class='co'># This is the code that was used to extract the data</span>
<span class='no'>scenario_path</span> <span class='kw'>&lt;-</span> <span class='st'>"inst/extdata/FOCUS_Step_12_scenarios.txt"</span>
- <span class='no'>scenarios</span> <span class='kw'>&lt;-</span> <span class='fu'>readLines</span>(<span class='no'>scenario_path</span>)[<span class='fl'>9</span>:<span class='fl'>38</span>]
- <span class='no'>FOCUS_Step_12_scenarios</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>()
- <span class='no'>sce</span> <span class='kw'>&lt;-</span> <span class='fu'>read.table</span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>scenarios</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>, <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>check.names</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='no'>scenarios</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/readLines'>readLines</a></span>(<span class='no'>scenario_path</span>)[<span class='fl'>9</span>:<span class='fl'>38</span>]
+ <span class='no'>FOCUS_Step_12_scenarios</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>()
+ <span class='no'>sce</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/read.table'>read.table</a></span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>scenarios</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>, <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>check.names</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span> <span class='kw'>=</span> <span class='no'>sce</span>$<span class='no'>Crop</span>
- <span class='fu'>rownames</span>(<span class='no'>sce</span>) <span class='kw'>&lt;-</span> <span class='no'>sce</span>$<span class='no'>Crop</span>
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>rownames</a></span>(<span class='no'>sce</span>) <span class='kw'>&lt;-</span> <span class='no'>sce</span>$<span class='no'>Crop</span>
<span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>drift</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>3</span>:<span class='fl'>11</span>]
<span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>interception</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>12</span>:<span class='fl'>15</span>]
- <span class='no'>sce_2</span> <span class='kw'>&lt;-</span> <span class='fu'>readLines</span>(<span class='no'>scenario_path</span>)[<span class='fl'>41</span>:<span class='fl'>46</span>]
- <span class='no'>rd</span> <span class='kw'>&lt;-</span> <span class='fu'>read.table</span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>sce_2</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>)[<span class='fl'>1</span>:<span class='fl'>2</span>]
- <span class='no'>rd_mat</span> <span class='kw'>&lt;-</span> <span class='fu'>matrix</span>(<span class='no'>rd</span>$<span class='no'>V2</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
- <span class='fu'>dimnames</span>(<span class='no'>rd_mat</span>) <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>Time</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Oct-Feb"</span>, <span class='st'>"Mar-May"</span>, <span class='st'>"Jun-Sep"</span>),
- <span class='kw'>Region</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"North"</span>, <span class='st'>"South"</span>))
+ <span class='no'>sce_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/readLines'>readLines</a></span>(<span class='no'>scenario_path</span>)[<span class='fl'>41</span>:<span class='fl'>46</span>]
+ <span class='no'>rd</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/read.table'>read.table</a></span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>sce_2</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>)[<span class='fl'>1</span>:<span class='fl'>2</span>]
+ <span class='no'>rd_mat</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/matrix'>matrix</a></span>(<span class='no'>rd</span>$<span class='no'>V2</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/dimnames'>dimnames</a></span>(<span class='no'>rd_mat</span>) <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>Time</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Oct-Feb"</span>, <span class='st'>"Mar-May"</span>, <span class='st'>"Jun-Sep"</span>),
+ <span class='kw'>Region</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"North"</span>, <span class='st'>"South"</span>))
<span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>rd</span> <span class='kw'>=</span> <span class='no'>rd_mat</span>
- <span class='fu'>save</span>(<span class='no'>FOCUS_Step_12_scenarios</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/FOCUS_Step_12_scenarios.RData"</span>)
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/save'>save</a></span>(<span class='no'>FOCUS_Step_12_scenarios</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/FOCUS_Step_12_scenarios.RData"</span>)
<span class='co'># }</span><div class='input'>
<span class='co'># And this is the resulting data</span>
<span class='no'>FOCUS_Step_12_scenarios</span></div><div class='output co'>#&gt; $names
@@ -308,9 +310,8 @@ 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="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html
index 070788b..9963761 100644
--- a/docs/reference/FOMC_actual_twa.html
+++ b/docs/reference/FOMC_actual_twa.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -38,7 +38,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -54,14 +55,15 @@
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -108,8 +110,8 @@
</div>
- <pre class="usage"><span class='fu'>FOMC_actual_twa</span>(<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1.0001</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, <span class='fl'>14</span>,
- <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, <span class='fl'>50</span>, <span class='fl'>100</span>))</pre>
+ <pre class="usage"><span class='fu'>FOMC_actual_twa</span>(<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1.0001</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>,
+ <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, <span class='fl'>50</span>, <span class='fl'>100</span>))</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -160,9 +162,7 @@
</ul>
<h2>Author</h2>
-
-Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -172,9 +172,8 @@ Johannes Ranke
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html
index 59fd888..18f59be 100644
--- a/docs/reference/GUS.html
+++ b/docs/reference/GUS.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Groundwater ubiquity score based on Gustafson (1989) — GUS • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -56,14 +57,15 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -119,11 +121,12 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p>
<span class='co'># S3 method for chent</span>
<span class='fu'>GUS</span>(<span class='no'>chent</span>, <span class='kw'>degradation_value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>,
- <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>, <span class='kw'>sorption_value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>,
- <span class='kw'>degradation_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>sorption_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='no'>...</span>)
+ <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>,
+ <span class='kw'>sorption_value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>, <span class='kw'>degradation_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>,
+ <span class='kw'>sorption_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='no'>...</span>)
<span class='co'># S3 method for GUS_result</span>
-<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -221,9 +224,7 @@ toxicology and chemistry</em> <b>8</b>(4) 339–57.</p>
</ul>
<h2>Author</h2>
-
-Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -233,9 +234,8 @@ Johannes Ranke
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/PEC_FOMC_accu_rel.html b/docs/reference/PEC_FOMC_accu_rel.html
index 7999e32..a81683d 100644
--- a/docs/reference/PEC_FOMC_accu_rel.html
+++ b/docs/reference/PEC_FOMC_accu_rel.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -38,7 +38,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -54,14 +55,15 @@
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -150,9 +152,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html
index d746c2d..db09110 100644
--- a/docs/reference/PEC_soil.html
+++ b/docs/reference/PEC_soil.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Calculate predicted environmental concentrations in soil — PEC_soil • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -42,7 +42,8 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -58,14 +59,15 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." />
<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">
+ <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>
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- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
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@@ -116,13 +118,14 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).</p>
</div>
- <pre class="usage"><span class='fu'>PEC_soil</span>(<span class='no'>rate</span>, <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>mixing_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>,
- <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"mg/kg"</span>, <span class='kw'>PEC_pw_units</span> <span class='kw'>=</span> <span class='st'>"mg/L"</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
- <span class='kw'>n_periods</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, <span class='kw'>tillage_depth</span> <span class='kw'>=</span> <span class='fl'>20</span>, <span class='kw'>leaching_depth</span> <span class='kw'>=</span> <span class='no'>tillage_depth</span>,
- <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"annual"</span>, <span class='kw'>cultivation</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>chent</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
- <span class='kw'>FOMC</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='no'>Koc</span>/<span class='fl'>1.724</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fl'>0</span>,
- <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"default"</span>, <span class='st'>"EFSA_2017"</span>, <span class='st'>"EFSA_2015"</span>), <span class='kw'>leaching</span> <span class='kw'>=</span> <span class='no'>scenarios</span>
- <span class='kw'>==</span> <span class='st'>"EFSA_2017"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
+ <pre class="usage"><span class='fu'>PEC_soil</span>(<span class='no'>rate</span>, <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>,
+ <span class='kw'>mixing_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"mg/kg"</span>, <span class='kw'>PEC_pw_units</span> <span class='kw'>=</span> <span class='st'>"mg/L"</span>,
+ <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>n_periods</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, <span class='kw'>tillage_depth</span> <span class='kw'>=</span> <span class='fl'>20</span>,
+ <span class='kw'>leaching_depth</span> <span class='kw'>=</span> <span class='no'>tillage_depth</span>, <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"annual"</span>,
+ <span class='kw'>cultivation</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>chent</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>FOMC</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+ <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='no'>Koc</span>/<span class='fl'>1.724</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>t_act</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+ <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"default"</span>, <span class='st'>"EFSA_2017"</span>, <span class='st'>"EFSA_2015"</span>),
+ <span class='kw'>leaching</span> <span class='kw'>=</span> <span class='no'>scenarios</span> <span class='kw'>==</span> <span class='st'>"EFSA_2017"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -216,6 +219,10 @@ as Kom here</p></td>
<td><p>Averaging times for time weighted average concentrations</p></td>
</tr>
<tr>
+ <th>t_act</th>
+ <td><p>Time series for actual concentrations</p></td>
+ </tr>
+ <tr>
<th>scenarios</th>
<td><p>If this is 'default', the DT50 will be used without correction
and soil properties as specified in the REACH guidance (R.16, Table
@@ -296,21 +303,21 @@ from 2017 (p. 92).</p>
<span class='co'># This is example 1 starting at p. 92 of the EFSA guidance (2017)</span>
<span class='co'># Note that TWA concentrations differ from the ones given in the guidance</span>
<span class='co'># for an unknown reason (the values from EFSA (2015) can be reproduced).</span>
-<span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
+<span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
<span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2017"</span>)</div><div class='output co'>#&gt; scenario
#&gt; t_avg CTN CTC CTS
#&gt; 0 19.76834 13.8619 10.53795
-#&gt; 21 19.59345 13.7169 10.39882</div><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
+#&gt; 21 19.59345 13.7169 10.39882</div><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
<span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2017"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; scenario
#&gt; t_avg CLN CLC CLS
#&gt; 0 0.5541984 0.6779249 0.9816693
#&gt; 21 0.5484576 0.6693125 0.9609119</div><div class='input'>
<span class='co'># This is example 1 starting at p. 79 of the EFSA guidance (2015)</span>
-<span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
+<span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
<span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>)</div><div class='output co'>#&gt; scenario
#&gt; t_avg CTN CTC CTS
#&gt; 0 21.96827 11.53750 9.145259
-#&gt; 21 21.78517 11.40701 9.017370</div><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
+#&gt; 21 21.78517 11.40701 9.017370</div><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
<span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; scenario
#&gt; t_avg CLN CLC CLS
#&gt; 0 0.7589401 0.6674322 0.9147861
@@ -319,9 +326,9 @@ from 2017 (p. 92).</p>
<span class='co'># Metabolite M2</span>
<span class='co'># Calculate total and porewater soil concentrations for tier 1 scenarios</span>
<span class='co'># Relative molar mass is 100/300, formation fraction is 0.7 * 1</span>
-<span class='no'>results_pfm</span> <span class='kw'>&lt;-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
+<span class='no'>results_pfm</span> <span class='kw'>&lt;-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
<span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>)
-<span class='no'>results_pfm_pw</span> <span class='kw'>&lt;-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
+<span class='no'>results_pfm_pw</span> <span class='kw'>&lt;-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
<span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -341,9 +348,7 @@ from 2017 (p. 92).</p>
</ul>
<h2>Author</h2>
-
-Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -353,9 +358,8 @@ Johannes Ranke
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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diff --git a/docs/reference/PEC_soil_mets.html b/docs/reference/PEC_soil_mets.html
new file mode 100644
index 0000000..e60cc70
--- /dev/null
+++ b/docs/reference/PEC_soil_mets.html
@@ -0,0 +1,168 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
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+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Calculate initial and accumulation PEC soil for a set of metabolites</h1>
+ <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PEC_soil.R'><code>R/PEC_soil.R</code></a></small>
+ <div class="hidden name"><code>PEC_soil_mets.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+
+ <p>Calculate initial and accumulation PEC soil for a set of metabolites</p>
+
+ </div>
+
+ <pre class="usage"><span class='fu'>PEC_soil_mets</span>(<span class='no'>rate</span>, <span class='no'>mw_parent</span>, <span class='no'>mets</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>rate</th>
+ <td><p>Application rate in units specified below</p></td>
+ </tr>
+ <tr>
+ <th>mw_parent</th>
+ <td><p>The molecular weight of the parent compound</p></td>
+ </tr>
+ <tr>
+ <th>mets</th>
+ <td><p>A dataframe with metabolite identifiers as rownames
+and columns "mw", "occ" and "DT50" holding their molecular weight,
+maximum occurrence in soil and their soil DT50</p></td>
+ </tr>
+ <tr>
+ <th>interval</th>
+ <td><p>The interval for accumulation calculations</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Further arguments are passed to PEC_soil</p></td>
+ </tr>
+ </table>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
+</div>
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+
diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html
index 80dd7fa..b924c99 100644
--- a/docs/reference/PEC_sw_drainage_UK.html
+++ b/docs/reference/PEC_sw_drainage_UK.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK • pfm</title>
<!-- jquery -->
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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@@ -39,7 +39,8 @@ published on the CRC website" />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
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@@ -55,14 +56,15 @@ published on the CRC website" />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -110,8 +112,9 @@ published on the CRC website</p>
</div>
- <pre class="usage"><span class='fu'>PEC_sw_drainage_UK</span>(<span class='no'>rate</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>Koc</span>, <span class='kw'>latest_application</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>soil_DT50</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>model_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+ <pre class="usage"><span class='fu'>PEC_sw_drainage_UK</span>(<span class='no'>rate</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>Koc</span>,
+ <span class='kw'>latest_application</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>soil_DT50</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+ <span class='kw'>model_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -166,9 +169,7 @@ published on the CRC website</p>
</ul>
<h2>Author</h2>
-
-Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -178,9 +179,8 @@ Johannes Ranke
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html
index f537d5d..cb16371 100644
--- a/docs/reference/PEC_sw_drift.html
+++ b/docs/reference/PEC_sw_drift.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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@@ -40,7 +40,8 @@ with input via spray drift." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -56,14 +57,15 @@ with input via spray drift." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -114,7 +116,8 @@ with input via spray drift.</p>
<pre class="usage"><span class='fu'>PEC_sw_drift</span>(<span class='no'>rate</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>,
<span class='kw'>drift_percentages</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='st'>"JKI"</span>, <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"Ackerbau"</span>,
- <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>), <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"µg/L"</span>)</pre>
+ <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>), <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>,
+ <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"µg/L"</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -178,9 +181,7 @@ with input via spray drift.</p>
</ul>
<h2>Author</h2>
-
-Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -190,9 +191,8 @@ Johannes Ranke
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html
index b57c2f9..f86ad1e 100644
--- a/docs/reference/PEC_sw_exposit_runoff.html
+++ b/docs/reference/PEC_sw_exposit_runoff.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
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<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -39,7 +39,8 @@ in the worksheet &quot;Konzept Runoff&quot;. Calculation of sediment PEC values
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -55,14 +56,15 @@ in the worksheet &quot;Konzept Runoff&quot;. Calculation of sediment PEC values
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -111,7 +113,7 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp
</div>
<pre class="usage"><span class='fu'>PEC_sw_exposit_runoff</span>(<span class='no'>rate</span>, <span class='no'>Koc</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, <span class='kw'>t_runoff</span> <span class='kw'>=</span> <span class='fl'>3</span>,
- <span class='kw'>exposit_reduction_version</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"3.01"</span>, <span class='st'>"2.0"</span>), <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>,
+ <span class='kw'>exposit_reduction_version</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"3.01"</span>, <span class='st'>"2.0"</span>), <span class='kw'>V_ditch</span> <span class='kw'>=</span> <span class='fl'>30</span>,
<span class='kw'>V_event</span> <span class='kw'>=</span> <span class='fl'>100</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -210,9 +212,8 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html
index 93d5d44..76a7ec4 100644
--- a/docs/reference/PEC_sw_focus.html
+++ b/docs/reference/PEC_sw_focus.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -44,7 +44,8 @@ to be used with the FOCUS calculator." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -60,14 +61,15 @@ to be used with the FOCUS calculator." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -122,8 +124,8 @@ to be used with the FOCUS calculator.</p>
<pre class="usage"><span class='fu'>PEC_sw_focus</span>(<span class='no'>parent</span>, <span class='no'>rate</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>f_rd</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span>,
- <span class='kw'>region</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"n"</span>, <span class='st'>"s"</span>), <span class='kw'>season</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='st'>"of"</span>, <span class='st'>"mm"</span>, <span class='st'>"js"</span>),
- <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"no interception"</span>, <span class='st'>"minimal crop cover"</span>,
+ <span class='kw'>region</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"n"</span>, <span class='st'>"s"</span>), <span class='kw'>season</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"of"</span>, <span class='st'>"mm"</span>, <span class='st'>"js"</span>),
+ <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"no interception"</span>, <span class='st'>"minimal crop cover"</span>,
<span class='st'>"average crop cover"</span>, <span class='st'>"full canopy"</span>), <span class='kw'>met_form_water</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>txt_file</span> <span class='kw'>=</span> <span class='st'>"pesticide.txt"</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
@@ -353,9 +355,8 @@ should be written</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html
index 28dae7c..2e4fddc 100644
--- a/docs/reference/PEC_sw_sed.html
+++ b/docs/reference/PEC_sw_sed.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -10,17 +10,17 @@
water concentrations — PEC_sw_sed • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ PEC calculator" />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -57,14 +58,15 @@ PEC calculator" />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -115,7 +117,7 @@ PEC calculator</p>
<pre class="usage"><span class='fu'>PEC_sw_sed</span>(<span class='no'>PEC_sw</span>, <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"percentage"</span>,
<span class='kw'>sediment_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>sediment_density</span> <span class='kw'>=</span> <span class='fl'>1.3</span>,
- <span class='kw'>PEC_sed_units</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"µg/kg"</span>, <span class='st'>"mg/kg"</span>))</pre>
+ <span class='kw'>PEC_sed_units</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"µg/kg"</span>, <span class='st'>"mg/kg"</span>))</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -172,9 +174,7 @@ g/cm3)</p></td>
</ul>
<h2>Author</h2>
-
-Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -184,9 +184,8 @@ Johannes Ranke
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html
index 65ca58e..1361ded 100644
--- a/docs/reference/SFO_actual_twa.html
+++ b/docs/reference/SFO_actual_twa.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -38,7 +38,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -54,14 +55,15 @@
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -108,8 +110,8 @@
</div>
- <pre class="usage"><span class='fu'>SFO_actual_twa</span>(<span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, <span class='fl'>50</span>,
- <span class='fl'>100</span>))</pre>
+ <pre class="usage"><span class='fu'>SFO_actual_twa</span>(<span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>,
+ <span class='fl'>50</span>, <span class='fl'>100</span>))</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -156,9 +158,7 @@
</ul>
<h2>Author</h2>
-
-Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -168,9 +168,8 @@ Johannes Ranke
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html
index a0e592a..5c78362 100644
--- a/docs/reference/SSLRC_mobility_classification.html
+++ b/docs/reference/SSLRC_mobility_classification.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -39,7 +39,8 @@ checked against the spreadsheet published on the CRC website" />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -55,14 +56,15 @@ checked against the spreadsheet published on the CRC website" />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -146,9 +148,7 @@ checked against the spreadsheet published on the CRC website</p>
</ul>
<h2>Author</h2>
-
-Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -158,9 +158,8 @@ Johannes Ranke
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html
index 6941fa9..357fb59 100644
--- a/docs/reference/TOXSWA_cwa.html
+++ b/docs/reference/TOXSWA_cwa.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -39,7 +39,8 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -55,14 +56,15 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -147,11 +149,11 @@ for the requested moving window sizes in days.</p></dd>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>H_sw_R1_stream</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>,
<span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>,
- <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>,
+ <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.file'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>,
<span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))
-<span class='no'>H_sw_R1_stream</span>$<span class='fu'>get_events</span>(<span class='fu'>c</span>(<span class='fl'>2</span>, <span class='fl'>10</span>))
-<span class='no'>H_sw_R1_stream</span>$<span class='fu'>moving_windows</span>(<span class='fu'>c</span>(<span class='fl'>7</span>, <span class='fl'>21</span>))
-<span class='fu'>print</span>(<span class='no'>H_sw_R1_stream</span>)</div><div class='output co'>#&gt; &lt;TOXSWA_cwa&gt; data from file 00003s_pa.cwa segment 20
+<span class='no'>H_sw_R1_stream</span>$<span class='fu'>get_events</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>2</span>, <span class='fl'>10</span>))
+<span class='no'>H_sw_R1_stream</span>$<span class='fu'>moving_windows</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>7</span>, <span class='fl'>21</span>))
+<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>H_sw_R1_stream</span>)</div><div class='output co'>#&gt; &lt;TOXSWA_cwa&gt; data from file 00003s_pa.cwa segment 20
#&gt; datetime t t_firstjan t_rel_to_max cwa_mug_per_L
#&gt; 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0
#&gt; 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0
@@ -200,9 +202,8 @@ for the requested moving window sizes in days.</p></dd>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html
index 680efa6..f4c2281 100644
--- a/docs/reference/chent_focus_sw.html
+++ b/docs/reference/chent_focus_sw.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -38,7 +38,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -54,14 +55,15 @@
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -108,8 +110,9 @@
</div>
- <pre class="usage"><span class='fu'>chent_focus_sw</span>(<span class='no'>name</span>, <span class='no'>Koc</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50_soil</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50_water</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
- <span class='kw'>DT50_sediment</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
+ <pre class="usage"><span class='fu'>chent_focus_sw</span>(<span class='no'>name</span>, <span class='no'>Koc</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50_soil</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+ <span class='kw'>DT50_water</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50_sediment</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+ <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -181,9 +184,8 @@ systems</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html
index 71cd2d9..1b44852 100644
--- a/docs/reference/drift_data_JKI.html
+++ b/docs/reference/drift_data_JKI.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -10,17 +10,17 @@
published by the JKI — drift_data_JKI • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ published by the German Julius-Kühn Institute (JKI)." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -57,14 +58,15 @@ published by the German Julius-Kühn Institute (JKI)." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -138,20 +140,20 @@ as its licence is not clear.</p>
<pre class="examples"><div class='input'>
</div><span class='co'># NOT RUN {</span>
<span class='co'># This is the code that was used to extract the data</span>
- <span class='fu'>library</span>(<span class='no'>readxl</span>)
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>readxl</span>)
<span class='no'>abdrift_path</span> <span class='kw'>&lt;-</span> <span class='st'>"inst/extdata/Tabelle der Abdrifteckwerte.xls"</span>
- <span class='no'>JKI_crops</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>"Ackerbau"</span>, <span class='st'>"Obstbau frueh"</span>, <span class='st'>"Obstbau spaet"</span>)
- <span class='fu'>names</span>(<span class='no'>JKI_crops</span>) <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>"Field crops"</span>, <span class='st'>"Pome/stone fruit, early"</span>, <span class='st'>"Pome/stone fruit, late"</span>)
- <span class='no'>drift_data_JKI</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>()
+ <span class='no'>JKI_crops</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Ackerbau"</span>, <span class='st'>"Obstbau frueh"</span>, <span class='st'>"Obstbau spaet"</span>)
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>JKI_crops</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Field crops"</span>, <span class='st'>"Pome/stone fruit, early"</span>, <span class='st'>"Pome/stone fruit, late"</span>)
+ <span class='no'>drift_data_JKI</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>()
<span class='kw'>for</span> (<span class='no'>n</span> <span class='kw'>in</span> <span class='fl'>1</span>:<span class='fl'>8</span>) {
- <span class='no'>drift_data_raw</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/readxl/topics/read_excel'>read_excel</a></span>(<span class='no'>abdrift_path</span>, <span class='kw'>sheet</span> <span class='kw'>=</span> <span class='no'>n</span> + <span class='fl'>1</span>, <span class='kw'>skip</span> <span class='kw'>=</span> <span class='fl'>2</span>)
- <span class='no'>drift_data</span> <span class='kw'>&lt;-</span> <span class='fu'>as.matrix</span>(<span class='no'>drift_data_raw</span>[<span class='fl'>1</span>:<span class='fl'>9</span>, <span class='fl'>2</span>:<span class='fl'>4</span>])
- <span class='fu'>dimnames</span>(<span class='no'>drift_data</span>) <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='kw'>distance</span> <span class='kw'>=</span> <span class='fu'>as.integer</span>(<span class='no'>drift_data_raw</span>[<span class='fl'>1</span>:<span class='fl'>9</span>, <span class='fl'>1</span>]),
+ <span class='no'>drift_data_raw</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://readxl.tidyverse.org/reference/read_excel.html'>read_excel</a></span>(<span class='no'>abdrift_path</span>, <span class='kw'>sheet</span> <span class='kw'>=</span> <span class='no'>n</span> + <span class='fl'>1</span>, <span class='kw'>skip</span> <span class='kw'>=</span> <span class='fl'>2</span>)
+ <span class='no'>drift_data</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/matrix'>as.matrix</a></span>(<span class='no'>drift_data_raw</span>[<span class='fl'>1</span>:<span class='fl'>9</span>, <span class='fl'>2</span>:<span class='fl'>4</span>])
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/dimnames'>dimnames</a></span>(<span class='no'>drift_data</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>distance</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/integer'>as.integer</a></span>(<span class='no'>drift_data_raw</span>[<span class='fl'>1</span>:<span class='fl'>9</span>, <span class='fl'>1</span>]),
<span class='kw'>crop</span> <span class='kw'>=</span> <span class='no'>JKI_crops</span>)
<span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='no'>n</span>]] <span class='kw'>&lt;-</span> <span class='no'>drift_data</span>
}
- <span class='fu'>save</span>(<span class='no'>drift_data_JKI</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/drift_data_JKI.RData"</span>)
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/save'>save</a></span>(<span class='no'>drift_data_JKI</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/drift_data_JKI.RData"</span>)
<span class='co'># }</span><div class='input'>
<span class='co'># And this is the resulting data</span>
<span class='no'>drift_data_JKI</span></div><div class='output co'>#&gt; [[1]]
@@ -281,9 +283,8 @@ as its licence is not clear.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html
index 0c0eb66..b4e4516 100644
--- a/docs/reference/endpoint.html
+++ b/docs/reference/endpoint.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ this function." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -57,14 +58,15 @@ this function." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -114,10 +116,10 @@ this function.</p>
</div>
- <pre class="usage"><span class='fu'>endpoint</span>(<span class='no'>chent</span>, <span class='kw'>medium</span> <span class='kw'>=</span> <span class='st'>"soil"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"degradation"</span>, <span class='st'>"sorption"</span>),
- <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='st'>"laboratory"</span>, <span class='st'>"field"</span>), <span class='kw'>redox</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='st'>"aerobic"</span>,
- <span class='st'>"anaerobic"</span>), <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"DT50ref"</span>, <span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>,
- <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>)
+ <pre class="usage"><span class='fu'>endpoint</span>(<span class='no'>chent</span>, <span class='kw'>medium</span> <span class='kw'>=</span> <span class='st'>"soil"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"degradation"</span>, <span class='st'>"sorption"</span>),
+ <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"laboratory"</span>, <span class='st'>"field"</span>), <span class='kw'>redox</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>NA</span>, <span class='st'>"aerobic"</span>,
+ <span class='st'>"anaerobic"</span>), <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"DT50ref"</span>, <span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>),
+ <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>)
<span class='fu'>soil_DT50</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>,
<span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>, <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>,
@@ -128,8 +130,8 @@ this function.</p>
<span class='fu'>soil_N</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>mean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-<span class='fu'>soil_sorption</span>(<span class='no'>chent</span>, <span class='kw'>values</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), <span class='kw'>aggregators</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span>
- <span class='no'>geomean</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='no'>mean</span>), <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='fl'>3</span>),
+<span class='fu'>soil_sorption</span>(<span class='no'>chent</span>, <span class='kw'>values</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), <span class='kw'>aggregators</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span>
+ <span class='no'>geomean</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='no'>mean</span>), <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='fl'>3</span>),
<span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@@ -221,9 +223,8 @@ exponent is often called 1/n.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html
index b676773..80684b5 100644
--- a/docs/reference/geomean.html
+++ b/docs/reference/geomean.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Calculate the geometric mean — geomean • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -41,7 +41,8 @@ returns 0 if at least one element of the vector is 0." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -57,14 +58,15 @@ returns 0 if at least one element of the vector is 0." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -135,8 +137,8 @@ returns 0 if at least one element of the vector is 0.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='fu'>geomean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#&gt; [1] 3</div><div class='input'><span class='fu'>geomean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>NA</span>, <span class='fl'>9</span>))</div><div class='output co'>#&gt; [1] 3</div><span class='co'># NOT RUN {</span>
-<span class='fu'>geomean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>, -<span class='fl'>3</span>, <span class='fl'>9</span>)) <span class='co'># returns an error</span>
+ <pre class="examples"><div class='input'><span class='fu'>geomean</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#&gt; [1] 3</div><div class='input'><span class='fu'>geomean</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>NA</span>, <span class='fl'>9</span>))</div><div class='output co'>#&gt; [1] 3</div><span class='co'># NOT RUN {</span>
+<span class='fu'>geomean</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, -<span class='fl'>3</span>, <span class='fl'>9</span>)) <span class='co'># returns an error</span>
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -150,9 +152,7 @@ returns 0 if at least one element of the vector is 0.</p>
</ul>
<h2>Author</h2>
-
-Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -162,9 +162,8 @@ Johannes Ranke
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/get_vertex.html b/docs/reference/get_vertex.html
index 6878553..1e123f1 100644
--- a/docs/reference/get_vertex.html
+++ b/docs/reference/get_vertex.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Fit a parabola through three points — get_vertex • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -39,7 +39,8 @@ https://stackoverflow.com/a/717791" />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -55,14 +56,15 @@ https://stackoverflow.com/a/717791" />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -111,12 +113,26 @@ https://stackoverflow.com/a/717791</p>
</div>
<pre class="usage"><span class='fu'>get_vertex</span>(<span class='no'>x</span>, <span class='no'>y</span>)</pre>
-
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>x</th>
+ <td><p>Three x coordinates</p></td>
+ </tr>
+ <tr>
+ <th>y</th>
+ <td><p>Three y coordinates</p></td>
+ </tr>
+ </table>
+
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
</ul>
</div>
@@ -128,9 +144,8 @@ https://stackoverflow.com/a/717791</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index d57bc84..dd8d213 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Function reference • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -35,7 +35,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -51,14 +52,15 @@
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -183,6 +185,12 @@
</tr><tr>
<td>
+ <p><code><a href="PEC_soil_mets.html">PEC_soil_mets()</a></code> </p>
+ </td>
+ <td><p>Calculate initial and accumulation PEC soil for a set of metabolites</p></td>
+ </tr><tr>
+
+ <td>
<p><code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code> </p>
</td>
<td><p>Properties of the predefined scenarios from the EFSA guidance from 2015</p></td>
@@ -192,6 +200,12 @@
<p><code><a href="soil_scenario_data_EFSA_2017.html">soil_scenario_data_EFSA_2017</a></code> </p>
</td>
<td><p>Properties of the predefined scenarios from the EFSA guidance from 2017</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="PEC_FOMC_accu_rel.html">PEC_FOMC_accu_rel()</a></code> </p>
+ </td>
+ <td><p>Get the relative accumulation of an FOMC model over multiples of an interval</p></td>
</tr>
</tbody><tbody>
<tr>
@@ -206,48 +220,6 @@
<p><code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code> </p>
</td>
<td><p>A very small subset of the FOCUS Groundwater scenario definitions</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="create_run_list.html">create_run_list()</a></code> </p>
- </td>
- <td><p>Create a list of runs that we can traverse</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="PELMO_runs.html">PELMO_runs()</a></code> <code><a href="PELMO_runs.html">run_PELMO()</a></code> <code><a href="PELMO_runs.html">evaluate_PELMO()</a></code> </p>
- </td>
- <td><p>Set up runs for FOCUS PELMO</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="PELMO_path.html">PELMO_path()</a></code> </p>
- </td>
- <td><p>Create a path of run directories as the PELMO GUI does</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="FOCUS_PELMO_crop_sze_names.html">FOCUS_PELMO_crop_sze_names</a></code> </p>
- </td>
- <td><p>FOCUS PELMO crop acronyms used for naming sceneario files</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="FOCUS_PELMO_crops.html">FOCUS_PELMO_crops</a></code> </p>
- </td>
- <td><p>FOCUS PELMO crop names</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="FOCUS_PELMO_location_codes.html">FOCUS_PELMO_location_codes</a></code> </p>
- </td>
- <td><p>Location codes in FOCUS PELMO</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="focus_80th.html">focus_80th()</a></code> </p>
- </td>
- <td><p>Calculate the 80th percentile according to FOCUS guidance</p></td>
</tr>
</tbody><tbody>
<tr>
@@ -357,6 +329,20 @@ water concentrations</p></td>
</td>
<td><p>Groundwater ubiquity score based on Gustafson (1989)</p></td>
</tr>
+ </tbody><tbody>
+ <tr>
+ <th colspan="2">
+ <h2 id="section-utilities" class="hasAnchor"><a href="#section-utilities" class="anchor"></a>Utilities</h2>
+ <p class="section-desc"></p>
+ </th>
+ </tr>
+ <tr>
+
+ <td>
+ <p><code><a href="get_vertex.html">get_vertex()</a></code> </p>
+ </td>
+ <td><p>Fit a parabola through three points</p></td>
+ </tr>
</tbody>
</table>
</div>
@@ -369,6 +355,7 @@ water concentrations</p></td>
<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>
</div>
@@ -379,9 +366,8 @@ water concentrations</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html
index 838b00f..d38e382 100644
--- a/docs/reference/max_twa.html
+++ b/docs/reference/max_twa.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>The maximum time weighted average concentration for a moving window — max_twa • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -42,7 +42,8 @@ max_twa." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -58,14 +59,15 @@ max_twa." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -152,7 +154,7 @@ SFO, FOMC and DFOP models and to the parent compound</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>),
- <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>1</span>)))
+ <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>1</span>)))
<span class='fu'>max_twa</span>(<span class='no'>pred</span>)</div><div class='output co'>#&gt; $max
#&gt; parent
#&gt; 0.9537545
@@ -191,9 +193,8 @@ SFO, FOMC and DFOP models and to the parent compound</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html
index 78daced..799ca6c 100644
--- a/docs/reference/one_box.html
+++ b/docs/reference/one_box.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Create a time series of decline data — one_box • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -38,7 +38,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -54,14 +55,15 @@
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -118,7 +120,8 @@
<span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
<span class='co'># S3 method for mkinfit</span>
-<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)</pre>
+<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>, <span class='no'>...</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>,
+ <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -159,22 +162,22 @@ all observed variables.</p></td>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
- <p>An object of class <code>one_box</code>, inheriting from <code>ts</code>.</p>
+ <p>An object of class <code>one_box</code>, inheriting from <code><a href='https://www.rdocumentation.org/packages/stats/topics/ts'>ts</a></code>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Only use a half-life</span>
<span class='no'>pred_0</span> <span class='kw'>&lt;-</span> <span class='fu'>one_box</span>(<span class='fl'>10</span>)
-<span class='fu'>plot</span>(<span class='no'>pred_0</span>)</div><div class='img'><img src='one_box-1.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>pred_0</span>)</div><div class='img'><img src='one_box-1.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># Use a fitted mkinfit model</span>
-<span class='fu'>require</span>(<span class='no'>mkin</span>)
-<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinfit'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>require</a></span>(<span class='no'>mkin</span>)
+<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mkin/topics/mkinfit'>mkinfit</a></span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>pred_1</span> <span class='kw'>&lt;-</span> <span class='fu'>one_box</span>(<span class='no'>fit</span>)
-<span class='fu'>plot</span>(<span class='no'>pred_1</span>)</div><div class='img'><img src='one_box-2.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>pred_1</span>)</div><div class='img'><img src='one_box-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># Use a model with more than one observed variable</span>
-<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinmod'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinsub'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinsub'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinfit'>mkinfit</a></span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mkin/topics/mkinmod'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mkin/topics/mkinsub'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mkin/topics/mkinsub'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mkin/topics/mkinfit'>mkinfit</a></span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>pred_2</span> <span class='kw'>&lt;-</span> <span class='fu'>one_box</span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>)
-<span class='fu'>plot</span>(<span class='no'>pred_2</span>)</div><div class='img'><img src='one_box-3.png' alt='' width='700' height='433' /></div></pre>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>pred_2</span>)</div><div class='img'><img src='one_box-3.png' alt='' width='700' height='433' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -195,9 +198,8 @@ all observed variables.</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html
index 2899a26..e600a1c 100644
--- a/docs/reference/perc_runoff_exposit.html
+++ b/docs/reference/perc_runoff_exposit.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -38,7 +38,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -54,14 +55,15 @@
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -127,7 +129,7 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='fu'>print</span>(<span class='no'>perc_runoff_exposit</span>)</div><div class='output co'>#&gt; Koc_lower_bound dissolved bound
+ <pre class="examples"><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>perc_runoff_exposit</span>)</div><div class='output co'>#&gt; Koc_lower_bound dissolved bound
#&gt; 0-20 0 0.110 0.000
#&gt; &gt;20-50 20 0.151 0.000
#&gt; &gt;50-100 50 0.197 0.000
@@ -161,9 +163,8 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html
index 865f1cf..9170b37 100644
--- a/docs/reference/perc_runoff_reduction_exposit.html
+++ b/docs/reference/perc_runoff_reduction_exposit.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -38,7 +38,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -54,14 +55,15 @@
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -127,7 +129,7 @@ from which the values were taken.</p><dl class='dl-horizontal'>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='fu'>print</span>(<span class='no'>perc_runoff_reduction_exposit</span>)</div><div class='output co'>#&gt; $`3.01`
+ <pre class="examples"><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>perc_runoff_reduction_exposit</span>)</div><div class='output co'>#&gt; $`3.01`
#&gt; dissolved bound
#&gt; No buffer 0 0
#&gt; 5 m 40 40
@@ -160,9 +162,8 @@ from which the values were taken.</p><dl class='dl-horizontal'>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt
index e524f3c..38d58ba 100644
--- a/docs/reference/pesticide.txt
+++ b/docs/reference/pesticide.txt
@@ -43,3 +43,7 @@ Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Du
M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00
Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00
M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00
+Dummy 1 cereals, spring n NA Dummy 1 cereals, spring n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00
+M1 cereals, winter n NA M1 cereals, winter n NA 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00
+Dummy 1 cereals, spring n NA Dummy 1 cereals, spring n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00
+M1 cereals, winter n NA M1 cereals, winter n NA 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00
diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html
index e09eff8..a9c94fb 100644
--- a/docs/reference/pfm_degradation.html
+++ b/docs/reference/pfm_degradation.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -38,7 +38,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -54,14 +55,15 @@
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -108,9 +110,9 @@
</div>
- <pre class="usage"><span class='fu'>pfm_degradation</span>(<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span>
- <span class='fu'>log</span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>), <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>, <span class='kw'>by</span> <span class='kw'>=</span>
- <span class='no'>step_days</span>))</pre>
+ <pre class="usage"><span class='fu'>pfm_degradation</span>(<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span>
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Log'>log</a></span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>), <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>,
+ <span class='kw'>by</span> <span class='kw'>=</span> <span class='no'>step_days</span>))</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -145,7 +147,7 @@ is calculated (SFO model).</p></td>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='fu'>head</span>(<span class='fu'>pfm_degradation</span>(<span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>10</span>))</div><div class='output co'>#&gt; time parent
+ <pre class="examples"><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(<span class='fu'>pfm_degradation</span>(<span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>10</span>))</div><div class='output co'>#&gt; time parent
#&gt; 1 0 1.0000000
#&gt; 2 1 0.9330330
#&gt; 3 2 0.8705506
@@ -162,9 +164,7 @@ is calculated (SFO model).</p></td>
</ul>
<h2>Author</h2>
-
-Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -174,9 +174,8 @@ Johannes Ranke
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html
index 6a98359..80a8095 100644
--- a/docs/reference/plot.TOXSWA_cwa.html
+++ b/docs/reference/plot.TOXSWA_cwa.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -39,7 +39,8 @@ segment of a TOXSWA surface water body." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -55,14 +56,15 @@ segment of a TOXSWA surface water body." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -111,10 +113,10 @@ segment of a TOXSWA surface water body.</p>
</div>
<pre class="usage"><span class='co'># S3 method for TOXSWA_cwa</span>
-<span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"datetime"</span>, <span class='st'>"t"</span>, <span class='st'>"t_firstjan"</span>,
- <span class='st'>"t_rel_to_max"</span>), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>threshold_factor</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>thin_low</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>LC_TIME</span> <span class='kw'>=</span> <span class='st'>"C"</span>,
- <span class='no'>...</span>)</pre>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"datetime"</span>, <span class='st'>"t"</span>,
+ <span class='st'>"t_firstjan"</span>, <span class='st'>"t_rel_to_max"</span>), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"default"</span>,
+ <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>threshold_factor</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>thin_low</span> <span class='kw'>=</span> <span class='fl'>1</span>,
+ <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>LC_TIME</span> <span class='kw'>=</span> <span class='st'>"C"</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -166,12 +168,12 @@ to suspended matter?</p></td>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00001p_pa.cwa"</span>,
<span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>,
- <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))
-<span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_firstjan"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-4.png' alt='' width='700' height='433' /></div><div class='input'>
+ <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.file'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_firstjan"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-4.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='no'>H_sw_R1_stream</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>,
<span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>,
- <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))
-<span class='fu'>plot</span>(<span class='no'>H_sw_R1_stream</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-5.png' alt='' width='700' height='433' /></div></pre>
+ <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.file'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>H_sw_R1_stream</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-5.png' alt='' width='700' height='433' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -182,9 +184,7 @@ to suspended matter?</p></td>
</ul>
<h2>Author</h2>
-
-Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -194,9 +194,8 @@ Johannes Ranke
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html
index 6081c71..bdbece5 100644
--- a/docs/reference/plot.one_box.html
+++ b/docs/reference/plot.one_box.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Plot time series of decline data — plot.one_box • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -38,7 +38,8 @@
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -54,14 +55,15 @@
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -109,9 +111,9 @@
</div>
<pre class="usage"><span class='co'># S3 method for one_box</span>
-<span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'>range</span>(<span class='fu'>time</span>(<span class='no'>x</span>)), <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fu'>max</span>(<span class='no'>x</span>)),
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>x</span>, <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/range'>range</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/time'>time</a></span>(<span class='no'>x</span>)), <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Extremes'>max</a></span>(<span class='no'>x</span>)),
<span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='fu'>dimnames</span>(<span class='no'>x</span>)<span class='kw'>[[</span><span class='fl'>2</span>]][<span class='fl'>1</span>], <span class='no'>...</span>)</pre>
+ <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/dimnames'>dimnames</a></span>(<span class='no'>x</span>)<span class='kw'>[[</span><span class='fl'>2</span>]][<span class='fl'>1</span>], <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -158,13 +160,13 @@ be shown if max_twa is not NULL.</p></td>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>dfop_pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='st'>"DFOP"</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>))
-<span class='fu'>plot</span>(<span class='no'>dfop_pred</span>)</div><div class='img'><img src='plot.one_box-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>plot</span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>dfop_pred</span>, <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><div class='img'><img src='plot.one_box-2.png' alt='' width='700' height='433' /></div><div class='input'>
+ <pre class="examples"><div class='input'><span class='no'>dfop_pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='st'>"DFOP"</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>))
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>dfop_pred</span>)</div><div class='img'><img src='plot.one_box-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>dfop_pred</span>, <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><div class='img'><img src='plot.one_box-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># Use a fitted mkinfit model</span>
<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>pred_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='no'>pred_2_saw</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>)
-<span class='fu'>plot</span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='plot.one_box-3.png' alt='' width='700' height='433' /></div></pre>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='plot.one_box-3.png' alt='' width='700' height='433' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -185,9 +187,8 @@ be shown if max_twa is not NULL.</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html
index 2f036de..6a0ee74 100644
--- a/docs/reference/read.TOXSWA_cwa.html
+++ b/docs/reference/read.TOXSWA_cwa.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -43,7 +43,8 @@ renamed to ConLiqWatLay in the out file." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -59,14 +60,15 @@ renamed to ConLiqWatLay in the out file." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -118,9 +120,9 @@ renamed to ConLiqWatLay in the out file.</p>
</div>
- <pre class="usage"><span class='fu'>read.TOXSWA_cwa</span>(<span class='no'>filename</span>, <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>,
- <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>windows</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>thresholds</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+ <pre class="usage"><span class='fu'>read.TOXSWA_cwa</span>(<span class='no'>filename</span>, <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+ <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>, <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>windows</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>thresholds</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -176,7 +178,7 @@ generating event statistics.</p></td>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'>&lt;-</span> <span class='fu'>read.TOXSWA_cwa</span>(<span class='st'>"00001p_pa.cwa"</span>,
<span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>,
- <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>,
+ <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.file'>system.file</a></span>(<span class='st'>"testdata/SwashProjects.zip"</span>,
<span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -190,9 +192,7 @@ generating event statistics.</p></td>
</ul>
<h2>Author</h2>
-
-Johannes Ranke
-
+ <p>Johannes Ranke</p>
</div>
</div>
@@ -202,9 +202,8 @@ Johannes Ranke
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html
index 128d1f9..638d290 100644
--- a/docs/reference/sawtooth.html
+++ b/docs/reference/sawtooth.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Create decline time series for multiple applications — sawtooth • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@ times, with an interval i." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -56,14 +57,15 @@ times, with an interval i." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -112,8 +114,8 @@ times, with an interval <code>i</code>.</p>
</div>
- <pre class="usage"><span class='fu'>sawtooth</span>(<span class='no'>x</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>seq</span>(<span class='fl'>0</span>, (<span class='no'>n</span> -
- <span class='fl'>1</span>) * <span class='no'>i</span>, <span class='kw'>length.out</span> <span class='kw'>=</span> <span class='no'>n</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fl'>1</span>))</pre>
+ <pre class="usage"><span class='fu'>sawtooth</span>(<span class='no'>x</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>,
+ (<span class='no'>n</span> - <span class='fl'>1</span>) * <span class='no'>i</span>, <span class='kw'>length.out</span> <span class='kw'>=</span> <span class='no'>n</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fl'>1</span>))</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -140,13 +142,13 @@ the corresponding amounts applied in the second column.</p></td>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>14</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>3</span>))
+ <pre class="examples"><div class='input'><span class='no'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>14</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>3</span>))
<span class='no'>pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>)
-<span class='fu'>plot</span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><div class='img'><img src='sawtooth-1.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><div class='img'><img src='sawtooth-1.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>pred_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='no'>pred_2_saw</span> <span class='kw'>&lt;-</span> <span class='fu'>sawtooth</span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>)
-<span class='fu'>plot</span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='sawtooth-2.png' alt='' width='700' height='433' /></div><div class='input'>
+<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='sawtooth-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred_2_saw</span>)</div><div class='output co'>#&gt; $max
#&gt; parent m1
#&gt; 0.7834480 0.8617048
@@ -177,9 +179,8 @@ the corresponding amounts applied in the second column.</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html
index 7565ef7..6051cc2 100644
--- a/docs/reference/soil_scenario_data_EFSA_2015.html
+++ b/docs/reference/soil_scenario_data_EFSA_2015.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -56,14 +57,15 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -131,21 +133,21 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='co'># This is the code that was used to define the data</span>
- <span class='no'>soil_scenario_data_EFSA_2015</span> <span class='kw'>&lt;-</span> <span class='fu'>data.frame</span>(
- <span class='kw'>Zone</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fu'>c</span>(<span class='st'>"North"</span>, <span class='st'>"Central"</span>, <span class='st'>"South"</span>), <span class='fl'>2</span>),
- <span class='kw'>Country</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Estonia"</span>, <span class='st'>"Germany"</span>, <span class='st'>"France"</span>, <span class='st'>"Denmark"</span>, <span class='st'>"Czech Republik"</span>, <span class='st'>"Spain"</span>),
- <span class='kw'>T_arit</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>4.7</span>, <span class='fl'>8.0</span>, <span class='fl'>11.0</span>, <span class='fl'>8.2</span>, <span class='fl'>9.1</span>, <span class='fl'>12.8</span>),
- <span class='kw'>T_arr</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>7.0</span>, <span class='fl'>10.1</span>, <span class='fl'>12.3</span>, <span class='fl'>9.8</span>, <span class='fl'>11.2</span>, <span class='fl'>14.7</span>),
- <span class='kw'>Texture</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Coarse"</span>, <span class='st'>"Coarse"</span>, <span class='st'>"Medium fine"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>),
- <span class='kw'>f_om</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.118</span>, <span class='fl'>0.086</span>, <span class='fl'>0.048</span>, <span class='fl'>0.023</span>, <span class='fl'>0.018</span>, <span class='fl'>0.011</span>),
- <span class='kw'>theta_fc</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.244</span>, <span class='fl'>0.244</span>, <span class='fl'>0.385</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>),
- <span class='kw'>rho</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.95</span>, <span class='fl'>1.05</span>, <span class='fl'>1.22</span>, <span class='fl'>1.39</span>, <span class='fl'>1.43</span>, <span class='fl'>1.51</span>),
- <span class='kw'>f_sce</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>3</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>1.5</span>, <span class='fl'>1.5</span>),
- <span class='kw'>f_mod</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>4</span>, <span class='fl'>4</span>),
+ <span class='no'>soil_scenario_data_EFSA_2015</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(
+ <span class='kw'>Zone</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/rep'>rep</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"North"</span>, <span class='st'>"Central"</span>, <span class='st'>"South"</span>), <span class='fl'>2</span>),
+ <span class='kw'>Country</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Estonia"</span>, <span class='st'>"Germany"</span>, <span class='st'>"France"</span>, <span class='st'>"Denmark"</span>, <span class='st'>"Czech Republik"</span>, <span class='st'>"Spain"</span>),
+ <span class='kw'>T_arit</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>4.7</span>, <span class='fl'>8.0</span>, <span class='fl'>11.0</span>, <span class='fl'>8.2</span>, <span class='fl'>9.1</span>, <span class='fl'>12.8</span>),
+ <span class='kw'>T_arr</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>7.0</span>, <span class='fl'>10.1</span>, <span class='fl'>12.3</span>, <span class='fl'>9.8</span>, <span class='fl'>11.2</span>, <span class='fl'>14.7</span>),
+ <span class='kw'>Texture</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Coarse"</span>, <span class='st'>"Coarse"</span>, <span class='st'>"Medium fine"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>),
+ <span class='kw'>f_om</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0.118</span>, <span class='fl'>0.086</span>, <span class='fl'>0.048</span>, <span class='fl'>0.023</span>, <span class='fl'>0.018</span>, <span class='fl'>0.011</span>),
+ <span class='kw'>theta_fc</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0.244</span>, <span class='fl'>0.244</span>, <span class='fl'>0.385</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>),
+ <span class='kw'>rho</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0.95</span>, <span class='fl'>1.05</span>, <span class='fl'>1.22</span>, <span class='fl'>1.39</span>, <span class='fl'>1.43</span>, <span class='fl'>1.51</span>),
+ <span class='kw'>f_sce</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>1.5</span>, <span class='fl'>1.5</span>),
+ <span class='kw'>f_mod</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>4</span>, <span class='fl'>4</span>),
<span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"CTN"</span>, <span class='st'>"CTC"</span>, <span class='st'>"CTS"</span>, <span class='st'>"CLN"</span>, <span class='st'>"CLC"</span>, <span class='st'>"CLS"</span>)
+ <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"CTN"</span>, <span class='st'>"CTC"</span>, <span class='st'>"CTS"</span>, <span class='st'>"CLN"</span>, <span class='st'>"CLC"</span>, <span class='st'>"CLS"</span>)
)
- <span class='fu'>save</span>(<span class='no'>soil_scenario_data_EFSA_2015</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>'../data/soil_scenario_data_EFSA_2015.RData'</span>)
+ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/save'>save</a></span>(<span class='no'>soil_scenario_data_EFSA_2015</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>'../data/soil_scenario_data_EFSA_2015.RData'</span>)
<span class='co'># }</span><div class='input'>
<span class='co'># And this is the resulting dataframe</span>
<span class='no'>soil_scenario_data_EFSA_2015</span></div><div class='output co'>#&gt; Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce
@@ -183,9 +185,8 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html
index 21bf797..082fb7b 100644
--- a/docs/reference/soil_scenario_data_EFSA_2017.html
+++ b/docs/reference/soil_scenario_data_EFSA_2017.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -56,14 +57,15 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -164,9 +166,8 @@ scenario and model adjustment factors from p. 16 and p. 18 are included.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
</div>
diff --git a/docs/reference/twa.html b/docs/reference/twa.html
index f493a29..69efa7f 100644
--- a/docs/reference/twa.html
+++ b/docs/reference/twa.html
@@ -1,6 +1,6 @@
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
-<html>
+<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
<title>Calculate a time weighted average concentration — twa • pfm</title>
<!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<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 href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
-<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
-<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" />
<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -40,7 +40,8 @@ is after one window has passed." />
<!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<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>
@@ -56,14 +57,15 @@ is after one window has passed." />
<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">
+ <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="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.3</span>
</span>
</div>
@@ -137,7 +139,7 @@ is after one window has passed.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>),
- <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>1</span>)))
+ <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>1</span>)))
<span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred</span>)</div><div class='output co'>#&gt; $max
#&gt; parent
#&gt; 0.9537545
@@ -170,9 +172,8 @@ is after one window has passed.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
-
</footer>
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