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-rw-r--r--docs/README.html144
-rw-r--r--docs/docsearch.css148
-rw-r--r--docs/docsearch.js85
-rw-r--r--docs/pkgdown.yml5
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diff --git a/docs/README.html b/docs/README.html
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+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
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+
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+ <div class="contents col-md-12">
+ <div class="page-header">
+ <h1>/home/jranke/git/pfm/README.md</h1>
+ </div>
+
+<div id="pfm" class="section level1">
+<h1 class="hasAnchor">
+<a href="#pfm" class="anchor"></a>pfm</h1>
+<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"><pre class="sourceCode R"><code class="sourceCode r">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
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version <span class="dv">3</span> of the License, <span class="kw">or</span> (at your option) any later
+version.
+
+This program is distributed <span class="cf">in</span> the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License <span class="cf">for</span> more
+details.
+
+You should have received a copy of the GNU General Public License along with
+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></code></pre></div>
+<div id="installation" class="section level2">
+<h2 class="hasAnchor">
+<a href="#installation" class="anchor"></a>Installation</h2>
+<p>You can install the package from <a href="http://github.com/jranke/pfm">github</a>, e.g. using the <code>devtools</code> package. Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and vignettes, to make installation as fast and painless as possible.</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(devtools)
+<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>)</code></pre></div>
+</div>
+<div id="use" class="section level2">
+<h2 class="hasAnchor">
+<a href="#use" class="anchor"></a>Use</h2>
+<p>Please refer to the <a href="http://pkgdown.jrwb.de/pfm/reference/index.html">reference</a>.</p>
+</div>
+<div id="examples" class="section level2">
+<h2 class="hasAnchor">
+<a href="#examples" class="anchor"></a>Examples</h2>
+<p>One recent nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown <a href="http://pkgdown.jrwb.de/pfm/reference/plot.one_box.html">here</a>.</p>
+<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>
+
+
+ <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>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
+
diff --git a/docs/docsearch.css b/docs/docsearch.css
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+ background-repeat: no-repeat;
+ background-position: 50%;
+ background-size: 100%;
+ overflow: hidden;
+ text-indent: -9000px;
+ width: 100%;
+ height: 100%;
+ display: block;
+ transform: translate(-8px);
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--highlight {
+ color: #FF8C00;
+ background: rgba(232, 189, 54, 0.1)
+}
+
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
+ box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+}
+
+.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
+ background-color: rgba(192, 192, 192, .15)
+}
diff --git a/docs/docsearch.js b/docs/docsearch.js
new file mode 100644
index 0000000..b35504c
--- /dev/null
+++ b/docs/docsearch.js
@@ -0,0 +1,85 @@
+$(function() {
+
+ // register a handler to move the focus to the search bar
+ // upon pressing shift + "/" (i.e. "?")
+ $(document).on('keydown', function(e) {
+ if (e.shiftKey && e.keyCode == 191) {
+ e.preventDefault();
+ $("#search-input").focus();
+ }
+ });
+
+ $(document).ready(function() {
+ // do keyword highlighting
+ /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
+ var mark = function() {
+
+ var referrer = document.URL ;
+ var paramKey = "q" ;
+
+ if (referrer.indexOf("?") !== -1) {
+ var qs = referrer.substr(referrer.indexOf('?') + 1);
+ var qs_noanchor = qs.split('#')[0];
+ var qsa = qs_noanchor.split('&');
+ var keyword = "";
+
+ for (var i = 0; i < qsa.length; i++) {
+ var currentParam = qsa[i].split('=');
+
+ if (currentParam.length !== 2) {
+ continue;
+ }
+
+ if (currentParam[0] == paramKey) {
+ keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
+ }
+ }
+
+ if (keyword !== "") {
+ $(".contents").unmark({
+ done: function() {
+ $(".contents").mark(keyword);
+ }
+ });
+ }
+ }
+ };
+
+ mark();
+ });
+});
+
+/* Search term highlighting ------------------------------*/
+
+function matchedWords(hit) {
+ var words = [];
+
+ var hierarchy = hit._highlightResult.hierarchy;
+ // loop to fetch from lvl0, lvl1, etc.
+ for (var idx in hierarchy) {
+ words = words.concat(hierarchy[idx].matchedWords);
+ }
+
+ var content = hit._highlightResult.content;
+ if (content) {
+ words = words.concat(content.matchedWords);
+ }
+
+ // return unique words
+ var words_uniq = [...new Set(words)];
+ return words_uniq;
+}
+
+function updateHitURL(hit) {
+
+ var words = matchedWords(hit);
+ var url = "";
+
+ if (hit.anchor) {
+ url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+ } else {
+ url = hit.url + '?q=' + escape(words.join(" "));
+ }
+
+ return url;
+}
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
new file mode 100644
index 0000000..6e67788
--- /dev/null
+++ b/docs/pkgdown.yml
@@ -0,0 +1,5 @@
+pandoc: 1.19.2.4
+pkgdown: 1.1.0
+pkgdown_sha: ~
+articles: []
+

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