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<!DOCTYPE html>
-<html lang="en">
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-<title>Home. pfm 0.3-8</title>
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+<title>Utilities for Pesticide Fate Modelling • pfm</title>
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+ <a class="navbar-brand" href="index.html">pfm</a>
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+ <div id="navbar" class="navbar-collapse collapse">
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-
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- <h1>pfm</h1>
-
-<p>The R package <strong>pfm</strong> provides some utilities for dealing with FOCUS pesticide fate modelling tools,
-(currently only TOXSWA cwa and out files), made available under the GNU public license.
-This means:</p>
-
-<pre><code>This program is free software: you can redistribute it and/or modify it under
+ </header><div class="row">
+ <div class="contents col-md-9">
+ <div id="pfm" class="section level1">
+<div class="page-header"><h1 class="hasAnchor">
+<a href="#pfm" class="anchor"> </a>pfm</h1></div>
+<p>The R package <strong>pfm</strong> provides some utilities for 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="st"> </span>you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
-Foundation, either version 3 of the License, or (at your option) any later
+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 in the hope that it will be useful, but WITHOUT
@@ -68,49 +58,32 @@ FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
details.
You should have received a copy of the GNU General Public License along with
-this program. If not, see &lt;http://www.gnu.org/licenses/&gt;
-</code></pre>
-
-<h2>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>
-
-<pre><code class="r">library(devtools)
-install_github(&quot;jranke/pfm&quot;, subdir = &quot;pkg&quot;, quick = TRUE)
-</code></pre>
-
-<h2>Use</h2>
-
-<h3>Analyse TOXSWA output</h3>
-
+this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/licenses/<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">install_github</span>(<span class="st">"jranke/pfm"</span>, <span class="dt">subdir =</span> <span class="st">"pkg"</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>
+<div id="analyse-toxswa-output" class="section level3">
+<h3 class="hasAnchor">
+<a href="#analyse-toxswa-output" class="anchor"> </a>Analyse TOXSWA output</h3>
<p>Read in and analyse a cwa file:</p>
-
-<pre><code class="r">library(pfm, quietly = TRUE)
-</code></pre>
-
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(pfm, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</code></pre></div>
<pre><code>##
## Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10)
-## [GCC 4.9.2]
-</code></pre>
-
-<pre><code class="r">example_cwa &lt;- read.TOXSWA_cwa(&quot;00003s_pa.cwa&quot;)
-plot(example_cwa)
-</code></pre>
-
-<p><img src="README_files/figure-html/unnamed-chunk-3-1.png" width="672" /></p>
-
-<p>Get events above thresholds of 20 and 100 µg/L,
-and do a moving window analysis for windows of 7 days
-and 21 days, print the results:</p>
-
-<pre><code class="r">example_cwa$get_events(c(20, 100))
-example_cwa$moving_windows(c(7, 21))
-print(example_cwa)
-</code></pre>
-
+## [GCC 4.9.2]</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">example_cwa &lt;-<span class="st"> </span><span class="kw"><a href="reference/read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span>(<span class="st">"00003s_pa.cwa"</span>)
+<span class="kw">plot</span>(example_cwa)</code></pre></div>
+<p><img src="README_files/figure-html/unnamed-chunk-3-1.png" width="672"></p>
+<p>Get events above thresholds of 20 and 100 µg/L, and do a moving window analysis for windows of 7 days and 21 days, print the results:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">example_cwa$<span class="kw">get_events</span>(<span class="kw">c</span>(<span class="dv">20</span>, <span class="dv">100</span>))
+example_cwa$<span class="kw">moving_windows</span>(<span class="kw">c</span>(<span class="dv">7</span>, <span class="dv">21</span>))
+<span class="kw">print</span>(example_cwa)</code></pre></div>
<pre><code>## &lt;TOXSWA_cwa&gt; data from file 00003s_pa.cwa segment 20
## datetime t t_firstjan t_rel_to_max cwa_mug_per_L
## 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0
@@ -134,35 +107,23 @@ print(example_cwa)
## t_start cwa_max duration pre_interval AUC_h AUC_d
## 1 55.083 40.58401 0.417 55.083 365.7912 15.2413
## Event statistics for threshold 100
-## No events found
-</code></pre>
-
-<p>This can also be done with out files, the function reads
-out files from current TOXSWA versions as well as cwa files
-from old TOXSWA versions.</p>
-
-<h3>Calculate PEC soil</h3>
-
-<p>Simple PEC soil calculation for an application rate of 100 g/ha and
-25% interception, assuming complete mixing into 5 cm and a soil bulk
-density of 1.5 kg/L, output in mg/kg:</p>
-
-<pre><code class="r">PEC_soil(100, interception = 0.25)
-</code></pre>
-
+## No events found</code></pre>
+<p>This can also be done with out files, the function reads out files from current TOXSWA versions as well as cwa files from old TOXSWA versions.</p>
+</div>
+<div id="calculate-pec-soil" class="section level3">
+<h3 class="hasAnchor">
+<a href="#calculate-pec-soil" class="anchor"> </a>Calculate PEC soil</h3>
+<p>Simple PEC soil calculation for an application rate of 100 g/ha and 25% interception, assuming complete mixing into 5 cm and a soil bulk density of 1.5 kg/L, output in mg/kg:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="reference/PEC_soil.html">PEC_soil</a></span>(<span class="dv">100</span>, <span class="dt">interception =</span> <span class="fl">0.25</span>)</code></pre></div>
<pre><code>## scenario
## t_avg default
-## 0 0.1
-</code></pre>
-
-<h3>Rautmann drift data</h3>
-
-<p>Some of the drift percentage data published by the JKI are included. To
-see the data for one application:</p>
-
-<pre><code class="r">drift_data_JKI[1]
-</code></pre>
-
+## 0 0.1</code></pre>
+</div>
+<div id="rautmann-drift-data" class="section level3">
+<h3 class="hasAnchor">
+<a href="#rautmann-drift-data" class="anchor"> </a>Rautmann drift data</h3>
+<p>Some of the drift percentage data published by the JKI are included. To see the data for one application:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">drift_data_JKI[<span class="dv">1</span>]</code></pre></div>
<pre><code>## [[1]]
## crop
## distance Ackerbau Obstbau frueh Obstbau spaet
@@ -174,35 +135,41 @@ see the data for one application:</p>
## 20 0.15 2.77 1.09
## 30 0.10 1.04 0.54
## 40 0.07 0.52 0.32
-## 50 0.06 0.30 0.22
-</code></pre>
-
-<h3>PEC surface water due to drift</h3>
-
-<p>Initial PEC values for an application of 100 g/ha in the vicinity of a 30 cm
-deep water body are obtained using</p>
+## 50 0.06 0.30 0.22</code></pre>
+</div>
+<div id="pec-surface-water-due-to-drift" class="section level3">
+<h3 class="hasAnchor">
+<a href="#pec-surface-water-due-to-drift" class="anchor"> </a>PEC surface water due to drift</h3>
+<p>Initial PEC values for an application of 100 g/ha in the vicinity of a 30 cm deep water body are obtained using</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="reference/PEC_sw_drift.html">PEC_sw_drift</a></span>(<span class="dv">100</span>, <span class="dt">applications =</span> <span class="dv">1</span>)</code></pre></div>
+<pre><code>## 1 m 5 m 10 m 20 m
+## 0.92333333 0.19000000 0.09666667 0.05000000</code></pre>
+</div>
+</div>
+</div>
+ </div>
-<pre><code class="r">PEC_sw_drift(100, applications = 1)
-</code></pre>
+ <div class="col-md-3" id="sidebar">
+ <h2>License</h2>
+<p>GPL</p>
+<h2>Developers</h2>
+<ul class="list-unstyled">
+<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li>
+</ul>
+</div>
+</div>
-<pre><code>## 1 m 5 m 10 m 20 m
-## 0.92333333 0.19000000 0.09666667 0.05000000
-</code></pre>
- </div>
+ <footer><div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
- <div class="span3 offset1 sidebar">
- <h2>Authors</h2>
- <ul>
- <li><a href='mailto:jranke@uni-bremen.de'>Johannes Ranke</a> [aut, cre, cph]</li>
- </ul>
- </div>
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