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authorJohannes Ranke <jranke@uni-bremen.de>2016-09-27 23:00:48 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-09-27 23:00:48 +0200
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+<title>Home. pfm 0.3-8</title>
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+ <li><a href="index.html">Home</a></li>
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+
+ <div class="row">
+ <div class="span8">
+ <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
+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
+version.
+
+This program is distributed in 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 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>
+
+<p>Read in and analyse a cwa file:</p>
+
+<pre><code class="r">library(pfm, quietly = TRUE)
+</code></pre>
+
+<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>
+
+<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
+## 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0
+## 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0
+## 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0
+## 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0
+## 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0
+## cwa_tot_mug_per_L
+## 20 0
+## 40 0
+## 60 0
+## 80 0
+## 100 0
+## 120 0
+## Moving window analysis
+## window max_TWAC max_AUC_h max_AUC_d
+## 1 7 days 2.3926551 401.9660 16.74859
+## 2 21 days 0.8369248 421.8101 17.57542
+## Event statistics for threshold 20
+## 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>
+
+<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>
+
+<pre><code>## [[1]]
+## crop
+## distance Ackerbau Obstbau frueh Obstbau spaet
+## 1 2.77 NA NA
+## 3 NA 29.20 15.73
+## 5 0.57 19.89 8.41
+## 10 0.29 11.81 3.60
+## 15 0.20 5.55 1.81
+## 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>
+
+<pre><code class="r">PEC_sw_drift(100, applications = 1)
+</code></pre>
+
+<pre><code>## 1 m 5 m 10 m 20 m
+## 0.92333333 0.19000000 0.09666667 0.05000000
+</code></pre>
+
+ </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>
+</div>
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