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<title>Utilities for Pesticide Fate Modelling • pfm</title>
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<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 <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
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 <http:<span class="er">//</span>www.gnu.org/licenses/<span class="er">></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>
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<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>
<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>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">example_cwa <-<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>## <TOXSWA_cwa> 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>
</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>
</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
## 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>
</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>
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