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diff --git a/docs/index.html b/docs/index.html new file mode 100644 index 0000000..a82dcae --- /dev/null +++ b/docs/index.html @@ -0,0 +1,208 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>Home. pfm 0.3-8</title> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<meta name="author" content=""> + +<link href="css/bootstrap.css" rel="stylesheet"> +<link href="css/bootstrap-responsive.css" rel="stylesheet"> +<link href="css/highlight.css" rel="stylesheet"> +<link href="css/staticdocs.css" rel="stylesheet"> + +<!--[if lt IE 9]> + <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> +<![endif]--> + +<script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + processEscapes: true + } + }); +</script> +<script type="text/javascript" + src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> +</script> + </head> + + <body> + <div class="navbar"> + <div class="navbar-inner"> + <div class="container"> + <a class="brand" href="index.html">pfm 0.3-8</a> + <div class="nav"> + <ul class="nav"> + <li><a href="index.html">Home</a></li> + <li><a href="reference.html">Reference</a></li> + </ul> + </div> + </div> + </div> +</div> + + + <div class="container"> + <header> + + </header> + + <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 <http://www.gnu.org/licenses/> +</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("jranke/pfm", subdir = "pkg", 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 <- read.TOXSWA_cwa("00003s_pa.cwa") +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>## <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> + +<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> + + <footer> + <p class="pull-right"><a href="#">Back to top</a></p> +<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. 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