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# pfm
The R package **pfm** 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:
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/>
## Installation
You can install the package from [github](http://github.com/jranke/pfm), e.g.
using the `devtools` package. Using `quick = TRUE` skips docs,
multiple-architecture builds, demos, and vignettes, to make installation as
fast and painless as possible.
```r
library(devtools)
install_github("jranke/pfm", subdir = "pkg", quick = TRUE)
```
## Use
### Analyse TOXSWA output
Read in and analyse a cwa file:
```r
library(pfm, quietly = TRUE)
```
```
##
## Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10)
## [GCC 4.9.2]
```
```r
example_cwa <- read.TOXSWA_cwa("00003s_pa.cwa")
plot(example_cwa)
```
<img src="README_files/figure-html/unnamed-chunk-3-1.png" width="672" />
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:
```r
example_cwa$get_events(c(20, 100))
example_cwa$moving_windows(c(7, 21))
print(example_cwa)
```
```
## <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
```
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.
### Calculate PEC soil
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:
```r
PEC_soil(100, interception = 0.25)
```
```
## scenario
## t_avg default
## 0 0.1
```
### Rautmann drift data
Some of the drift percentage data published by the JKI are included. To
see the data for one application:
```r
drift_data_JKI[1]
```
```
## [[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
```
### PEC surface water due to drift
Initial PEC values for an application of 100 g/ha in the vicinity of a 30 cm
deep water body are obtained using
```r
PEC_sw_drift(100, applications = 1)
```
```
## 1 m 5 m 10 m 20 m
## 0.92333333 0.19000000 0.09666667 0.05000000
```
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