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, 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.

library(devtools)
-install_github("jranke/pfm", subdir = "pkg", quick = TRUE)

Use

Analyse TOXSWA output

Read in and analyse a cwa file:

library(pfm, quietly = TRUE)

## 
-## Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10) 
-## [GCC 4.9.2]

example_cwa <- read.TOXSWA_cwa("00003s_pa.cwa")
-plot(example_cwa)

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:

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:

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:

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

PEC_sw_drift(100, applications = 1)

##        1 m        5 m       10 m       20 m 
-## 0.92333333 0.19000000 0.09666667 0.05000000