From 12a31f4c130c551f82232d9ef7dfb608bd52c53f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 27 Sep 2016 23:00:48 +0200 Subject: Reorganise repository using standard package layout --- docs/index.html | 208 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 208 insertions(+) create mode 100644 docs/index.html (limited to 'docs/index.html') 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 @@ + + + + +Home. pfm 0.3-8 + + + + + + + + + + + + + + + +
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+ pfm 0.3-8 +
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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, 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
+
+ +
+ +
+

Authors

+ +
+
+ + +
+ + \ No newline at end of file -- cgit v1.2.1