R6 class for holding TOXSWA cwa concentration data and associated statistics

Date: Wed, 20 Jun 2018 14:53:02 +0200 Subject: Update static docs --- docs/reference/PELMO_runs.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'docs/reference/PELMO_runs.html') diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html index dc068c3..72e3c39 100644 --- a/docs/reference/PELMO_runs.html +++ b/docs/reference/PELMO_runs.html @@ -67,7 +67,7 @@ and run using wine." /> @@ -229,7 +229,7 @@ the period.plm file generated by the FOCUS PELMO GUI.

#> #>

# We get exactly the same PECgw values (on Linux, calling PELMO using Wine). print(time_1)

#> User System verstrichen -#> 0.388 0.088 30.344

if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { +#> 0.390 0.084 30.914

if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]])) }

#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor

# Demonstrate some results with metabolites. -- cgit v1.2.3 From 6ca8bdb8636141fac592688a6794ae092f0bc85a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 20 Jun 2018 14:58:44 +0200 Subject: Advertise drat repo --- README.md | 14 +++++++++++--- docs/index.html | 6 +++++- docs/reference/PELMO_runs.html | 2 +- docs/reference/pesticide.txt | 2 ++ 4 files changed, 19 insertions(+), 5 deletions(-) (limited to 'docs/reference/PELMO_runs.html') diff --git a/README.md b/README.md index b4b2caa..68874f2 100644 --- a/README.md +++ b/README.md @@ -20,10 +20,18 @@ This means: ## Installation -You can install the package from [github](http://github.com/jranke/pfm), e.g. +The easiest way to install the package is probably to use +[drat](http://cran.r-project.org/package=drat): + +```r +install.packages("drat") +drat::addRepo("jranke") +install.packages("pfm") +``` + +Alternatively you can install the package using the `devtools` package. Using `quick = TRUE` skips docs, -multiple-architecture builds, demos, and vignettes, to make installation as -fast and painless as possible. +multiple-architecture builds, demos, and vignettes. ```r diff --git a/docs/index.html b/docs/index.html index fc6e0f8..b7f32cc 100644 --- a/docs/index.html +++ b/docs/index.html @@ -84,7 +84,11 @@ this program. If not, see <http:

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.

The easiest way to install the package is probably to use drat:

install.packages("drat")
+drat::addRepo("jranke")
+install.packages("pfm")

Alternatively you can install the package using the devtools package. Using quick = TRUE skips docs, multiple-architecture builds, demos, and vignettes.

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

diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html index 72e3c39..1eac49b 100644 --- a/docs/reference/PELMO_runs.html +++ b/docs/reference/PELMO_runs.html @@ -229,7 +229,7 @@ the period.plm file generated by the FOCUS PELMO GUI.

#> #>

# We get exactly the same PECgw values (on Linux, calling PELMO using Wine). print(time_1)

#> User System verstrichen -#> 0.390 0.084 30.914

if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { +#> 0.398 0.100 30.624

if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]])) }

#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor

# Demonstrate some results with metabolites. diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt index 0f03e9a..85f103d 100644 --- a/docs/reference/pesticide.txt +++ b/docs/reference/pesticide.txt @@ -33,3 +33,5 @@ Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Du M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 -- cgit v1.2.3 From 8989a484b9b2d23463c95e0a3927e307ec0a5e64 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 4 Jul 2018 10:59:47 +0200 Subject: Some documentation updates Document that TOXSWA 5.5.3 is supported in the help files --- ChangeLog | 18 ++++++++++++++++++ DESCRIPTION | 2 +- R/PEC_soil.R | 4 ++-- R/TOXSWA_cwa.R | 11 ++++++----- README.html | 8 ++++++-- docs/reference/PEC_soil.html | 2 +- docs/reference/PELMO_runs.html | 2 +- docs/reference/TOXSWA_cwa.html | 10 +++++----- docs/reference/index.html | 2 +- docs/reference/pesticide.txt | 2 ++ docs/reference/read.TOXSWA_cwa.html | 10 ++++++---- man/PEC_soil.Rd | 2 +- man/TOXSWA_cwa.Rd | 4 ++-- man/read.TOXSWA_cwa.Rd | 7 ++++--- 14 files changed, 56 insertions(+), 28 deletions(-) (limited to 'docs/reference/PELMO_runs.html') diff --git a/ChangeLog b/ChangeLog index 926bcd6..2960fbe 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,21 @@ +commit 6ca8bdb8636141fac592688a6794ae092f0bc85a +Author: Johannes Ranke +Date: 2018-06-20 14:58:44 +0200 + + Advertise drat repo + +commit 6acfd0dfb2670e3eeab6144c90586f28105583a8 +Author: Johannes Ranke +Date: 2018-06-20 14:53:02 +0200 + + Update static docs + +commit cac29c8c1cc0f6004ef0cd63229cfb993a24496c +Author: Johannes Ranke +Date: 2018-06-11 16:27:22 +0200 + + Adapt to TOXSWA 5.5.3 + commit bd15236d5dedb4067bd29e58e655c5352aca1db4 Author: Johannes Ranke Date: 2018-06-08 16:20:40 +0200 diff --git a/DESCRIPTION b/DESCRIPTION index 0851224..c1d967f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling Version: 0.4-6 -Date: 2018-06-11 +Date: 2018-07-04 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-4371-6538")) diff --git a/R/PEC_soil.R b/R/PEC_soil.R index ea1cb71..15ccc90 100644 --- a/R/PEC_soil.R +++ b/R/PEC_soil.R @@ -1,4 +1,4 @@ -# Copyright (C) 2015 Johannes Ranke +# Copyright (C) 2015,2016,2018 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package pfm @@ -44,7 +44,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_typ #' @param interception The fraction of the application rate that does not reach the soil #' @param mixing_depth Mixing depth in cm #' @param interval Period of the deeper mixing, defaults to 365, which is a year if -#' rate units are in days +#' degradation rate units are in days #' @param n_periods Number of periods to be considered for long term PEC calculations #' @param PEC_units Requested units for the calculated PEC. Only mg/kg currently supported #' @param PEC_pw_units Only mg/L currently supported diff --git a/R/TOXSWA_cwa.R b/R/TOXSWA_cwa.R index 576c7d3..5b1e8f2 100644 --- a/R/TOXSWA_cwa.R +++ b/R/TOXSWA_cwa.R @@ -22,10 +22,11 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("cwa")) #' segment of a TOXSWA surface water body. Per default, the data for the last #' segment are imported. As TOXSWA 4 reports the values at the end of the hour #' (ConLiqWatLayCur) in its summary file, we use this value as well instead -#' of the hourly averages (ConLiqWatLay). +#' of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was +#' renamed to ConLiqWatLay in the out file. #' #' @param filename The filename of the cwa file (TOXSWA 2.x.y or similar) or the -#' out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar). +#' out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher. #' @param basedir The path to the directory where the cwa file resides. #' @param zipfile Optional path to a zip file containing the cwa file. #' @param segment The segment for which the data should be read. Either "last", or @@ -33,7 +34,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("cwa")) #' @param total Set this to TRUE in order to read total concentrations as well. This is #' only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa #' files. For .cwa files, the total concentration is always read as well. -#' @param substance For TOXSWA 4 .out files, the default value "parent" leads +#' @param substance For .out files, the default value "parent" leads #' to reading concentrations of the parent compound. Alternatively, the substance #' of interested can be selected by its code name. #' @param windows Numeric vector of width of moving windows in days, for calculating @@ -155,9 +156,9 @@ plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t tmp <- Sys.setlocale("LC_TIME", lct) } -#' R6 class for holding TOXSWA cwa concentration data and associated statistics +#' R6 class for holding TOXSWA water concentration data and associated statistics #' -#' An R6 class for holding TOXSWA cwa concentration data and some associated statistics. +#' An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. #' Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. #' #' @docType class diff --git a/README.html b/README.html index 026f011..ef6dfca 100644 --- a/README.html +++ b/README.html @@ -15,7 +15,7 @@ - + @@ -138,7 +138,11 @@ 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

The easiest way to install the package is probably to use drat:

install.packages("drat")
+drat::addRepo("jranke")
+install.packages("pfm")

Alternatively you can install the package using the devtools package. Using quick = TRUE skips docs, multiple-architecture builds, demos, and vignettes.

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

diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index feed9d5..5073067 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -150,7 +150,7 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012).

interval

Period of the deeper mixing, defaults to 365, which is a year if -rate units are in days

+degradation rate units are in days

n_periods diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html index 1eac49b..5d53104 100644 --- a/docs/reference/PELMO_runs.html +++ b/docs/reference/PELMO_runs.html @@ -229,7 +229,7 @@ the period.plm file generated by the FOCUS PELMO GUI.

#> #>

# We get exactly the same PECgw values (on Linux, calling PELMO using Wine). print(time_1)

#> User System verstrichen -#> 0.398 0.100 30.624

if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { +#> 0.384 0.095 30.954

if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) { cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]])) }

#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor

# Demonstrate some results with metabolites. diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 3b11804..932e6ef 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -6,7 +6,7 @@ -R6 class for holding TOXSWA cwa concentration data and associated statistics — TOXSWA_cwa • pfm +R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm @@ -30,9 +30,9 @@ - + - @@ -98,14 +98,14 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />

An R6 class for holding TOXSWA cwa concentration data and some associated statistics. +

An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. Usually, an instance of this class will be generated by read.TOXSWA_cwa.

diff --git a/docs/reference/index.html b/docs/reference/index.html index c153b50..162298b 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -311,7 +311,7 @@ water concentrations

TOXSWA_cwa

R6 class for holding TOXSWA cwa concentration data and associated statistics

R6 class for holding TOXSWA water concentration data and associated statistics

diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt index 85f103d..d4fd84e 100644 --- a/docs/reference/pesticide.txt +++ b/docs/reference/pesticide.txt @@ -35,3 +35,5 @@ Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Du M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index 60e236a..aa18ec4 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -36,7 +36,8 @@ segment of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead -of the hourly averages (ConLiqWatLay)." /> +of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was +renamed to ConLiqWatLay in the out file." /> @@ -112,7 +113,8 @@ of the hourly averages (ConLiqWatLay)." /> segment of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead -of the hourly averages (ConLiqWatLay).

+of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was +renamed to ConLiqWatLay in the out file.

@@ -126,7 +128,7 @@ of the hourly averages (ConLiqWatLay).

filename

The filename of the cwa file (TOXSWA 2.x.y or similar) or the -out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).

+out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.

basedir @@ -143,7 +145,7 @@ the segment number.

substance -

For TOXSWA 4 .out files, the default value "parent" leads +

For .out files, the default value "parent" leads to reading concentrations of the parent compound. Alternatively, the substance of interested can be selected by its code name.

diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd index dd780cf..1491790 100644 --- a/man/PEC_soil.Rd +++ b/man/PEC_soil.Rd @@ -24,7 +24,7 @@ PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5, \item{PEC_pw_units}{Only mg/L currently supported} \item{interval}{Period of the deeper mixing, defaults to 365, which is a year if -rate units are in days} +degradation rate units are in days} \item{n_periods}{Number of periods to be considered for long term PEC calculations} diff --git a/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd index 3152c6e..f073180 100644 --- a/man/TOXSWA_cwa.Rd +++ b/man/TOXSWA_cwa.Rd @@ -3,13 +3,13 @@ \docType{class} \name{TOXSWA_cwa} \alias{TOXSWA_cwa} -\title{R6 class for holding TOXSWA cwa concentration data and associated statistics} +\title{R6 class for holding TOXSWA water concentration data and associated statistics} \format{An \code{\link{R6Class}} generator object.} \usage{ TOXSWA_cwa } \description{ -An R6 class for holding TOXSWA cwa concentration data and some associated statistics. +An R6 class for holding TOXSWA water concentration (cwa) data and some associated statistics. Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. } \section{Fields}{ diff --git a/man/read.TOXSWA_cwa.Rd b/man/read.TOXSWA_cwa.Rd index 2541c9b..c76fdbd 100644 --- a/man/read.TOXSWA_cwa.Rd +++ b/man/read.TOXSWA_cwa.Rd @@ -10,7 +10,7 @@ read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", } \arguments{ \item{filename}{The filename of the cwa file (TOXSWA 2.x.y or similar) or the -out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).} +out file when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher.} \item{basedir}{The path to the directory where the cwa file resides.} @@ -19,7 +19,7 @@ out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).} \item{segment}{The segment for which the data should be read. Either "last", or the segment number.} -\item{substance}{For TOXSWA 4 .out files, the default value "parent" leads +\item{substance}{For .out files, the default value "parent" leads to reading concentrations of the parent compound. Alternatively, the substance of interested can be selected by its code name.} @@ -42,7 +42,8 @@ Read TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead -of the hourly averages (ConLiqWatLay). +of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this variable was +renamed to ConLiqWatLay in the out file. } \examples{ H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", -- cgit v1.2.3 From 22b36c824fe5e1561868a649216fe079c6fbfb85 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 10 Jul 2018 18:06:29 +0200 Subject: Update static docs --- _pkgdown.yml | 2 + docs/authors.html | 2 +- docs/index.html | 4 +- docs/reference/FOCUS_GW_scenarios_2012.html | 2 +- docs/reference/FOCUS_PELMO_crop_sze_names.html | 2 +- docs/reference/FOCUS_PELMO_crops.html | 2 +- docs/reference/FOCUS_PELMO_location_codes.html | 2 +- docs/reference/FOCUS_Step_12_scenarios.html | 2 +- docs/reference/FOMC_actual_twa.html | 2 +- docs/reference/GUS.html | 2 +- docs/reference/PEC_soil.html | 77 ++++++++-- docs/reference/PEC_sw_drainage_UK.html | 2 +- docs/reference/PEC_sw_drift.html | 2 +- docs/reference/PEC_sw_exposit_runoff.html | 2 +- docs/reference/PEC_sw_focus.html | 2 +- docs/reference/PEC_sw_sed.html | 2 +- docs/reference/PELMO_path.html | 2 +- docs/reference/PELMO_runs.html | 4 +- docs/reference/SFO_actual_twa.html | 2 +- docs/reference/SSLRC_mobility_classification.html | 2 +- docs/reference/TOXSWA_cwa.html | 2 +- docs/reference/chent_focus_sw.html | 2 +- docs/reference/create_run_list.html | 2 +- docs/reference/drift_data_JKI.html | 2 +- docs/reference/endpoint.html | 2 +- docs/reference/focus_80th.html | 2 +- docs/reference/geomean.html | 2 +- docs/reference/get_flux.html | 2 +- docs/reference/get_interval.html | 2 +- docs/reference/index.html | 14 +- docs/reference/max_twa.html | 2 +- docs/reference/one_box.html | 2 +- docs/reference/perc_runoff_exposit.html | 3 +- docs/reference/perc_runoff_reduction_exposit.html | 2 +- docs/reference/pesticide.txt | 4 + docs/reference/pfm_degradation.html | 2 +- docs/reference/plot.TOXSWA_cwa.html | 2 +- docs/reference/plot.one_box.html | 2 +- docs/reference/read.TOXSWA_cwa.html | 2 +- docs/reference/sawtooth.html | 2 +- docs/reference/soil_scenario_data_EFSA_2015.html | 10 +- docs/reference/soil_scenario_data_EFSA_2017.html | 177 ++++++++++++++++++++++ docs/reference/sum_periods.html | 2 +- docs/reference/twa.html | 2 +- 44 files changed, 308 insertions(+), 57 deletions(-) create mode 100644 docs/reference/soil_scenario_data_EFSA_2017.html (limited to 'docs/reference/PELMO_runs.html') diff --git a/_pkgdown.yml b/_pkgdown.yml index 4f16d24..7252624 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -15,10 +15,12 @@ reference: - max_twa - pfm_degradation - SFO_actual_twa + - FOMC_actual_twa - title: Predicted environmental concentrations in soil contents: - PEC_soil - soil_scenario_data_EFSA_2015 + - soil_scenario_data_EFSA_2017 - title: Predicted environmental concentrations in groundwater contents: - FOCUS_GW_scenarios_2012 diff --git a/docs/authors.html b/docs/authors.html index 27e5e7c..e128b4d 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -58,7 +58,7 @@

diff --git a/docs/index.html b/docs/index.html index b7f32cc..70a1fed 100644 --- a/docs/index.html +++ b/docs/index.html @@ -31,7 +31,7 @@

@@ -84,7 +84,7 @@ this program. If not, see <http:

Installation

The easiest way to install the package is probably to use drat:

install.packages("drat")
 drat::addRepo("jranke")
 install.packages("pfm")

diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 1a9d513..af6d243 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -62,7 +62,7 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> diff --git a/docs/reference/FOCUS_PELMO_crop_sze_names.html b/docs/reference/FOCUS_PELMO_crop_sze_names.html index 89348f6..4eed679 100644 --- a/docs/reference/FOCUS_PELMO_crop_sze_names.html +++ b/docs/reference/FOCUS_PELMO_crop_sze_names.html @@ -64,7 +64,7 @@ files used for Beans (field) and Beans (vegetable) are the same." /> diff --git a/docs/reference/FOCUS_PELMO_crops.html b/docs/reference/FOCUS_PELMO_crops.html index 16653d9..e4928cd 100644 --- a/docs/reference/FOCUS_PELMO_crops.html +++ b/docs/reference/FOCUS_PELMO_crops.html @@ -65,7 +65,7 @@ in the three letter code, i.e. 'Peas (animals)' has the code ape." /> diff --git a/docs/reference/FOCUS_PELMO_location_codes.html b/docs/reference/FOCUS_PELMO_location_codes.html index 817d888..8177747 100644 --- a/docs/reference/FOCUS_PELMO_location_codes.html +++ b/docs/reference/FOCUS_PELMO_location_codes.html @@ -62,7 +62,7 @@ indexed by three letter acronyms." /> diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index 9ceb79d..b9f2e0d 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -62,7 +62,7 @@ The text file is not included in the package as its licence is not clear." /> diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html index 7a62183..685edc3 100644 --- a/docs/reference/FOMC_actual_twa.html +++ b/docs/reference/FOMC_actual_twa.html @@ -61,7 +61,7 @@ diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index 87714e0..65763bc 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -63,7 +63,7 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 5073067..8903470 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -33,9 +33,10 @@ +the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012 +and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> @@ -64,7 +65,7 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012)." /> @@ -108,17 +109,20 @@ the concepts layed out for example in the PPR panel opinion (EFSA 2012)." />

This is a basic calculation of a contaminant concentration in bulk soil -based on complete, instantaneous mixing. If an interval is given, an +based on complete, instantaneous mixing. If an interval is given, an attempt is made at calculating a long term maximum concentration using -the concepts layed out for example in the PPR panel opinion (EFSA 2012).

+the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012 +and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).

PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5,
   PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA,
-  n_periods = Inf, tillage_depth = 20, chent = NA, DT50 = NA,
+  n_periods = Inf, tillage_depth = 20, leaching_depth = tillage_depth,
+  crop = "annual", cultivation = FALSE, chent = NA, DT50 = NA,
   Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default",
-  "EFSA_2015"), porewater = FALSE)

+ "EFSA_2017", "EFSA_2015"), leaching = scenarios == "EFSA_2017", + porewater = FALSE)

Arguments

@@ -160,9 +164,28 @@ degradation rate units are in days

+ + + + + + + + + + + + - @@ -193,6 +216,11 @@ the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when 'chents' is specified, the DegT50 with destination 'PECgw' will be used), and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also model and scenario adjustment factors from the EFSA guidance are used.

+ + + + @@ -212,14 +240,24 @@ p. 13).

This assumes that the complete load to soil during the time specified by 'interval' (typically 365 days) is dosed at once. As in the PPR panel -opinion cited below (PPR panel 2012), only temperature correction using the +opinion cited below (EFSA PPR panel 2012), only temperature correction using the Arrhenius equation is performed.

Total soil and porewater PEC values for the scenarios as defined in the EFSA -guidance (2015, p. 13) can easily be calculated.

+guidance (2017, p. 14/15) can easily be calculated.

Note

If temperature information is available in the selected scenarios, as +

While time weighted average (TWA) concentrations given in the examples +from the EFSA guidance from 2015 (p. 80) are be reproduced, this is not +true for the TWA concentrations given for the same example in the EFSA guidance +from 2017 (p. 92).

According to the EFSA guidance (EFSA, 2017, p. 43), leaching should be + taken into account for the EFSA 2017 scenarios, using the evaluation depth + (here mixing depth) as the depth of the layer from which leaching takes + place. However, as the amount leaching below the evaluation depth + (often 5 cm) will partly be mixed back during tillage, the default in this function + is to use the tillage depth for the calculation of the leaching rate.

If temperature information is available in the selected scenarios, as e.g. in the EFSA scenarios, the DT50 for groundwater modelling (destination 'PECgw') is taken from the chent object, otherwise the DT50 with destination 'PECsoil'.

@@ -231,6 +269,11 @@ guidance (2015, p. 13) can easily be calculated.

selection and scenario parameterisation for predicting environmental concentrations of plant protection products in soil. EFSA Journal10(2) 2562, doi:10.2903/j.efsa.2012.2562

EFSA (European Food Safety Authority) 2017) EFSA guidance document for + predicting environmental concentrations of active substances of plant + protection products and transformation products of these active substances + in soil. EFSA Journal 15(10) 4982 + doi:10.2903/j.efsa.2017.4982

EFSA (European Food Safety Authority) (2015) EFSA guidance document for predicting environmental concentrations of active substances of plant protection products and transformation products of these active substances @@ -242,6 +285,18 @@ guidance (2015, p. 13) can easily be calculated.

PEC_soil(100, interception = 0.25)
#>      scenario
 #> t_avg default
 #>     0     0.1

+# This is example 1 starting at p. 92 of the EFSA guidance (2017)
+# Note that TWA concentrations differ from the ones given in the guidance
+# for an unknown reason (the values from EFSA (2015) can be reproduced).
+PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
+               Kom = 1000, scenarios = "EFSA_2017")
#>      scenario
+#> t_avg      CTN     CTC      CTS
+#>    0  19.76834 13.8619 10.53795
+#>    21 19.59345 13.7169 10.39882
PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21),
+               Kom = 1000, scenarios = "EFSA_2017", porewater = TRUE)
#>      scenario
+#> t_avg       CLN       CLC       CLS
+#>    0  0.5541984 0.6779249 0.9816693
+#>    21 0.5484576 0.6693125 0.9609119

 # This is example 1 starting at p. 79 of the EFSA guidance (2015)
 PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
                scenarios = "EFSA_2015")
#>      scenario
diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html
index 91eeccb..e183ae2 100644
--- a/docs/reference/PEC_sw_drainage_UK.html
+++ b/docs/reference/PEC_sw_drainage_UK.html
@@ -62,7 +62,7 @@ published on the CRC website" />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html
index 02b641f..b5608db 100644
--- a/docs/reference/PEC_sw_drift.html
+++ b/docs/reference/PEC_sw_drift.html
@@ -63,7 +63,7 @@ with input via spray drift." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html
index 2942ebb..9fab616 100644
--- a/docs/reference/PEC_sw_exposit_runoff.html
+++ b/docs/reference/PEC_sw_exposit_runoff.html
@@ -62,7 +62,7 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html
index 535e82e..88f5b43 100644
--- a/docs/reference/PEC_sw_focus.html
+++ b/docs/reference/PEC_sw_focus.html
@@ -67,7 +67,7 @@ to be used with the FOCUS calculator." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html
index 532031b..01ccf29 100644
--- a/docs/reference/PEC_sw_sed.html
+++ b/docs/reference/PEC_sw_sed.html
@@ -64,7 +64,7 @@ PEC calculator" />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html
index a678cb6..b390917 100644
--- a/docs/reference/PELMO_path.html
+++ b/docs/reference/PELMO_path.html
@@ -61,7 +61,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html
index 5d53104..12a4244 100644
--- a/docs/reference/PELMO_runs.html
+++ b/docs/reference/PELMO_runs.html
@@ -67,7 +67,7 @@ and run using wine." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
@@ -229,7 +229,7 @@ the period.plm file generated by the FOCUS PELMO GUI.
 #> 
 #> # We get exactly the same PECgw values (on Linux, calling PELMO using Wine).
 print(time_1)
#>        User      System verstrichen 
-#>       0.384       0.095      30.954 
if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) {
+#>       0.383       0.129      30.547 
if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) {
   cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]]))
 }
#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor

 # Demonstrate some results with metabolites.
diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html
index e5b1e8a..b7b65f5 100644
--- a/docs/reference/SFO_actual_twa.html
+++ b/docs/reference/SFO_actual_twa.html
@@ -61,7 +61,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html
index 49b80e7..06be24e 100644
--- a/docs/reference/SSLRC_mobility_classification.html
+++ b/docs/reference/SSLRC_mobility_classification.html
@@ -62,7 +62,7 @@ checked against the spreadsheet published on the CRC website" />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html
index 932e6ef..a1b6bfe 100644
--- a/docs/reference/TOXSWA_cwa.html
+++ b/docs/reference/TOXSWA_cwa.html
@@ -62,7 +62,7 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html
index 1683067..39b3c9e 100644
--- a/docs/reference/chent_focus_sw.html
+++ b/docs/reference/chent_focus_sw.html
@@ -61,7 +61,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/create_run_list.html b/docs/reference/create_run_list.html
index 255aa1d..c52719d 100644
--- a/docs/reference/create_run_list.html
+++ b/docs/reference/create_run_list.html
@@ -61,7 +61,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html
index ada93e7..c3f1f4d 100644
--- a/docs/reference/drift_data_JKI.html
+++ b/docs/reference/drift_data_JKI.html
@@ -64,7 +64,7 @@ published by the German Julius-Kühn Institute (JKI)." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html
index a078bd8..819d8bc 100644
--- a/docs/reference/endpoint.html
+++ b/docs/reference/endpoint.html
@@ -64,7 +64,7 @@ this function." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/focus_80th.html b/docs/reference/focus_80th.html
index 375e15a..0604fa7 100644
--- a/docs/reference/focus_80th.html
+++ b/docs/reference/focus_80th.html
@@ -64,7 +64,7 @@ values obtained by PELMO." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html
index 5673322..dfcd15e 100644
--- a/docs/reference/geomean.html
+++ b/docs/reference/geomean.html
@@ -64,7 +64,7 @@ returns 0 if at least one element of the vector is 0." />
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/get_flux.html b/docs/reference/get_flux.html
index 025b4ad..518b09c 100644
--- a/docs/reference/get_flux.html
+++ b/docs/reference/get_flux.html
@@ -61,7 +61,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/get_interval.html b/docs/reference/get_interval.html
index 0cd69f3..4b73ca2 100644
--- a/docs/reference/get_interval.html
+++ b/docs/reference/get_interval.html
@@ -61,7 +61,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 162298b..12abbd4 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -58,7 +58,7 @@
       
       
         pfm
-        0.4.6
+        0.5.1
       
     
 
@@ -160,6 +160,12 @@
           SFO_actual_twa()

+ + + + @@ -180,6 +186,12 @@

soil_scenario_data_EFSA_2015

+ + + + diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html index 6e5ee67..c603fb4 100644 --- a/docs/reference/max_twa.html +++ b/docs/reference/max_twa.html @@ -65,7 +65,7 @@ max_twa." /> diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index 9cd4d61..f3a6324 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -61,7 +61,7 @@ diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html index e243efb..2c7dd2a 100644 --- a/docs/reference/perc_runoff_exposit.html +++ b/docs/reference/perc_runoff_exposit.html @@ -61,7 +61,7 @@ @@ -113,6 +113,7 @@

A data frame with percentage values for the dissolved fraction and the fraction bound to eroding particles, with Koc classes used as row names

Koc_lower_bound

The lower bound of the Koc class

dissolved

The percentage of the applied substance transferred to an adjacent water body in the dissolved phase

bound

The percentage of the applied substance transferred to an diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html index 4e10a64..9a8f10a 100644 --- a/docs/reference/perc_runoff_reduction_exposit.html +++ b/docs/reference/perc_runoff_reduction_exposit.html @@ -61,7 +61,7 @@ pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt index d4fd84e..1f9181a 100644 --- a/docs/reference/pesticide.txt +++ b/docs/reference/pesticide.txt @@ -37,3 +37,7 @@ Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Du M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html index e547ed1..16df913 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -61,7 +61,7 @@ pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html index 8612bac..65703e8 100644 --- a/docs/reference/plot.TOXSWA_cwa.html +++ b/docs/reference/plot.TOXSWA_cwa.html @@ -62,7 +62,7 @@ segment of a TOXSWA surface water body." /> pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html index a8f62d4..473243a 100644 --- a/docs/reference/plot.one_box.html +++ b/docs/reference/plot.one_box.html @@ -61,7 +61,7 @@ pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index aa18ec4..5f6aba2 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -66,7 +66,7 @@ renamed to ConLiqWatLay in the out file." /> pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index 175e045..87dcab2 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -63,7 +63,7 @@ times, with an interval i." /> pfm - 0.4.6 + 0.5.1 diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index 64c9c28..23fe106 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -63,7 +63,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> pfm - 0.4.6 + 0.5.1 @@ -122,10 +122,10 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.

Source

EFSA (European Food Safety Authority) (2015) -EFSA guidance document for predicting environmental concentrations -of active substances of plant protection products and transformation products of these -active substances in soil. EFSA Journal 13(4) 4093 -doi:10.2903/j.efsa.2015.4093

+ EFSA guidance document for predicting environmental concentrations + of active substances of plant protection products and transformation products of these + active substances in soil. EFSA Journal 13(4) 4093 + doi:10.2903/j.efsa.2015.4093

Examples

diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html new file mode 100644 index 0000000..be49263 --- /dev/null +++ b/docs/reference/soil_scenario_data_EFSA_2017.html @@ -0,0 +1,177 @@ + + + + + + + + +Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + +

+ +

Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +concentration in soil as given in the EFSA guidance (2017, p. 14/15). Also, the +scenario and model adjustment factors from p. 16 and p. 18 are included.

+ +

+ + +

Format

+ +

A data frame with one row for each scenario. Row names are the scenario codes, + e.g. CTN for the Northern scenario for the total concentration in soil. Columns are + mostly self-explanatory. rho is the dry bulk density of the top soil.

+ +

Source

+ +

EFSA (European Food Safety Authority) (2017) + EFSA guidance document for predicting environmental concentrations + of active substances of plant protection products and transformation products of these + active substances in soil. EFSA Journal 15(10) 4982 + doi:10.2903/j.efsa.2017.4982

+ + +

Examples

soil_scenario_data_EFSA_2017
#>        Zone Country T_arit T_arr Texture  f_om theta_fc   rho f_sce f_mod
+#> CTN   North Estonia    5.7   7.6  Coarse 0.220    0.244 0.707   1.4     3
+#> CTC Central  Poland    7.4   9.3  Coarse 0.122    0.244 0.934   1.4     3
+#> CTS   South  France   10.2  11.7  Medium 0.070    0.349 1.117   1.4     3
+#> CLN   North Denmark    8.0   9.2  Medium 0.025    0.349 1.371   1.6     4
+#> CLC Central Austria    9.3  11.3  Medium 0.018    0.349 1.432   1.6     4
+#> CLS   South   Spain   15.4  16.7  Medium 0.010    0.349 1.521   1.6     4
+#>     FOCUS_zone prec
+#> CTN    Hamburg  639
+#> CTC    Hamburg  617
+#> CTS    Hamburg  667
+#> CLN    Hamburg  602
+#> CLC Châteaudun  589
+#> CLS    Sevilla  526

+ +

+ + +

+ + + + + + diff --git a/docs/reference/sum_periods.html b/docs/reference/sum_periods.html index ec0c34b..109d9e7 100644 --- a/docs/reference/sum_periods.html +++ b/docs/reference/sum_periods.html @@ -61,7 +61,7 @@ diff --git a/docs/reference/twa.html b/docs/reference/twa.html index da44f92..f74399c 100644 --- a/docs/reference/twa.html +++ b/docs/reference/twa.html @@ -63,7 +63,7 @@ is after one window has passed." /> -- cgit v1.2.3

tillage_depth	Periodic (see interval) deeper mixing in cm
leaching_depth	EFSA (2017) uses the mixing depth (ecotoxicological +evaluation depth) to calculate leaching for annual crops where tillage +takes place. By default, losses from the layer down to the tillage +depth are taken into account in this implementation.
crop	Ignored for scenarios other than EFSA_2017. Only annual crops +are supported when these scenarios are used. Only crops with a single cropping +cycle per year are currently supported.
cultivation	Does mechanical cultivation in the sense of EFSA (2017) +take place, i.e. twice a year to a depth of 5 cm? Ignored for scenarios +other than EFSA_2017
chent	An optional chent object holding substance specific information. Can +	An optional chent object holding substance specific information. Can also be a name for the substance as a character string
leaching	Should leaching be taken into account? The default is FALSE, +except when the EFSA_2017 scenarios are used.
porewater	Actual and maximum moving window time average concentrations for SFO kinetics
+ `FOMC_actual_twa()` +	Actual and maximum moving window time average concentrations for FOMC kinetics
Properties of the predefined scenarios from the EFSA guidance from 2015
+ `soil_scenario_data_EFSA_2017` +	Properties of the predefined scenarios from the EFSA guidance from 2017

Installation

Installation

R6 class for holding TOXSWA cwa concentration data and associated statistics

R6 class for holding TOXSWA water concentration data and associated statistics

Installation

Arguments

Note

Source

Examples

Properties of the predefined scenarios from the EFSA guidance from 2017

Format

Source

Examples

Contents