R6 class for holding TOXSWA cwa concentration data and associated statistics

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

# 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/read.TOXSWA_cwa.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 @@

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

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