diff options
Diffstat (limited to 'pkg/man')
-rw-r--r-- | pkg/man/PEC_sw_drainage_UK_ini.Rd | 40 | ||||
-rw-r--r-- | pkg/man/PEC_sw_drift.Rd | 42 | ||||
-rw-r--r-- | pkg/man/PEC_sw_drift_ini.Rd | 42 | ||||
-rw-r--r-- | pkg/man/PEC_sw_sed.Rd | 42 | ||||
-rw-r--r-- | pkg/man/SFO_actual_twa.Rd | 29 | ||||
-rw-r--r-- | pkg/man/SSLRC_mobility_classification.Rd | 26 | ||||
-rw-r--r-- | pkg/man/drift_data_JKI.Rd | 46 | ||||
-rw-r--r-- | pkg/man/pfm_degradation.Rd | 35 |
8 files changed, 302 insertions, 0 deletions
diff --git a/pkg/man/PEC_sw_drainage_UK_ini.Rd b/pkg/man/PEC_sw_drainage_UK_ini.Rd new file mode 100644 index 0000000..1b2009d --- /dev/null +++ b/pkg/man/PEC_sw_drainage_UK_ini.Rd @@ -0,0 +1,40 @@ +% Generated by roxygen2 (4.1.0.9001): do not edit by hand +% Please edit documentation in R/PEC_sw_drainage_UK.R +\name{PEC_sw_drainage_UK_ini} +\alias{PEC_sw_drainage_UK_ini} +\title{Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method} +\usage{ +PEC_sw_drainage_UK_ini(rate, interception = 0, Koc, + latest_application = NULL, soil_DT50 = NULL, model = NULL, + model_parms = NULL) +} +\arguments{ +\item{rate}{Application rate in g/ha} + +\item{interception}{The fraction of the application rate that does not reach the soil} + +\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg} + +\item{latest_application}{Latest application date, formatted as e.g. "01 July"} + +\item{soil_DT50}{Soil degradation half-life, if SFO kinetics are to be used} + +\item{model}{The degradation model to be used. Either one of "FOMC", "DFOP", +"HS", or "IORE", or an mkinmod object} + +\item{model_parms}{A named numeric vector containing the model parameters} +} +\value{ +The predicted concentration in surface water in µg/L +} +\description{ +This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet +published on the CRC website +} +\examples{ +PEC_sw_drainage_UK_ini(150, Koc = 100) +} +\author{ +Johannes Ranke +} + diff --git a/pkg/man/PEC_sw_drift.Rd b/pkg/man/PEC_sw_drift.Rd new file mode 100644 index 0000000..20299a5 --- /dev/null +++ b/pkg/man/PEC_sw_drift.Rd @@ -0,0 +1,42 @@ +% Generated by roxygen2 (4.1.0.9001): do not edit by hand +% Please edit documentation in R/PEC_sw_drift.R +\name{PEC_sw_drift} +\alias{PEC_sw_drift} +\title{Calculate predicted environmental concentrations in surface water due to drift} +\usage{ +PEC_sw_drift(rate, applications = 1, water_depth = 30, drift_data = "JKI", + crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha", + PEC_units = "µg/L") +} +\arguments{ +\item{rate}{Application rate in units specified below} + +\item{applications}{Number of applications for selection of drift percentile} + +\item{water_depth}{Depth of the water body in cm} + +\item{drift_data}{Source of drift percentage data} + +\item{crop}{Crop name (use German names for JKI data), defaults to "Ackerbau"} + +\item{distances}{The distances in m for which to get PEC values} + +\item{rate_units}{Defaults to g/ha} + +\item{PEC_units}{Requested units for the calculated PEC. Only µg/L currently supported} +} +\value{ +The predicted concentration in surface water +} +\description{ +This is a basic, vectorised form of a simple calculation of a contaminant +concentration in surface water based on complete, instantaneous mixing +with input via spray drift. +} +\examples{ +PEC_sw_drift(100) +} +\author{ +Johannes Ranke +} + diff --git a/pkg/man/PEC_sw_drift_ini.Rd b/pkg/man/PEC_sw_drift_ini.Rd new file mode 100644 index 0000000..0bcbf97 --- /dev/null +++ b/pkg/man/PEC_sw_drift_ini.Rd @@ -0,0 +1,42 @@ +% Generated by roxygen2 (4.1.0.9001): do not edit by hand +% Please edit documentation in R/PEC_sw_drift_ini.R +\name{PEC_sw_drift_ini} +\alias{PEC_sw_drift_ini} +\title{Calculate initial predicted environmental concentrations in surface water due to drift} +\usage{ +PEC_sw_drift_ini(rate, applications = 1, water_depth = 30, + drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20), + rate_units = "g/ha", PEC_units = "µg/L") +} +\arguments{ +\item{rate}{Application rate in units specified below} + +\item{applications}{Number of applications for selection of drift percentile} + +\item{water_depth}{Depth of the water body in cm} + +\item{drift_data}{Source of drift percentage data} + +\item{crop}{Crop name (use German names for JKI data), defaults to "Ackerbau"} + +\item{distances}{The distances in m for which to get PEC values} + +\item{rate_units}{Defaults to g/ha} + +\item{PEC_units}{Requested units for the calculated PEC. Only µg/L currently supported} +} +\value{ +The predicted concentration in surface water +} +\description{ +This is a basic, vectorised form of a simple calculation of a contaminant +concentration in surface water based on complete, instantaneous mixing +with input via spray drift. +} +\examples{ +PEC_sw_drift_ini(100) +} +\author{ +Johannes Ranke +} + diff --git a/pkg/man/PEC_sw_sed.Rd b/pkg/man/PEC_sw_sed.Rd new file mode 100644 index 0000000..ee496d1 --- /dev/null +++ b/pkg/man/PEC_sw_sed.Rd @@ -0,0 +1,42 @@ +% Generated by roxygen2 (4.1.0.9001): do not edit by hand +% Please edit documentation in R/PEC_sw_sed.R +\name{PEC_sw_sed} +\alias{PEC_sw_sed} +\title{Calculate initial predicted environmental concentrations in sediment from +surface water concentrations} +\usage{ +PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage", + sediment_depth = 5, water_depth = 30, sediment_density = 1.3, + PEC_sed_units = c("µg/kg", "mg/kg")) +} +\arguments{ +\item{PEC_sw}{Numeric vector or matrix of surface water concentrations in µg/L for +which the corresponding sediment concentration is to be estimated} + +\item{percentage}{The percentage in sediment, used for the percentage method} + +\item{method}{The method used for the calculation} + +\item{sediment_depth}{Depth of the sediment layer} + +\item{water_depth}{Depth of the water body in cm} + +\item{sediment_density}{The density of the sediment in L/kg (equivalent to +g/cm3)} + +\item{PEC_sed_units}{The units of the estimated sediment PEC value} +} +\value{ +The predicted concentration in sediment +} +\description{ +The method 'percentage' is equivalent to what is used in the CRD spreadsheet +PEC calculator +} +\examples{ +PEC_sw_sed(PEC_sw_drift_ini(100, distances = 1), percentage = 50) +} +\author{ +Johannes Ranke +} + diff --git a/pkg/man/SFO_actual_twa.Rd b/pkg/man/SFO_actual_twa.Rd new file mode 100644 index 0000000..967b60f --- /dev/null +++ b/pkg/man/SFO_actual_twa.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2 (4.1.0.9001): do not edit by hand +% Please edit documentation in R/SFO_actual_twa.R +\name{SFO_actual_twa} +\alias{SFO_actual_twa} +\title{Actual and maximum moving window time average concentrations for SFO kinetics} +\source{ +FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation + Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, + 18 December 2014, p. 251 +} +\usage{ +SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, + 100)) +} +\arguments{ +\item{DT50}{The half-life.} + +\item{times}{The output times, and window sizes for time weighted average concentrations} +} +\description{ +Actual and maximum moving window time average concentrations for SFO kinetics +} +\examples{ +SFO_actual_twa(10) +} +\author{ +Johannes Ranke +} + diff --git a/pkg/man/SSLRC_mobility_classification.Rd b/pkg/man/SSLRC_mobility_classification.Rd new file mode 100644 index 0000000..62a345b --- /dev/null +++ b/pkg/man/SSLRC_mobility_classification.Rd @@ -0,0 +1,26 @@ +% Generated by roxygen2 (4.1.0.9001): do not edit by hand +% Please edit documentation in R/SSLRC_mobility_classification.R +\name{SSLRC_mobility_classification} +\alias{SSLRC_mobility_classification} +\title{Determine the SSLRC mobility classification for a chemical substance from its Koc} +\usage{ +SSLRC_mobility_classification(Koc) +} +\arguments{ +\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg} +} +\value{ +A list containing the classification and the percentage of the + compound transported per 10 mm drain water +} +\description{ +This implements the method specified in the UK data requirements handbook and was +checked against the spreadsheet published on the CRC website +} +\examples{ +SSLRC_mobility_classification(100) +} +\author{ +Johannes Ranke +} + diff --git a/pkg/man/drift_data_JKI.Rd b/pkg/man/drift_data_JKI.Rd new file mode 100644 index 0000000..a2bbb77 --- /dev/null +++ b/pkg/man/drift_data_JKI.Rd @@ -0,0 +1,46 @@ +% Generated by roxygen2 (4.1.0.9001): do not edit by hand +% Please edit documentation in R/drift_data_JKI.R +\docType{data} +\name{drift_data_JKI} +\alias{drift_data_JKI} +\title{Deposition from spray drift expressed as percent of the applied dose as +published by the JKI} +\format{A list currently containing matrices with spray drift percentage +data for field crops (Ackerbau), and Pome/stone fruit, early and late +(Obstbau früh, spät).} +\source{ +JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved +from +http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html +on 2015-06-11 +} +\description{ +Deposition from spray drift expressed as percent of the applied dose as +published by the German Julius-Kühn Institute (JKI). +} +\details{ +The data were extracted from the spreadsheet cited below using the R code +given in the example section. The spreadsheet is not included in the package +as its licence is not clear. +} +\examples{ +\dontrun{ + # This is the code that was used to extract the data + library(readxl) + abdrift_path <- "../inst/extdata/Tabelle der Abdrifteckwerte.xls" + JKI_crops <- c("Ackerbau", "Obstbau früh", "Obstbau spät") + names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late") + drift_data_JKI <- list() + + for (n in 1:8) { + drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) + drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) + dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]), + crop = JKI_crops) + drift_data_JKI[[n]] <- drift_data + } + save(drift_data_JKI, file = "../data/drift_data_JKI.RData") +} +} +\keyword{datasets} + diff --git a/pkg/man/pfm_degradation.Rd b/pkg/man/pfm_degradation.Rd new file mode 100644 index 0000000..b875434 --- /dev/null +++ b/pkg/man/pfm_degradation.Rd @@ -0,0 +1,35 @@ +% Generated by roxygen2 (4.1.0.9001): do not edit by hand +% Please edit documentation in R/pfm_degradation.R +\name{pfm_degradation} +\alias{pfm_degradation} +\title{Calculate a time course of relative concentrations based on an mkinmod model} +\usage{ +pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = + log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by = + step_days)) +} +\arguments{ +\item{model}{The degradation model to be used. Either a parent only model like +'SFO' or 'FOMC', or an mkinmod object} + +\item{DT50}{The half-life. This is only used when simple exponential decline +is calculated (SFO model).} + +\item{parms}{The parameters used for the degradation model} + +\item{years}{For how many years should the degradation be predicted?} + +\item{step_days}{What step size in days should the output have?} + +\item{times}{The output times} +} +\description{ +Calculate a time course of relative concentrations based on an mkinmod model +} +\examples{ +pfm_degradation("SFO", DT50 = 10) +} +\author{ +Johannes Ranke +} + |