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 --- man/FOCUS_GW_scenarios_2012.Rd | 17 +++++ man/GUS.Rd | 81 ++++++++++++++++++++++++ man/PEC_soil.Rd | 119 +++++++++++++++++++++++++++++++++++ man/PEC_sw_drainage_UK.Rd | 39 ++++++++++++ man/PEC_sw_drift.Rd | 45 +++++++++++++ man/PEC_sw_sed.Rd | 42 +++++++++++++ man/SFO_actual_twa.Rd | 29 +++++++++ man/SSLRC_mobility_classification.Rd | 26 ++++++++ man/TOXSWA_cwa.Rd | 58 +++++++++++++++++ man/drift_data_JKI.Rd | 50 +++++++++++++++ man/endpoint.Rd | 75 ++++++++++++++++++++++ man/geomean.Rd | 31 +++++++++ man/pfm_degradation.Rd | 35 +++++++++++ man/plot.TOXSWA_cwa.Rd | 42 +++++++++++++ man/read.TOXSWA_cwa.Rd | 56 +++++++++++++++++ man/soil_scenario_data_EFSA_2015.Rd | 46 ++++++++++++++ 16 files changed, 791 insertions(+) create mode 100644 man/FOCUS_GW_scenarios_2012.Rd create mode 100644 man/GUS.Rd create mode 100644 man/PEC_soil.Rd create mode 100644 man/PEC_sw_drainage_UK.Rd create mode 100644 man/PEC_sw_drift.Rd create mode 100644 man/PEC_sw_sed.Rd create mode 100644 man/SFO_actual_twa.Rd create mode 100644 man/SSLRC_mobility_classification.Rd create mode 100644 man/TOXSWA_cwa.Rd create mode 100644 man/drift_data_JKI.Rd create mode 100644 man/endpoint.Rd create mode 100644 man/geomean.Rd create mode 100644 man/pfm_degradation.Rd create mode 100644 man/plot.TOXSWA_cwa.Rd create mode 100644 man/read.TOXSWA_cwa.Rd create mode 100644 man/soil_scenario_data_EFSA_2015.Rd (limited to 'man') diff --git a/man/FOCUS_GW_scenarios_2012.Rd b/man/FOCUS_GW_scenarios_2012.Rd new file mode 100644 index 0000000..3ae151b --- /dev/null +++ b/man/FOCUS_GW_scenarios_2012.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/FOCUS_GW_scenarios_2012.R +\name{FOCUS_GW_scenarios_2012} +\alias{FOCUS_GW_scenarios_2012} +\title{A very small subset of the FOCUS Groundwater scenario defitions} +\description{ +Currently, only a small subset of the soil definitions are provided. +} +\examples{ +FOCUS_GW_scenarios_2012 +} +\references{ +FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. + FOrum for the Co-ordination of pesticde fate models and their USe. + http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf +} + diff --git a/man/GUS.Rd b/man/GUS.Rd new file mode 100644 index 0000000..f1f5f28 --- /dev/null +++ b/man/GUS.Rd @@ -0,0 +1,81 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/GUS.R +\name{GUS} +\alias{GUS} +\alias{GUS.chent} +\alias{GUS.numeric} +\alias{print.GUS_result} +\title{Groundwater ubiquity score based on Gustafson (1989)} +\usage{ +GUS(...) + +\method{GUS}{numeric}(DT50, Koc, ...) + +\method{GUS}{chent}(chent, degradation_value = "DT50ref", + lab_field = "laboratory", redox = "aerobic", sorption_value = "Kfoc", + degradation_aggregator = geomean, sorption_aggregator = geomean, ...) + +\method{print}{GUS_result}(x, ..., digits = 1) +} +\arguments{ +\item{...}{Included in the generic to allow for further arguments later. Therefore +this also had to be added to the specific methods.} + +\item{DT50}{Half-life of the chemical in soil. Should be a field +half-life according to Gustafson (1989). However, leaching to the sub-soil +can not completely be excluded in field dissipation experiments and Gustafson +did not refer to any normalisation procedure, but says the field study should +be conducted under use conditions.} + +\item{Koc}{The sorption constant normalised to organic carbon. Gustafson +does not mention the nonlinearity of the sorption constant commonly +found and usually described by Freundlich sorption, therefore it is +unclear at which reference concentration the Koc should be observed +(and if the reference concentration would be in soil or in porewater).} + +\item{chent}{If a chent is given with appropriate information present in its +chyaml field, this information is used, with defaults specified below.} + +\item{degradation_value}{Which of the available degradation values should +be used?} + +\item{lab_field}{Should laboratory or field half-lives be used? This +defaults to lab in this implementation, in order to avoid +double-accounting for mobility. If comparability with the original GUS +values given by Gustafson (1989) is desired, non-normalised first-order +field half-lives obtained under actual use conditions should be used.} + +\item{redox}{Aerobic or anaerobic degradation data} + +\item{sorption_value}{Which of the available sorption values should be used? +Defaults to Kfoc as this is what is generally available from the European +pesticide peer review process. These values generally use a reference +concentration of 1 mg/L in porewater, that means they would be expected to +be Koc values at a concentration of 1 mg/L in the water phase.} + +\item{degradation_aggregator}{Function for aggregating half-lives} + +\item{sorption_aggregator}{Function for aggregation Koc values} + +\item{x}{An object of class GUS_result to be printed} + +\item{digits}{The number of digits used in the print method} +} +\value{ +A list with the DT50 and Koc used as well as the resulting score + of class GUS_result +} +\description{ +The groundwater ubiquity score GUS is calculated according to +the following equation +\deqn{GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})}{GUS = log10 DT50soil * (4 - log10 Koc)} +} +\author{ +Johannes Ranke +} +\references{ +Gustafson, David I. (1989) Groundwater ubiquity score: a simple +method for assessing pesticide leachability. \emph{Environmental +toxicology and chemistry} \bold{8}(4) 339–57. +} + diff --git a/man/PEC_soil.Rd b/man/PEC_soil.Rd new file mode 100644 index 0000000..c0b5201 --- /dev/null +++ b/man/PEC_soil.Rd @@ -0,0 +1,119 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PEC_soil.R +\name{PEC_soil} +\alias{PEC_soil} +\title{Calculate predicted environmental concentrations in soil} +\usage{ +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, + Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default", + "EFSA_2015"), porewater = FALSE) +} +\arguments{ +\item{rate}{Application rate in units specified below} + +\item{rate_units}{Defaults to g/ha} + +\item{interception}{The fraction of the application rate that does not reach the soil} + +\item{mixing_depth}{Mixing depth in cm} + +\item{PEC_units}{Requested units for the calculated PEC. Only mg/kg currently supported} + +\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} + +\item{n_periods}{Number of periods to be considered for long term PEC calculations} + +\item{tillage_depth}{Periodic (see interval) deeper mixing in cm} + +\item{chent}{An optional chent object holding substance specific information. Can +also be a name for the substance as a character string} + +\item{DT50}{If specified, overrides soil DT50 endpoints from a chent object +If DT50 is not specified here and not available from the chent object, zero +degradation is assumed} + +\item{Koc}{If specified, overrides Koc endpoints from a chent object} + +\item{Kom}{Calculated from Koc by default, but can explicitly be specified +as Kom here} + +\item{t_avg}{Averaging times for time weighted average concentrations} + +\item{scenarios}{If this is 'default', the DT50 will be used without correction +and soil properties as specified in the REACH guidance (R.16, Table +R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", +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.} + +\item{porewater}{Should equilibrium porewater concentrations be estimated +based on Kom and the organic carbon fraction of the soil instead of total +soil concentrations? Based on equation (7) given in the PPR panel opinion +(EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, +p. 13).} +} +\value{ +The predicted concentration in soil +} +\description{ +This is a basic calculation of a contaminant concentration in bulk soil +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). +} +\details{ +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 +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. +} +\note{ +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'. +} +\examples{ +PEC_soil(100, interception = 0.25) + +# 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") +PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), + Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) + +# The following is from example 4 starting at p. 85 of the EFSA guidance (2015) +# Metabolite M2 +# Calculate total and porewater soil concentrations for tier 1 scenarios +# Relative molar mass is 100/300, formation fraction is 0.7 * 1 +results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), + scenarios = "EFSA_2015") +results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), + Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) +} +\author{ +Johannes Ranke +} +\references{ +EFSA Panel on Plant Protection Products and their Residues (2012) + Scientific Opinion on the science behind the guidance for scenario + selection and scenario parameterisation for predicting environmental + concentrations of plant protection products in soil. \emph{EFSA Journal} + \bold{10}(2) 2562, doi:10.2903/j.efsa.2012.2562 + + 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. \emph{EFSA Journal} \bold{13}(4) 4093 + doi:10.2903/j.efsa.2015.4093 +} + diff --git a/man/PEC_sw_drainage_UK.Rd b/man/PEC_sw_drainage_UK.Rd new file mode 100644 index 0000000..cb64bde --- /dev/null +++ b/man/PEC_sw_drainage_UK.Rd @@ -0,0 +1,39 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PEC_sw_drainage_UK.R +\name{PEC_sw_drainage_UK} +\alias{PEC_sw_drainage_UK} +\title{Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method} +\usage{ +PEC_sw_drainage_UK(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 soil 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(150, Koc = 100) +} +\author{ +Johannes Ranke +} + diff --git a/man/PEC_sw_drift.Rd b/man/PEC_sw_drift.Rd new file mode 100644 index 0000000..20fa921 --- /dev/null +++ b/man/PEC_sw_drift.Rd @@ -0,0 +1,45 @@ +% Generated by roxygen2: 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_percentages = NULL, 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_percentages}{Percentage drift values for which to calculate PECsw. +'drift_data' and 'distances' if not NULL.} + +\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/man/PEC_sw_sed.Rd b/man/PEC_sw_sed.Rd new file mode 100644 index 0000000..3140eb0 --- /dev/null +++ b/man/PEC_sw_sed.Rd @@ -0,0 +1,42 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PEC_sw_sed.R +\name{PEC_sw_sed} +\alias{PEC_sw_sed} +\title{Calculate 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(100, distances = 1), percentage = 50) +} +\author{ +Johannes Ranke +} + diff --git a/man/SFO_actual_twa.Rd b/man/SFO_actual_twa.Rd new file mode 100644 index 0000000..573ea03 --- /dev/null +++ b/man/SFO_actual_twa.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2: 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/man/SSLRC_mobility_classification.Rd b/man/SSLRC_mobility_classification.Rd new file mode 100644 index 0000000..04aa01d --- /dev/null +++ b/man/SSLRC_mobility_classification.Rd @@ -0,0 +1,26 @@ +% Generated by roxygen2: 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/man/TOXSWA_cwa.Rd b/man/TOXSWA_cwa.Rd new file mode 100644 index 0000000..de87510 --- /dev/null +++ b/man/TOXSWA_cwa.Rd @@ -0,0 +1,58 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/TOXSWA_cwa.R +\docType{class} +\name{TOXSWA_cwa} +\alias{TOXSWA_cwa} +\title{R6 class for holding TOXSWA cwa 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. +Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_cwa}}. +} +\section{Fields}{ + +\describe{ +\item{\code{filename}}{Length one character vector.} + +\item{\code{basedir}}{Length one character vector.} + +\item{\code{segment}}{Length one integer, specifying for which segment the cwa data were read.} + +\item{\code{cwas}}{Dataframe holding the concentrations.} + +\item{\code{events}}{List of dataframes holding the event statistics for each threshold.} + +\item{\code{windows}}{Matrix of maximum time weighted average concentrations (TWAC_max) +and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) +for the requested moving window sizes in days.} +}} +\section{Methods}{ + +\describe{ + \item{\code{get_events(threshold, total = FALSE)}}{ + Populate a datataframe with event information for the specified threshold value + in µg/L. If \code{total = TRUE}, the total concentration including the amount + adsorbed to suspended matter will be used. The resulting dataframe is stored in the + \code{events} field of the object. + } + \item{\code{moving_windows(windows, total = FALSE)}}{ + Add to the \code{windows} field described above. + Again, if \code{total = TRUE}, the total concentration including the amount + adsorbed to suspended matter will be used. + } +} +} +\examples{ +H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", + basedir = "SwashProjects/project_H_sw/TOXSWA", + zipfile = system.file("testdata/SwashProjects.zip", + package = "pfm")) +H_sw_R1_stream$get_events(c(2, 10)) +H_sw_R1_stream$moving_windows(c(7, 21)) +print(H_sw_R1_stream) +} +\keyword{data} + diff --git a/man/drift_data_JKI.Rd b/man/drift_data_JKI.Rd new file mode 100644 index 0000000..c193c0d --- /dev/null +++ b/man/drift_data_JKI.Rd @@ -0,0 +1,50 @@ +% Generated by roxygen2: 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 frueh, spaet).} +\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 frueh", "Obstbau spaet") + 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") +} + +# And this is the resulting data +drift_data_JKI +} +\keyword{datasets} + diff --git a/man/endpoint.Rd b/man/endpoint.Rd new file mode 100644 index 0000000..0350a51 --- /dev/null +++ b/man/endpoint.Rd @@ -0,0 +1,75 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/endpoint.R +\name{endpoint} +\alias{endpoint} +\alias{soil_DT50} +\alias{soil_Kfoc} +\alias{soil_N} +\alias{soil_sorption} +\title{Retrieve endpoint information from the chyaml field of a chent object} +\usage{ +endpoint(chent, medium = "soil", type = c("degradation", "sorption"), + lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic", + "anaerobic"), value = c("DT50ref", "Kfoc", "N"), aggregator = geomean, + raw = FALSE, signif = 3) + +soil_DT50(chent, aggregator = geomean, signif = 3, + lab_field = "laboratory", value = "DT50ref", redox = "aerobic", + raw = FALSE) + +soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", + raw = FALSE) + +soil_N(chent, aggregator = mean, signif = 3, raw = FALSE) + +soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = + geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), + raw = FALSE) +} +\arguments{ +\item{chent}{The chent object to get the information from} + +\item{medium}{The medium for which information is sought} + +\item{type}{The information type} + +\item{lab_field}{If not NA, do we want laboratory or field endpoints} + +\item{redox}{If not NA, are we looking for aerobic or anaerobic data} + +\item{value}{The name of the value we want. The list given in the +usage section is not exclusive} + +\item{aggregator}{The aggregator function. Can be mean, +\code{\link{geomean}}, or identity, for example.} + +\item{raw}{Should the number(s) be returned as stored in the chent +object (could be a character value) to retain original information +about precision?} + +\item{signif}{How many significant digits do we want} + +\item{values}{The values to be returned} + +\item{aggregators}{A named vector of aggregator functions to be used} +} +\value{ +The result from applying the aggregator function to + the values converted to a numeric vector, rounded to the + given number of significant digits, or, if raw = TRUE, + the values as a character value, retaining any implicit + information on precision that may be present. +} +\description{ +R6 class objects of class chent represent chemical entities +and can hold a list of information loaded from a chemical yaml file in their +chyaml field. Such information is extracted and optionally aggregated by +this function. +} +\details{ +The functions \code{soil_*} are functions to extract soil specific endpoints. +For the Freundlich exponent, the capital letter \code{N} is used in order to +facilitate dealing with such data in R. In pesticide fate modelling, this +exponent is often called 1/n. +} + diff --git a/man/geomean.Rd b/man/geomean.Rd new file mode 100644 index 0000000..ed82294 --- /dev/null +++ b/man/geomean.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/geomean.R +\name{geomean} +\alias{geomean} +\title{Calculate the geometric mean} +\usage{ +geomean(x, na.rm = TRUE) +} +\arguments{ +\item{x}{Vector of numbers} + +\item{na.rm}{Should NA values be omitted?} +} +\value{ +The geometric mean +} +\description{ +Based on some posts in a thread on Stackoverflow +\url{http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in} +This function checks for negative values, removes NA values per default and +returns 0 if at least one element of the vector is 0. +} +\examples{ +geomean(c(1, 3, 9)) +geomean(c(1, 3, NA, 9)) +\dontrun{geomean(c(1, -3, 9)) # returns an error} +} +\author{ +Johannes Ranke +} + diff --git a/man/pfm_degradation.Rd b/man/pfm_degradation.Rd new file mode 100644 index 0000000..9ab1d0a --- /dev/null +++ b/man/pfm_degradation.Rd @@ -0,0 +1,35 @@ +% Generated by roxygen2: 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{ +head(pfm_degradation("SFO", DT50 = 10)) +} +\author{ +Johannes Ranke +} + diff --git a/man/plot.TOXSWA_cwa.Rd b/man/plot.TOXSWA_cwa.Rd new file mode 100644 index 0000000..b5f0163 --- /dev/null +++ b/man/plot.TOXSWA_cwa.Rd @@ -0,0 +1,42 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/TOXSWA_cwa.R +\name{plot.TOXSWA_cwa} +\alias{plot.TOXSWA_cwa} +\title{Plot TOXSWA surface water concentrations} +\usage{ +\method{plot}{TOXSWA_cwa}(x, time_column = c("datetime", "t", "t_firstjan", + "t_rel_to_max"), xlab = "default", ylab = "default", add = FALSE, + total = FALSE, LC_TIME = "C", ...) +} +\arguments{ +\item{x}{The TOXSWA_cwa object to be plotted.} + +\item{time_column}{What should be used for the time axis. If "t_firstjan" is chosen, +the time is given in days relative to the first of January in the first year.} + +\item{xlab, ylab}{Labels for x and y axis.} + +\item{add}{Should we add to an existing plot?} + +\item{total}{Should the total concentration in water be plotted, including substance sorbed +to suspended matter?} + +\item{LC_TIME}{Specification of the locale used to format dates} + +\item{...}{Further arguments passed to \code{plot} if we are not adding to an existing plot} +} +\description{ +Plot TOXSWA hourly concentrations of a chemical substance in a specific +segment of a TOXSWA surface water body. +} +\examples{ +H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", + basedir = "SwashProjects/project_H_sw/TOXSWA", + zipfile = system.file("testdata/SwashProjects.zip", + package = "pfm")) +plot(H_sw_D4_pond) +} +\author{ +Johannes Ranke +} + diff --git a/man/read.TOXSWA_cwa.Rd b/man/read.TOXSWA_cwa.Rd new file mode 100644 index 0000000..84ef3da --- /dev/null +++ b/man/read.TOXSWA_cwa.Rd @@ -0,0 +1,56 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/TOXSWA_cwa.R +\name{read.TOXSWA_cwa} +\alias{read.TOXSWA_cwa} +\title{Read TOXSWA surface water concentrations} +\usage{ +read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", + substance = "parent", total = FALSE, windows = NULL, + thresholds = NULL) +} +\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).} + +\item{basedir}{The path to the directory where the cwa file resides.} + +\item{zipfile}{Optional path to a zip file containing the cwa file.} + +\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 +to reading concentrations of the parent compound. Alternatively, the substance +of interested can be selected by its code name.} + +\item{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.} + +\item{windows}{Numeric vector of width of moving windows in days, for calculating +maximum time weighted average concentrations and areas under the curve.} + +\item{thresholds}{Numeric vector of threshold concentrations in µg/L for +generating event statistics.} +} +\value{ +An instance of an R6 object of class +\code{\link{TOXSWA_cwa}}. +} +\description{ +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). +} +\examples{ +H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", + basedir = "SwashProjects/project_H_sw/TOXSWA", + zipfile = system.file("testdata/SwashProjects.zip", + package = "pfm")) +} +\author{ +Johannes Ranke +} + diff --git a/man/soil_scenario_data_EFSA_2015.Rd b/man/soil_scenario_data_EFSA_2015.Rd new file mode 100644 index 0000000..b45af4a --- /dev/null +++ b/man/soil_scenario_data_EFSA_2015.Rd @@ -0,0 +1,46 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/soil_scenario_data_EFSA_2015.R +\docType{data} +\name{soil_scenario_data_EFSA_2015} +\alias{soil_scenario_data_EFSA_2015} +\title{Properties of the predefined scenarios from the EFSA guidance from 2015} +\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. \code{rho} is the dry bulk density of the top soil.} +\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. \emph{EFSA Journal} \bold{13}(4) 4093 +doi:10.2903/j.efsa.2015.4093 +} +\description{ +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 (2015, p. 13/14). Also, the +scenario and model adjustment factors from p. 15 and p. 17 are included. +} +\examples{ +\dontrun{ + # This is the code that was used to define the data + soil_scenario_data_EFSA_2015 <- data.frame( + Zone = rep(c("North", "Central", "South"), 2), + Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"), + T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8), + T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7), + Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"), + f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011), + theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347), + rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51), + f_sce = c(3, 2, 2, 2, 1.5, 1.5), + f_mod = c(2, 2, 2, 4, 4, 4), + stringsAsFactors = FALSE, + row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS") + ) + save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData') +} + +# And this is the resulting dataframe +soil_scenario_data_EFSA_2015 +} +\keyword{datasets} + -- cgit v1.2.1