diff options
Diffstat (limited to 'pkg')
| -rw-r--r-- | pkg/DESCRIPTION | 18 | ||||
| -rw-r--r-- | pkg/NAMESPACE | 12 | ||||
| -rw-r--r-- | pkg/R/GUS.R | 74 | ||||
| -rw-r--r-- | pkg/R/endpoint.R | 102 | ||||
| -rw-r--r-- | pkg/man/FOCUS_GW_scenarios_2012.Rd | 6 | ||||
| -rw-r--r-- | pkg/man/GUS.Rd | 70 | ||||
| -rw-r--r-- | pkg/man/PEC_soil.Rd | 2 | ||||
| -rw-r--r-- | pkg/man/PEC_soil_product.Rd | 2 | ||||
| -rw-r--r-- | pkg/man/PEC_sw_drainage_UK_ini.Rd | 4 | ||||
| -rw-r--r-- | pkg/man/PEC_sw_drift.Rd | 2 | ||||
| -rw-r--r-- | pkg/man/PEC_sw_drift_ini.Rd | 2 | ||||
| -rw-r--r-- | pkg/man/PEC_sw_sed.Rd | 2 | ||||
| -rw-r--r-- | pkg/man/SFO_actual_twa.Rd | 4 | ||||
| -rw-r--r-- | pkg/man/SSLRC_mobility_classification.Rd | 4 | ||||
| -rw-r--r-- | pkg/man/TOXSWA_cwa.Rd | 6 | ||||
| -rw-r--r-- | pkg/man/drift_data_JKI.Rd | 8 | ||||
| -rw-r--r-- | pkg/man/endpoint.Rd | 45 | ||||
| -rw-r--r-- | pkg/man/geomean.Rd | 2 | ||||
| -rw-r--r-- | pkg/man/pfm_degradation.Rd | 2 | ||||
| -rw-r--r-- | pkg/man/plot.TOXSWA_cwa.Rd | 4 | ||||
| -rw-r--r-- | pkg/man/read.TOXSWA_cwa.Rd | 4 | ||||
| -rw-r--r-- | pkg/man/soil_DT50.Rd | 29 | ||||
| -rw-r--r-- | pkg/man/soil_Kfoc.Rd | 24 | ||||
| -rw-r--r-- | pkg/man/soil_N.Rd | 21 | ||||
| -rw-r--r-- | pkg/man/soil_sorption.Rd | 23 |
25 files changed, 440 insertions, 32 deletions
diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION index 55e5814..fb9171f 100644 --- a/pkg/DESCRIPTION +++ b/pkg/DESCRIPTION @@ -2,16 +2,22 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling Version: 0.2-4 -Date: 2015-10-01 +Date: 2015-10-15 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph")) Description: Utilities for simple calculations of predicted environmental - concentrations (PECs) and for dealing with data from some FOCUS pesticide - fate modelling software packages. -Depends: R6, mkin -Imports: graphics -Suggests: testthat, chents + concentrations (PECs) and for dealing with data from some FOCUS pesticide + fate modelling software packages. +Depends: + R6, + mkin +Imports: + graphics +Suggests: + testthat, + chents License: GPL LazyLoad: yes LazyData: yes Encoding: UTF-8 +RoxygenNote: 4.1.1.9001 diff --git a/pkg/NAMESPACE b/pkg/NAMESPACE index a1c5df2..4214464 100644 --- a/pkg/NAMESPACE +++ b/pkg/NAMESPACE @@ -1,6 +1,10 @@ -# Generated by roxygen2 (4.1.1): do not edit by hand +# Generated by roxygen2: do not edit by hand +S3method(GUS,chent) +S3method(GUS,numeric) S3method(plot,TOXSWA_cwa) +S3method(print,GUS_result) +export(GUS) export(PEC_soil) export(PEC_soil_product) export(PEC_sw_drainage_UK_ini) @@ -10,9 +14,15 @@ export(PEC_sw_sed) export(SFO_actual_twa) export(SSLRC_mobility_classification) export(TOXSWA_cwa) +export(endpoint) export(geomean) export(pfm_degradation) export(read.TOXSWA_cwa) +export(soil_DT50) +export(soil_Kfoc) +export(soil_N) +export(soil_sorption) +import(chents) import(graphics) import(mkin) importFrom(R6,R6Class) diff --git a/pkg/R/GUS.R b/pkg/R/GUS.R new file mode 100644 index 0000000..2690f50 --- /dev/null +++ b/pkg/R/GUS.R @@ -0,0 +1,74 @@ +#' Groundwater ubiquity score based on Gustafson (1989) +#' +#' 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)} +#' +#' @references Gustafson, David I. (1989) Groundwater ubiquity score: a simple +#' method for assessing pesticide leachability. _Environmental +#' toxicology and chemistry_ *8*(4) 339–57. +#' @inheritParams endpoint +#' @param chent If a chent is given with appropriate information present in its +#' chyaml field, this information is used, with defaults specified below. +#' @param 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. +#' @param 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). +#' @param 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. +#' @param degradation_value Which of the available degradation values should +#' be used? +#' @param 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. +#' @param degradation_aggregator Function for aggregating half-lives +#' @param sorption_aggregator Function for aggregation Koc values +#' @return A list with the DT50 and Koc used as well as the resulting score +#' of class GUS_result +#' @author Johannes Ranke +#' @export +GUS <- function(...) UseMethod("GUS") + +#' @rdname GUS +#' @export +GUS.numeric <- function(DT50, Koc) { + score <- log10(DT50) * (4 - log10(Koc)) + res <- list(DT50 = DT50, Koc = Koc, score = score) + class(res) <- "GUS_result" + return(res) +} + +#' @rdname GUS +#' @export +GUS.chent <- function(chent, lab_field = "laboratory", + aerobic = TRUE, + degradation_value = "DT50ref", + sorption_value = "Kfoc", + degradation_aggregator = geomean, + sorption_aggregator = geomean, + digits = 1) +{ + DT50 = soil_DT50(chent, lab_field = lab_field, redox = aerobic, + value = degradation_value, + aggregator = degradation_aggregator, signif = 5) + Koc = soil_Kfoc(chent, value = sorption_value, + aggregator = sorption_aggregator, signif = 5) + GUS.numeric(DT50, Koc) +} + +#' @export +print.GUS_result = function(x, ..., digits = 1) { + cat("GUS: ", round(x$score, digits = 1), "\n") + cat("calculated from DT50 ", x$DT50, " and Koc ", x$Koc, "\n") +} diff --git a/pkg/R/endpoint.R b/pkg/R/endpoint.R new file mode 100644 index 0000000..f9b9102 --- /dev/null +++ b/pkg/R/endpoint.R @@ -0,0 +1,102 @@ +#' Retrieve endpoint information from the chyaml field of a chent object +#' +#' R6 class objects of class \code{\link{chent}} represent chemical entities +#' and can hold a list of information loaded from a chemical yaml file in their +#' chyaml field. Such information is extracted and optionally aggregated by +#' this function. +#' +#' @import chents +#' @export +#' @param chent The \code{\link{chent}} object to get the information from +#' @param medium The medium for which information is sought +#' @param type The information type +#' @param lab_field If not NA, do we want laboratory or field endpoints +#' @param redox If not NA, are we looking for aerobic or anaerobic data +#' @param value The name of the value we want. The list given in the +#' usage section is not exclusive +#' @param aggregator The aggregator function. Can be mean, +#' \code{\link{geomean}}, or identity, for example. +#' @param signif How many significant digits do we want +#' @return The result from applying the aggregator function to +#' the values converted to a numeric vector, rounded to the +#' given number of significant digits, or, if raw = TRUE, +#' the values as a character value, retaining any implicit +#' information on precision that may be present. +#' +endpoint <- function(chent, + medium = "soil", + type = c("degradation", "sorption"), + lab_field = c(NA, "laboratory", "field"), + redox = c(NA, "aerobic", "anaerobic"), + value = c("DT50ref", "Kfoc", "N"), + aggregator = geomean, + raw = FALSE, + signif = 3) +{ + ep_list <- chent$chyaml[[medium]][[type]] + if (!is.na(lab_field[1])) { + ep_list <- ep_list[[lab_field]] + } + if (!is.na(redox[1])) { + ep_list <- ep_list[[redox]] + } + values <- ep_list$data[[value]] + if (raw) return(values) + else return(signif(aggregator(as.numeric(values)), signif)) +} + +#' Obtain soil DT50 +#' +#' @inheritParams endpoint +#' @export +soil_DT50 <- function(chent, aggregator = geomean, signif = 3, + lab_field = "laboratory", value = "DT50ref", + redox = "aerobic", raw = FALSE) { + ep <- endpoint(chent, medium = "soil", type = "degradation", + lab_field = "laboratory", redox = redox, + value = value, aggregator = aggregator, raw = raw) + return(ep) +} + +#' Obtain soil Kfoc +#' +#' @inheritParams endpoint +#' @export +soil_Kfoc <- function(chent, aggregator = geomean, signif = 3, + value = "Kfoc", raw = FALSE) { + ep <- endpoint(chent, medium = "soil", type = "sorption", + value = value, aggregator = aggregator, raw = raw) + return(ep) +} + +#' Obtain soil Freundlich exponent +#' +#' In pesticide fate modelling, this exponent is often called 1/n. Here, in +#' order to facilitate dealing with such data in R, it is called N. +#' +#' @inheritParams endpoint +#' @export +soil_N <- function(chent, aggregator = mean, signif = 3, raw = FALSE) { + ep <- endpoint(chent, medium = "soil", type = "sorption", + value = "N", aggregator = aggregator, raw = raw) + return(ep) +} + +#' Obtain soil sorption data +#' +#' @inheritParams endpoint +#' @param values The values to be returned +#' @param aggregators A named vector of aggregator functions to be used +#' @export +soil_sorption <- function(chent, values = c("Kfoc", "N"), + aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), + signif = rep(3, length(values)), + raw = FALSE) { + res <- sapply(values, + function(x) { + endpoint(chent, medium = "soil", type = "sorption", + value = x, aggregator = aggregators[[x]], raw = raw) + } + ) + return(res) +} diff --git a/pkg/man/FOCUS_GW_scenarios_2012.Rd b/pkg/man/FOCUS_GW_scenarios_2012.Rd index 5fcf4b1..5494d16 100644 --- a/pkg/man/FOCUS_GW_scenarios_2012.Rd +++ b/pkg/man/FOCUS_GW_scenarios_2012.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% 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} @@ -7,8 +7,8 @@ Currently, only a small subset of the soil definitions are provided. } \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. +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/pkg/man/GUS.Rd b/pkg/man/GUS.Rd new file mode 100644 index 0000000..5e2c936 --- /dev/null +++ b/pkg/man/GUS.Rd @@ -0,0 +1,70 @@ +% 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} +\title{Groundwater ubiquity score based on Gustafson (1989)} +\usage{ +GUS(...) + +\method{GUS}{numeric}(DT50, Koc) + +\method{GUS}{chent}(chent, lab_field = "laboratory", aerobic = TRUE, + degradation_value = "DT50ref", sorption_value = "Kfoc", + degradation_aggregator = geomean, sorption_aggregator = geomean, + digits = 1) +} +\arguments{ +\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{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{degradation_value}{Which of the available degradation values should +be used?} + +\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} +} +\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. _Environmental +toxicology and chemistry_ *8*(4) 339–57. +} + diff --git a/pkg/man/PEC_soil.Rd b/pkg/man/PEC_soil.Rd index 1ced69a..2433ecc 100644 --- a/pkg/man/PEC_soil.Rd +++ b/pkg/man/PEC_soil.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/PEC_soil.R \name{PEC_soil} \alias{PEC_soil} diff --git a/pkg/man/PEC_soil_product.Rd b/pkg/man/PEC_soil_product.Rd index 28cb5fd..b3afc8e 100644 --- a/pkg/man/PEC_soil_product.Rd +++ b/pkg/man/PEC_soil_product.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/PEC_soil.R \name{PEC_soil_product} \alias{PEC_soil_product} diff --git a/pkg/man/PEC_sw_drainage_UK_ini.Rd b/pkg/man/PEC_sw_drainage_UK_ini.Rd index 1715b39..c75b846 100644 --- a/pkg/man/PEC_sw_drainage_UK_ini.Rd +++ b/pkg/man/PEC_sw_drainage_UK_ini.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: 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} @@ -19,7 +19,7 @@ PEC_sw_drainage_UK_ini(rate, interception = 0, Koc, \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", +\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} diff --git a/pkg/man/PEC_sw_drift.Rd b/pkg/man/PEC_sw_drift.Rd index 99d3d65..c486831 100644 --- a/pkg/man/PEC_sw_drift.Rd +++ b/pkg/man/PEC_sw_drift.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% 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} diff --git a/pkg/man/PEC_sw_drift_ini.Rd b/pkg/man/PEC_sw_drift_ini.Rd index 994a07e..26ef40a 100644 --- a/pkg/man/PEC_sw_drift_ini.Rd +++ b/pkg/man/PEC_sw_drift_ini.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: 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} diff --git a/pkg/man/PEC_sw_sed.Rd b/pkg/man/PEC_sw_sed.Rd index 515562c..ecd57f5 100644 --- a/pkg/man/PEC_sw_sed.Rd +++ b/pkg/man/PEC_sw_sed.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% 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} diff --git a/pkg/man/SFO_actual_twa.Rd b/pkg/man/SFO_actual_twa.Rd index 7a9c2f1..573ea03 100644 --- a/pkg/man/SFO_actual_twa.Rd +++ b/pkg/man/SFO_actual_twa.Rd @@ -1,11 +1,11 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% 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, + Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, 18 December 2014, p. 251 } \usage{ diff --git a/pkg/man/SSLRC_mobility_classification.Rd b/pkg/man/SSLRC_mobility_classification.Rd index 0b441ae..04aa01d 100644 --- a/pkg/man/SSLRC_mobility_classification.Rd +++ b/pkg/man/SSLRC_mobility_classification.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% 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} @@ -14,7 +14,7 @@ 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 +This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website } \examples{ diff --git a/pkg/man/TOXSWA_cwa.Rd b/pkg/man/TOXSWA_cwa.Rd index b14f654..de87510 100644 --- a/pkg/man/TOXSWA_cwa.Rd +++ b/pkg/man/TOXSWA_cwa.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/TOXSWA_cwa.R \docType{class} \name{TOXSWA_cwa} @@ -26,7 +26,7 @@ Usually, an instance of this class will be generated by \code{\link{read.TOXSWA_ \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) +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}{ @@ -35,7 +35,7 @@ for the requested moving window sizes in days.} \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 + 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)}}{ diff --git a/pkg/man/drift_data_JKI.Rd b/pkg/man/drift_data_JKI.Rd index d7e6d3b..cc27985 100644 --- a/pkg/man/drift_data_JKI.Rd +++ b/pkg/man/drift_data_JKI.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/drift_data_JKI.R \docType{data} \name{drift_data_JKI} @@ -22,8 +22,11 @@ published by the German Julius-Kühn Institute (JKI). 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) @@ -34,13 +37,14 @@ as its licence is not clear. 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]) + 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/endpoint.Rd b/pkg/man/endpoint.Rd new file mode 100644 index 0000000..6c93022 --- /dev/null +++ b/pkg/man/endpoint.Rd @@ -0,0 +1,45 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/endpoint.R +\name{endpoint} +\alias{endpoint} +\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) +} +\arguments{ +\item{chent}{The \code{\link{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{signif}{How many significant digits do we want} +} +\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 \code{\link{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. +} + diff --git a/pkg/man/geomean.Rd b/pkg/man/geomean.Rd index be9f26a..ed82294 100644 --- a/pkg/man/geomean.Rd +++ b/pkg/man/geomean.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/geomean.R \name{geomean} \alias{geomean} diff --git a/pkg/man/pfm_degradation.Rd b/pkg/man/pfm_degradation.Rd index 04a692f..6e5ce03 100644 --- a/pkg/man/pfm_degradation.Rd +++ b/pkg/man/pfm_degradation.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/pfm_degradation.R \name{pfm_degradation} \alias{pfm_degradation} diff --git a/pkg/man/plot.TOXSWA_cwa.Rd b/pkg/man/plot.TOXSWA_cwa.Rd index 8a5ada4..fdc11f5 100644 --- a/pkg/man/plot.TOXSWA_cwa.Rd +++ b/pkg/man/plot.TOXSWA_cwa.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/TOXSWA_cwa.R \name{plot.TOXSWA_cwa} \alias{plot.TOXSWA_cwa} @@ -14,7 +14,7 @@ \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{xlab, ylab}{Labels for x and y axis.} \item{add}{Should we add to an existing plot?} diff --git a/pkg/man/read.TOXSWA_cwa.Rd b/pkg/man/read.TOXSWA_cwa.Rd index 5d97bb2..acc384c 100644 --- a/pkg/man/read.TOXSWA_cwa.Rd +++ b/pkg/man/read.TOXSWA_cwa.Rd @@ -1,4 +1,4 @@ -% Generated by roxygen2 (4.1.1): do not edit by hand +% Generated by roxygen2: do not edit by hand % Please edit documentation in R/TOXSWA_cwa.R \name{read.TOXSWA_cwa} \alias{read.TOXSWA_cwa} @@ -14,7 +14,7 @@ read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", \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 +\item{segment}{The segment for which the data should be read. Either "last", or the segment number.} \item{windows}{Numeric vector of width of moving windows in days, for calculating diff --git a/pkg/man/soil_DT50.Rd b/pkg/man/soil_DT50.Rd new file mode 100644 index 0000000..cbec234 --- /dev/null +++ b/pkg/man/soil_DT50.Rd @@ -0,0 +1,29 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/endpoint.R +\name{soil_DT50} +\alias{soil_DT50} +\title{Obtain soil DT50} +\usage{ +soil_DT50(chent, aggregator = geomean, signif = 3, + lab_field = "laboratory", value = "DT50ref", redox = "aerobic", + raw = FALSE) +} +\arguments{ +\item{chent}{The \code{\link{chent}} object to get the information from} + +\item{aggregator}{The aggregator function. Can be mean, +\code{\link{geomean}}, or identity, for example.} + +\item{signif}{How many significant digits do we want} + +\item{lab_field}{If not NA, do we want laboratory or field endpoints} + +\item{value}{The name of the value we want. The list given in the +usage section is not exclusive} + +\item{redox}{If not NA, are we looking for aerobic or anaerobic data} +} +\description{ +Obtain soil DT50 +} + diff --git a/pkg/man/soil_Kfoc.Rd b/pkg/man/soil_Kfoc.Rd new file mode 100644 index 0000000..3cc67cd --- /dev/null +++ b/pkg/man/soil_Kfoc.Rd @@ -0,0 +1,24 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/endpoint.R +\name{soil_Kfoc} +\alias{soil_Kfoc} +\title{Obtain soil Kfoc} +\usage{ +soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", + raw = FALSE) +} +\arguments{ +\item{chent}{The \code{\link{chent}} object to get the information from} + +\item{aggregator}{The aggregator function. Can be mean, +\code{\link{geomean}}, or identity, for example.} + +\item{signif}{How many significant digits do we want} + +\item{value}{The name of the value we want. The list given in the +usage section is not exclusive} +} +\description{ +Obtain soil Kfoc +} + diff --git a/pkg/man/soil_N.Rd b/pkg/man/soil_N.Rd new file mode 100644 index 0000000..9045ea8 --- /dev/null +++ b/pkg/man/soil_N.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/endpoint.R +\name{soil_N} +\alias{soil_N} +\title{Obtain soil Freundlich exponent} +\usage{ +soil_N(chent, aggregator = mean, signif = 3, raw = FALSE) +} +\arguments{ +\item{chent}{The \code{\link{chent}} object to get the information from} + +\item{aggregator}{The aggregator function. Can be mean, +\code{\link{geomean}}, or identity, for example.} + +\item{signif}{How many significant digits do we want} +} +\description{ +In pesticide fate modelling, this exponent is often called 1/n. Here, in +order to facilitate dealing with such data in R, it is called N. +} + diff --git a/pkg/man/soil_sorption.Rd b/pkg/man/soil_sorption.Rd new file mode 100644 index 0000000..41b8794 --- /dev/null +++ b/pkg/man/soil_sorption.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/endpoint.R +\name{soil_sorption} +\alias{soil_sorption} +\title{Obtain soil sorption data} +\usage{ +soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = + geomean, Koc = geomean, N = mean), signif = rep(3, length(values)), + raw = FALSE) +} +\arguments{ +\item{chent}{The \code{\link{chent}} object to get the information from} + +\item{values}{The values to be returned} + +\item{aggregators}{A named vector of aggregator functions to be used} + +\item{signif}{How many significant digits do we want} +} +\description{ +Obtain soil sorption data +} + |