diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/GUS.R | 1 | ||||
| -rw-r--r-- | R/TOXSWA_cwa.R | 56 | ||||
| -rw-r--r-- | R/drift_data_JKI.R | 4 | ||||
| -rw-r--r-- | R/endpoint.R | 4 |
4 files changed, 37 insertions, 28 deletions
@@ -7,7 +7,6 @@ #' @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. -#' @inheritParams endpoint #' @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 diff --git a/R/TOXSWA_cwa.R b/R/TOXSWA_cwa.R index 42cdd35..6521349 100644 --- a/R/TOXSWA_cwa.R +++ b/R/TOXSWA_cwa.R @@ -142,35 +142,24 @@ plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t #' R6 class for holding TOXSWA water concentration data and 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}}. +#' @description An R6 class for holding TOXSWA water concentration (cwa) data +#' and some associated statistics. like maximum moving window average +#' concentrations, and dataframes holding the events exceeding specified +#' thresholds. Usually, an instance of this class will be generated +#' by \code{\link{read.TOXSWA_cwa}}. #' -#' @docType class -#' @importFrom R6 R6Class #' @export #' @format An \code{\link{R6Class}} generator object. -#' @field filename Length one character vector. -#' @field basedir Length one character vector. +#' @field filename Length one character vector holding the filename. +#' @field basedir Length one character vector holding the directory where the file came from. +#' @field zipfile If not null, giving the path to the zip file from which the file was read. #' @field segment Length one integer, specifying for which segment the cwa data were read. +#' @field substance The TOXSWA name of the substance. #' @field cwas Dataframe holding the concentrations. #' @field events List of dataframes holding the event statistics for each threshold. #' @field 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", @@ -180,7 +169,6 @@ plot.TOXSWA_cwa <- function(x, time_column = c("datetime", "t", "t_firstjan", "t #' H_sw_R1_stream$moving_windows(c(7, 21)) #' print(H_sw_R1_stream) #' @keywords data - TOXSWA_cwa <- R6Class("TOXSWA_cwa", public = list( filename = NULL, @@ -191,6 +179,15 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa", cwas = NULL, windows = NULL, events = list(), + + #' @description + #' Create a TOXSWA_cwa object from a file + #' @param filename The filename + #' @param basedir The directory to look in + #' @param zipfile Optional path to a zipfile holding the file + #' @param segment Either "last" or the number of the segment for which to read the data + #' @param substance The TOXSWA substance name (for TOXSWA 4 or higher) + #' @param total Should total concentrations be read in? If FALSE, free concentrations are read initialize = function(filename, basedir, zipfile = NULL, segment = "last", substance = "parent", total = FALSE) { self$filename <- filename @@ -327,6 +324,12 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa", } } }, + + #' @description + #' Add to the `windows` field described above. + #' @param windows Window sizes in days + #' @param total If TRUE, the total concentration including the amount adsorbed to + #' suspended matter will be used. moving_windows = function(windows, total = FALSE) { window_names = paste(windows, "days") n = length(window_names) @@ -350,6 +353,14 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa", } invisible(self) }, + + #' @description + #' Populate a datataframe with event information for the specified + #' threshold value. The resulting dataframe is stored in the `events` + #' field of the object. + #' @param thresholds Threshold values in µg/L. + #' @param total If TRUE, the total concentration including the amount adsorbed to + #' suspended matter will be used. get_events = function(thresholds, total = FALSE) { if (missing(thresholds)) { stop("You need to specify at least one threshold concentration in \u03bcg/L") @@ -397,6 +408,9 @@ TOXSWA_cwa <- R6Class("TOXSWA_cwa", } invisible(self) }, + + #' @description + #' Print a `TOXSWA_cwa` object print = function() { cat("<TOXSWA_cwa> data from file", self$filename, "segment", self$segment, "\n") print(head(self$cwas)) diff --git a/R/drift_data_JKI.R b/R/drift_data_JKI.R index e44079d..3b02f43 100644 --- a/R/drift_data_JKI.R +++ b/R/drift_data_JKI.R @@ -30,7 +30,7 @@ #' from #' http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html #' on 2015-06-11 -#' +#' #' Rautmann, D., Streloke, M and Winkler, R (2001) New basic drift values in #' the authorization procedure for plant protection products Mitt. Biol. #' Bundesanst. Land- Forstwirtsch. 383, 133-141 @@ -82,6 +82,6 @@ #' save(drift_data_JKI, file = "data/drift_data_JKI.RData") #' } #' -#' # And this is the resulting data +#' # And these are the resulting data #' drift_data_JKI NULL diff --git a/R/endpoint.R b/R/endpoint.R index 56a314b..08856f9 100644 --- a/R/endpoint.R +++ b/R/endpoint.R @@ -55,7 +55,6 @@ endpoint <- function(chent, else return(signif(aggregator(as.numeric(values)), signif)) } -#' @inheritParams endpoint #' @rdname endpoint #' @export soil_DT50 <- function(chent, aggregator = geomean, signif = 3, @@ -68,7 +67,6 @@ soil_DT50 <- function(chent, aggregator = geomean, signif = 3, return(ep) } -#' @inheritParams endpoint #' @rdname endpoint #' @export soil_Kfoc <- function(chent, aggregator = geomean, signif = 3, @@ -79,7 +77,6 @@ soil_Kfoc <- function(chent, aggregator = geomean, signif = 3, return(ep) } -#' @inheritParams endpoint #' @rdname endpoint #' @export soil_N <- function(chent, aggregator = mean, signif = 3, raw = FALSE) { @@ -89,7 +86,6 @@ soil_N <- function(chent, aggregator = mean, signif = 3, raw = FALSE) { return(ep) } -#' @inheritParams endpoint #' @rdname endpoint #' @param values The values to be returned #' @param aggregators A named vector of aggregator functions to be used |