diff options
Diffstat (limited to 'pkg/R')
| -rw-r--r-- | pkg/R/GUS.R | 29 | ||||
| -rw-r--r-- | pkg/R/endpoint.R | 3 |
2 files changed, 21 insertions, 11 deletions
diff --git a/pkg/R/GUS.R b/pkg/R/GUS.R index 2690f50..8a20561 100644 --- a/pkg/R/GUS.R +++ b/pkg/R/GUS.R @@ -5,11 +5,9 @@ #' \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. +#' method for assessing pesticide leachability. \emph{Environmental +#' toxicology and chemistry} \bold{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 @@ -20,13 +18,16 @@ #' 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 chent If a chent is given with appropriate information present in its +#' chyaml field, this information is used, with defaults specified below. +#' @param degradation_value Which of the available degradation values should +#' be used? #' @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 redox Aerobic or anaerobic degradation data #' @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 @@ -34,6 +35,8 @@ #' 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 +#' @param ... Included in the generic to allow for further arguments later. Therefore +#' this also had to be added to the specific methods. #' @return A list with the DT50 and Koc used as well as the resulting score #' of class GUS_result #' @author Johannes Ranke @@ -42,7 +45,7 @@ GUS <- function(...) UseMethod("GUS") #' @rdname GUS #' @export -GUS.numeric <- function(DT50, Koc) { +GUS.numeric <- function(DT50, Koc, ...) { score <- log10(DT50) * (4 - log10(Koc)) res <- list(DT50 = DT50, Koc = Koc, score = score) class(res) <- "GUS_result" @@ -51,15 +54,16 @@ GUS.numeric <- function(DT50, Koc) { #' @rdname GUS #' @export -GUS.chent <- function(chent, lab_field = "laboratory", - aerobic = TRUE, +GUS.chent <- function(chent, degradation_value = "DT50ref", + lab_field = "laboratory", + redox = "aerobic", sorption_value = "Kfoc", degradation_aggregator = geomean, sorption_aggregator = geomean, - digits = 1) + ...) { - DT50 = soil_DT50(chent, lab_field = lab_field, redox = aerobic, + DT50 = soil_DT50(chent, lab_field = lab_field, redox = redox, value = degradation_value, aggregator = degradation_aggregator, signif = 5) Koc = soil_Kfoc(chent, value = sorption_value, @@ -67,7 +71,10 @@ GUS.chent <- function(chent, lab_field = "laboratory", GUS.numeric(DT50, Koc) } +#' @rdname GUS #' @export +#' @param x An object of class GUS_result to be printed +#' @param digits The number of digits used in the print method 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 index f9b9102..6cc253a 100644 --- a/pkg/R/endpoint.R +++ b/pkg/R/endpoint.R @@ -16,6 +16,9 @@ #' usage section is not exclusive #' @param aggregator The aggregator function. Can be mean, #' \code{\link{geomean}}, or identity, for example. +#' @param raw Should the number(s) be returned as stored in the chent +#' object (could be a character value) to retain original information +#' about precision? #' @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 |