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 --- pkg/R/GUS.R | 98 ------------------------------------------------------------- 1 file changed, 98 deletions(-) delete mode 100644 pkg/R/GUS.R (limited to 'pkg/R/GUS.R') diff --git a/pkg/R/GUS.R b/pkg/R/GUS.R deleted file mode 100644 index 4a6532d..0000000 --- a/pkg/R/GUS.R +++ /dev/null @@ -1,98 +0,0 @@ -# Copyright (C) 2015 Johannes Ranke -# Contact: jranke@uni-bremen.de -# This file is part of the R package pfm - -# This program is free software: you can redistribute it and/or modify it under -# the terms of the GNU General Public License as published by the Free Software -# Foundation, either version 3 of the License, or (at your option) any later -# version. - -# This program is distributed in the hope that it will be useful, but WITHOUT -# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS -# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more -# details. - -# You should have received a copy of the GNU General Public License along with -# this program. If not, see - -#' 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. \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 -#' 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 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 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 -#' 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 -#' @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 -#' @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, - degradation_value = "DT50ref", - lab_field = "laboratory", - redox = "aerobic", - sorption_value = "Kfoc", - degradation_aggregator = geomean, - sorption_aggregator = geomean, - ...) -{ - 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, - aggregator = sorption_aggregator, signif = 5) - 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") -} -- cgit v1.2.1