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# 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 <http://www.gnu.org/licenses/>
#' 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")
}
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