From 12a31f4c130c551f82232d9ef7dfb608bd52c53f Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 27 Sep 2016 23:00:48 +0200
Subject: Reorganise repository using standard package layout

---
 R/GUS.R | 98 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 98 insertions(+)
 create mode 100644 R/GUS.R

(limited to 'R/GUS.R')

diff --git a/R/GUS.R b/R/GUS.R
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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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