Reorganise repository using standard package layout

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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")
-}