Reorganise repository using standard package layout

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diff --git a/R/PEC_sw_drainage_UK.R b/R/PEC_sw_drainage_UK.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/>
+
+#' Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method
+#'
+#' This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet
+#' published on the CRC website
+#'
+#' @param rate Application rate in g/ha
+#' @param interception The fraction of the application rate that does not reach the soil
+#' @param Koc The sorption coefficient normalised to organic carbon in L/kg
+#' @param latest_application Latest application date, formatted as e.g. "01 July"
+#' @param soil_DT50 Soil degradation half-life, if SFO kinetics are to be used
+#' @param model The soil degradation model to be used. Either one of "FOMC",
+#'   "DFOP", "HS", or "IORE", or an mkinmod object
+#' @param model_parms A named numeric vector containing the model parameters
+#' @return The predicted concentration in surface water in µg/L
+#' @export
+#' @author Johannes Ranke
+#' @examples
+#' PEC_sw_drainage_UK(150, Koc = 100)
+PEC_sw_drainage_UK <- function(rate, interception = 0, Koc,
+                                   latest_application = NULL, soil_DT50 = NULL,
+                                   model = NULL, model_parms = NULL)
+{
+  percentage_lost <- SSLRC_mobility_classification(Koc)[[2]]
+  amount_available <- rate * (1 - interception) # g/ha
+
+  if (!missing(latest_application)) {
+    lct <- Sys.getlocale("LC_TIME")
+    tmp <- Sys.setlocale("LC_TIME", "C")
+    latest <- as.Date(paste(latest_application, "1999"), "%d %b %Y")
+    tmp <- Sys.setlocale("LC_TIME", lct)
+    degradation_time <- as.numeric(difftime(as.Date("1999-10-01"), units = "days", latest))
+    if (!missing(soil_DT50)) {
+      k = log(2)/soil_DT50
+      as.Date(paste(latest_application, "1999"), "%d %B %Y")
+
+      amount_available <- amount_available * exp(-k * degradation_time)
+      if (!missing(model)) stop("You already supplied a soil_DT50 value, implying SFO kinetics")
+    }
+    if (!missing(model)) {
+      fraction_left <- pfm_degradation(model, parms = model_parms, 
+                                       times = degradation_time)[1, "parent"]
+      amount_available <- fraction_left * amount_available
+    }
+  } 
+
+  volume = 130000 # L/ha
+  PEC = 1e6 * (percentage_lost/100) * amount_available / volume
+  return(PEC)
+}