Add simplest PEC soil calcs, use testthat

1 files changed, 45 insertions, 0 deletions

diff --git a/pkg/R/PEC_soil.R b/pkg/R/PEC_soil.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 predicted environmental concentrations in soil
+#'
+#' This is a basic, vectorised form of a simple calculation of a contaminant
+#' concentration in bulk soil based on complete, instantaneous mixing.
+#'
+#' @param rate Application rate in units specified below
+#' @param rate_units Defaults to g/ha
+#' @param interception The fraction of the application rate that does not reach the soil
+#' @param mixing_depth Mixing depth in cm
+#' @param bulk_density Bulk density of the soil. Defaults to 1.5 kg/L, or 1500 kg/m3
+#' @param PEC_units Requested units for the calculated PEC. Only mg/kg currently supported
+#' @return The predicted concentration in soil
+#' @export
+#' @author Johannes Ranke
+#' @examples
+#' PEC_soil(100, interception = 0.25)
+PEC_soil <- function(rate, rate_units = "g/ha", interception = 0,
+                     mixing_depth = 5, bulk_density = 1.5,
+                     PEC_units = "mg/kg")
+{
+  rate_to_soil = (1 - interception) * rate
+  rate_units = match.arg(rate_units)
+  PEC_units = match.arg(PEC_units)
+  soil_volume = 100 * 100 * (mixing_depth/100)   # in m3
+  soil_mass = soil_volume * bulk_density * 1000  # in kg
+  PEC_soil = rate_to_soil * 1000 / soil_mass     # in mg/kg
+  return(PEC_soil)
+}