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Diffstat (limited to 'pkg/R/PEC_soil.R')
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diff --git a/pkg/R/PEC_soil.R b/pkg/R/PEC_soil.R deleted file mode 100644 index 0263e47..0000000 --- a/pkg/R/PEC_soil.R +++ /dev/null @@ -1,215 +0,0 @@ -# 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/> - -# Register global variables -if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_type", "TP_identifier", - "soil_scenario_data_EFSA_2015")) - -#' Calculate predicted environmental concentrations in soil -#' -#' This is a basic calculation of a contaminant concentration in bulk soil -#' based on complete, instantaneous mixing. If an interval is given, an -#' attempt is made at calculating a long term maximum concentration using -#' the concepts layed out for example in the PPR panel opinion (EFSA 2012). -#' -#' This assumes that the complete load to soil during the time specified by -#' 'interval' (typically 365 days) is dosed at once. As in the PPR panel -#' opinion cited below (PPR panel 2012), only temperature correction using the -#' Arrhenius equation is performed. -#' -#' Total soil and porewater PEC values for the scenarios as defined in the EFSA -#' guidance (2015, p. 13) can easily be calculated. -#' -#' @note If temperature information is available in the selected scenarios, as -#' e.g. in the EFSA scenarios, the DT50 for groundwater modelling -#' (destination 'PECgw') is taken from the chent object, otherwise the DT50 -#' with destination 'PECsoil'. -#' @importFrom methods is -#' @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 interval Period of the deeper mixing, defaults to 365, which is a year if -#' rate units are in days -#' @param n_periods Number of periods to be considered for long term PEC calculations -#' @param PEC_units Requested units for the calculated PEC. Only mg/kg currently supported -#' @param PEC_pw_units Only mg/L currently supported -#' @param tillage_depth Periodic (see interval) deeper mixing in cm -#' @param chent An optional chent object holding substance specific information. Can -#' also be a name for the substance as a character string -#' @param DT50 If specified, overrides soil DT50 endpoints from a chent object -#' If DT50 is not specified here and not available from the chent object, zero -#' degradation is assumed -#' @param Koc If specified, overrides Koc endpoints from a chent object -#' @param Kom Calculated from Koc by default, but can explicitly be specified -#' as Kom here -#' @param t_avg Averaging times for time weighted average concentrations -#' @param scenarios If this is 'default', the DT50 will be used without correction -#' and soil properties as specified in the REACH guidance (R.16, Table -#' R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", -#' the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when -#' 'chents' is specified, the DegT50 with destination 'PECgw' will be used), -#' and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also -#' model and scenario adjustment factors from the EFSA guidance are used. -#' @param porewater Should equilibrium porewater concentrations be estimated -#' based on Kom and the organic carbon fraction of the soil instead of total -#' soil concentrations? Based on equation (7) given in the PPR panel opinion -#' (EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, -#' p. 13). -#' @return The predicted concentration in soil -#' @references EFSA Panel on Plant Protection Products and their Residues (2012) -#' Scientific Opinion on the science behind the guidance for scenario -#' selection and scenario parameterisation for predicting environmental -#' concentrations of plant protection products in soil. \emph{EFSA Journal} -#' \bold{10}(2) 2562, doi:10.2903/j.efsa.2012.2562 -#' -#' EFSA (European Food Safety Authority) (2015) EFSA guidance document for -#' predicting environmental concentrations of active substances of plant -#' protection products and transformation products of these active substances -#' in soil. \emph{EFSA Journal} \bold{13}(4) 4093 -#' doi:10.2903/j.efsa.2015.4093 -#' @author Johannes Ranke -#' @export -#' @examples -#' PEC_soil(100, interception = 0.25) -#' -#' # This is example 1 starting at p. 79 of the EFSA guidance (2015) -#' PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), -#' scenarios = "EFSA_2015") -#' PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), -#' Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) -#' -#' # The following is from example 4 starting at p. 85 of the EFSA guidance (2015) -#' # Metabolite M2 -#' # Calculate total and porewater soil concentrations for tier 1 scenarios -#' # Relative molar mass is 100/300, formation fraction is 0.7 * 1 -#' results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), -#' scenarios = "EFSA_2015") -#' results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), -#' Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) - -PEC_soil <- function(rate, rate_units = "g/ha", interception = 0, - mixing_depth = 5, - PEC_units = "mg/kg", PEC_pw_units = "mg/L", - interval = NA, n_periods = Inf, - tillage_depth = 20, - chent = NA, - DT50 = NA, - Koc = NA, Kom = Koc / 1.724, - t_avg = 0, - scenarios = c("default", "EFSA_2015"), - porewater = FALSE) -{ - rate_to_soil = (1 - interception) * rate - rate_units = match.arg(rate_units) - PEC_units = match.arg(PEC_units) - scenarios = match.arg(scenarios) - sce <- switch(scenarios, - default = data.frame(rho = 1.5, T_arr = NA, theta_fc = 0.2, f_oc = 0.02, - f_sce = 1, f_mod = 1, row.names = "default"), - EFSA_2015 = if (porewater) soil_scenario_data_EFSA_2015[4:6, ] - else soil_scenario_data_EFSA_2015[1:3, ] - ) - n_sce = nrow(sce) - - soil_volume = 100 * 100 * (mixing_depth/100) # in m3 - soil_mass = soil_volume * sce$rho * 1000 # in kg - - # The following is C_T,ini from EFSA 2012, p. 22, but potentially with interception > 0 - PEC_soil_ini = rate_to_soil * 1000 / soil_mass # in mg/kg - - # Decide which DT50 to take, or set degradation to zero if no DT50 available - if (is.na(DT50) & is(chent, "chent")) { - if (all(is.na(sce$T_arr))) { # No temperature correction - DT50 <- subset(chent$soil_degradation_endpoints, destination == "PECsoil")$DT50 - } else { - DT50 <- subset(chent$soil_degradation_endpoints, destination == "PECgw")$DT50 - } - if (length(DT50) > 1) stop("More than one PECsoil DT50 in chent object") - if (length(DT50) == 0) DT50 <- Inf - } - k = log(2)/DT50 - - # Temperature correction of degradation (accumulation) - if (all(is.na(sce$T_arr))) { # No temperature correction - f_T = 1 - } else { - # Temperature correction as in EFSA 2012 p. 23 - f_T = ifelse(sce$T_arr == 0, - 0, - exp(- (65.4 / 0.008314) * (1/(sce$T_arr + 273.15) - 1/293.15))) - } - - # X is the fraction left after one period (EFSA guidance p. 23) - X = exp(- k * f_T * interval) - - # f_accu is the fraction left after n periods (X + X^2 + ...) - f_accu = 0 - if (!is.na(interval)) { - if (n_periods == Inf) { - f_accu = X/(1 - X) - } else { - for (i in 1:n_periods) { - f_accu = f_accu + X^i - } - } - } - - f_tillage = mixing_depth / tillage_depth - - PEC_background = f_accu * f_tillage * PEC_soil_ini - - PEC_soil = (1 + f_accu * f_tillage) * PEC_soil_ini - - # Get porewater PEC if requested - if (porewater) { - - # If Kom is not specified, try to get K(f)oc - if (is.na(Kom)) { - # If Koc not specified, try to get K(f)oc from chent - if (is.na(Koc) & is(chent, "chent")) { - Koc <- soil_Kfoc(chent) - } - Kom <- Koc / 1.724 - } - - if (is.na(Kom)) stop("No Kom information specified") - - PEC_soil = PEC_soil/((sce$theta_fc/sce$rho) + sce$f_om * Kom) - } - - # Scenario adjustment factors - PEC_soil_sce = PEC_soil * sce$f_sce - - # Model adjustment factors - PEC_soil_sce_mod = PEC_soil_sce * sce$f_mod - - result <- matrix(NA, ncol = n_sce, nrow = length(t_avg), - dimnames = list(t_avg = t_avg, scenario = rownames(sce))) - - result[1, ] <- PEC_soil_sce_mod - - for (i in seq_along(t_avg)) { - t_av_i <- t_avg[i] - if (t_av_i > 0) { - # Equation 10 from p. 24 (EFSA 2015) - result[i, ] <- PEC_soil_sce_mod/(t_av_i * f_T * k) * (1 - exp(- f_T * k * t_av_i)) - } - } - - return(result) -} |