diff options
| -rw-r--r-- | R/PEC_soil.R | 93 | ||||
| -rw-r--r-- | man/PEC_soil_mets.Rd | 24 |
2 files changed, 103 insertions, 14 deletions
diff --git a/R/PEC_soil.R b/R/PEC_soil.R index 091149c..541184f 100644 --- a/R/PEC_soil.R +++ b/R/PEC_soil.R @@ -1,4 +1,4 @@ -# Copyright (C) 2015,2016,2018 Johannes Ranke +# Copyright (C) 2015,2016,2018,2019 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package pfm @@ -84,6 +84,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_typ #' @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 t_act Time series for actual 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", @@ -158,6 +159,7 @@ PEC_soil <- function(rate, rate_units = "g/ha", interception = 0, FOMC = NA, Koc = NA, Kom = Koc / 1.724, t_avg = 0, + t_act = NULL, scenarios = c("default", "EFSA_2017", "EFSA_2015"), leaching = scenarios == "EFSA_2017", porewater = FALSE) @@ -336,23 +338,46 @@ PEC_soil <- function(rate, rate_units = "g/ha", interception = 0, # 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))) + if (is.null(t_act)) { + 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 + result[1, ] <- PEC_soil_sce_mod - for (i in seq_along(t_avg)) { - t_av_i <- t_avg[i] - k_avg <- f_T * k_ref # Leaching not taken into account, EFSA 2017 p. 43 - if (t_av_i > 0) { - # Equation 10 from p. 24 (EFSA 2015) - if (!is.na(FOMC[1])) { - result[i, ] <- PEC_soil_sce_mod * (FOMC[["beta"]])/(t_av_i * (1 - FOMC[["alpha"]])) * - ((t_av_i/FOMC[["beta"]] + 1)^(1 - FOMC[["alpha"]]) - 1) - } else { - result[i, ] <- PEC_soil_sce_mod/(t_av_i * k_avg) * (1 - exp(- k_avg * t_av_i)) # (A8) + for (i in seq_along(t_avg)) { + t_av_i <- t_avg[i] + k_avg <- f_T * k_ref # Leaching not taken into account, EFSA 2017 p. 43 + if (t_av_i > 0) { + # Equation 10 from p. 24 (EFSA 2015) + if (!is.na(FOMC[1])) { + result[i, ] <- PEC_soil_sce_mod * (FOMC[["beta"]])/(t_av_i * (1 - FOMC[["alpha"]])) * + ((t_av_i/FOMC[["beta"]] + 1)^(1 - FOMC[["alpha"]]) - 1) + } else { + result[i, ] <- PEC_soil_sce_mod/(t_av_i * k_avg) * (1 - exp(- k_avg * t_av_i)) # (A8) + } + } + } + } else { + if (!identical(t_avg, 0)) stop("Either t_act or t_avg can be specified") + result <- matrix(NA, ncol = n_sce, nrow = length(t_act), + dimnames = list(t_act = t_act, scenario = rownames(sce))) + + result[1, ] <- PEC_soil_sce_mod + + for (i in seq_along(t_act)) { + t_ac_i <- t_act[i] + k_act <- f_T * k_ref # Leaching not taken into account + if (t_ac_i > 0) { + # Equation 10 from p. 24 (EFSA 2015) + if (!is.na(FOMC[1])) { + result[i, ] <- + PEC_soil_sce_mod / ((t_ac_i/FOMC[["beta"]] + 1)^(FOMC[["alpha"]])) + } else { + result[i, ] <- PEC_soil_sce_mod * exp(- k_act * t_ac_i) + } } } + } return(result) @@ -377,6 +402,8 @@ PEC_FOMC_accu_rel <- function(n, interval, FOMC) { #' #' This was inspired by an answer on stackoverflow #' https://stackoverflow.com/a/717791 +#' @param x Three x coordinates +#' @param y Three y coordinates get_vertex <- function(x, y) { m <- cbind(x^2, x, 1) m_inv <- solve(m) @@ -388,3 +415,41 @@ get_vertex <- function(x, y) { yv = C - B**2 / (4*A) return(list(xv = xv, yv = yv, A = A, B = B, C = C)) } + +#' Calculate initial and accumulation PEC soil for a set of metabolites +#' +#' @param rate Application rate in units specified below +#' @param mw_parent The molecular weight of the parent compound +#' @param mets A dataframe with metabolite identifiers as rownames +#' and columns "mw", "occ" and "DT50" holding their molecular weight, +#' maximum occurrence in soil and their soil DT50 +#' @param interval The interval for accumulation calculations +#' @param ... Further arguments are passed to PEC_soil +#' @export +PEC_soil_mets <- function(rate, mw_parent, mets, interval = 365, ...) +{ + result <- matrix(NA, nrow = nrow(mets), ncol = 3, + dimnames = list(mets = rownames(mets), + PECs = c("Initial", + "Plateau", + "Accumulation"))) + result[, "Initial"] <- sapply(rownames(mets), + function(x) { + PEC_soil(mets[x, "occ"] * (mets[x, "mw"] / mw_parent) * rate, + interval = NA, ...) + } + ) + + result[, "Accumulation"] <- sapply(rownames(mets), + function(x) { + PEC_soil(mets[x, "occ"] * (mets[x, "mw"] / mw_parent) * rate, + DT50 = mets[x, "DT50"], + interval = interval, ...) + } + ) + + result[, "Plateau"] <- result[, "Accumulation"] - + result[, "Initial"] + + return(result) +} diff --git a/man/PEC_soil_mets.Rd b/man/PEC_soil_mets.Rd new file mode 100644 index 0000000..637f1c0 --- /dev/null +++ b/man/PEC_soil_mets.Rd @@ -0,0 +1,24 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/PEC_soil.R +\name{PEC_soil_mets} +\alias{PEC_soil_mets} +\title{Calculate initial and accumulation PEC soil for a set of metabolites} +\usage{ +PEC_soil_mets(rate, mw_parent, mets, interval = 365, ...) +} +\arguments{ +\item{rate}{Application rate in units specified below} + +\item{mw_parent}{The molecular weight of the parent compound} + +\item{mets}{A dataframe with metabolite identifiers as rownames +and columns "mw", "occ" and "DT50" holding their molecular weight, +maximum occurrence in soil and their soil DT50} + +\item{interval}{The interval for accumulation calculations} + +\item{...}{Further arguments are passed to PEC_soil} +} +\description{ +Calculate initial and accumulation PEC soil for a set of metabolites +} |