1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
|
# 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)
}
if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_type", "TP_identifier"))
#' Calculate predicted environmental concentrations in soil for a product
#'
#' Calculates long term accumulation PEC values
#'
#' @param product An object of class pp
#' @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 tillage_depth Periodic (see interval) deeper mixing in cm
#' @param interval Period of the deeper mixing, defaults to 365, which is a year if
#' rate units are in days
#' @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 A data frame with compound names, and initial, plateau maximum, plateau minimum (background)
#' and long term maximum predicted concentrations in soil
#' @export PEC_soil_product
#' @author Johannes Ranke
PEC_soil_product <- function(product, rate, rate_units = "L/ha", interception = 0,
mixing_depth = 5, tillage_depth = 20,
interval = 365,
bulk_density = 1.5,
PEC_units = "mg/kg") {
rate_units = match.arg(rate_units)
PEC_units = match.arg(PEC_units)
if (product$density_units != "g/L") stop("Product density other than g/L not supported")
if (product$concentration_units != "g/L") {
stop("Active ingredient concentration units other than g/L not supported")
}
results <- data.frame(compound = character(0), initial = numeric(0),
plateau_max = numeric(0), plateau_min = numeric(0),
long_term_max = numeric(0),
stringsAsFactors = FALSE)
for (ai_name in names(product$ais)) {
ai <- product$ais[[ai_name]]
ai_rate <- rate * product$concentrations[ai_name]
ini <- PEC_soil(ai_rate,
interception = interception, mixing_depth = mixing_depth,
bulk_density = bulk_density)
results[ai_name, "compound"] <- ai$identifier
results[ai_name, "initial"] <- ini
ini_tillage <- ini * mixing_depth / tillage_depth
DT50 <- subset(ai$soil_degradation_endpoints, destination == "PECsoil")$DT50
if (length(DT50) > 1) stop("More than one PECsoil DT50 for", ai_name)
if (length(DT50) > 0) {
if (!is.na(DT50)) {
k <- log(2) / DT50
plateau_max <- ini_tillage / (1 - exp( - k * interval))
plateau_min <- plateau_max * exp( - k * interval)
long_term_max <- plateau_min + ini
results[ai_name, c("plateau_max", "plateau_min", "long_term_max")] <-
c(plateau_max, plateau_min, long_term_max)
}
}
for (TP_name in names(ai$TPs)) {
TP <- ai$TPs[[TP_name]]
max_occurrence = max(subset(ai$transformations,
grepl("soil", study_type) &
TP_identifier == TP$identifier, max_occurrence))
TP_rate <- ai_rate * TP$mw / ai$mw * max_occurrence
ini <- PEC_soil(TP_rate, interception = interception, mixing_depth = mixing_depth,
bulk_density = bulk_density)
results[TP_name, "compound"] <- TP$identifier
results[TP_name, "initial"] <- ini
ini_tillage <- ini * mixing_depth / tillage_depth
DT50 <- subset(TP$soil_degradation_endpoints, destination == "PECsoil")$DT50
if (length(DT50) > 1) stop("More than one PECsoil DT50 for", TP_name)
if (length(DT50) > 0) {
if (!is.na(DT50)) {
k <- log(2) / DT50
plateau_max <- ini_tillage / (1 - exp( - k * interval))
plateau_min <- plateau_max * exp( - k * interval)
results[TP_name, c("plateau_max", "plateau_min")] <- c(plateau_max, plateau_min)
long_term_max <- plateau_min + ini
results[TP_name, c("plateau_max", "plateau_min", "long_term_max")] <-
c(plateau_max, plateau_min, long_term_max)
}
}
}
}
return(results)
}
|
