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authorJohannes Ranke <jranke@uni-bremen.de>2018-07-10 17:57:33 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2018-07-10 17:59:19 +0200
commitcb3695dd434b3a3273217fb22c5ffb86065ae96d (patch)
treec37fbe68273e25d2741c0845665458357ac05450 /R
parentc4c3ca282c6aadca82e392692ae4100fec1dd834 (diff)
EFSA PEC soil guidance from 2017
- Implement the new guidance as well as possible - Maintenance work addressing CRAN checks
Diffstat (limited to 'R')
-rw-r--r--R/PEC_soil.R213
-rw-r--r--R/PEC_sw_exposit_runoff.R1
-rw-r--r--R/soil_scenario_data_EFSA_2015.R8
-rw-r--r--R/soil_scenario_data_EFSA_2017.R20
4 files changed, 192 insertions, 50 deletions
diff --git a/R/PEC_soil.R b/R/PEC_soil.R
index 15ccc90..1227f6a 100644
--- a/R/PEC_soil.R
+++ b/R/PEC_soil.R
@@ -17,23 +17,34 @@
# Register global variables
if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_type", "TP_identifier",
- "soil_scenario_data_EFSA_2015"))
+ "soil_scenario_data_EFSA_2015",
+ "soil_scenario_data_EFSA_2017", "bottom"))
#' 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
+#' 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).
-#'
+#' the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012
+#' and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).
+#'
#' 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.
-#'
+#' opinion cited below (EFSA 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.
-#'
+#' guidance (2017, p. 14/15) can easily be calculated.
+#' @note While time weighted average (TWA) concentrations given in the examples
+#' from the EFSA guidance from 2015 (p. 80) are be reproduced, this is not
+#' true for the TWA concentrations given for the same example in the EFSA guidance
+#' from 2017 (p. 92).
+#' @note According to the EFSA guidance (EFSA, 2017, p. 43), leaching should be
+#' taken into account for the EFSA 2017 scenarios, using the evaluation depth
+#' (here mixing depth) as the depth of the layer from which leaching takes
+#' place. However, as the amount leaching below the evaluation depth
+#' (often 5 cm) will partly be mixed back during tillage, the default in this function
+#' is to use the tillage depth for the calculation of the leaching rate.
#' @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
@@ -49,7 +60,17 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_typ
#' @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
+#' @param leaching_depth EFSA (2017) uses the mixing depth (ecotoxicological
+#' evaluation depth) to calculate leaching for annual crops where tillage
+#' takes place. By default, losses from the layer down to the tillage
+#' depth are taken into account in this implementation.
+#' @param cultivation Does mechanical cultivation in the sense of EFSA (2017)
+#' take place, i.e. twice a year to a depth of 5 cm? Ignored for scenarios
+#' other than EFSA_2017
+#' @param crop Ignored for scenarios other than EFSA_2017. Only annual crops
+#' are supported when these scenarios are used. Only crops with a single cropping
+#' cycle per year are currently supported.
+#' @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
@@ -65,6 +86,8 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_typ
#' '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 leaching Should leaching be taken into account? The default is FALSE,
+#' except when the EFSA_2017 scenarios 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
@@ -76,23 +99,38 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_typ
#' 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) 2017) 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{15}(10) 4982
+#' doi:10.2903/j.efsa.2017.4982
+#'
#' 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. 92 of the EFSA guidance (2017)
+#' # Note that TWA concentrations differ from the ones given in the guidance
+#' # for an unknown reason (the values from EFSA (2015) can be reproduced).
+#' PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
+#' Kom = 1000, scenarios = "EFSA_2017")
+#' PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21),
+#' Kom = 1000, scenarios = "EFSA_2017", porewater = TRUE)
+#'
#' # 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
@@ -103,34 +141,97 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("destination", "study_typ
#' Kom = 100, scenarios = "EFSA_2015", porewater = TRUE)
PEC_soil <- function(rate, rate_units = "g/ha", interception = 0,
- mixing_depth = 5,
+ mixing_depth = 5,
PEC_units = "mg/kg", PEC_pw_units = "mg/L",
interval = NA, n_periods = Inf,
- tillage_depth = 20,
- chent = NA,
- DT50 = NA,
+ tillage_depth = 20,
+ leaching_depth = tillage_depth,
+ crop = "annual",
+ cultivation = FALSE,
+ chent = NA,
+ DT50 = NA,
Koc = NA, Kom = Koc / 1.724,
t_avg = 0,
- scenarios = c("default", "EFSA_2015"),
+ scenarios = c("default", "EFSA_2017", "EFSA_2015"),
+ leaching = scenarios == "EFSA_2017",
porewater = FALSE)
{
+ # Comments with equation numbers in parentheses refer to
+ # the numbering in the EFSA guidance from 2017, appendix A
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,
+ if (scenarios == "EFSA_2017") {
+ if (crop != "annual") stop("Only annual crops are currently supported")
+ if (cultivation) stop("Permanent crops with mechanical cultivation are currently not supported")
+ }
+ sce <- switch(scenarios,
default = data.frame(rho = 1.5, T_arr = NA, theta_fc = 0.2, f_om = 1.724 * 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, ]
+ EFSA_2015 = if (porewater) soil_scenario_data_EFSA_2015[4:6, ]
+ else soil_scenario_data_EFSA_2015[1:3, ],
+ EFSA_2017 = if (porewater) soil_scenario_data_EFSA_2017[4:6, ]
+ else soil_scenario_data_EFSA_2017[1:3, ]
)
n_sce = nrow(sce)
soil_volume = 100 * 100 * (mixing_depth/100) # in m3
soil_mass = soil_volume * sce$rho * 1000 # in kg
+ # In EFSA (2017), f_om is depth dependent for permanent crops
+ # For annual crops, the correction factor is 1 (uniform f_om is
+ # assumed)
+ mixing_depth_string <- paste(mixing_depth, "cm")
+ tillage_depth_string <- paste(tillage_depth, "cm")
+ if (scenarios == "EFSA_2017" & crop != "annual") {
+ # Correction factors f_f_om with depth according to EFSA 2017, p. 15
+ f_f_om_depth = data.frame(
+ depth = c("0-5", "5-10", "10-20", "20-30"),
+ bottom = c(5, 10, 20, 30),
+ thickness = c(5, 5, 10, 10),
+ f_f_om_no_cultivation = c(1.95, 1.30, 0.76, 0.62),
+ f_f_om_cultivation = c(1.50, 1.20, 0.90, 0.75))
+ # Averages for the 0-5 cm and 0-20 cm layers
+ f_f_om_layer = data.frame(
+ layer = c("0-5", "0-20"),
+ f_f_om_no_cultivation = c(1.95, (5 * 1.95 + 5 * 1.3 + 10 * 0.76)/20),
+ f_f_om_cultivation = c(1.50, (5 * 1.5 + 5 * 1.2 + 10 * 0.9)/20))
+ # The resulting mean value for 0-20 cm and no cultivation of 1.1925 is
+ # consistent with the value of 1.19 given in Table B.4 on p. 54 of the
+ # 2017 EFSA guidance
+
+ f_f_om_average <- function(depth, cultivation) {
+ rownames(f_f_om_layer) = paste(f_f_om_layer$layer, "cm")
+ if (depth %in% c(5, 20)) {
+ if (cultivation) {
+ return(f_f_om_layer[paste0("0-", depth, " cm"), "f_f_om_cultivation"])
+ } else {
+ return(f_f_om_layer[paste0("0-", depth, " cm"), "f_f_om_no_cultivation"])
+ }
+ } else {
+ stop("Depths other than 5 and 20 cm are not supported when using EFSA 2017 scenarios for permanent crops")
+ }
+ }
+
+ # For the loss via leaching, the equilibrium and therefore the f_om at the
+ # bottom of the layer is probably most relevant. Unfortunately this is not
+ # clarified in the guidance.
+ f_f_om_bottom <- function(depth, cultivation) {
+ bottom_depth <- depth # rename to avoid confusion when subsetting
+ if (cultivation) {
+ f_f_om <- subset(f_f_om_depth, bottom == bottom_depth)$f_f_om_cultivation
+ } else {
+ f_f_om <- subset(f_f_om_depth, bottom == bottom_depth)$f_f_om_no_cultivation
+ }
+ return(f_f_om)
+ }
+ } else {
+ f_f_om_average <- f_f_om_bottom <- function(depth, cultivation) 1
+ }
+
# 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
+ PEC_soil_ini = rate_to_soil * 1000 / soil_mass # in mg/kg (A1)
# Decide which DT50 to take, or set degradation to zero if no DT50 available
if (is.na(DT50) & is(chent, "chent")) {
@@ -142,26 +243,56 @@ PEC_soil <- function(rate, rate_units = "g/ha", interception = 0,
if (length(DT50) > 1) stop("More than one PECsoil DT50 in chent object")
if (length(DT50) == 0) DT50 <- Inf
}
- k = log(2)/DT50
+ k_ref = log(2)/DT50 # (A5)
# 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$T_arr + 273.15) - 1/293.15)))
+ f_T = ifelse(sce$T_arr == 0,
+ 0, # (A4b)
+ exp(- (65.4 / 0.008314) * (1/(sce$T_arr + 273.15) - 1/293.15))) # (A4a)
}
- # X is the fraction left after one period (EFSA guidance p. 23)
- X = exp(- k * f_T * interval)
-
+ # Define Kom if needed
+ if (leaching | porewater) {
+ # If Kom is not specified, try to get K(f)oc
+ if (is.na(Kom)) {
+ # If Koc not specified, try to get K(f)oc from chent
+ if (is.na(Koc) & is(chent, "chent")) {
+ Koc <- soil_Kfoc(chent)
+ } else {
+ stop("No Kom information specified")
+ }
+ Kom <- Koc / 1.724
+ }
+ }
+
+ if (leaching) {
+ leaching_depth_string <- paste(leaching_depth, "cm")
+ f_q <- c("1 cm" = 0.8, "2.5 cm" = 0.75, "5 cm" = 0.7, "20 cm" = 0.5) # EFSA 2017 p. 54
+ if (leaching_depth_string %in% names(f_q)) {
+ q_mm_year = f_q[leaching_depth_string] * sce$prec # Irrigation at tier 1? I have not found values for Tier 1
+ q_dm_day = q_mm_year / (100 * 365)
+ leaching_depth_dm <- leaching_depth / 10
+
+ k_leach = q_dm_day/(leaching_depth_dm * (sce$theta_fc + sce$rho * f_f_om_average(leaching_depth, cultivation) * sce$f_om * Kom))
+ } else {
+ stop("Leaching can not be calculated, because f_q for this leaching depth is undefined")
+ }
+ } else {
+ k_leach = 0
+ }
+
+ # X is the fraction left after one period (EFSA 2017 guidance p. 23)
+ X = exp(- (k_ref * f_T + k_leach) * interval) # (A3)
+
# f_accu is the fraction left after n periods (X + X^2 + ...)
- f_accu = 0
+ f_accu = 0
if (!is.na(interval)) {
if (n_periods == Inf) {
- f_accu = X/(1 - X)
+ f_accu = X/(1 - X) # part of (A2)
} else {
for (i in 1:n_periods) {
f_accu = f_accu + X^i
@@ -171,25 +302,14 @@ PEC_soil <- function(rate, rate_units = "g/ha", interception = 0,
f_tillage = mixing_depth / tillage_depth
- PEC_background = f_accu * f_tillage * PEC_soil_ini
+ PEC_background = f_accu * f_tillage * PEC_soil_ini # (A2)
- PEC_soil = (1 + f_accu * f_tillage) * PEC_soil_ini
+ PEC_soil = PEC_soil_ini + PEC_background # (A6)
# Get porewater PEC if requested
if (porewater) {
- # If Kom is not specified, try to get K(f)oc
- if (is.na(Kom)) {
- # If Koc not specified, try to get K(f)oc from chent
- if (is.na(Koc) & is(chent, "chent")) {
- Koc <- soil_Kfoc(chent)
- }
- Kom <- Koc / 1.724
- }
-
- if (is.na(Kom)) stop("No Kom information specified")
-
- PEC_soil = PEC_soil/((sce$theta_fc/sce$rho) + sce$f_om * Kom)
+ PEC_soil = PEC_soil/((sce$theta_fc/sce$rho) + f_f_om_average(mixing_depth, cultivation) * sce$f_om * Kom) # (A7)
}
# Scenario adjustment factors
@@ -200,14 +320,15 @@ PEC_soil <- function(rate, rate_units = "g/ha", interception = 0,
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]
+ 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)
- result[i, ] <- PEC_soil_sce_mod/(t_av_i * f_T * k) * (1 - exp(- f_T * k * t_av_i))
+ result[i, ] <- PEC_soil_sce_mod/(t_av_i * k_avg) * (1 - exp(- k_avg * t_av_i)) # (A8)
}
}
diff --git a/R/PEC_sw_exposit_runoff.R b/R/PEC_sw_exposit_runoff.R
index f56b8f8..733f621 100644
--- a/R/PEC_sw_exposit_runoff.R
+++ b/R/PEC_sw_exposit_runoff.R
@@ -6,6 +6,7 @@
#' @format A data frame with percentage values for the dissolved fraction and the fraction
#' bound to eroding particles, with Koc classes used as row names
#' \describe{
+#' \item{Koc_lower_bound}{The lower bound of the Koc class}
#' \item{dissolved}{The percentage of the applied substance transferred to an
#' adjacent water body in the dissolved phase}
#' \item{bound}{The percentage of the applied substance transferred to an
diff --git a/R/soil_scenario_data_EFSA_2015.R b/R/soil_scenario_data_EFSA_2015.R
index fb096bc..660cafe 100644
--- a/R/soil_scenario_data_EFSA_2015.R
+++ b/R/soil_scenario_data_EFSA_2015.R
@@ -10,10 +10,10 @@
#' e.g. CTN for the Northern scenario for the total concentration in soil. Columns are
#' mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.
#' @source 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
+#' 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
#' @keywords datasets
#' @examples
#' \dontrun{
diff --git a/R/soil_scenario_data_EFSA_2017.R b/R/soil_scenario_data_EFSA_2017.R
new file mode 100644
index 0000000..79ee15f
--- /dev/null
+++ b/R/soil_scenario_data_EFSA_2017.R
@@ -0,0 +1,20 @@
+#' Properties of the predefined scenarios from the EFSA guidance from 2017
+#'
+#' Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the
+#' concentration in soil as given in the EFSA guidance (2017, p. 14/15). Also, the
+#' scenario and model adjustment factors from p. 16 and p. 18 are included.
+#'
+#' @name soil_scenario_data_EFSA_2017
+#' @docType data
+#' @format A data frame with one row for each scenario. Row names are the scenario codes,
+#' e.g. CTN for the Northern scenario for the total concentration in soil. Columns are
+#' mostly self-explanatory. \code{rho} is the dry bulk density of the top soil.
+#' @source EFSA (European Food Safety Authority) (2017)
+#' 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{15}(10) 4982
+#' doi:10.2903/j.efsa.2017.4982
+#' @keywords datasets
+#' @examples
+#' soil_scenario_data_EFSA_2017
+NULL

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