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authorJohannes Ranke <jranke@uni-bremen.de>2015-06-11 16:57:43 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-06-11 16:57:43 +0200
commitdd803b191062925eda830543236836e7822fd884 (patch)
treefc10d2c230b0e3b4fd777bf3124127d90921a0c4
parent09cf970942706cfab43753d298b42e8d85216d80 (diff)
Add UK tier 1 drainage PEC calculations
-rw-r--r--pkg/NAMESPACE2
-rw-r--r--pkg/R/PEC_sw_drainage_UK.R53
-rw-r--r--pkg/R/SSLRC_mobility_classification.R42
-rw-r--r--pkg/man/PEC_sw_drainage_UK_ini.Rd30
-rw-r--r--pkg/man/SSLRC_mobility_classification.Rd26
-rw-r--r--pkg/tests/testthat/test_UK_drainage.R33
6 files changed, 186 insertions, 0 deletions
diff --git a/pkg/NAMESPACE b/pkg/NAMESPACE
index 2d95da4..771739a 100644
--- a/pkg/NAMESPACE
+++ b/pkg/NAMESPACE
@@ -2,9 +2,11 @@
S3method(plot,TOXSWA_cwa)
export(PEC_soil)
+export(PEC_sw_drainage_UK_ini)
export(PEC_sw_drift)
export(PEC_sw_drift_ini)
export(SFO_actual_twa)
+export(SSLRC_mobility_classification)
export(TOXSWA_cwa)
export(geomean)
export(pfm_degradation)
diff --git a/pkg/R/PEC_sw_drainage_UK.R b/pkg/R/PEC_sw_drainage_UK.R
new file mode 100644
index 0000000..03c56c0
--- /dev/null
+++ b/pkg/R/PEC_sw_drainage_UK.R
@@ -0,0 +1,53 @@
+# 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 initial predicted environmental concentrations in surface water due to drainage using the UK method
+#'
+#' This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet
+#' published on the CRC website
+#'
+#' @param rate Application rate in g/ha
+#' @param interception The fraction of the application rate that does not reach the soil
+#' @param Koc The sorption coefficient normalised to organic carbon in L/kg
+#' @return The predicted concentration in surface water in µg/L
+#' @export
+#' @author Johannes Ranke
+#' @examples
+#' PEC_sw_drainage_UK_ini(100)
+PEC_sw_drainage_UK_ini <- function(rate, interception = 0, Koc,
+ latest_application = NULL, soil_DT50 = NULL)
+{
+ percentage_lost <- SSLRC_mobility_classification(Koc)[[2]]
+ amount_available <- rate * (1 - interception) # g/ha
+
+ if (!missing(latest_application)) {
+ if (missing(soil_DT50)) stop("You need to supply a soil DT50 value")
+ k = log(2)/soil_DT50
+ as.Date(paste(latest_application, "1999"), "%d %B %Y")
+
+ lct <- Sys.getlocale("LC_TIME")
+ tmp <- Sys.setlocale("LC_TIME", "C")
+ latest <- as.Date(paste(latest_application, "1999"), "%d %b %Y")
+ tmp <- Sys.setlocale("LC_TIME", lct)
+ degradation_time <- as.numeric(difftime(as.Date("1999-10-01"), units = "days", latest))
+ amount_available <- amount_available * exp(-k * degradation_time)
+ }
+
+ volume = 130000 # L/ha
+ PEC = 1e6 * (percentage_lost/100) * amount_available / volume
+ return(PEC)
+}
diff --git a/pkg/R/SSLRC_mobility_classification.R b/pkg/R/SSLRC_mobility_classification.R
new file mode 100644
index 0000000..e04d472
--- /dev/null
+++ b/pkg/R/SSLRC_mobility_classification.R
@@ -0,0 +1,42 @@
+# 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/>
+
+#' Determine the SSLRC mobility classification for a chemical substance from its Koc
+#'
+#' This implements the method specified in the UK data requirements handbook and was
+#' checked against the spreadsheet published on the CRC website
+#'
+#' @param Koc The sorption coefficient normalised to organic carbon in L/kg
+#' @return A list containing the classification and the percentage of the
+#' compound transported per 10 mm drain water
+#' @export
+#' @author Johannes Ranke
+#' @examples
+#' SSLRC_mobility_classification(Koc)
+SSLRC_mobility_classification <- function(Koc)
+{
+ if (!is.numeric(Koc) | length(Koc) != 1) stop("Please give a single number")
+ result <- list("Non mobile", 0.01)
+ if (Koc < 4000) result <- list("Slightly mobile", 0.02)
+ if (Koc < 1000) result <- list("Slightly mobile", 0.5)
+ if (Koc < 500) result <- list("Moderately mobile", 0.7)
+ if (Koc < 75) result <- list("Mobile", 1.9)
+ if (Koc < 15) result <- list("Very mobile", 1.9)
+ names(result) <- c("Mobility classification",
+ "Percentage drained per mm of drain water")
+ return(result)
+}
diff --git a/pkg/man/PEC_sw_drainage_UK_ini.Rd b/pkg/man/PEC_sw_drainage_UK_ini.Rd
new file mode 100644
index 0000000..c39a5c9
--- /dev/null
+++ b/pkg/man/PEC_sw_drainage_UK_ini.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Please edit documentation in R/PEC_sw_drainage_UK.R
+\name{PEC_sw_drainage_UK_ini}
+\alias{PEC_sw_drainage_UK_ini}
+\title{Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method}
+\usage{
+PEC_sw_drainage_UK_ini(rate, interception = 0, Koc,
+ latest_application = NULL, soil_DT50 = NULL)
+}
+\arguments{
+\item{rate}{Application rate in g/ha}
+
+\item{interception}{The fraction of the application rate that does not reach the soil}
+
+\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg}
+}
+\value{
+The predicted concentration in surface water in µg/L
+}
+\description{
+This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet
+published on the CRC website
+}
+\examples{
+PEC_sw_drainage_UK_ini(100)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/pkg/man/SSLRC_mobility_classification.Rd b/pkg/man/SSLRC_mobility_classification.Rd
new file mode 100644
index 0000000..a1bb413
--- /dev/null
+++ b/pkg/man/SSLRC_mobility_classification.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2 (4.1.0.9001): do not edit by hand
+% Please edit documentation in R/SSLRC_mobility_classification.R
+\name{SSLRC_mobility_classification}
+\alias{SSLRC_mobility_classification}
+\title{Determine the SSLRC mobility classification for a chemical substance from its Koc}
+\usage{
+SSLRC_mobility_classification(Koc)
+}
+\arguments{
+\item{Koc}{The sorption coefficient normalised to organic carbon in L/kg}
+}
+\value{
+A list containing the classification and the percentage of the
+ compound transported per 10 mm drain water
+}
+\description{
+This implements the method specified in the UK data requirements handbook and was
+checked against the spreadsheet published on the CRC website
+}
+\examples{
+SSLRC_mobility_classification(Koc)
+}
+\author{
+Johannes Ranke
+}
+
diff --git a/pkg/tests/testthat/test_UK_drainage.R b/pkg/tests/testthat/test_UK_drainage.R
new file mode 100644
index 0000000..3a57db8
--- /dev/null
+++ b/pkg/tests/testthat/test_UK_drainage.R
@@ -0,0 +1,33 @@
+library(pfm)
+context("UK drainage PEC calculations")
+
+test_that("The mobility classification and the drained percentage are correct", {
+ # Expected results are from the CRD drainage calculator, retrieved 2015-06-11
+
+ expect_equivalent(SSLRC_mobility_classification(1), list("Very mobile", 1.9))
+ expect_equivalent(SSLRC_mobility_classification(15), list("Mobile", 1.9))
+ expect_equivalent(SSLRC_mobility_classification(30), list("Mobile", 1.9))
+ expect_equivalent(SSLRC_mobility_classification(74.9), list("Mobile", 1.9))
+ expect_equivalent(SSLRC_mobility_classification(75), list("Moderately mobile", 0.7))
+ expect_equivalent(SSLRC_mobility_classification(100), list("Moderately mobile", 0.7))
+ expect_equivalent(SSLRC_mobility_classification(800), list("Slightly mobile", 0.5))
+ expect_equivalent(SSLRC_mobility_classification(2000), list("Slightly mobile", 0.02))
+ expect_equivalent(SSLRC_mobility_classification(5000), list("Non mobile", 0.01))
+})
+
+test_that("UK drainflow PECs are correct", {
+ # Expected results are from the CRD drainage calculator, retrieved 2015-06-11, except
+ # for the third example from the data requirements handbook
+
+ # This is the first example calculation from the data requirements handbook, where they give
+ # 8.07 µg/L as the result (obviously a rounding error).
+ expect_equal(round(PEC_sw_drainage_UK_ini(150, interception = 0, Koc = 100), 4), 8.0769)
+
+ # This is the second example calculation from the data requirements handbook
+ expect_equal(round(PEC_sw_drainage_UK_ini(90, interception = 0, Koc = 10), 4), 13.1538)
+
+ # This is the third example calculation from the data requirements handbook,
+ expect_equal(round(PEC_sw_drainage_UK_ini(60, interception = 0.5, Koc = 550,
+ latest_application = "01 July",
+ soil_DT50 = 200), 2), 0.84)
+})

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