library(pfm)
library(testthat)
context("Simple PEC soil calculations")
test_that("PEC_soil calculates correctly", {
# Application of 100 g/ha gives 0.133 mg/kg under default assumptions
expect_equal(as.numeric(PEC_soil(100)), 0.1 * 4/3)
# or 0.1 mg/kg assuming 25% interception
expect_equal(as.numeric(PEC_soil(100, interception = 0.25)), 0.1)
# Mixing depth of 1 cm gives five-fold PEC
expect_equal(as.numeric(PEC_soil(100, interception = 0.25, mixing_depth = 1)), 0.5)
})
test_that("Tier 1 PEC soil example for Pesticide A in EFSA guidance from 2017 can be reproduced", {
# Calculate total soil concentrations for tier 1 scenarios
# Leaching is calculated from the 5 cm layer to be able to reproduce the
# results from the guidance
results_pfm_2017 <- PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
scenarios = "EFSA_2017", Kom = 1000,
leaching_depth = 5)
# From Table G.2, p. 92
results_guidance_2017 <- matrix(c(18.6, 13.0, 9.9, 18.2, 12.7, 9.6),
ncol = 3, byrow = TRUE)
dimnames(results_guidance_2017) <- list(t_avg = c(0, 21),
scenario = c("CTN", "CTC", "CTS"))
expect_equal(round(results_pfm_2017, 1)[1, ], results_guidance_2017[1, ])
# I do not get the same TWA concentrations as in the 2017 guidance on p. 92
# Calculate porewater soil concentrations for tier 1 scenarios
results_pfm_pw_2017 <- PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21),
Kom = 1000, scenarios = "EFSA_2017", porewater = TRUE,
leaching_depth = 5)
# From Table I.5, p. 80
results_guidance_pw_2017 <- matrix(c(0.48, 0.60, 0.91, 0.47, 0.58, 0.86),
ncol = 3, byrow = TRUE)
dimnames(results_guidance_pw_2017) <- list(t_avg = c(0, 21),
scenario = c("CLN", "CLC", "CLS"))
expect_equal(round(results_pfm_pw_2017, 2)[1, ], results_guidance_pw_2017[1, ])
# Here I also do not get the same TWA concentrations as in the guidance p. 92
})
test_that("Tier 1 PEC soil example for Pesticide A in EFSA guidance from 2015 can be reproduced", {
# Calculate total soil concentrations for tier 1 scenarios
results_pfm_2015 <- PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
scenarios = "EFSA_2015")
# From Table I.5, p. 80
results_guidance_2015 <- matrix(c(22.0, 11.5, 9.1, 21.8, 11.4, 9.0),
ncol = 3, byrow = TRUE)
dimnames(results_guidance_2015) <- list(t_avg = c(0, 21),
scenario = c("CTN", "CTC", "CTS"))
expect_equal(round(results_pfm_2015, 1), results_guidance_2015)
# Calculate porewater soil concentrations for tier 1 scenarios
results_pfm_pw_2015 <- PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21),
Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE)
# From Table I.5, p. 80
results_guidance_pw_2015 <- matrix(c(0.76, 0.67, 0.91, 0.75, 0.66, 0.90),
ncol = 3, byrow = TRUE)
dimnames(results_guidance_pw_2015) <- list(t_avg = c(0, 21),
scenario = c("CLN", "CLC", "CLS"))
expect_equal(round(results_pfm_pw_2015, 2), results_guidance_pw_2015)
})
test_that("Tier 1 PEC soil example for Pesticide F in EFSA guidance from 2015 can be reproduced", {
# Parent F
# Calculate total and porewater soil concentrations for tier 1 scenarios
results_pfm <- PEC_soil(1000, interval = 365, DT50 = 25, t_avg = c(0, 21),
scenarios = "EFSA_2015")
results_pfm_pw <- PEC_soil(1000, interval = 365, DT50 = 25, t_av = c(0, 21),
Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE)
# From Table I.14, p. 88
results_guidance <- matrix(c(12.8, 7.7, 6.6, 11.8, 6.8, 5.7),
ncol = 3, byrow = TRUE)
results_guidance_pw <- matrix(c(0.50, 0.46, 0.71, 0.45, 0.41, 0.60),
ncol = 3, byrow = TRUE)
# Skip checking dimnames by using expect_equivalent()
expect_equivalent(round(results_pfm, 1), results_guidance)
expect_equivalent(round(results_pfm_pw, 2), results_guidance_pw)
# Metabolite M1
# Calculate total and porewater soil concentrations for tier 1 scenarios
# Relative molar mass is 200/300, formation fraction is 0.7
results_pfm <- PEC_soil(200/300 * 0.7 * 1000, interval = 365, DT50 = 100, t_avg = c(0, 21),
scenarios = "EFSA_2015")
results_pfm_pw <- PEC_soil(200/300 * 0.7 * 1000, interval = 365, DT50 = 100, t_av = c(0, 21),
Kom = 10, scenarios = "EFSA_2015", porewater = TRUE)
# From Table I.15, p. 88
results_guidance <- matrix(c(7.27, 4.08, 3.38, 7.12, 3.97, 3.26),
ncol = 3, byrow = TRUE)
results_guidance_pw <- matrix(c(12.93, 10.42, 11.66, 12.58, 10.09, 11.15),
ncol = 3, byrow = TRUE)
# Skip checking dimnames by using expect_equivalent()
expect_equivalent(round(results_pfm, 2), results_guidance)
expect_equivalent(round(results_pfm_pw, 2), results_guidance_pw)
# 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)
# From Table I.16, p. 89
results_guidance <- matrix(c(5.13, 2.69, 2.13, 5.08, 2.66, 2.10),
ncol = 3, byrow = TRUE)
results_guidance_pw <- matrix(c(1.61, 1.39, 1.80, 1.60, 1.37, 1.77),
ncol = 3, byrow = TRUE)
# Skip checking dimnames by using expect_equivalent()
expect_equivalent(round(results_pfm, 2), results_guidance)
expect_equivalent(round(results_pfm_pw, 2), results_guidance_pw)
})
test_that("Long term FOMC PEC soil from ESCAPE can be reproduced", {
# Application of 100 g/ha with 25% interception and FOMC degradation type a
fomc_50_a <- PEC_soil(100, interception = 0.25, FOMC = c(alpha = 1, beta = 10),
interval = 365, tillage_depth = 20, n_periods = 50)
expect_warning(
fomc_long_a <- PEC_soil(100, interception = 0.25, FOMC = c(alpha = 1, beta = 10),
interval = 365, tillage_depth = 20),
"pseudo-plateau"
)
# Application of 100 g/ha with 25% interception and FOMC degradation type b
# The long term PEC is much lower than when adding FOMC curves for 50 years
fomc_50_b <- PEC_soil(100, interception = 0.25, FOMC = c(alpha = 0.5, beta = 20),
interval = 365, tillage_depth = 20, n_periods = 50)
expect_warning(
fomc_long_b <- PEC_soil(100, interception = 0.25, FOMC = c(alpha = 0.5, beta = 20),
interval = 365, tillage_depth = 20),
"pseudo-plateau"
)
expect_true(fomc_50_b > fomc_long_b)
# The benchmark results were obtained with ESCAPE
expect_equivalent(round(fomc_long_b, 4), 0.1424)
})
