Reorganise repository using standard package layout

1 files changed, 0 insertions, 95 deletions

diff --git a/pkg/tests/testthat/test_PEC_soil.R b/pkg/tests/testthat/test_PEC_soil.R
deleted file mode 100644
index 0661a52..0000000
--- a/pkg/tests/testthat/test_PEC_soil.R
+++ /dev/null
@@ -1,95 +0,0 @@
-library(pfm)
-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 can be reproduced", {
-  # Calculate total soil concentrations for tier 1 scenarios
-  results_pfm <- PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
-                          scenarios = "EFSA_2015")
-
-  # From Table I.5, p. 80
-  results_guidance <- matrix(c(22.0, 11.5, 9.1, 21.8, 11.4, 9.0), 
-                             ncol = 3, byrow = TRUE)
-  dimnames(results_guidance) <- list(t_avg = c(0, 21), 
-                                     scenario = c("CTN", "CTC", "CTS"))
-
-
-  expect_equal(round(results_pfm, 1), results_guidance)
-
-  # Calculate porewater soil concentrations for tier 1 scenarios
-  results_pfm_pw <- 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 <- matrix(c(0.76, 0.67, 0.91, 0.75, 0.66, 0.90), 
-                                ncol = 3, byrow = TRUE)
-  dimnames(results_guidance_pw) <- list(t_avg = c(0, 21), 
-                                        scenario = c("CLN", "CLC", "CLS"))
-
-  expect_equal(round(results_pfm_pw, 2), results_guidance_pw)
-})
-
-test_that("Tier 1 PEC soil example for Pesticide F in EFSA guidance 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)
-})