Reorganise repository using standard package layout

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diff --git a/tests/testthat/test_PEC_soil.R b/tests/testthat/test_PEC_soil.R
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+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)
+})