Reorganise repository using standard package layout

12 files changed, 262 insertions, 0 deletions

diff --git a/tests/testthat/EXSW2_R1_stream_printed.txt b/tests/testthat/EXSW2_R1_stream_printed.txt
new file mode 100644
index 0000000..60bb5ac
--- /dev/null
+++ b/tests/testthat/EXSW2_R1_stream_printed.txt
@@ -0,0 +1,10 @@
+<TOXSWA_cwa> data from file 3.out segment 20 
+             datetime     t t_firstjan t_rel_to_max cwa_mug_per_L
+1 1978-10-01 00:00:00 0.000   273.0000      -55.083             0
+2 1978-10-01 01:00:00 0.042   273.0417      -55.041             0
+3 1978-10-01 02:00:00 0.083   273.0833      -55.000             0
+4 1978-10-01 03:00:00 0.125   273.1250      -54.958             0
+5 1978-10-01 04:00:00 0.167   273.1667      -54.916             0
+6 1978-10-01 05:00:00 0.208   273.2083      -54.875             0
+Moving window analysis
+NULL
diff --git a/tests/testthat/H_sw_D4_pond_printed.txt b/tests/testthat/H_sw_D4_pond_printed.txt
new file mode 100644
index 0000000..5730be6
--- /dev/null
+++ b/tests/testthat/H_sw_D4_pond_printed.txt
@@ -0,0 +1,10 @@
+<TOXSWA_cwa> data from file 00001p_pa.cwa segment 1 
+             datetime     t t_firstjan t_rel_to_max cwa_mug_per_L cwa_tot_mug_per_L
+1 1985-01-01 00:00:00 0.000 0.00000000     -396.167    0.00000000        0.00000000
+2 1985-01-01 01:00:00 0.042 0.04166667     -396.125    0.08323064        0.08323716
+3 1985-01-01 02:00:00 0.083 0.08333333     -396.084    0.16626900        0.16628210
+4 1985-01-01 03:00:00 0.125 0.12500000     -396.042    0.24911240        0.24913190
+5 1985-01-01 04:00:00 0.167 0.16666667     -396.000    0.33172050        0.33174650
+6 1985-01-01 05:00:00 0.208 0.20833333     -395.959    0.41401430        0.41404670
+Moving window analysis
+NULL
diff --git a/tests/testthat/H_sw_R1_stream_events.rds b/tests/testthat/H_sw_R1_stream_events.rds
new file mode 100644
index 0000000..ba6557b
--- /dev/null
+++ b/tests/testthat/H_sw_R1_stream_events.rds
diff --git a/tests/testthat/H_sw_R1_stream_printed.txt b/tests/testthat/H_sw_R1_stream_printed.txt
new file mode 100644
index 0000000..572ad6d
--- /dev/null
+++ b/tests/testthat/H_sw_R1_stream_printed.txt
@@ -0,0 +1,10 @@
+<TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 
+               datetime     t t_firstjan t_rel_to_max cwa_mug_per_L cwa_tot_mug_per_L
+20  1978-10-01 00:00:00 0.000   273.0000      -55.333             0                 0
+40  1978-10-01 01:00:00 0.042   273.0417      -55.291             0                 0
+60  1978-10-01 02:00:00 0.083   273.0833      -55.250             0                 0
+80  1978-10-01 03:00:00 0.125   273.1250      -55.208             0                 0
+100 1978-10-01 04:00:00 0.167   273.1667      -55.166             0                 0
+120 1978-10-01 05:00:00 0.208   273.2083      -55.125             0                 0
+Moving window analysis
+NULL
diff --git a/tests/testthat/H_sw_R1_stream_windows.rds b/tests/testthat/H_sw_R1_stream_windows.rds
new file mode 100644
index 0000000..2531189
--- /dev/null
+++ b/tests/testthat/H_sw_R1_stream_windows.rds
diff --git a/tests/testthat/test_PEC_sed.R b/tests/testthat/test_PEC_sed.R
new file mode 100644
index 0000000..443f789
--- /dev/null
+++ b/tests/testthat/test_PEC_sed.R
@@ -0,0 +1,9 @@
+context("Simple PEC sediment calculations")
+
+test_that("PEC_sw_sed calculates correctly using the percentage method", {
+  # Application of 100 g/ha, 1 m spray drift distance (2.77% drift input), 50% in sediment,
+  # default assumptions of CRD spreadsheet (5 cm sediment depth, 1.3 kg/L sediment density)
+  # Reference value calculated with CRD spreadsheet
+  PEC_sw_100_1_m <- PEC_sw_drift(100, distances = 1)
+  expect_equivalent(round(PEC_sw_sed(PEC_sw_100_1_m, percentage = 50), 3), 2.131)
+})
diff --git a/tests/testthat/test_PEC_soil.R b/tests/testthat/test_PEC_soil.R
new file mode 100644
index 0000000..0661a52
--- /dev/null
+++ b/tests/testthat/test_PEC_soil.R
@@ -0,0 +1,95 @@
+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)
+})
diff --git a/tests/testthat/test_PEC_sw_drift.R b/tests/testthat/test_PEC_sw_drift.R
new file mode 100644
index 0000000..d09d578
--- /dev/null
+++ b/tests/testthat/test_PEC_sw_drift.R
@@ -0,0 +1,15 @@
+library(pfm)
+context("Simple PEC surface water calculations with drift entry")
+
+test_that("PEC_sw_drift gives the same results as the CRD PEC calculator", {
+  # One application of 30 g/ha to field crops calculated with UK PEC calculator published by CRD
+  expect_equal(round(PEC_sw_drift(30), 3), 
+               c('1 m' = 0.277, '5 m' = 0.057, '10 m' = 0.029, '20 m' = 0.015))
+
+  # 7 applications of 30 g/ha to field crops calculated with UK PEC calculator, initial PEC
+  expect_equal(round(PEC_sw_drift(30, 7), 3), 
+               c('1 m' = 0.161, '5 m' = 0.033, '10 m' = 0.017, '20 m' = 0.008))
+
+  # 4 applications of 30 g/ha to late fruit crops calculated with UK PEC calculator published by CRD (uses different drift values from SANCO aquatic guidance)
+  #expect_equal(round(PEC_sw_drift(30, 4, crop = "Obstbau spät", distances = c(3, 20, 50)), 3), c('3 m' = 1.101, '20 m' = 0.080, '50 m' = 0.013))
+})
diff --git a/tests/testthat/test_SFO_actual_twa.R b/tests/testthat/test_SFO_actual_twa.R
new file mode 100644
index 0000000..b0a5537
--- /dev/null
+++ b/tests/testthat/test_SFO_actual_twa.R
@@ -0,0 +1,13 @@
+library(pfm)
+context("Actual and time weighted average concentrations for SFO kinetics")
+
+test_that("SFO_actual_twa calculates correctly", {
+  test_times <- c(0, 1, 7, 21, 42)
+  # This was calculated with the CRD spreadsheet for multiple applications
+  reference <- data.frame(
+    actual = c(10, 9.330, 6.156, 2.333, 0.544),
+    twa = c(NaN, 9.661, 7.923, 5.267, 3.248),
+    row.names = test_times)
+  result <- round(10 * SFO_actual_twa(10, times = test_times), 3)
+  expect_equal(result, reference)
+})
diff --git a/tests/testthat/test_TOXSWA_cwa.R b/tests/testthat/test_TOXSWA_cwa.R
new file mode 100644
index 0000000..7c9a73c
--- /dev/null
+++ b/tests/testthat/test_TOXSWA_cwa.R
@@ -0,0 +1,56 @@
+library(pfm)
+context("Read and analyse TOXSWA cwa files")
+
+zipfile_test = system.file("testdata/SwashProjects.zip", package = "pfm")
+basedir_test = "SwashProjects/project_H_sw/TOXSWA"
+
+H_sw_D4_pond  <- read.TOXSWA_cwa("00001p_pa.cwa",
+                                 basedir = basedir_test,
+                                 zipfile = zipfile_test)
+
+H_sw_R1_stream  <- read.TOXSWA_cwa("00003s_pa.cwa",
+                                 basedir = basedir_test,
+                                 zipfile = zipfile_test)
+
+basedir_test_2 = "SwashProjects/Project_1/TOXSWA"
+
+EXSW2_R1_stream  <- read.TOXSWA_cwa("3.out",
+                                 basedir = basedir_test_2,
+                                 zipfile = zipfile_test)
+
+
+
+test_that("TOXSWA cwa file is correctly read and printed", {
+
+  # This was the setting when printing the output into text files
+  options(width = 100)
+
+  # Most content of the R6 object is at least partially printed
+
+  H_sw_D4_pond_printed <- capture.output(print(H_sw_D4_pond))
+
+  expect_equal(H_sw_D4_pond_printed, readLines("H_sw_D4_pond_printed.txt"))
+
+  H_sw_R1_stream_printed <- capture.output(print(H_sw_R1_stream))
+  expect_equal(H_sw_R1_stream_printed, readLines("H_sw_R1_stream_printed.txt"))
+
+  # The basedir is not printed, therefore tested separately
+  expect_equal(H_sw_D4_pond$basedir, basedir_test)
+
+  EXSW2_R1_stream_printed <- capture.output(print(EXSW2_R1_stream))
+  expect_equal(EXSW2_R1_stream_printed, readLines("EXSW2_R1_stream_printed.txt"))
+
+  # The basedir is not printed, therefore tested separately
+  expect_equal(H_sw_D4_pond$basedir, basedir_test)
+})
+
+test_that("Getting events and moving window analysis works", {
+
+  # Event analysis with two different thresholds
+  H_sw_R1_stream$get_events(c(2, 10))
+  expect_equal_to_reference(H_sw_R1_stream$events, file = "H_sw_R1_stream_events.rds")
+
+  # Moving window analysis
+  H_sw_R1_stream$moving_windows(c(7, 21))
+  expect_equal_to_reference(H_sw_R1_stream$windows, file = "H_sw_R1_stream_windows.rds")
+})
diff --git a/tests/testthat/test_UK_drainage.R b/tests/testthat/test_UK_drainage.R
new file mode 100644
index 0000000..859f145
--- /dev/null
+++ b/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(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(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(60, interception = 0.5, Koc = 550,
+                                        latest_application = "01 July",
+                                        soil_DT50 = 200), 2), 0.84)
+})
diff --git a/tests/testthat/test_geomean.R b/tests/testthat/test_geomean.R
new file mode 100644
index 0000000..0cc3416
--- /dev/null
+++ b/tests/testthat/test_geomean.R
@@ -0,0 +1,11 @@
+library(pfm)
+context("Geometric mean calculation")
+
+test_that("The geometric mean is correctly calculated", {
+  expect_equal(geomean(c(1, 3, 9)), 3)
+  expect_equal(geomean(c(0, 3, 9)), 0)
+  expect_error(geomean(c(1, 3, NA, 9), na.rm = FALSE), "NA")
+  expect_equal(geomean(c(1, 3, NA, 9), na.rm = TRUE), 3)
+  expect_error(geomean(c(1, -3, 9)), "positive")
+  expect_error(geomean(c(1, -3, NA, 9)), "positive")
+})