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-rw-r--r--pkg/tests/testthat.R4
-rw-r--r--pkg/tests/testthat/EXSW2_R1_stream_printed.txt10
-rw-r--r--pkg/tests/testthat/H_sw_D4_pond_printed.txt10
-rw-r--r--pkg/tests/testthat/H_sw_R1_stream_events.rdsbin334 -> 0 bytes
-rw-r--r--pkg/tests/testthat/H_sw_R1_stream_printed.txt10
-rw-r--r--pkg/tests/testthat/H_sw_R1_stream_windows.rdsbin235 -> 0 bytes
-rw-r--r--pkg/tests/testthat/test_PEC_sed.R9
-rw-r--r--pkg/tests/testthat/test_PEC_soil.R95
-rw-r--r--pkg/tests/testthat/test_PEC_sw_drift.R15
-rw-r--r--pkg/tests/testthat/test_SFO_actual_twa.R13
-rw-r--r--pkg/tests/testthat/test_TOXSWA_cwa.R56
-rw-r--r--pkg/tests/testthat/test_UK_drainage.R33
-rw-r--r--pkg/tests/testthat/test_geomean.R11
13 files changed, 0 insertions, 266 deletions
diff --git a/pkg/tests/testthat.R b/pkg/tests/testthat.R
deleted file mode 100644
index d2df1cc..0000000
--- a/pkg/tests/testthat.R
+++ /dev/null
@@ -1,4 +0,0 @@
-library(testthat)
-library(pfm)
-
-test_check("pfm")
diff --git a/pkg/tests/testthat/EXSW2_R1_stream_printed.txt b/pkg/tests/testthat/EXSW2_R1_stream_printed.txt
deleted file mode 100644
index 60bb5ac..0000000
--- a/pkg/tests/testthat/EXSW2_R1_stream_printed.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-<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/pkg/tests/testthat/H_sw_D4_pond_printed.txt b/pkg/tests/testthat/H_sw_D4_pond_printed.txt
deleted file mode 100644
index 5730be6..0000000
--- a/pkg/tests/testthat/H_sw_D4_pond_printed.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-<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/pkg/tests/testthat/H_sw_R1_stream_events.rds b/pkg/tests/testthat/H_sw_R1_stream_events.rds
deleted file mode 100644
index ba6557b..0000000
--- a/pkg/tests/testthat/H_sw_R1_stream_events.rds
+++ /dev/null
Binary files differ
diff --git a/pkg/tests/testthat/H_sw_R1_stream_printed.txt b/pkg/tests/testthat/H_sw_R1_stream_printed.txt
deleted file mode 100644
index 572ad6d..0000000
--- a/pkg/tests/testthat/H_sw_R1_stream_printed.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-<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/pkg/tests/testthat/H_sw_R1_stream_windows.rds b/pkg/tests/testthat/H_sw_R1_stream_windows.rds
deleted file mode 100644
index 2531189..0000000
--- a/pkg/tests/testthat/H_sw_R1_stream_windows.rds
+++ /dev/null
Binary files differ
diff --git a/pkg/tests/testthat/test_PEC_sed.R b/pkg/tests/testthat/test_PEC_sed.R
deleted file mode 100644
index 443f789..0000000
--- a/pkg/tests/testthat/test_PEC_sed.R
+++ /dev/null
@@ -1,9 +0,0 @@
-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/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)
-})
diff --git a/pkg/tests/testthat/test_PEC_sw_drift.R b/pkg/tests/testthat/test_PEC_sw_drift.R
deleted file mode 100644
index d09d578..0000000
--- a/pkg/tests/testthat/test_PEC_sw_drift.R
+++ /dev/null
@@ -1,15 +0,0 @@
-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/pkg/tests/testthat/test_SFO_actual_twa.R b/pkg/tests/testthat/test_SFO_actual_twa.R
deleted file mode 100644
index b0a5537..0000000
--- a/pkg/tests/testthat/test_SFO_actual_twa.R
+++ /dev/null
@@ -1,13 +0,0 @@
-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/pkg/tests/testthat/test_TOXSWA_cwa.R b/pkg/tests/testthat/test_TOXSWA_cwa.R
deleted file mode 100644
index 7c9a73c..0000000
--- a/pkg/tests/testthat/test_TOXSWA_cwa.R
+++ /dev/null
@@ -1,56 +0,0 @@
-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/pkg/tests/testthat/test_UK_drainage.R b/pkg/tests/testthat/test_UK_drainage.R
deleted file mode 100644
index 859f145..0000000
--- a/pkg/tests/testthat/test_UK_drainage.R
+++ /dev/null
@@ -1,33 +0,0 @@
-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/pkg/tests/testthat/test_geomean.R b/pkg/tests/testthat/test_geomean.R
deleted file mode 100644
index 0cc3416..0000000
--- a/pkg/tests/testthat/test_geomean.R
+++ /dev/null
@@ -1,11 +0,0 @@
-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")
-})

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