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authorJohannes Ranke <jranke@uni-bremen.de>2016-09-27 23:00:48 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-09-27 23:00:48 +0200
commit12a31f4c130c551f82232d9ef7dfb608bd52c53f (patch)
tree2525ab1ea4102a6edddbd0c2f03f4a851bf2f9c5 /tests/testthat
parent0d958ab6f84b569b5437f231c56004890c4ae23b (diff)
Reorganise repository using standard package layout
Diffstat (limited to 'tests/testthat')
-rw-r--r--tests/testthat/EXSW2_R1_stream_printed.txt10
-rw-r--r--tests/testthat/H_sw_D4_pond_printed.txt10
-rw-r--r--tests/testthat/H_sw_R1_stream_events.rdsbin0 -> 334 bytes
-rw-r--r--tests/testthat/H_sw_R1_stream_printed.txt10
-rw-r--r--tests/testthat/H_sw_R1_stream_windows.rdsbin0 -> 235 bytes
-rw-r--r--tests/testthat/test_PEC_sed.R9
-rw-r--r--tests/testthat/test_PEC_soil.R95
-rw-r--r--tests/testthat/test_PEC_sw_drift.R15
-rw-r--r--tests/testthat/test_SFO_actual_twa.R13
-rw-r--r--tests/testthat/test_TOXSWA_cwa.R56
-rw-r--r--tests/testthat/test_UK_drainage.R33
-rw-r--r--tests/testthat/test_geomean.R11
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
Binary files differ
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
Binary files differ
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")
+})

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