From 12a31f4c130c551f82232d9ef7dfb608bd52c53f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 27 Sep 2016 23:00:48 +0200 Subject: Reorganise repository using standard package layout --- pkg/tests/testthat/EXSW2_R1_stream_printed.txt | 10 --- pkg/tests/testthat/H_sw_D4_pond_printed.txt | 10 --- pkg/tests/testthat/H_sw_R1_stream_events.rds | Bin 334 -> 0 bytes pkg/tests/testthat/H_sw_R1_stream_printed.txt | 10 --- pkg/tests/testthat/H_sw_R1_stream_windows.rds | Bin 235 -> 0 bytes pkg/tests/testthat/test_PEC_sed.R | 9 --- pkg/tests/testthat/test_PEC_soil.R | 95 ------------------------- pkg/tests/testthat/test_PEC_sw_drift.R | 15 ---- pkg/tests/testthat/test_SFO_actual_twa.R | 13 ---- pkg/tests/testthat/test_TOXSWA_cwa.R | 56 --------------- pkg/tests/testthat/test_UK_drainage.R | 33 --------- pkg/tests/testthat/test_geomean.R | 11 --- 12 files changed, 262 deletions(-) delete mode 100644 pkg/tests/testthat/EXSW2_R1_stream_printed.txt delete mode 100644 pkg/tests/testthat/H_sw_D4_pond_printed.txt delete mode 100644 pkg/tests/testthat/H_sw_R1_stream_events.rds delete mode 100644 pkg/tests/testthat/H_sw_R1_stream_printed.txt delete mode 100644 pkg/tests/testthat/H_sw_R1_stream_windows.rds delete mode 100644 pkg/tests/testthat/test_PEC_sed.R delete mode 100644 pkg/tests/testthat/test_PEC_soil.R delete mode 100644 pkg/tests/testthat/test_PEC_sw_drift.R delete mode 100644 pkg/tests/testthat/test_SFO_actual_twa.R delete mode 100644 pkg/tests/testthat/test_TOXSWA_cwa.R delete mode 100644 pkg/tests/testthat/test_UK_drainage.R delete mode 100644 pkg/tests/testthat/test_geomean.R (limited to 'pkg/tests/testthat') 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 @@ - 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 @@ - 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 Binary files a/pkg/tests/testthat/H_sw_R1_stream_events.rds and /dev/null 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 @@ - 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 Binary files a/pkg/tests/testthat/H_sw_R1_stream_windows.rds and /dev/null 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") -}) -- cgit v1.2.1