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-rw-r--r--tests/testthat/test_step_1.R172
1 files changed, 104 insertions, 68 deletions
diff --git a/tests/testthat/test_step_1.R b/tests/testthat/test_step_1.R
index 0c8710b..2a65f36 100644
--- a/tests/testthat/test_step_1.R
+++ b/tests/testthat/test_step_1.R
@@ -1,125 +1,161 @@
-context("FOCUS Step 1 calculations")
+context("FOCUS Step 1 and 2 calculations")
-t_out <- c(0, 1, 2, 4) # Checking the first four days is sufficient for Step 1
test_txt <- readLines(
system.file("testdata/Steps_12_pesticide.txt", package = "pfm")
)
+# Define test compounds as in pesticide.txt
+dummy_1 <- chent_focus_sw("Dummy 1", cwsat = 6000, DT50_ws = 6, DT50_soil = 6, Koc = 344.8,
+ DT50_water = 6, DT50_sediment = 6)
+dummy_2 <- chent_focus_sw("Dummy 2", cwsat = 30, DT50_ws = 26, Koc = 110)
+dummy_4 <- chent_focus_sw("Dummy 4", cwsat = 2e-3, DT50_ws = 4, Koc = 970)
+dummy_5 <- chent_focus_sw("Dummy 5", cwsat = 1.15, DT50_ws = 118, Koc = 860)
+dummy_7 <- chent_focus_sw("Dummy 7", cwsat = 2.60, DT50_ws = 28, Koc = 500)
+new_dummy <- chent_focus_sw("New Dummy", mw = 250, Koc = 100)
+M1 <- chent_focus_sw("M1", mw = 100, cwsat = 100, DT50_ws = 100,
+ Koc = 50, max_ws = 0, max_soil = 0.5)
+M2 <- chent_focus_sw("M2", mw = 100, cwsat = 100, DT50_ws = 100,
+ Koc = 50, max_ws = 0.5, max_soil = 0)
+
+# When we compare the generated input file with the test file,
+# we can ignore some fields
+field_index <- c(ai = 1, compound = 2, comment = 3,
+ mw_ai = 4, mw_met = 5,
+ cwsat = 6, Koc_assessed = 7,
+ Koc_parent = 8,
+ DT50_ws = 9,
+ max_ws = 10, max_soil = 11,
+ rate = 12, n = 13, i = 14, app_type = 15,
+ DT50_soil_parent = 16, DT50_soil = 17, DT50_water = 18, DT50_sediment = 19,
+ reg_sea = 20, int_class = 21)
+field_index_parent <- field_index[-c(4:5, 8, 10:11, 16)]
+
+t_out_1 <- c(0, 1, 2, 4) # Checking the first four days is sufficient for Step 1
+PEC_template_1 <- matrix(NA, nrow = length(t_out_1), ncol = 4,
+ dimnames = list(Time = t_out_1, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
+
+t_out_2 <- c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100) # We read in text from rtf reports for Step 2
+
test_that("Results of Steps 1/2 calculator for Dummy 1 are reproduced", {
- dummy_1 <- chent_focus_sw("Dummy 1", cwsat = 6000, DT50_ws = 6, Koc = 344.8)
- res_dummy_1 <- PEC_sw_focus(dummy_1, 3000,
+ res_step_1_1 <- PEC_sw_focus(dummy_1, 3000,
comment = "Potatoes, Southern Europe, spring, 1 app/season, soil incorporation",
- f_drift = 0,
+ scenario = "no drift (incorp or seed trtmt)",
+ region = "s", season = "mm",
append = FALSE, overwrite = TRUE)
pest_txt <- readLines("pesticide.txt")
- expect_equal(test_txt[1], pest_txt[1])
- strsplit(test_txt[2], "\t")[[1]]
-
- PEC_orig_1 = matrix(NA, nrow = length(t_out), ncol = 4,
- dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
-
- PEC_orig_1[, "PECsw"] = c(685.06, 610.32, 543.73, 431.56)
- PEC_orig_1[, "TWAECsw"] = c(NA, 647.69, 612.03, 548.76)
- PEC_orig_1[, "PECsed"] = c(2.36, 2.1, 1.87, 1.49) * 1e3
- PEC_orig_1[, "TWAECsed"] = c(NA, 2.23e3, 2.11e3, 1.89e3)
-
- expect_equal(res_dummy_1$PEC[1:4, c(1, 2)], PEC_orig_1[, c(1, 2)], tolerance = 0.01, scale = 1)
- expect_equal(res_dummy_1$PEC[1:4, c(3, 4)], PEC_orig_1[, c(3, 4)], tolerance = 10, scale = 1)
+ expect_equal(test_txt[1], pest_txt[1]) # Header
+ test_1 <- strsplit(test_txt[2], "\t")[[1]][field_index_parent]
+ pest_1 <- strsplit(pest_txt[2], "\t")[[1]][field_index_parent]
+ expect_equal(test_1, pest_1) # Parent fields
+
+ PEC_step_1_1 <- PEC_template_1
+ PEC_step_1_1[, "PECsw"] = c(685.06, 610.32, 543.73, 431.56)
+ PEC_step_1_1[, "TWAECsw"] = c(NA, 647.69, 612.03, 548.76)
+ PEC_step_1_1[, "PECsed"] = c(2.36, 2.1, 1.87, 1.49) * 1e3
+ PEC_step_1_1[, "TWAECsed"] = c(NA, 2.23e3, 2.11e3, 1.89e3)
+
+ expect_equal(res_step_1_1$PEC[1:4, c(1, 2)], PEC_step_1_1[, c(1, 2)], tolerance = 0.01, scale = 1)
+ expect_equal(res_step_1_1$PEC[1:4, c(3, 4)], PEC_step_1_1[, c(3, 4)], tolerance = 10, scale = 1)
+
+ # This is pasted from the file "Dummy 1 step 2.rtf" generated with Steps12 version 3.2 from 15/05/2017
+ PEC_step_2_1_raw <- read.table(text = "0 172.6235 NA 595.2057 NA
+1 153.7900 163.2067 530.2680 562.7368
+2 137.0113 154.3037 472.4151 532.0392
+4 108.7460 138.3873 374.9561 477.1595
+7 76.8950 118.5090 265.1340 408.6191
+14 34.2528 85.6494 118.1038 295.3191
+21 15.2579 64.9380 52.6092 223.9062
+28 6.7966 51.3222 23.4348 176.9589
+42 1.3486 35.3389 4.6500 121.8484
+50 0.5352 29.8256 1.8454 102.8388
+100 0.0017 14.9591 0.0057 51.5788")
+ PEC_step_2_1 = PEC_step_2_1_raw[, 2:5]
+ dimnames(PEC_step_2_1) = list(Time = t_out_2,
+ type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed"))
+
+ # Step 2 is not implemented.
})
test_that("Results of Steps 1/2 calculator for Dummy 2 are reproduced", {
- dummy_2 <- chent_focus_sw(cwsat = 30, DT50_ws = 26, Koc = 110)
res_dummy_2 <- PEC_sw_focus(dummy_2, 1000)
- PEC_orig_2 = matrix(NA, nrow = length(t_out), ncol = 4,
- dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
+ PEC_step_1_2 = PEC_template_1
- PEC_orig_2[, "PECsw"] = c(299.89, 290.86, 283.21, 268.50)
- PEC_orig_2[, "TWAECsw"] = c(NA, 295.38, 291.20, 283.49)
- PEC_orig_2[, "PECsed"] = c(319.77, 319.95, 311.53, 295.35)
- PEC_orig_2[, "TWAECsed"] = c(NA, 319.86, 317.79, 310.58)
+ PEC_step_1_2[, "PECsw"] = c(299.89, 290.86, 283.21, 268.50)
+ PEC_step_1_2[, "TWAECsw"] = c(NA, 295.38, 291.20, 283.49)
+ PEC_step_1_2[, "PECsed"] = c(319.77, 319.95, 311.53, 295.35)
+ PEC_step_1_2[, "TWAECsed"] = c(NA, 319.86, 317.79, 310.58)
- expect_equal(res_dummy_2$PEC[1:4, ], PEC_orig_2[, ], tolerance = 0.01, scale = 1)
+ expect_equal(res_dummy_2$PEC[1:4, ], PEC_step_1_2[, ], tolerance = 0.01, scale = 1)
})
test_that("Results of Steps 1/2 calculator for Dummy 4 are reproduced", {
- dummy_4 <- chent_focus_sw(cwsat = 2e-3, DT50_ws = 4, Koc = 970)
res_dummy_4 <- PEC_sw_focus(dummy_4, 7.5, n = 3, i = 14,
scenario = "pome / stone fruit, early")
- PEC_orig_4 = matrix(NA, nrow = length(t_out), ncol = 4,
- dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
+ PEC_step_1_4 = PEC_template_1
- PEC_orig_4[, "PECsw"] = c(1.82, 1.18, 1.00, 0.70)
- PEC_orig_4[, "TWAECsw"] = c(NA, 1.50, 1.29, 1.07)
- PEC_orig_4[, "PECsed"] = c(10.57, 11.49, 9.66, 6.83)
- PEC_orig_4[, "TWAECsed"] = c(NA, 11.03, 10.79, 9.48)
+ PEC_step_1_4[, "PECsw"] = c(1.82, 1.18, 1.00, 0.70)
+ PEC_step_1_4[, "TWAECsw"] = c(NA, 1.50, 1.29, 1.07)
+ PEC_step_1_4[, "PECsed"] = c(10.57, 11.49, 9.66, 6.83)
+ PEC_step_1_4[, "TWAECsed"] = c(NA, 11.03, 10.79, 9.48)
- expect_equal(res_dummy_4$PEC[1:4, ], PEC_orig_4[, ], tolerance = 0.01, scale = 1)
+ expect_equal(res_dummy_4$PEC[1:4, ], PEC_step_1_4[, ], tolerance = 0.01, scale = 1)
})
test_that("Results of Steps 1/2 calculator for Dummy 5 are reproduced", {
- dummy_5 <- chent_focus_sw(cwsat = 1.15, DT50_ws = 118, Koc = 860)
res_dummy_5 <- PEC_sw_focus(dummy_5, 75, n = 5, i = 14,
scenario = "vines, early")
- PEC_orig_5 = matrix(NA, nrow = length(t_out), ncol = 4,
- dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
+ PEC_step_1_5 = PEC_template_1
- PEC_orig_5[, "PECsw"] = c(61.60, 59.45, 59.10, 58.41)
- PEC_orig_5[, "TWAECsw"] = c(NA, 60.53, 59.90, 59.33)
- PEC_orig_5[, "PECsed"] = c(500.78, 511.28, 508.29, 502.35)
- PEC_orig_5[, "TWAECsed"] = c(NA, 506.03, 507.90, 506.61)
+ PEC_step_1_5[, "PECsw"] = c(61.60, 59.45, 59.10, 58.41)
+ PEC_step_1_5[, "TWAECsw"] = c(NA, 60.53, 59.90, 59.33)
+ PEC_step_1_5[, "PECsed"] = c(500.78, 511.28, 508.29, 502.35)
+ PEC_step_1_5[, "TWAECsed"] = c(NA, 506.03, 507.90, 506.61)
- expect_equal(res_dummy_5$PEC[1:4, ], PEC_orig_5[, ], tolerance = 0.01, scale = 1)
+ expect_equal(res_dummy_5$PEC[1:4, ], PEC_step_1_5[, ], tolerance = 0.01, scale = 1)
})
test_that("Results of Steps 1/2 calculator for Dummy 7 are reproduced", {
- dummy_7 <- chent_focus_sw(cwsat = 2.60, DT50_ws = 28, Koc = 500)
res_dummy_7 <- PEC_sw_focus(dummy_7, 750, n = 4, i = 14,
scenario = "vines, early")
- PEC_orig_7 = matrix(NA, nrow = length(t_out), ncol = 4,
- dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
+ PEC_step_1_7 = PEC_template_1
- PEC_orig_7[, "PECsw"] = c(626.99, 601.13, 586.43, 558.10)
- PEC_orig_7[, "TWAECsw"] = c(NA, 614.06, 603.90, 588.03)
- PEC_orig_7[, "PECsed"] = c(3.0, 3.01, 2.93, 2.79) * 1e3
- PEC_orig_7[, "TWAECsed"] = c(NA, 3.01e3, 2.99e3, 2.92e3)
+ PEC_step_1_7[, "PECsw"] = c(626.99, 601.13, 586.43, 558.10)
+ PEC_step_1_7[, "TWAECsw"] = c(NA, 614.06, 603.90, 588.03)
+ PEC_step_1_7[, "PECsed"] = c(3.0, 3.01, 2.93, 2.79) * 1e3
+ PEC_step_1_7[, "TWAECsed"] = c(NA, 3.01e3, 2.99e3, 2.92e3)
- expect_equal(res_dummy_7$PEC[1:4, c(1, 2)], PEC_orig_7[, c(1, 2)], tolerance = 0.01, scale = 1)
- expect_equal(res_dummy_7$PEC[1:4, c(3, 4)], PEC_orig_7[, c(3, 4)], tolerance = 10, scale = 1)
+ expect_equal(res_dummy_7$PEC[1:4, c(1, 2)], PEC_step_1_7[, c(1, 2)], tolerance = 0.01, scale = 1)
+ expect_equal(res_dummy_7$PEC[1:4, c(3, 4)], PEC_step_1_7[, c(3, 4)], tolerance = 10, scale = 1)
})
test_that("Results of Steps 1/2 calculator for New Dummy (M1-M3) are reproduced", {
- new_dummy <- chent_focus_sw(mw = 250, Koc = 100)
- M1 <- chent_focus_sw(mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, max_ws = 0, max_soil = 0.5)
res_M1 <- PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter",
met = M1)
- PEC_orig_M1 = matrix(NA, nrow = length(t_out), ncol = 4,
- dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
+ PEC_step_1_M1 = PEC_template_1
- PEC_orig_M1[, "PECsw"] = c(62.5, 62.07, 61.64, 60.79)
- PEC_orig_M1[, "TWAECsw"] = c(NA, 62.28, 62.07, 61.64)
- PEC_orig_M1[, "PECsed"] = c(31.25, 31.03, 30.82, 30.40)
- PEC_orig_M1[, "TWAECsed"] = c(NA, 31.14, 31.03, 30.82)
+ PEC_step_1_M1[, "PECsw"] = c(62.5, 62.07, 61.64, 60.79)
+ PEC_step_1_M1[, "TWAECsw"] = c(NA, 62.28, 62.07, 61.64)
+ PEC_step_1_M1[, "PECsed"] = c(31.25, 31.03, 30.82, 30.40)
+ PEC_step_1_M1[, "TWAECsed"] = c(NA, 31.14, 31.03, 30.82)
- expect_equal(res_M1$PEC[1:4, ], PEC_orig_M1[, ], tolerance = 0.01, scale = 1)
+ expect_equal(res_M1$PEC[1:4, ], PEC_step_1_M1[, ], tolerance = 0.01, scale = 1)
- M2 <- chent_focus_sw(mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, max_ws = 0.5, max_soil = 0)
res_M2 <- PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter",
met = M2)
- PEC_orig_M2 = matrix(NA, nrow = length(t_out), ncol = 4,
- dimnames = list(Time = t_out, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")))
+ PEC_step_1_M2 = PEC_template_1
- PEC_orig_M2[, "PECsw"] = c(64.34, 63.78, 63.34, 62.47)
- PEC_orig_M2[, "TWAECsw"] = c(NA, 64.06, 63.81, 63.36)
- PEC_orig_M2[, "PECsed"] = c(31.25, 31.89, 31.67, 31.23)
- PEC_orig_M2[, "TWAECsed"] = c(NA, 31.57, 31.68, 31.56)
+ PEC_step_1_M2[, "PECsw"] = c(64.34, 63.78, 63.34, 62.47)
+ PEC_step_1_M2[, "TWAECsw"] = c(NA, 64.06, 63.81, 63.36)
+ PEC_step_1_M2[, "PECsed"] = c(31.25, 31.89, 31.67, 31.23)
+ PEC_step_1_M2[, "TWAECsed"] = c(NA, 31.57, 31.68, 31.56)
- expect_equal(res_M2$PEC[1:4, ], PEC_orig_M2[, ], tolerance = 0.01, scale = 1)
+ expect_equal(res_M2$PEC[1:4, ], PEC_step_1_M2[, ], tolerance = 0.01, scale = 1)
})
unlink("pesticide.txt")

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