Single line of generated Step12 input file partially validated

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")