diff options
| -rw-r--r-- | ChangeLog | 16 | ||||
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | build.log | 3 | ||||
| -rw-r--r-- | test.log | 28 | ||||
| -rw-r--r-- | tests/testthat/test_step_1.R | 116 |
5 files changed, 131 insertions, 34 deletions
@@ -1,3 +1,19 @@ +commit 34d4915297faf6236479f0e6474f8aa6b8d4b416 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2017-06-20 04:30:52 +0200 + + Fix generation of input files + + - Write header only if not appending + - Write max_soil and max_ws for metabolites + - Formatting + +commit 7233eed00b799e08c31ae971f997b4b3c14eaea2 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2017-06-19 20:10:21 +0200 + + Single line of generated Step12 input file partially validated + commit c9bcd8e68db61515080ff377c6a04fa807337258 Author: Johannes Ranke <jranke@uni-bremen.de> Date: 2017-06-17 16:36:13 +0200 diff --git a/DESCRIPTION b/DESCRIPTION index 6173a49..c456607 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling Version: 0.4-3 -Date: 2017-06-19 +Date: 2017-06-20 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph")) Description: Utilities for simple calculations of predicted environmental @@ -1,9 +1,6 @@ * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘pfm’: * checking DESCRIPTION meta-information ... OK -* excluding invalid files -Subdirectory 'R' contains invalid file names: - ‘pesticide.txt’ ‘xxx.txt’ * checking for LF line-endings in source and make files * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added @@ -13,10 +13,34 @@ Check max_twa for parent mkinfit models against analytical solutions: . Simple PEC sediment calculations: . Simple PEC soil calculations: ........... Simple PEC surface water calculations with drift entry: .. -Create PELMO runs from psm files and execute them: ........................................................................................................................................................................................................................... +Create PELMO runs from psm files and execute them: ..................................................1...........2............................................................................................................................................................ Actual and time weighted average concentrations for SFO kinetics: . -FOCUS Step 1 and 2 calculations: ........... +FOCUS Step 1 calculations: ......... +FOCUS Steps 12 input files: ........ Read and analyse TOXSWA cwa files: ....... UK drainage PEC calculations: ............ +Failed --------------------------------------------------------------------------------------------- +1. Failure: PELMO runs can be run and give the expected result files (@test_PELMO.R#93) ------------ +`new` not identical to `test`. +1/17288 mismatches +x[15376]: " 14958 24 0.900E-01 0.420E-01 0.000E+00 0.000E+00 0.292E+00 0.292E+00 0.2 +x[15376]: 68E+01\xa00.244E+01 0.000E+00 0.753E-04 0.209E-05 0.175E-02 0.000E+00 0.00 +x[15376]: 0E+00 0.000E+00" +y[15376]: " 14958 24 0.900E-01 0.420E-01 0.000E+00 0.000E+00 0.292E+00 0.292E+00 0.2 +y[15376]: 68E+01 0.244E+01 0.000E+00 0.753E-04 0.209E-05 0.175E-02 0.000E+00 0.000E+ +y[15376]: 00 0.000E+00" + + +2. Failure: PELMO runs can be run and give the expected result files (@test_PELMO.R#93) ------------ +`new` not identical to `test`. +1/17460 mismatches +x[16928]: " 16293 24 0.510E+00 0.480E+00 0.000E+00 0.000E+00 0.334E+00 0.2\xb57E+00 +x[16928]: 0.232E+02 0.235E+02 0.000E+00 0.190E-02 0.695E-04 0.992E-02 0.000E+00 0.00 +x[16928]: 0E+00 0.000E+00" +y[16928]: " 16293 24 0.510E+00 0.480E+00 0.000E+00 0.000E+00 0.334E+00 0.257E+00 0.2 +y[16928]: 32E+02 0.235E+02 0.000E+00 0.190E-02 0.695E-04 0.992E-02 0.000E+00 0.000E+ +y[16928]: 00 0.000E+00" + + DONE =============================================================================================== diff --git a/tests/testthat/test_step_1.R b/tests/testthat/test_step_1.R index 2a65f36..024a25a 100644 --- a/tests/testthat/test_step_1.R +++ b/tests/testthat/test_step_1.R @@ -1,4 +1,4 @@ -context("FOCUS Step 1 and 2 calculations") +context("FOCUS Step 1 calculations") # {{{1 test_txt <- readLines( system.file("testdata/Steps_12_pesticide.txt", package = "pfm") @@ -7,18 +7,27 @@ test_txt <- readLines( # 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) +dummy_2 <- chent_focus_sw("Dummy 2", cwsat = 30, DT50_ws = 26, DT50_soil = 56, Koc = 110, + DT50_water = 26, DT50_sediment = 26) +dummy_4 <- chent_focus_sw("Dummy 4", cwsat = 2e-3, DT50_ws = 4, Koc = 970, + DT50_soil = 19, DT50_water = 4, DT50_sediment = 4) +dummy_5 <- chent_focus_sw("Dummy 5", cwsat = 1.15, DT50_ws = 118, Koc = 860, + DT50_soil = 250, DT50_water = 6, DT50_sediment = 118) +dummy_7 <- chent_focus_sw("Dummy 7", cwsat = 2.60, DT50_ws = 28, Koc = 500, + DT50_soil = 50, DT50_water = 2.5, DT50_sediment = 28) +new_dummy <- chent_focus_sw("New Dummy", mw = 250, Koc = 100, + DT50_soil = 10) +M1 <- chent_focus_sw("Metabolite M1", + mw = 100, cwsat = 100, DT50_ws = 100, + Koc = 50, max_ws = 0, max_soil = 0.5, + DT50_soil = 20, DT50_water = 10, DT50_sediment = 100) +M2 <- chent_focus_sw("Metabolite M2", + mw = 100, cwsat = 100, DT50_ws = 100, + Koc = 50, max_ws = 0.5, max_soil = 0, + DT50_soil = 20, DT50_water = 10, DT50_sediment = 100) # When we compare the generated input file with the test file, -# we can ignore some fields +# we can ignore some fields if we are looking at the parent ai field_index <- c(ai = 1, compound = 2, comment = 3, mw_ai = 4, mw_met = 5, cwsat = 6, Koc_assessed = 7, @@ -36,19 +45,13 @@ PEC_template_1 <- matrix(NA, nrow = length(t_out_1), ncol = 4, 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", { +test_that("Results of Steps 1/2 calculator for Dummy 1 are reproduced", { # {{{1 res_step_1_1 <- PEC_sw_focus(dummy_1, 3000, comment = "Potatoes, Southern Europe, spring, 1 app/season, soil incorporation", 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]) # 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) @@ -74,11 +77,14 @@ test_that("Results of Steps 1/2 calculator for Dummy 1 are reproduced", { dimnames(PEC_step_2_1) = list(Time = t_out_2, type = c("PECsw", "TWAECsw", "PECsed", "TWAECsed")) - # Step 2 is not implemented. + # Step 2 is not implemented, so this can not be tested. }) -test_that("Results of Steps 1/2 calculator for Dummy 2 are reproduced", { - res_dummy_2 <- PEC_sw_focus(dummy_2, 1000) +test_that("Results of Steps 1/2 calculator for Dummy 2 are reproduced", { # {{{1 + res_dummy_2 <- PEC_sw_focus(dummy_2, 1000, + comment = "Maize, Southern Europe, spring, 1 app/season", + scenario = "maize", + region = "s", season = "mm") PEC_step_1_2 = PEC_template_1 @@ -90,9 +96,11 @@ test_that("Results of Steps 1/2 calculator for Dummy 2 are reproduced", { expect_equal(res_dummy_2$PEC[1:4, ], PEC_step_1_2[, ], tolerance = 0.01, scale = 1) }) -test_that("Results of Steps 1/2 calculator for Dummy 4 are reproduced", { +test_that("Results of Steps 1/2 calculator for Dummy 4 are reproduced", { # {{{1 res_dummy_4 <- PEC_sw_focus(dummy_4, 7.5, n = 3, i = 14, - scenario = "pome / stone fruit, early") + comment = "Apples, Southern Europe, spring, 3 app./season, 14 d int, orchards", + region = "s", season = "mm", + scenario = "pome / stone fruit, early") PEC_step_1_4 = PEC_template_1 @@ -104,9 +112,11 @@ test_that("Results of Steps 1/2 calculator for Dummy 4 are reproduced", { expect_equal(res_dummy_4$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", { +test_that("Results of Steps 1/2 calculator for Dummy 5 are reproduced", { # {{{1 res_dummy_5 <- PEC_sw_focus(dummy_5, 75, n = 5, i = 14, - scenario = "vines, early") + comment = "Vines, Northern Europe, spring, 5 app/seaon 14 d int.", + region = "n", season = "mm", + scenario = "vines, early") PEC_step_1_5 = PEC_template_1 @@ -118,9 +128,11 @@ test_that("Results of Steps 1/2 calculator for Dummy 5 are reproduced", { expect_equal(res_dummy_5$PEC[1:4, ], PEC_step_1_5[, ], tolerance = 0.01, scale = 1) }) -test_that("Results of Steps 1/2 calculator for Dummy 7 are reproduced", { +test_that("Results of Steps 1/2 calculator for Dummy 7 are reproduced", { # {{{1 res_dummy_7 <- PEC_sw_focus(dummy_7, 750, n = 4, i = 14, - scenario = "vines, early") + comment = "Vines, Southern Europe, spring, 4 app/seaon 14 d int.", + region = "s", season = "mm", + scenario = "vines, early") PEC_step_1_7 = PEC_template_1 @@ -133,8 +145,10 @@ test_that("Results of Steps 1/2 calculator for Dummy 7 are reproduced", { expect_equal(res_dummy_7$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", { +test_that("Results of Steps 1/2 calculator for New Dummy (M1-M2) are reproduced", { # {{{1 res_M1 <- PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter", + comment = "Soil Metabolite", + region = "n", season = "of", met = M1) PEC_step_1_M1 = PEC_template_1 @@ -147,6 +161,8 @@ test_that("Results of Steps 1/2 calculator for New Dummy (M1-M3) are reproduced" expect_equal(res_M1$PEC[1:4, ], PEC_step_1_M1[, ], tolerance = 0.01, scale = 1) res_M2 <- PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter", + comment = "Water Metabolite", + region = "n", season = "of", met = M2) PEC_step_1_M2 = PEC_template_1 @@ -158,4 +174,48 @@ test_that("Results of Steps 1/2 calculator for New Dummy (M1-M3) are reproduced" expect_equal(res_M2$PEC[1:4, ], PEC_step_1_M2[, ], tolerance = 0.01, scale = 1) }) + +context("FOCUS Steps 12 input files") # {{{1 +test_that("Runs are correctly defined in the Steps 12 input file", { # {{{1 + + pest_txt <- readLines("pesticide.txt") + expect_equal(test_txt[1], pest_txt[1]) # Header + + # Dummy 1 + 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 + + # Dummy 2 + test_2 <- strsplit(test_txt[3], "\t")[[1]][field_index_parent] + pest_2 <- strsplit(pest_txt[3], "\t")[[1]][field_index_parent] + expect_equal(test_2, pest_2) # Parent fields + + # Dummy 4 + test_4 <- strsplit(test_txt[5], "\t")[[1]][field_index_parent] + pest_4 <- strsplit(pest_txt[4], "\t")[[1]][field_index_parent] + expect_equal(test_4, pest_4) # Parent fields + + # Dummy 5 + test_5 <- strsplit(test_txt[6], "\t")[[1]][field_index_parent] + pest_5 <- strsplit(pest_txt[5], "\t")[[1]][field_index_parent] + expect_equal(test_5, pest_5) # Parent fields + + # Dummy 7 + test_7 <- strsplit(test_txt[9], "\t")[[1]][field_index_parent] + pest_7 <- strsplit(pest_txt[6], "\t")[[1]][field_index_parent] + expect_equal(test_7, pest_7) # Parent fields + + # New Dummy / M1 + test_m1 <- strsplit(test_txt[10], "\t")[[1]] + pest_m1 <- strsplit(pest_txt[7], "\t")[[1]] + expect_equal(test_m1, pest_m1) # All fields + + # New Dummy / M2 + test_m2 <- strsplit(test_txt[11], "\t")[[1]] + pest_m2 <- strsplit(pest_txt[8], "\t")[[1]] + expect_equal(test_m2, pest_m2) # All fields + +}) unlink("pesticide.txt") +# vim: set foldmethod=marker: {{{ |