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library(testthat)
library(pfm)
context("Create PELMO runs from psm files and execute them")
PELMO_base <- system.file("FOCUSPELMO.553", package = "PELMO.installeR")
test_archive <- system.file("testdata/FOCUS_PELMO.tar.bz2", package = "pfm")
test_dir <- tempdir()
untar(test_archive, exdir = test_dir, compressed = "bzip2")
runs <- list(
list(
psm = "Pesticide_D",
fbe = c("Por"),
vbe = c("Por")),
list(
psm = "Pesticide_D_1_day_pre_em_every_third_year",
pot = c("Cha", "Ham")),
list(
psm = "Pesticide_D_1_May_every_other_year_mets",
win = names(FOCUS_GW_scenarios_2012$names)))
test_that("PELMO paths are correctly created", {
psm_paths = c(
PELMO_path(runs[[1]]$psm, "fbe", "Por"),
PELMO_path(runs[[2]]$psm, "pot", "Ham"),
PELMO_path(runs[[3]]$psm, "win", "Cha"))
for (i in seq_along(psm_paths)) {
psm_file <- file.path(test_dir, psm_paths[i], paste0(runs[[i]]$psm, ".psm"))
expect_true(file.exists(psm_file))
psm_new_location <- file.path(PELMO_base, basename(psm_file))
file.copy(psm_file, psm_new_location, overwrite = TRUE)
}
})
test_that("PELMO runs are correctly set up", {
# Prepare runs in analogy to the test archive
PELMO_runs(runs, psm_dir = PELMO_base, execute = FALSE, evaluate = FALSE, overwrite = TRUE)
# Check that input files are correctly generated in the right location
for (run in runs) {
psm <- run$psm
crops <- setdiff(names(run), "psm")
for (crop in crops) {
for (scenario in run[[crop]]) {
pp <- PELMO_path(psm, crop, scenario)
input_new <- readLines(file.path(PELMO_base, "FOCUS", pp, "pelmo.inp"))
input_test <- readLines(file.path(test_dir, pp, "pelmo.inp"))
# Check if the input files are correctly reproduced
expect_identical(input_new, input_test)
}
}
}
})
test_that("PELMO runs can be run and give the expected result files", {
run_PELMO(runs, cores = 7)
plm_files <- c("CHEM.PLM", "ECHO.PLM",
"KONZCHEM.PLM", "KONZC_A1", "KONZC_B1",
"PLNTPEST.plm", "PLOT.PLM", "WASSER.PLM")
# Check that if output is the same as in the test archive
for (run in runs) {
psm <- run$psm
crops <- setdiff(names(run), "psm")
for (crop in crops) {
for (scenario in run[[crop]]) {
pp <- PELMO_path(psm, crop, scenario)
for (plm in plm_files) {
if (file.exists(file.path(test_dir, pp, plm))) {
new <- readLines(file.path(PELMO_base, "FOCUS", pp, plm))
test <- readLines(file.path(test_dir, pp, plm))
# Check if the ouput files are correctly reproduced
expect_identical(new, test)
}
}
}
}
}
})
test_that("PELMO runs are correctly evaluated", {
results <- evaluate_PELMO(runs)
# Check that if output is the same as in the test archive
for (run in runs) {
psm <- run$psm
crops <- setdiff(names(run), "psm")
for (crop in crops) {
for (scenario in run[[crop]]) {
pp <- PELMO_path(psm, crop, scenario)
period_file <- readLines(file.path(test_dir, pp, "period.plm"), encoding = "latin1")
result_lines <- grep("^\tResults for.*in the percolate at 1 m soil depth$", period_file)
acronyms <- gsub(".*\\((.*)\\).*", "\\1", period_file[result_lines])
names(result_lines) <- acronyms
results <- list()
for (acronym in acronyms) {
results[[acronym]] <- list()
conc_lines <- result_lines[acronym] + 5:24
tmp <- read.table(text = period_file[conc_lines], sep = "\t")
results[[acronym]]$periods <- data.frame(
period = as.integer(tmp$V2),
flux = tmp$V3,
percolate = tmp$V4,
conc = tmp$V5)
tmp80 <- read.table(text = period_file[result_lines[acronym] + 27], sep = "\t")
results[[acronym]]$focus <- tmp80[[1, "V5"]]
}
period_pfm_file <- file.path(PELMO_base, "FOCUS", pp, "period_pfm.rda")
load(period_pfm_file)
# Test for equality of all the components separately,
# as we need to adapt the tolerance
for (acronym in acronyms) {
p_pelmo <- results[[acronym]]$periods
p_test <- results_pfm[[acronym]]$periods
expect_equal(p_test$flux, p_pelmo$flux, tol = 1e-6, scale = 1)
expect_equal(p_test$percolate, p_pelmo$percolate)
# PELMO sets the concentration to 0 when the percolate is zero.
# We get NaN, which is more reasonable, but we need to
# take this into account for testing
p_test$conc <- ifelse(is.na(p_test$conc), 0, p_test$conc)
expect_equal(p_test$conc, p_pelmo$conc, tol = 1e-3, scale = 1)
# FOCUS PEC
expect_equal(results_pfm[[acronym]]$focus, results[[acronym]]$focus,
tol = 1e-3, scale = 1)
}
}
}
}
})
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