Separate out PELMO utilities into rPELMO

1 files changed, 0 insertions, 201 deletions

diff --git a/tests/testthat/test_PELMO.R b/tests/testthat/test_PELMO.R
deleted file mode 100644
index ba6a04a..0000000
--- a/tests/testthat/test_PELMO.R
+++ /dev/null
@@ -1,201 +0,0 @@
-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$names)))
-
-# Check if we have wine on the path
-wine_installed <- system('wine --version', ignore.stdout = TRUE) == 0
-skip_if_no_wine <- function() {
-  if (!wine_installed) skip("wine is not available")
-}
-
-test_that("PELMO paths are correctly created", {
-  skip_if_no_wine()
-  psm_paths = c(
-     PELMO_path(runs[[1]]$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]]$psm, ".psm"))
-    expect_true(file.exists(psm_file))
-    psm_new_location <- file.path(PELMO_base, basename(psm_file))
-    file.copy(psm_file, psm_new_location, overwrite = TRUE)
-  }
-})
-
-test_that("PELMO runs are correctly set up", {
-  skip_if_no_wine()
-
-  # Prepare runs in analogy to the test archive
-  skip_on_cran()
-  PELMO_runs(runs, psm_dir = PELMO_base, execute = FALSE, evaluate = FALSE, overwrite = TRUE)
-
-  # Check that input files are correctly generated in the right location
-  for (run in runs) {
-    psm <- run$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", {
-  skip_if_no_wine()
-  skip_on_cran()
-
-  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$psm
-    crops <- setdiff(names(run), "psm")
-    for (crop in crops) {
-      for (scenario in run[[crop]]) {
-        pp <- PELMO_path(psm, crop, scenario)
-
-        for (plm in plm_files) {
-          if (file.exists(file.path(test_dir, pp, plm))) {
-            new <- readLines(file.path(PELMO_base, "FOCUS", pp, plm))
-            test <- readLines(file.path(test_dir, pp, plm))
-
-            # Don't check for differences in the PESTICIDE BALANCE ERROR
-            pest_balance_error <- suppressWarnings(grep("PESTICIDE BALANCE ERROR", new))
-            # Suppress warnings about invalid strings in this locale caused by the files
-
-            # Check if the ouput files are correctly reproduced
-            expect_identical(new[!pest_balance_error], test[!pest_balance_error])
-          }
-        }
-      }
-    }
-  }
-})
-
-test_that("PELMO runs are correctly evaluated", {
-  skip_if_no_wine()
-  skip_on_cran()
-
-  pfm_PECgw <- evaluate_PELMO(runs)
-
-  # Check that if output is the same as in the test archive
-  for (run in runs) {
-    psm <- run$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]]$focus <- tmp80[[1, "V5"]]
-        }
-
-        period_pfm_file <- file.path(PELMO_base, "FOCUS", pp, "period_pfm.rda")
-        load(period_pfm_file)
-
-        #message(psm, " ", crop, " ", scenario)
-
-        # Test for equality of all the components separately,
-        # as we need to adapt the tolerance
-        for (acronym in acronyms) {
-          p_pelmo <- results[[acronym]]$periods
-          p_test <- results_pfm[[acronym]]$periods
-          expect_equal(p_test$flux, p_pelmo$flux, tol = 1e-6)
-          expect_equal(p_test$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)
-        }
-      }
-    }
-  }
-})
-
-test_that("PECgw from FOCUS summary files can be reproduced", {
-  skip_if_no_wine()
-  skip_on_cran()
-
-  pfm_PECgw <- evaluate_PELMO(runs)
-  
-  focus_summary <- list()
-
-  for (run in runs) {
-    psm <- run$psm
-    focus_summary[[psm]] <- list()
-
-    crops <- setdiff(names(run), "psm")
-    for (crop in crops) {
-      scenarios <- run[[crop]]
-
-      # Read contents of summary text file copied from the GUI output. We only
-      # have results for one crop per psm file, so the crop is not in the file
-      # name.
-      sumfile_path <- system.file(paste0("testdata/FOCUS_Summary_", psm,
-                                         ".txt"), package = "pfm")
-      sumfile <- readLines(sumfile_path, encoding = "latin1")
-      result_anchors <- grep("Results for", sumfile)
-      acronyms <- gsub(".*\\((.*)\\).*", "\\1", sumfile[result_anchors])
-      names(result_anchors) <- acronyms
-      focus_summary[[psm]][[crop]] <- matrix(nrow = length(scenarios), ncol = length(acronyms),
-                                             dimnames = list(scenarios, acronyms))
-      for (acronym in acronyms) {
-        tmp <- sumfile[result_anchors[acronym] + 4 + (1:length(scenarios))]
-        tmp_frame <- read.table(text = tmp, sep = "\t")
-        PECgw <- tmp_frame$V5
-        focus_summary[[psm]][[crop]][, acronym] <- PECgw
-      }
-    }
-  }
-  expect_equal(pfm_PECgw, focus_summary)
-})