Tests(#66): unit test evaluation and fixes

R/load-nc-physics.R

@@ -21,11 +21,13 @@
 #' nc <- file.path(d, "outputSETAS.nc")
 #' prm_run <- file.path(d, "VMPA_setas_run_fishing_F_Trunk.prm")
 #' bboxes <- get_boundary(boxinfo = load_box(file.path(d, bgm = "VMPA_setas.bgm")))
+#' select_physics = c("salt", "NO3", "NH3", "Temp", "Chl_a", "Denitrifiction")
 #'
 #' test <- load_nc_physics(nc, select_physics, prm_run, bboxes)
-#' str(test)
+#' head(test)
 #'
 #' test <- load_nc_physics(nc, select_physics = "nominal_dz", prm_run, bboxes)
+#' head(test)
 
 load_nc_physics <- function(
   nc,

R/load-txt.R

@@ -41,7 +41,7 @@ load_txt <- function(file, id_col = "Time") {
       names_to = "code",
       values_to = "atoutput"
     ) |>
-    dplyr::arrange(id_col, code)
+    dplyr::arrange(dplyr::across(all_of(id_col)), code)
 
   data$code <- as.character(data$code)
   names(data) <- tolower(names(data))

data-raw/data-create-reference-dfs.R

@@ -12,8 +12,10 @@ ssb <- file.path(d, "outputSETASSSB.txt")
 prm_biol <- file.path(d, "VMPA_setas_biol_fishing_Trunk.prm")
 prm_run <- file.path(d, "VMPA_setas_run_fishing_F_Trunk.prm")
 
-boundary_boxes <- get_boundary(boxinfo = load_box(bgm = bgm))
-epibenthic_groups <- load_bps(fgs = fgs, init = init)
+boundary_boxes <- atlantistools::get_boundary(
+  boxinfo = atlantistools::load_box(bgm = bgm)
+)
+epibenthic_groups <- atlantistools::load_bps(fgs = fgs, init = init)
 groups <- c(
   "Planktiv_S_Fish",
   "Pisciv_S_Fish",
@@ -25,7 +27,7 @@ groups <- c(
 )
 groups_age <- groups[1:2]
 groups_rest <- groups[3:length(groups)]
-bio_conv <- get_conv_mgnbiot(prm_biol = prm_biol)
+bio_conv <- atlantistools::get_conv_mgnbiot(prm_biol = prm_biol)
 
 # Create reference dataframes ---------------------------------------------------------------------
 vars <- list("Nums", "StructN", "ResN", "Growth", "Eat", "Grazing", "N")
@@ -40,7 +42,7 @@ grps <- list(
   groups_rest
 )
 dfs <- Map(
-  load_nc,
+  atlantistools::load_nc,
   nc = ncs,
   select_variable = vars,
   select_groups = grps,
@@ -60,39 +62,39 @@ ref_eat <- dfs[[5]]
 ref_grazing <- dfs[[6]]
 ref_n <- dfs[[7]]
 
-ref_vol_dz <- load_nc_physics(
+ref_vol_dz <- atlantistools::load_nc_physics(
   nc = nc_gen,
   select_physics = c("volume", "dz"),
   prm_run = prm_run,
   bboxes = boundary_boxes,
   aggregate_layers = F
 )
 
-ref_vol <- load_nc_physics(
+ref_vol <- atlantistools::load_nc_physics(
   nc = nc_gen,
   select_physics = "volume",
   prm_run = prm_run,
   bboxes = boundary_boxes,
   aggregate_layers = F
 )
 
-ref_physics <- load_nc_physics(
+ref_physics <- atlantistools::load_nc_physics(
   nc = nc_gen,
   select_physics = c("salt", "NO3", "NH3", "Temp", "Chl_a", "Denitrifiction"),
   prm_run = prm_run,
   bboxes = boundary_boxes,
   aggregate_layers = F
 )
 
-ref_dm <- load_dietcheck(
+ref_dm <- atlantistools::load_dietcheck(
   dietcheck = dietcheck,
   fgs = fgs,
   prm_run = prm_run,
   version_flag = 2,
   convert_names = TRUE
 )
 
-ref_bio_sp <- calculate_biomass_spatial(
+ref_bio_sp <- atlantistools::calculate_biomass_spatial(
   nums = ref_nums,
   sn = ref_structn,
   rn = ref_resn,
@@ -102,25 +104,29 @@ ref_bio_sp <- calculate_biomass_spatial(
   bps = epibenthic_groups
 )
 
-ref_bio_cons <- calculate_consumed_biomass(
+ref_bio_cons <- atlantistools::calculate_consumed_biomass(
   eat = ref_eat,
   grazing = ref_grazing,
   dm = ref_dm,
   vol = ref_vol,
   bio_conv = bio_conv
 )
 
-ref_dietmatrix <- load_dietmatrix(prm_biol, fgs, convert_names = TRUE)
+ref_dietmatrix <- atlantistools::load_dietmatrix(
+  prm_biol,
+  fgs,
+  convert_names = TRUE
+)
 
-ref_agemat <- prm_to_df(
+ref_agemat <- atlantistools::prm_to_df(
   prm_biol = prm_biol,
   fgs = fgs,
-  group = get_age_acronyms(fgs = fgs),
+  group = atlantistools::get_age_acronyms(fgs = fgs),
   parameter = "age_mat"
 )
 
 # Save to HDD and cleanup -------------------------------------------------------------------------
-devtools::use_data(
+usethis::use_data(
   ref_eat,
   ref_grazing,
   ref_n,

tests/testthat/test-load-dietcheck.R

@@ -1,27 +1,23 @@
 context("load_dietcheck test datastructure")
 
-diet <- ref_dm
 
-d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
+test_that("test output numbers trunk", {
+  diet <- ref_dm
 
-diet2 <- load_dietcheck(
-  dietcheck = file.path(d, "outputSETASDietCheck.txt"),
-  fgs = file.path(d, "SETasGroupsDem_NoCep.csv"),
-  prm_run = file.path(d, "VMPA_setas_run_fishing_F_Trunk.prm"),
-  report = FALSE,
-  version_flag = 2
-)
+  d <- system.file(
+    "extdata",
+    "setas-model-new-trunk",
+    package = "atlantistools"
+  )
 
-# This is only used for code-coverage purposes.
-diet3 <- suppressWarnings(load_dietcheck(
-  dietcheck = file.path(d, "outputSETASDietCheck.txt"),
-  fgs = file.path(d, "SETasGroupsDem_NoCep.csv"),
-  prm_run = file.path(d, "VMPA_setas_run_fishing_F_Trunk.prm"),
-  report = TRUE,
-  version_flag = 2
-))
+  diet2 <- load_dietcheck(
+    dietcheck = file.path(d, "outputSETASDietCheck.txt"),
+    fgs = file.path(d, "SETasGroupsDem_NoCep.csv"),
+    prm_run = file.path(d, "VMPA_setas_run_fishing_F_Trunk.prm"),
+    report = FALSE,
+    version_flag = 2
+  )
 
-test_that("test output numbers trunk", {
   # expect_true(all(abs(test1$check - 1) < 0.001))
   expect_equal(dim(diet), c(241, 5))
   expect_is(diet$pred, "character")
@@ -55,7 +51,8 @@ test_that("test output numbers trunk", {
         diet2$agecl == 2 &
         diet2$prey == "PL"
     ],
-    2.680623e-001
+    2.680623e-001,
+    tolerance = 1e-3
   )
   expect_equal(
     diet2$atoutput[
@@ -64,6 +61,7 @@ test_that("test output numbers trunk", {
         diet2$agecl == 1 &
         diet2$prey == "CEP"
     ],
-    6.483338e-001
+    6.483338e-001,
+    tolerance = 1e-3
   )
 })