use new dataset in tests/

tests/testthat/test-fb_aggregate_site_data.R

@@ -86,9 +86,9 @@ test_that("fb_aggregate_site_data() works", {
   )
 
   expect_s4_class(ras, "SpatRaster")
-  expect_named(ras, c("sp_001", "sp_002"))
-  expect_equal(dim(ras), c(290, 405, 2))
-  expect_equal(ras[][1816], 1, tolerance = 0.000001)
+  expect_named(ras, c("country", "CGRA", "CLAC"))
+  expect_equal(dim(ras), c(290, 405, 3))
+  expect_equal(ras[][82006], 0, tolerance = 0.000001)
 
 
   # Projected raster
@@ -101,7 +101,7 @@ test_that("fb_aggregate_site_data() works", {
   )
 
   expect_s4_class(ras, "SpatRaster")
-  expect_named(ras, c("sp_001", "sp_002"))
+  expect_named(ras, c("country", "CGRA", "CLAC"))
 
 
   ## Polygon spatial data
@@ -111,17 +111,17 @@ test_that("fb_aggregate_site_data() works", {
   )
 
   expect_s4_class(ras, "SpatRaster")
-  expect_named(ras, c("sp_001", "sp_002"))
-  expect_equal(dim(ras), c(290, 405, 2))
-  expect_equal(ras[][1816], 1, tolerance = 0.000001)
+  expect_named(ras, c("country", "CGRA", "CLAC"))
+  expect_equal(dim(ras), c(290, 405, 3))
+  expect_equal(ras[][82006], 0, tolerance = 0.000001)
 
   # Projected Raster
   expect_silent(
     ras <- fb_aggregate_site_data(site_locations, site_species[, 1:3], tavg_prj)
   )
 
   expect_s4_class(ras, "SpatRaster")
-  expect_named(ras, c("sp_001", "sp_002"))
+  expect_named(ras, c("country", "CGRA", "CLAC"))
 
 
   ## Multiline spatial data
@@ -131,14 +131,14 @@ test_that("fb_aggregate_site_data() works", {
   )
 
   expect_s4_class(ras, "SpatRaster")
-  expect_named(ras, c("sp_001", "sp_002"))
-  expect_equal(dim(ras), c(290, 405, 2))
+  expect_named(ras, c("country", "CGRA", "CLAC"))
+  expect_equal(dim(ras), c(290, 405, 3))
 
   # Projected Raster
   expect_silent(
     ras <- fb_aggregate_site_data(site_lines, site_species[, 1:3], tavg_prj)
   )
 
   expect_s4_class(ras, "SpatRaster")
-  expect_named(ras, c("sp_001", "sp_002"))
+  expect_named(ras, c("country", "CGRA", "CLAC"))
 })

tests/testthat/test-fb_format_site_locations.R

@@ -1,6 +1,6 @@
 # Initial data -----------------------------------------------------------------
 
-filename <- system.file("extdata", "raw_mammals_data.csv", 
+filename <- system.file("extdata", "funbiogeo_raw_data.csv", 
                         package = "funbiogeo")
 all_data <- read.csv(filename)
 
@@ -230,10 +230,10 @@ test_that("fb_format_site_locations() works with valid input", {
   site_locations <- fb_format_site_locations(all_data, "site", "longitude", 
                                                "latitude")
   expect_true(is(site_locations, "sf"))
-  expect_equal(nrow(site_locations), 32L)
+  expect_equal(nrow(site_locations), 4723L)
   expect_equal(ncol(site_locations), 2L)
   expect_true("site" %in% colnames(site_locations))
-  expect_equal(sf::st_coordinates(site_locations)[1, 1][[1]], 59.097357)
+  expect_equal(sf::st_coordinates(site_locations)[1, 1][[1]], 1955000)
 
 
   # Including NA values
@@ -244,5 +244,5 @@ test_that("fb_format_site_locations() works with valid input", {
   site_locations <- fb_format_site_locations(all_data_test, "site", 
                                                "longitude", "latitude", 
                                                na_rm = TRUE)
-  expect_equal(nrow(site_locations), 32L)
+  expect_equal(nrow(site_locations), 4722L)
 })

tests/testthat/test-fb_format_site_species.R

@@ -1,6 +1,6 @@
 test_that("fb_format_site_species() works", {
 
-  filename <- system.file("extdata", "raw_mammals_data.csv", 
+  filename <- system.file("extdata", "funbiogeo_raw_data.csv", 
                           package = "funbiogeo")
   all_data <- read.csv(filename)
 
@@ -110,8 +110,8 @@ test_that("fb_format_site_species() works", {
   )
 
   expect_error(
-    fb_format_site_species(all_data, "site", "genus"),
-    "The column 'genus' is absent from 'data'",
+    fb_format_site_species(all_data, "site", "class"),
+    "The column 'class' is absent from 'data'",
     fixed = TRUE
   )
 
@@ -193,12 +193,12 @@ test_that("fb_format_site_species() works", {
   site_species <- fb_format_site_species(all_data, "site", "species", "count",
                                            na_to_zero = TRUE)
 
-  expect_equal(nrow(site_species), 32L)
-  expect_equal(ncol(site_species), 66L)
+  expect_equal(nrow(site_species), 4723L)
+  expect_equal(ncol(site_species), 27L)
   expect_true("site" %in% colnames(site_species))
-  expect_equal(site_species[1, 3], 0L)
+  expect_equal(site_species[1, 3], 1L)
 
   site_species <- fb_format_site_species(all_data, "site", "species", "count",
                                            na_to_zero = FALSE)
-  expect_equal(site_species[1, 3], NA_real_)
+  expect_equal(site_species[1, 3], 1L)
 })

tests/testthat/test-fb_format_species_categories.R

@@ -1,6 +1,6 @@
 test_that("fb_format_species_categories() works", {
 
-  filename <- system.file("extdata", "raw_mammals_data.csv", 
+  filename <- system.file("extdata", "funbiogeo_raw_data.csv", 
                           package = "funbiogeo")
   all_data <- read.csv(filename)
 
@@ -120,22 +120,22 @@ test_that("fb_format_species_categories() works", {
   # Non-unique categories per species ----
 
   test_data <- all_data
-  test_data[2, 2] <- "Carnivora"
+  test_data[1, "genus"] <- "Pyrus"
 
   expect_error(
-    fb_format_species_categories(test_data, "species", "order"),
+    fb_format_species_categories(test_data, "species", "genus"),
     "Some species have non-unique category values",
     fixed = TRUE
   )
 
   # Working ----
 
   species_categories <- fb_format_species_categories(
-    all_data, "species", "order"
+    all_data, "species", "genus"
   )
   expect_true(is.data.frame(species_categories))
-  expect_equal(nrow(species_categories), 65L)
+  expect_equal(nrow(species_categories), 26L)
   expect_equal(ncol(species_categories), 2L)
   expect_true("species" %in% colnames(species_categories))
-  expect_equal(species_categories[1, 2],"Cetartiodactyla")
+  expect_equal(species_categories[1, 2],"Crataegus")
 })

tests/testthat/test-fb_format_species_traits.R

@@ -1,6 +1,6 @@
 test_that("fb_format_species_traits() works", {
 
-  filename <- system.file("extdata", "raw_mammals_data.csv", 
+  filename <- system.file("extdata", "funbiogeo_raw_data.csv", 
                           package = "funbiogeo")
   all_data <- read.csv(filename)
 
@@ -120,30 +120,26 @@ test_that("fb_format_species_traits() works", {
 
   all_data_test <- all_data
   all_data_test <- rbind(all_data_test[1, ], all_data_test)
-  all_data_test[1, "adult_body_mass"] <- 9999
+  all_data_test[1, "plant_height"] <- 9999
 
   expect_error(
-    fb_format_species_traits(all_data_test, "species", c("adult_body_mass", 
-                                                         "gestation_length",
-                                                         "litter_size",
-                                                         "max_longevity",
-                                                         "sexual_maturity_age",
-                                                         "diet_breadth")),
+    fb_format_species_traits(all_data_test, "species", c("plant_height", 
+                                                         "seed_mass",
+                                                         "sla",
+                                                         "wood_density")),
     "Some species have non-unique trait values",
     fixed = TRUE
   )
 
   all_data_test <- all_data
   all_data_test <- rbind(all_data_test[1, ], all_data_test)
-  all_data_test[1, "adult_body_mass"] <- NA
+  all_data_test[1, "plant_height"] <- NA
 
   expect_error(
-    fb_format_species_traits(all_data_test, "species", c("adult_body_mass", 
-                                                         "gestation_length",
-                                                         "litter_size",
-                                                         "max_longevity",
-                                                         "sexual_maturity_age",
-                                                         "diet_breadth")),
+    fb_format_species_traits(all_data_test, "species", c("plant_height", 
+                                                         "seed_mass",
+                                                         "sla",
+                                                         "wood_density")),
     "Some species have non-unique trait values",
     fixed = TRUE
   )
@@ -153,12 +149,14 @@ test_that("fb_format_species_traits() works", {
 
   species_traits <- fb_format_species_traits(
     all_data, "species",
-    c("adult_body_mass", "gestation_length", "litter_size", "max_longevity",
-      "sexual_maturity_age", "diet_breadth")
+    c("plant_height", 
+      "seed_mass",
+      "sla",
+      "wood_density")
   )
   expect_true(is.data.frame(species_traits))
-  expect_equal(nrow(species_traits), 65L)
-  expect_equal(ncol(species_traits), 7L)
+  expect_equal(nrow(species_traits), 26L)
+  expect_equal(ncol(species_traits), 5L)
   expect_true("species" %in% colnames(species_traits))
   expect_equal(species_traits[1, 3], 235, tolerance = 7)
 })

tests/testthat/test-fb_get_all_trait_coverages_by_site.R

@@ -59,12 +59,12 @@ test_that(
     )
 
     expect_s3_class(res, "data.frame")
-    expect_equal(dim(res), c(1505, 8))
+    expect_equal(dim(res), c(4723, 6))
     expect_equal(
       colnames(res), c("site", "all_traits", colnames(species_traits)[-1])
     )
-    expect_equal(round(res[1, 2], 2), 0.73)
-    expect_equal(round(res[2, 5], 2), 0.97)
+    expect_equal(round(res[1, 2], 2), 1.0)
+    expect_equal(round(res[2, 5], 2), 1.0)
 
     # Without all traits
     expect_silent(
@@ -74,11 +74,11 @@ test_that(
     )
 
     expect_s3_class(res, "data.frame")
-    expect_equal(dim(res), c(1505, 7))
+    expect_equal(dim(res), c(0, 5))
     expect_equal(
       colnames(res), c("site", colnames(species_traits)[-1])
     )
-    expect_equal(round(res[2, 4], 2), 0.91)
+    expect_equal(round(res[2, 4], 2), NA_real_)
 
   }
 )
@@ -94,7 +94,7 @@ test_that("fb_get_all_trait_coverages_by_site() works for edge cases", {
     )
   )
   expect_s3_class(res, "data.frame")
-  expect_equal(dim(res), c(1505, 8))
+  expect_equal(dim(res), c(4723, 6))
   expect_equal(
     colnames(res), c("site", "all_traits", colnames(species_traits)[-1])
   )
@@ -106,7 +106,7 @@ test_that("fb_get_all_trait_coverages_by_site() works for edge cases", {
     )
   )
   expect_s3_class(res, "data.frame")
-  expect_equal(dim(res), c(1505, 8))
+  expect_equal(dim(res), c(4723, 6))
   expect_equal(
     colnames(res), c("site", "all_traits", colnames(species_traits)[-1])
   )
@@ -118,7 +118,7 @@ test_that("fb_get_all_trait_coverages_by_site() works for edge cases", {
     )
   )
   expect_s3_class(res, "data.frame")
-  expect_equal(dim(res), c(1505, 8))
+  expect_equal(dim(res), c(4723, 6))
   expect_equal(
     colnames(res), c("site", "all_traits", colnames(species_traits)[-1])
   )
@@ -132,7 +132,7 @@ test_that("fb_get_all_trait_coverages_by_site() works for edge cases", {
     )
   )
   expect_s3_class(res, "data.frame")
-  expect_equal(dim(res), c(1505, 7))
+  expect_equal(dim(res), c(0, 5))
   expect_equal(
     colnames(res), c("site", colnames(species_traits)[-1])
   )
@@ -144,7 +144,7 @@ test_that("fb_get_all_trait_coverages_by_site() works for edge cases", {
     )
   )
   expect_s3_class(res, "data.frame")
-  expect_equal(dim(res), c(1505, 7))
+  expect_equal(dim(res), c(0, 5))
   expect_equal(
     colnames(res), c("site", colnames(species_traits)[-1])
   )
@@ -156,7 +156,7 @@ test_that("fb_get_all_trait_coverages_by_site() works for edge cases", {
     )
   )
   expect_s3_class(res, "data.frame")
-  expect_equal(dim(res), c(1505, 7))
+  expect_equal(dim(res), c(0, 5))
   expect_equal(
     colnames(res), c("site", colnames(species_traits)[-1])
   )

tests/testthat/test-fb_get_environment.R

@@ -87,8 +87,8 @@ test_that("fb_get_environment() works", {
 
   expect_s3_class(env_value, "data.frame")
   expect_named(env_value, c("site", "annual_mean_temp", "annual_tot_prec"))
-  expect_equal(dim(env_value), c(1505, 3))
-  expect_equal(round(env_value[["annual_tot_prec"]][[1]]), 2620)
+  expect_equal(dim(env_value), c(4723, 3))
+  expect_equal(round(env_value[["annual_tot_prec"]][[3]]), 692)
 
   # Projected layers
   rob <- "+proj=robin +lon_0=0 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs"
@@ -99,8 +99,8 @@ test_that("fb_get_environment() works", {
 
   expect_s3_class(env_value, "data.frame")
   expect_named(env_value, c("site", "annual_mean_temp", "annual_tot_prec"))
-  expect_equal(dim(env_value), c(1505, 3))
-  expect_equal(env_value[["annual_mean_temp"]][[1]], 6.3, tolerance = 0.01)
+  expect_equal(dim(env_value), c(4723, 3))
+  expect_equal(env_value[["annual_mean_temp"]][[1]], 15.7, tolerance = 0.01)
 
 
   ## 'sf' polygons
@@ -109,16 +109,16 @@ test_that("fb_get_environment() works", {
 
   expect_s3_class(env_value, "data.frame")
   expect_named(env_value, c("site", "annual_mean_temp", "annual_tot_prec"))
-  expect_equal(dim(env_value), c(1505, 3))
-  expect_equal(round(env_value[["annual_tot_prec"]][[1]]), 2480)
+  expect_equal(dim(env_value), c(4723, 3))
+  expect_equal(round(env_value[["annual_tot_prec"]][[1]]), 671)
 
   # Projected Layer
   expect_silent(env_value <- fb_get_environment(site_locations, layers_prj))
 
   expect_s3_class(env_value, "data.frame")
   expect_named(env_value, c("site", "annual_mean_temp", "annual_tot_prec"))
-  expect_equal(dim(env_value), c(1505, 3))
-  expect_equal(env_value[["annual_mean_temp"]][[1]], 6.6, tolerance = 0.01)
+  expect_equal(dim(env_value), c(4723, 3))
+  expect_equal(env_value[["annual_mean_temp"]][[1]], 15.7, tolerance = 0.01)
 
 
   ## 'sf' line
@@ -128,13 +128,13 @@ test_that("fb_get_environment() works", {
   expect_s3_class(env_value, "data.frame")
   expect_named(env_value, c("site", "annual_mean_temp", "annual_tot_prec"))
   expect_equal(dim(env_value), c(1, 3))
-  expect_equal(env_value[["annual_mean_temp"]][[1]], 6.3, tolerance = 0.01)
+  expect_equal(env_value[["annual_mean_temp"]][[1]], 15.7, tolerance = 0.01)
 
   # Projected layer
   expect_silent(env_value <- fb_get_environment(site_lines, layers_prj))
 
   expect_s3_class(env_value, "data.frame")
   expect_named(env_value, c("site", "annual_mean_temp", "annual_tot_prec"))
   expect_equal(dim(env_value), c(1, 3))
-  expect_equal(env_value[["annual_mean_temp"]][[1]], 6.38, tolerance = 0.01)
+  expect_equal(env_value[["annual_mean_temp"]][[1]], 15.9, tolerance = 0.01)
 })

tests/testthat/test-fb_get_trait_combination_coverage.R

@@ -52,7 +52,7 @@ test_that("fb_get_trait_combination_coverage() works with good inputs", {
                      "trait_coverage")
   )
   expect_equal(res[1, 2], 1)
-  expect_equal(res[1, 3], "adult_body_mass")
+  expect_equal(res[1, 3], "plant_height")
 
   # Given trait combination
   expect_silent(
@@ -66,5 +66,5 @@ test_that("fb_get_trait_combination_coverage() works with good inputs", {
                      "trait_coverage")
   )
   expect_equal(res[1, 2], 2)
-  expect_equal(res[1, 3], "adult_body_mass__gestation_length")
+  expect_equal(res[1, 3], "plant_height__seed_mass")
 })