Nothing
test_that("get_pam works", {
require(terra)
#Load Brazilian Flora data
data("bf_data")
#Select endemic and native species of trees with occurrence only in Amazon
am_trees <- select_species(data = bf_data,
include_subspecies = FALSE,
include_variety = FALSE,
kingdom = "Plantae",
group = "All", subgroup = "All",
family = "All", genus = "All",
lifeForm = "Tree", filter_lifeForm = "only",
habitat = "All", filter_habitat = "in",
biome = "Amazon",
filter_biome = "only",
state = "All", filter_state = "and",
vegetation = "All",
filter_vegetation = "in",
endemism = "Endemic", origin = "Native",
taxonomicStatus = "Accepted",
nomenclaturalStatus = "All")
#Get presence-absence matrix
pam_am <- get_pam(data = am_trees, by_biome = TRUE, by_state = TRUE,
by_vegetation = FALSE, remove_empty_sites = TRUE,
return_richness_summary = TRUE,
return_spatial_richness = TRUE,
return_plot = TRUE)
expect_equal(class(pam_am), "list")
expect_equal(length(pam_am), 3)
expect_equal(class(pam_am[[1]]), "data.frame")
expect_equal(ncol(pam_am[[1]]), nrow(am_trees) + 2)
expect_equal(class(pam_am[[2]]), "data.frame")
expect_equal(class(pam_am[[3]]), "SpatVector", ignore_attr = TRUE)
#Get presence-absence matrix, without return richness summary
pam_am_not_richness <- get_pam(data = am_trees, by_biome = TRUE, by_state = TRUE,
by_vegetation = FALSE, remove_empty_sites = TRUE,
return_richness_summary = FALSE,
return_spatial_richness = TRUE,
return_plot = TRUE)
expect_equal(class(pam_am_not_richness), "list")
expect_equal(length(pam_am_not_richness), 2)
expect_equal(class(pam_am_not_richness[[1]]), "data.frame")
expect_equal(ncol(pam_am_not_richness[[1]]), nrow(am_trees) + 2)
expect_equal(class(pam_am_not_richness[[2]]), "SpatVector", ignore_attr = TRUE)
#Get presence-absence matrix, without return spatial_richness
pam_am_not_spatial <- get_pam(data = am_trees, by_biome = TRUE, by_state = TRUE,
by_vegetation = FALSE, remove_empty_sites = TRUE,
return_richness_summary = TRUE,
return_spatial_richness = FALSE,
return_plot = TRUE)
expect_equal(class(pam_am_not_spatial), "list")
expect_equal(length(pam_am_not_spatial), 2)
expect_equal(class(pam_am_not_spatial[[1]]), "data.frame")
expect_equal(ncol(pam_am_not_spatial[[1]]), nrow(am_trees) + 2)
expect_equal(class(pam_am_not_spatial[[2]]), "data.frame")
#Get presence-absence matrix, only PAM
pam_am_only_pam <- get_pam(data = am_trees, by_biome = TRUE, by_state = TRUE,
by_vegetation = FALSE, remove_empty_sites = TRUE,
return_richness_summary = FALSE,
return_spatial_richness = FALSE,
return_plot = TRUE)
expect_equal(class(pam_am_only_pam), "data.frame")
expect_equal(ncol(pam_am_only_pam), nrow(am_trees) + 2)
#Get presence-absence matrix, only PAM, using vegetation type
expect_no_error(get_pam(data = am_trees, by_biome = TRUE, by_state = TRUE,
by_vegetation = TRUE, remove_empty_sites = TRUE,
return_richness_summary = FALSE,
return_spatial_richness = FALSE,
return_plot = TRUE))
#Get presence-absence matrix, only PAM, using vegetation type, but not state
expect_no_error(get_pam(data = am_trees, by_biome = TRUE, by_state = FALSE,
by_vegetation = TRUE, remove_empty_sites = TRUE,
return_richness_summary = FALSE,
return_spatial_richness = FALSE,
return_plot = TRUE))
#Get presence-absence matrix, only PAM, using vegetation type, but not biome
expect_no_error(get_pam(data = am_trees, by_biome = FALSE, by_state = TRUE,
by_vegetation = TRUE, remove_empty_sites = TRUE,
return_richness_summary = FALSE,
return_spatial_richness = FALSE,
return_plot = TRUE))
####It does not work when we don't set data####
expect_error(get_pam(by_biome = TRUE, by_state = TRUE,
by_vegetation = FALSE, remove_empty_sites = TRUE,
return_richness_summary = FALSE,
return_spatial_richness = FALSE,
return_plot = TRUE))
####It does not work when we biome, state and Vegetatio are set to FALSE####
expect_error(get_pam(data = am_trees, by_biome = FALSE, by_state = FALSE,
by_vegetation = FALSE, remove_empty_sites = TRUE,
return_richness_summary = FALSE,
return_spatial_richness = FALSE,
return_plot = TRUE))
})
####Test errors####
test_that("get_pam does not work", {
require(terra)
#Load Brazilian Flora data
data("bf_data")
#Select endemic and native species of trees with occurrence only in Amazon
am_trees <- select_species(data = bf_data,
include_subspecies = FALSE,
include_variety = FALSE,
kingdom = "Plantae",
group = "All", subgroup = "All",
family = "All", genus = "All",
lifeForm = "Tree", filter_lifeForm = "only",
habitat = "All", filter_habitat = "in",
biome = "Amazon",
filter_biome = "only",
state = "All", filter_state = "and",
vegetation = "All",
filter_vegetation = "in",
endemism = "Endemic", origin = "Native",
taxonomicStatus = "Accepted",
nomenclaturalStatus = "All")
expect_error(get_pam(data = TRUE))
expect_error(get_pam(data = bf_data, by_biome = "TRUE"))
expect_error(get_pam(data = bf_data, by_state = "TRUE"))
expect_error(get_pam(data = bf_data, by_vegetation = "TRUE"))
expect_error(get_pam(data = bf_data, remove_empty_sites = "TRUE"))
expect_error(get_pam(data = bf_data, return_richness_summary = "TRUE"))
expect_error(get_pam(data = bf_data, return_spatial_richness = "TRUE"))
bf_data2 <- bf_data[, setdiff(colnames(bf_data), "species")]
expect_error(get_pam(data = bf_data2))
expect_error(get_pam(data = bf_data, by_biome = FALSE, by_state = FALSE,
by_vegetation = TRUE,
return_spatial_richness = TRUE))
})
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