# Preamble code ----------------------------------------------------------------
data("traits_birds")
traits_birds_sc <- scale(traits_birds)
# Tests for valid inputs -------------------------------------------------------
test_that("Functional Divergence output format", {
fdiv <- expect_silent(fd_fdiv(traits_birds))
expect_s3_class(fdiv, "data.frame")
expect_identical(dim(fdiv), c(1L, 2L))
expect_named(fdiv, c("site", "FDiv"))
expect_equal(fdiv$FDiv, 0.7282172, tolerance = 1e-7)
})
test_that("Functional Divergence works on subset of site/species", {
site_sp <- matrix(1, ncol = nrow(traits_birds))
colnames(site_sp) <- rownames(traits_birds)
rownames(site_sp) <- "s1"
expect_message(fd_fdiv(traits_birds, site_sp[, 2:ncol(site_sp),
drop = FALSE]),
paste0("Differing number of species between trait dataset ",
"and site-species matrix\nTaking subset of species"))
expect_message(fd_fdiv(traits_birds[2:nrow(traits_birds),], site_sp),
paste0("Differing number of species between trait dataset ",
"and site-species matrix\nTaking subset of species"))
})
test_that("Functional Divergence works for site with no species", {
data("traits_plants")
data("site_sp_plants")
fdiv <- expect_silent(
fd_fdiv(traits_plants, site_sp_plants[10,, drop = FALSE])
)
expect_identical(fdiv$FDiv[[1]], 0)
})
test_that("Functional Divergence works in 1D", {
expect_identical(
fd_fdiv(traits_birds[, 1]),
fd_fdiv(traits_birds[, 1, drop = FALSE])
)
})
test_that("Functional Divergence works with sparse matrices", {
skip_if_not_installed("Matrix")
site_sp <- matrix(1, ncol = nrow(traits_birds))
colnames(site_sp) <- rownames(traits_birds)
rownames(site_sp) <- "s1"
sparse_site_sp <- Matrix(site_sp, sparse = TRUE)
fdiv <- expect_silent(fd_fdiv(traits_birds, sparse_site_sp))
expect_s3_class(fdiv, "data.frame")
expect_identical(dim(fdiv), c(1L, 2L))
expect_named(fdiv, c("site", "FDiv"))
expect_equal(
fd_fdiv(traits_birds, sparse_site_sp),
fd_fdiv(traits_birds, site_sp)
)
})
test_that("Functional Divergence works with matrices without rownames", {
traits_birds_un <- traits_birds
rownames(traits_birds_un) <- NULL
expect_identical(
fd_fdiv(traits_birds_un),
fd_fdiv(traits_birds)
)
})
test_that("Functional Divergence works on data.frame as well as matrix", {
site_sp <- matrix(1, ncol = nrow(traits_birds))
colnames(site_sp) <- rownames(traits_birds)
rownames(site_sp) <- "s1"
site_sp_df <- as.data.frame(site_sp)
fdiv <- expect_silent(fd_fdiv(traits_birds, site_sp))
fdiv_df <- expect_silent(fd_fdiv(traits_birds, site_sp_df))
expect_s3_class(fdiv, "data.frame")
expect_identical(dim(fdiv), c(1L, 2L))
expect_named(fdiv, c("site", "FDiv"))
expect_equal(
fdiv,
fdiv_df
)
})
test_that("Functional Divergence works when sites have no names", {
site_sp_no_names <- site_sp_birds[1,, drop = FALSE]
rownames(site_sp_no_names) <- NULL
fdiv <- expect_silent(fd_fdiv(traits_birds, site_sp_no_names))
expect_s3_class(fdiv, "data.frame")
expect_identical(dim(fdiv), c(1L, 2L))
expect_named(fdiv, c("site", "FDiv"))
expect_equal(fdiv$FDiv, 0.6847251, tolerance = 1e-7)
expect_equal(fdiv[1, "site"], "s1")
})
test_that("Functional Divergence works with unmemoised version", {
withr::local_options(fundiversity.memoise = FALSE)
fdiv <- expect_silent(fd_fdiv(traits_birds))
expect_equal(fdiv$FDiv, 0.7282172, tolerance = 1e-7)
})
# Tests for invalid inputs -----------------------------------------------------
test_that("Functional Divergence fails gracefully", {
# No traits
expect_error(
fd_fdiv(NULL, matrix(1)),
"Please provide a trait dataset", fixed = TRUE
)
# Species matrix doesn't contain species from trait data
expect_error(
fd_fdiv(data.frame(a = 1, row.names = "sp1"), matrix(1)),
paste0("No species in common found between trait dataset ",
"and site-species matrix"),
fixed = TRUE
)
## Categorical trait data
# Add non-continuous traits
traits_birds_cat <- as.data.frame(traits_birds_sc)
traits_birds_cat$cat_trait <- "a"
expect_error(
fd_fdiv(traits_birds_cat, site_sp_birds),
paste0("Non-continuous trait data found in input traits. ",
"Please provide only continuous trait data"),
fixed = TRUE
)
})
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