context("ggd_create_phylo")
test_that("use, Non_endemic_MaxAge", {
phylo <- ggdaisie:::ggd_create_phylo(
clade_name = "Pyrocephalus rubinus",
status = "Non_endemic_MaxAge",
branching_times = 10.28,
island_age = 4
)
expect_true(class(phylo) == "phylo")
expect_true("status" %in% names(attributes(phylo)))
expect_true(all(attributes(phylo)$status %in% get_ggdaisy_states()))
expect_true(all(levels(attributes(phylo)$status) %in% get_ggdaisy_states()))
})
test_that("use, Non_endemic", {
phylo <- ggdaisie:::ggd_create_phylo(
clade_name = "Dendroica",
status = "Non_endemic",
branching_times = 1.0,
island_age = 4
)
expect_true(class(phylo) == "phylo")
expect_true("status" %in% names(attributes(phylo)))
expect_true(all(attributes(phylo)$status %in% get_ggdaisy_states()))
expect_true(all(levels(attributes(phylo)$status) %in% get_ggdaisy_states()))
})
test_that("use, Non_endemic, specialized function", {
island_age <- 4
phylo <- ggdaisie:::ggd_create_phylo_non_endemic(
taxon_label = "Dendroica",
immigration_time = 1.0,
island_age = island_age
)
expect_true(class(phylo) == "phylo")
expect_true("status" %in% names(attributes(phylo)))
expect_true(all(attributes(phylo)$status %in% get_ggdaisy_states()))
expect_true(all(levels(attributes(phylo)$status) %in% get_ggdaisy_states()))
expect_equal(ggdaisie:::get_crown_age(phylo), island_age)
})
test_that("use, Endemic, 3 branching times", {
phylo <- ggdaisie:::ggd_create_phylo(
clade_name = "Mimus",
status = "Endemic",
branching_times = c(3.958, 3.422,2.884,0.459),
island_age = 4
)
expect_true(class(phylo) == "phylo")
expect_true("status" %in% names(attributes(phylo)))
expect_true(all(attributes(phylo)$status %in% get_ggdaisy_states()))
expect_true(all(levels(attributes(phylo)$status) %in% get_ggdaisy_states()))
})
test_that("use, Endemic, 3 branching times, specialized function", {
island_age <- 4
phylo <- ggdaisie:::ggd_create_phylo_endemic(
clade_label = "Mimus",
immigration_time = 3.958,
branching_times = c(3.422,2.884,0.459),
island_age = island_age
)
expect_true(class(phylo) == "phylo")
expect_true("status" %in% names(attributes(phylo)))
expect_true(all(attributes(phylo)$status %in% get_ggdaisy_states()))
expect_true(all(levels(attributes(phylo)$status) %in% get_ggdaisy_states()))
expect_equal(ggdaisie:::get_crown_age(phylo), island_age)
expect_silent(ape::plot.phylo(phylo))
})
test_that("use, Endemic, 1 branching times", {
phylo <- ggdaisie:::ggd_create_phylo(
clade_name = "Mimus_subset",
status = "Endemic",
branching_times = c(3.958, 3.422),
island_age = 4
)
expect_true(class(phylo) == "phylo")
expect_true("status" %in% names(attributes(phylo)))
expect_true(all(attributes(phylo)$status %in% get_ggdaisy_states()))
expect_true(all(levels(attributes(phylo)$status) %in% get_ggdaisy_states()))
})
test_that("use, Endemic, 1 branching time, specialized function", {
island_age <- 4
phylo <- ggdaisie:::ggd_create_phylo_endemic(
clade_label = "Mimus_subset",
immigration_time = 3.958,
branching_times = c(3.422),
island_age = island_age
)
expect_true(class(phylo) == "phylo")
expect_true("status" %in% names(attributes(phylo)))
expect_true(all(attributes(phylo)$status %in% get_ggdaisy_states()))
expect_true(all(levels(attributes(phylo)$status) %in% get_ggdaisy_states()))
expect_equal(ggdaisie:::get_crown_age(phylo), island_age)
expect_silent(ape::plot.phylo(phylo))
})
test_that("use, Endemic, 0 branching times", {
phylo <- ggdaisie:::ggd_create_phylo(
clade_name = "Myiarchus",
status = "Endemic",
branching_times = c(0.855),
island_age = 4
)
expect_true(class(phylo) == "phylo")
expect_true("status" %in% names(attributes(phylo)))
expect_true(all(attributes(phylo)$status %in% get_ggdaisy_states()))
expect_true(all(levels(attributes(phylo)$status) %in% get_ggdaisy_states()))
})
test_that("use, Endemic, 0 branching times, specialized function", {
island_age <- 4
phylo <- ggdaisie:::ggd_create_phylo_endemic(
clade_label = "Myiarchus",
immigration_time = 0.855,
branching_times = c(),
island_age = island_age
)
expect_true(class(phylo) == "phylo")
expect_true("status" %in% names(attributes(phylo)))
expect_true(all(attributes(phylo)$status %in% get_ggdaisy_states()))
expect_true(all(levels(attributes(phylo)$status) %in% get_ggdaisy_states()))
expect_equal(ggdaisie:::get_crown_age(phylo), island_age)
expect_silent(ape::plot.phylo(phylo))
})
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