tests/testthat/test-create_non_empty_island.R
In joshwlambert/DAISIEmainland: Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics
# For reference on the appendix scenarios see: # nolint documentation
# inst/extdata/DAISIEmainland_appendix_a.pdf # nolint documentation
test_that("appendix scenario A1", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 1),
mainland_clade = create_test_mainland_clade(mainland_scenario = 1),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 4)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A2", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 2),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A3", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 3),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 4)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A4", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 4),
mainland_clade = create_test_mainland_clade(mainland_scenario = 3),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.99999))
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 5)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scnario A5", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 5),
mainland_clade = create_test_mainland_clade(mainland_scenario = 4),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A6", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 6),
mainland_clade = create_test_mainland_clade(mainland_scenario = 5),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.99999))
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 5)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A7", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 7),
mainland_clade = create_test_mainland_clade(mainland_scenario = 4),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 4)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A8", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 8),
mainland_clade = create_test_mainland_clade(mainland_scenario = 6),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.5))
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A9", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 9),
mainland_clade = create_test_mainland_clade(mainland_scenario = 5),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.99999))
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 5)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A10", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 10),
mainland_clade = create_test_mainland_clade(mainland_scenario = 1),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A11", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 11),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A12", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 12),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A13", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 13),
mainland_clade = create_test_mainland_clade(mainland_scenario = 3),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.99999))
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 5)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A14", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 14),
mainland_clade = create_test_mainland_clade(mainland_scenario = 7),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A15", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 15),
mainland_clade = create_test_mainland_clade(mainland_scenario = 8),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.99999))
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 5)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A16", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 16),
mainland_clade = create_test_mainland_clade(mainland_scenario = 4),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A17", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 17),
mainland_clade = create_test_mainland_clade(mainland_scenario = 6),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$ideal_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.5))
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A18", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 18),
mainland_clade = create_test_mainland_clade(mainland_scenario = 5),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.99999))
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 5)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A19", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 19),
mainland_clade = create_test_mainland_clade(mainland_scenario = 1),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.50))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A20", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 20),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.42))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A21", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 21),
mainland_clade = create_test_mainland_clade(mainland_scenario = 3),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.5))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.5)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A22", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 22),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33, 0.17))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A23", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 23),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.42))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A24", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 24),
mainland_clade = create_test_mainland_clade(mainland_scenario = 9),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.42))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.42)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A25", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 25),
mainland_clade = create_test_mainland_clade(mainland_scenario = 10),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33, 0.17))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A26", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 26),
mainland_clade = create_test_mainland_clade(mainland_scenario = 6),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33, 0.17))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.50, 0.17)
)
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A27", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 27),
mainland_clade = create_test_mainland_clade(mainland_scenario = 5),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33, 0.09))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.09)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A28", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 28),
mainland_clade = create_test_mainland_clade(mainland_scenario = 1),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.67))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A29", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 29),
mainland_clade = create_test_mainland_clade(mainland_scenario = 3),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.67))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.84, 0.67)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A30", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 30),
mainland_clade = create_test_mainland_clade(mainland_scenario = 11),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.67))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A31", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 31),
mainland_clade = create_test_mainland_clade(mainland_scenario = 12),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.67))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A32", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 32),
mainland_clade = create_test_mainland_clade(mainland_scenario = 13),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.67))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.84, 0.67)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A33", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 33),
mainland_clade = create_test_mainland_clade(mainland_scenario = 14),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.67, 0.5))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A34", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 34),
mainland_clade = create_test_mainland_clade(mainland_scenario = 15),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.67, 0.5))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.84, 0.67, 0.5)
)
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A35", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 35),
mainland_clade = create_test_mainland_clade(mainland_scenario = 16),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.67, 0.5))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.67, 0.5)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A36", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 36),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 4)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
})
test_that("appendix scenario A37", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 37),
mainland_clade = create_test_mainland_clade(mainland_scenario = 4),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 4)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
})
test_that("appendix scenario A38", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 38),
mainland_clade = create_test_mainland_clade(mainland_scenario = 6),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 2)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
expect_length(island$empirical_island, 2)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
expect_equal(island$empirical_island[[2]]$branching_times, c(1.00, 0.5))
expect_identical(island$empirical_island[[2]]$stac, 2)
expect_identical(island$empirical_island[[2]]$missing_species, 0)
})
test_that("appendix scenario A39", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 39),
mainland_clade = create_test_mainland_clade(mainland_scenario = 5),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 2)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.84)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A40", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 40),
mainland_clade = create_test_mainland_clade(mainland_scenario = 17),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.58))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 4)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
})
test_that("appendix scenario A41", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 41),
mainland_clade = create_test_mainland_clade(mainland_scenario = 18),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.58))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 4)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
})
test_that("appendix scenario A42", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 42),
mainland_clade = create_test_mainland_clade(mainland_scenario = 19),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.58))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 2)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
expect_length(island$empirical_island, 2)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.58))
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
expect_equal(island$empirical_island[[2]]$branching_times, c(1.00, 0.5))
expect_identical(island$empirical_island[[2]]$stac, 2)
expect_identical(island$empirical_island[[2]]$missing_species, 0)
})
test_that("appendix scenario A43", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 43),
mainland_clade = create_test_mainland_clade(mainland_scenario = 20),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.58))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 2)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.67, 0.58)
)
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
joshwlambert/DAISIEmainland documentation built on July 14, 2024, 5:40 p.m.
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# For reference on the appendix scenarios see: # nolint documentation
# inst/extdata/DAISIEmainland_appendix_a.pdf # nolint documentation
test_that("appendix scenario A1", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 1),
mainland_clade = create_test_mainland_clade(mainland_scenario = 1),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 4)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A2", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 2),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A3", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 3),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 4)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A4", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 4),
mainland_clade = create_test_mainland_clade(mainland_scenario = 3),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.99999))
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 5)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scnario A5", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 5),
mainland_clade = create_test_mainland_clade(mainland_scenario = 4),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A6", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 6),
mainland_clade = create_test_mainland_clade(mainland_scenario = 5),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.99999))
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 5)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A7", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 7),
mainland_clade = create_test_mainland_clade(mainland_scenario = 4),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 4)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A8", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 8),
mainland_clade = create_test_mainland_clade(mainland_scenario = 6),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.5))
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A9", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 9),
mainland_clade = create_test_mainland_clade(mainland_scenario = 5),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.99999))
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 5)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A10", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 10),
mainland_clade = create_test_mainland_clade(mainland_scenario = 1),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A11", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 11),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A12", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 12),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A13", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 13),
mainland_clade = create_test_mainland_clade(mainland_scenario = 3),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.99999))
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 5)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A14", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 14),
mainland_clade = create_test_mainland_clade(mainland_scenario = 7),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A15", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 15),
mainland_clade = create_test_mainland_clade(mainland_scenario = 8),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.99999))
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 5)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A16", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 16),
mainland_clade = create_test_mainland_clade(mainland_scenario = 4),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A17", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 17),
mainland_clade = create_test_mainland_clade(mainland_scenario = 6),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$ideal_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.5))
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A18", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 18),
mainland_clade = create_test_mainland_clade(mainland_scenario = 5),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.99999))
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 5)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A19", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 19),
mainland_clade = create_test_mainland_clade(mainland_scenario = 1),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.50))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A20", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 20),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.42))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A21", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 21),
mainland_clade = create_test_mainland_clade(mainland_scenario = 3),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.5))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.5)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A22", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 22),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33, 0.17))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A23", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 23),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.42))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A24", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 24),
mainland_clade = create_test_mainland_clade(mainland_scenario = 9),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.42))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.42)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A25", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 25),
mainland_clade = create_test_mainland_clade(mainland_scenario = 10),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33, 0.17))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A26", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 26),
mainland_clade = create_test_mainland_clade(mainland_scenario = 6),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33, 0.17))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.50, 0.17)
)
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A27", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 27),
mainland_clade = create_test_mainland_clade(mainland_scenario = 5),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.33, 0.09))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.09)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A28", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 28),
mainland_clade = create_test_mainland_clade(mainland_scenario = 1),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.67))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A29", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 29),
mainland_clade = create_test_mainland_clade(mainland_scenario = 3),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.67))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.84, 0.67)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A30", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 30),
mainland_clade = create_test_mainland_clade(mainland_scenario = 11),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.67))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A31", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 31),
mainland_clade = create_test_mainland_clade(mainland_scenario = 12),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.67))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A32", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 32),
mainland_clade = create_test_mainland_clade(mainland_scenario = 13),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84, 0.67))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.84, 0.67)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A33", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 33),
mainland_clade = create_test_mainland_clade(mainland_scenario = 14),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.67, 0.5))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A34", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 34),
mainland_clade = create_test_mainland_clade(mainland_scenario = 15),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.67, 0.5))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.84, 0.67, 0.5)
)
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A35", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 35),
mainland_clade = create_test_mainland_clade(mainland_scenario = 16),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 1)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.67, 0.5))
expect_identical(island$ideal_island[[1]]$stac, 3)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.67, 0.5)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A36", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 36),
mainland_clade = create_test_mainland_clade(mainland_scenario = 2),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 4)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
})
test_that("appendix scenario A37", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 37),
mainland_clade = create_test_mainland_clade(mainland_scenario = 4),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 4)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
})
test_that("appendix scenario A38", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 38),
mainland_clade = create_test_mainland_clade(mainland_scenario = 6),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 2)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
expect_length(island$empirical_island, 2)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
expect_equal(island$empirical_island[[2]]$branching_times, c(1.00, 0.5))
expect_identical(island$empirical_island[[2]]$stac, 2)
expect_identical(island$empirical_island[[2]]$missing_species, 0)
})
test_that("appendix scenario A39", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 39),
mainland_clade = create_test_mainland_clade(mainland_scenario = 5),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.84))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 2)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.99999, 0.84)
)
expect_identical(
island$empirical_island[[1]]$branching_times[1],
island$empirical_island[[1]]$branching_times[2] + 1e-5
)
expect_identical(island$empirical_island[[1]]$stac, 6)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
test_that("appendix scenario A40", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 40),
mainland_clade = create_test_mainland_clade(mainland_scenario = 17),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.58))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 4)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
})
test_that("appendix scenario A41", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 41),
mainland_clade = create_test_mainland_clade(mainland_scenario = 18),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_identical(island$ideal_island, island$empirical_island)
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.58))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 4)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
})
test_that("appendix scenario A42", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 42),
mainland_clade = create_test_mainland_clade(mainland_scenario = 19),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.58))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 2)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
expect_length(island$empirical_island, 2)
expect_equal(island$empirical_island[[1]]$branching_times, c(1.00, 0.58))
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
expect_equal(island$empirical_island[[2]]$branching_times, c(1.00, 0.5))
expect_identical(island$empirical_island[[2]]$stac, 2)
expect_identical(island$empirical_island[[2]]$missing_species, 0)
})
test_that("appendix scenario A43", {
set.seed(
1,
kind = "Mersenne-Twister",
normal.kind = "Inversion",
sample.kind = "Rejection"
)
island <- create_non_empty_island(
total_time = 1,
island_tbl = create_test_island_tbl(island_scenario = 43),
mainland_clade = create_test_mainland_clade(mainland_scenario = 20),
mainland_sample_prob = 1,
mainland_sample_type = "complete"
)
expect_false(identical(island$ideal_island, island$empirical_island))
expect_length(island$ideal_island, 2)
expect_equal(island$ideal_island[[1]]$branching_times, c(1.00, 0.58))
expect_identical(island$ideal_island[[1]]$stac, 2)
expect_identical(island$ideal_island[[1]]$missing_species, 0)
expect_equal(island$ideal_island[[2]]$branching_times, c(1.00, 0.33))
expect_identical(island$ideal_island[[2]]$stac, 2)
expect_identical(island$ideal_island[[2]]$missing_species, 0)
expect_length(island$empirical_island, 1)
expect_equal(
island$empirical_island[[1]]$branching_times,
c(1.00, 0.67, 0.58)
)
expect_identical(island$empirical_island[[1]]$stac, 2)
expect_identical(island$empirical_island[[1]]$missing_species, 0)
})
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