Nothing
test_that("Clean run should be silent", {
set.seed(42)
n_mainland_species <- 1
sim_time <- 10
clado_rate <- 1.0
ext_rate <- 0.1
carr_cap <- 4
imm_rate <- 1.0
ana_rate <- 1.0
area_pars <- create_area_pars(
max_area = 1,
current_area = 1,
proportional_peak_t = 0,
total_island_age = 0,
sea_level_amplitude = 0,
sea_level_frequency = 0,
island_gradient_angle = 0)
hyper_pars <- create_hyper_pars(d = 0, x = 0)
nonoceanic_pars <- c(0, 0)
testthat::expect_silent(
DAISIE_sim_core_cr(
time = sim_time,
mainland_n = n_mainland_species,
pars = c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate),
area_pars = area_pars,
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars
)
)
})
test_that("A non-oceanic run with non-zero sampling should have native
species on the island", {
area_pars <- create_area_pars(
max_area = 1,
current_area = 1,
proportional_peak_t = 0,
total_island_age = 0,
sea_level_amplitude = 0,
sea_level_frequency = 0,
island_gradient_angle = 0)
hyper_pars <- create_hyper_pars(d = 0, x = 0)
nonoceanic_sim <- DAISIE_sim_core_cr(
time = 0.4,
mainland_n = 1000,
pars = c(
2.550687345,
2.683454548,
10.0,
0.00933207,
1.010073119),
area_pars = area_pars,
hyper_pars = hyper_pars,
nonoceanic_pars = c(0.1, 0.9)
)
testthat::expect_gt(nonoceanic_sim$stt_table[1, 2], 0)
testthat::expect_gt(nonoceanic_sim$stt_table[1, 3], 0)
})
test_that("DAISIE_sim_core output is correct", {
time <- 1
mainland_n <- 100
set.seed(5)
area_pars <- create_area_pars(
max_area = 1,
current_area = 1,
proportional_peak_t = 0,
total_island_age = 0,
sea_level_amplitude = 0,
sea_level_frequency = 0,
island_gradient_angle = 0)
nonoceanic_pars <- c(0, 0)
hyper_pars <- create_hyper_pars(d = 0, x = 0)
sim_core <- DAISIE_sim_core_cr(
time = time,
mainland_n = mainland_n,
pars = c(2, 2, 20, 0.1, 1),
area_pars = area_pars,
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars
)
testthat::expect_true(is.matrix(sim_core$stt_table))
testthat::expect_true(sim_core$stt_table[1, 1] == time)
testthat::expect_true(sim_core$stt_table[nrow(sim_core$stt_table), 1] == 0)
testthat::expect_true(is.numeric(sim_core$taxon_list[[1]]$branching_times))
testthat::expect_true(is.numeric(sim_core$taxon_list[[1]]$stac))
testthat::expect_true(is.numeric(sim_core$taxon_list[[1]]$missing_species))
testthat::expect_true(length(sim_core$taxon_list) == 5)
testthat::expect_true("branching_times" %in% names(sim_core$taxon_list[[1]]))
testthat::expect_true("stac" %in% names(sim_core$taxon_list[[1]]))
testthat::expect_true("missing_species" %in% names(sim_core$taxon_list[[1]]))
})
test_that("DAISIE_sim_core with land-bridge starting at time = 0 for CS uses
the second parameter set at time = 0", {
area_pars <- create_area_pars(
max_area = 1,
current_area = 1,
proportional_peak_t = 0,
total_island_age = 0,
sea_level_amplitude = 0,
sea_level_frequency = 0,
island_gradient_angle = 0)
hyper_pars <- create_hyper_pars(d = 0, x = 0)
testthat::expect_silent(
DAISIE_sim_core_cr_shift(
time = 10,
mainland_n = 1,
pars = c(1, 1, 10, 0.1, 1, 2, 2, 20, 0.2, 1),
shift_times = 10,
area_pars = area_pars,
hyper_pars = hyper_pars
)
)
})
test_that("DAISIE_sim_core fails when pars[4] == 0 &&
nonoceanic_pars[1] == 0", {
area_pars <- create_area_pars(
max_area = 1,
current_area = 1,
proportional_peak_t = 0,
total_island_age = 0,
sea_level_amplitude = 0,
sea_level_frequency = 0,
island_gradient_angle = 0)
nonoceanic_pars <- c(0, 0)
hyper_pars <- create_hyper_pars(d = 0, x = 0)
testthat::expect_error(
DAISIE_sim_core_cr(
time = 1,
mainland_n = 100,
pars = c(2, 2, 20, 0, 1),
area_pars = area_pars,
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars
)
)
})
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