Nothing
test_that("sampled stt, 1 type, no geodynamics, oceanic island (same arguments as geodynamics, 5 pars)", {
pars <- c(0.5, 0.1, 10, 0.01, 0.5)
total_time <- 1
mainland_n <- 100
verbose <- FALSE
sample_freq <- 1
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)
replicates <- 1
cond <- 1
set.seed(1)
island_replicates <- list()
for (rep in seq_along(replicates)) {
if (cond == 0) {
number_present <- -1
} else {
number_present <- 0
}
while (number_present < cond) {
island_replicates[[rep]] <- DAISIE_sim_core_cr(
time = total_time,
mainland_n = mainland_n,
pars = pars,
nonoceanic_pars = nonoceanic_pars,
hyper_pars = hyper_pars,
area_pars = area_pars
)
stac_vec <- unlist(island_replicates)[which(
names(unlist(island_replicates)) == "taxon_list.stac"
)]
present <- which(stac_vec != 0)
number_present <- length(present)
}
}
testthat::expect_silent(
formatted_IW_sim <- DAISIE_format_IW_sampled_stt(
island_replicates = island_replicates,
total_time = total_time,
M = mainland_n,
sample_freq = sample_freq,
verbose = verbose
)
)
expected_IW_format <- list()
expected_IW_format[[1]] <- list()
stt_all <- matrix(ncol = 4, nrow = 2)
colnames(stt_all) <- c("Time", "nI", "nA", "nC")
stt_all[1, ] <- c(1, 0, 0, 0)
stt_all[2, ] <- c(0, 0, 0, 3)
expected_brts_table <- matrix(
data = c(
1.0, 0.0, 0.0, NA, NA,
0.244818166871655, 1, 1, 1, NA,
0.173128288990374, 1, 2, 1, NA,
0.029668240213840, 1, 3, 1, NA
),
ncol = 5,
byrow = TRUE
)
colnames(expected_brts_table) <- c("brt", "clade", "event", "endemic", "col")
expected_IW_format[[1]][[1]] <- list(island_age = 1,
not_present = 99,
stt_all = stt_all,
brts_table = expected_brts_table)
expected_IW_format[[1]][[2]] <- list(branching_times = c(1.000000000000000,
0.244818166871655,
0.173128288990374,
0.029668240213840),
stac = 2,
missing_species = 0)
testthat::expect_equal(object = formatted_IW_sim, expected = expected_IW_format)
})
test_that("sampled stt, 1 type, geodynamics, oceanic island (same arguments as no geodynamics, 5 pars)", {
total_time <- 1
mainland_n <- 100
verbose <- FALSE
sample_freq <- 25
set.seed(3)
island_replicates <- list()
out <- list()
ext_pars <- c(1, 100)
island_ontogeny <- 1
sea_level <- 0
pars <- c(0.0001, 2.2, 0.005, 1, 1)
area_pars <- create_area_pars(
max_area = 5000,
current_area = 2500,
proportional_peak_t = 0.5,
total_island_age = 5,
sea_level_amplitude = 0,
sea_level_frequency = 0,
island_gradient_angle = 0
)
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
peak <- calc_peak(total_time = total_time,
area_pars = area_pars)
Amax <- get_global_max_area(total_time = total_time,
area_pars = area_pars,
peak = peak,
island_ontogeny = island_ontogeny,
sea_level = sea_level)
Amin <- get_global_min_area(total_time = total_time,
area_pars = area_pars,
peak = peak,
island_ontogeny = island_ontogeny,
sea_level = sea_level)
nonoceanic_pars <- c(0, 0)
island_replicates[[1]] <- DAISIE_sim_core_time_dep(
time = total_time,
pars = pars,
mainland_n = mainland_n,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
hyper_pars = hyper_pars,
area_pars = area_pars,
peak = peak,
Amax = Amax,
Amin = Amin,
nonoceanic_pars = nonoceanic_pars
)
testthat::expect_silent(
formatted_IW_sim <- DAISIE_format_IW_sampled_stt(
island_replicates = island_replicates,
total_time = total_time,
M = mainland_n,
sample_freq = sample_freq,
verbose = verbose
)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$island_age,
total_time
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$not_present,
90
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$stt_all[5, ],
c(Time = 0.84, nI = 1.0, nA = 0.0, nC = 0.0)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$stt_all[12, ],
c(Time = 0.56, nI = 4.0, nA = 1.0, nC = 0.0)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$stt_all[25, ],
c(Time = 0.04, nI = 7.0, nA = 2.0, nC = 0.0)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[2]]$branching_times,
c(1.00000000000000, 0.982693734281605)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[2]]$stac,
2
)
testthat::expect_equal(
formatted_IW_sim[[1]][[2]]$missing_species,
0
)
})
test_that("sampled stt, 1 type, no geodynamics, nonoceanic (same arguments as geodynamics, 5 pars)", {
total_time <- 1
clado_rate <- 2.550687345 # cladogenesis rate
ext_rate <- 2.683454548 # extinction rate
clade_carr_cap <- 10.0 # clade-level carrying capacity
imm_rate <- 0.00933207 # immigration rate
ana_rate <- 1.010073119 # anagenesis rate
pars <- c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate)
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(0.1, 0.9)
sample_freq <- 25
mainland_n <- 100
verbose <- FALSE
set.seed(1)
island_replicates <- list()
island_replicates[[1]] <- DAISIE_sim_core_cr(
time = total_time,
pars = pars,
mainland_n = mainland_n,
area_pars = area_pars,
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars
)
testthat::expect_silent(
formatted_IW_sim <- DAISIE_format_IW_sampled_stt(
island_replicates = island_replicates,
total_time = total_time,
M = mainland_n,
sample_freq = sample_freq,
verbose = verbose
)
)
testthat::expect_gt(sum(formatted_IW_sim[[1]][[1]]$stt_all[1, ]), total_time)
})
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