Nothing
test_that("complete stt, 1 type, no geodynamics, oceanic island, one trait state
(same arguments as geodynamics, 5 pars)", {
pars <- c(0.6, 0.1, 10, 0.01, 0.5)
total_time <- 1
mainland_n <- 100
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)
verbose <- FALSE
set.seed(1)
replicates <- 2
cond <- 1
island_replicates <- list()
for (rep in seq_len(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_full_stt(
island_replicates = island_replicates,
total_time = total_time,
M = mainland_n,
verbose = verbose
)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$island_age,
1
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$not_present,
99
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$stt_all[2, ],
c(Time = 0.244818166871655, nI = 1.0, nA = 0.0, nC = 0.0)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$stt_all[4, ],
c(Time = 0.0, nI = 0.0, nA = 1.0, nC = 0.0)
)
expected_brts_table <- matrix(
c(1.0, 0.24481816687165, 0, 1, 0, 1, NA, 1, NA, NA),
nrow = 2
)
colnames(expected_brts_table) <- c("brt", "clade", "event", "endemic", "col")
rownames(expected_brts_table) <- c("", "brts_table")
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$brts_table, expected_brts_table
)
testthat::expect_equal(
formatted_IW_sim[[1]][[2]]$branching_times,
c(1.000000000000000, 0.244818166871655)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[2]]$stac,
2
)
testthat::expect_equal(
formatted_IW_sim[[1]][[2]]$missing_species,
0
)
testthat::expect_equal(
formatted_IW_sim[[2]][[1]]$island_age,
1
)
testthat::expect_equal(
formatted_IW_sim[[2]][[1]]$not_present,
99
)
testthat::expect_equal(
formatted_IW_sim[[2]][[1]]$stt_all[2, ],
c(Time = 0.741771912202239, nI = 1.0, nA = 0.0, nC = 0.0)
)
testthat::expect_equal(
formatted_IW_sim[[2]][[1]]$stt_all[3, ],
c(Time = 0.0, nI = 1.0, nA = 0.0, nC = 0.0)
)
expected_brts_table <- matrix(
c(1.0, 0.741771912202239, 0, 1, 0, 1, NA, 0, NA, NA),
nrow = 2
)
colnames(expected_brts_table) <- c("brt", "clade", "event", "endemic", "col")
rownames(expected_brts_table) <- c("", "brts_table")
testthat::expect_equal(
formatted_IW_sim[[2]][[1]]$brts_table, expected_brts_table
)
testthat::expect_equal(
formatted_IW_sim[[2]][[2]]$branching_times,
c(1.000000000000000, 0.741771912202239)
)
testthat::expect_equal(
formatted_IW_sim[[2]][[2]]$stac,
4
)
testthat::expect_equal(
formatted_IW_sim[[2]][[2]]$missing_species,
0
)
})
test_that("complete stt, 1 type, geodynamics, oceanic island, one trait state
(same arguments as no geodynamics, 5 pars)", {
total_time <- 5
mainland_n <- 100
verbose <- FALSE
set.seed(1)
replicates <- 2
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 = 15,
sea_level_amplitude = 0,
sea_level_frequency = 0,
island_gradient_angle = 0
)
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
nonoceanic_pars <- c(0, 0)
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)
cond <- 1
island_replicates <- list()
for (rep in seq_len(replicates)) {
if (cond == 0) {
number_present <- -1
} else {
number_present <- 0
}
while (number_present < cond) {
island_replicates[[rep]] <- DAISIE_sim_core_time_dep(
time = total_time,
mainland_n = mainland_n,
pars = pars,
nonoceanic_pars = nonoceanic_pars,
hyper_pars = hyper_pars,
area_pars = area_pars,
peak = peak,
Amax = Amax,
Amin = Amin,
island_ontogeny = island_ontogeny,
sea_level = sea_level
)
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_full_stt(
island_replicates = island_replicates,
total_time = total_time,
M = mainland_n,
verbose = verbose
)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$island_age,
5
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$not_present,
90
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$stt_all[2, ],
c(Time = 4.99244818166872, nI = 1.0, nA = 0.0, nC = 0.0)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$stt_all[5, ],
c(Time = 4.79587602350116, nI = 0.0, nA = 0.0, nC = 0.0)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[2]]$branching_times,
c(5.00000000000000, 1.38252473752213)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[2]]$stac,
4
)
testthat::expect_equal(
formatted_IW_sim[[1]][[2]]$missing_species,
0
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$brts_table[1, ],
c(brt = 5, clade = 0, event = 0, endemic = NA, col = NA)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$brts_table[5, ],
c(brt = 0.83094531417507, clade = 4, event = 1, endemic = 1, col = NA)
)
})
test_that("complete stt, 1 type, no geodynamics, nonoceanic, one trait state
(same arguments as geodynamics, 5 pars)", {
total_time <- 3
mainland_n <- 100
clado_rate <- 1 # cladogenesis rate
ext_rate <- 0.3 # extinction rate
clade_carr_cap <- 10.0 # clade-level carrying capacity
imm_rate <- 0.00933207 # immigration rate
ana_rate <- 1.010073119 # anagenesis rate
pars <- c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate)
replicates <- 2
hyper_pars <- create_hyper_pars(d = 0, x = 0)
nonoceanic_pars <- c(0.1, 0.9)
cond <- 1
verbose <- FALSE
area_pars <- create_area_pars(
max_area = 1,
current_area = 1,
proportional_peak_t = 0,
total_island_age = 0,
sea_level_amplitude = 0,
sea_level_frequency = 0,
island_gradient_angle = 0)
hyper_pars <- create_hyper_pars(d = 0, x = 0)
island_replicates <- list()
for (rep in seq_len(replicates)) {
if (cond == 0) {
number_present <- -1
} else {
number_present <- 0
}
while (number_present < cond) {
island_replicates[[rep]] <- DAISIE_sim_core_cr(
time = total_time,
mainland_n = mainland_n,
pars = pars,
area_pars = area_pars,
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars
)
stac_vec <- unlist(island_replicates)[which(
names(unlist(island_replicates)) == "taxon_list.stac"
)]
present <- which(stac_vec != 0)
number_present <- length(present)
}
}
# stt is not empty at start
testthat::expect_gt(sum(island_replicates[[1]]$stt_table[1, ]), expected = total_time)
testthat::expect_gt(sum(island_replicates[[2]]$stt_table[1, ]), expected = total_time)
testthat::expect_silent(
formatted_IW_sim <- DAISIE_format_IW_full_stt(
island_replicates = island_replicates,
total_time = total_time,
M = mainland_n,
verbose = verbose
)
)
})
test_that("complete stt, 1 type, no geodynamics, oceanic island, one trait
state (same arguments as geodynamics, 5 pars) verbose", {
pars <- c(0.4, 0.2, 10, 2, 0.8)
total_time <- 1
mainland_n <- 100
verbose <- TRUE
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)
set.seed(1)
replicates <- 2
island_ontogeny <- 0
sea_level <- 0
cond <- 1
island_replicates <- list()
for (rep in seq_len(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_message(
formatted_IW_sim <- DAISIE_format_IW_full_stt(
island_replicates = island_replicates,
total_time = total_time,
M = mainland_n,
verbose = verbose
),
regexp = "Island being formatted:*"
)
})
test_that("when no colonization happens returns 0", {
pars <- c(0.4, 0.2, 10, 0.000001, 0.5)
total_time <- 1
mainland_n <- 100
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)
verbose <- FALSE
set.seed(2)
replicates <- 1
island_replicates <- list()
island_replicates[[1]] <- list()
out <- DAISIE_sim_core_cr(
time = total_time,
mainland_n = 1,
pars = pars,
area_pars = area_pars,
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars
)
island_replicates <- list(out)
testthat::expect_silent(
formatted_IW_sim <- DAISIE_format_IW_full_stt(
island_replicates = island_replicates,
total_time = total_time,
M = mainland_n,
verbose = verbose
)
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$island_age,
1
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$not_present,
100
)
testthat::expect_equal(
formatted_IW_sim[[1]][[1]]$stt_all[2, ],
c(Time = 0, nI = 0.0, nA = 0.0, nC = 0.0)
)
})
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