Nothing
test_that("A clean CS ontogeny run should produce no output", {
n_mainland_species <- 1000
island_age <- 0.4
clado_rate <- 0.0001 # cladogenesis rate
ext_rate <- 0.5 # extinction rate
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.001 # immigration rate
ana_rate <- 0.1 # anagenesis rate
max_area <- 1000
current_area <- 500
peak_time <- 0.1
sharpness <- 1
total_island_age <- 10
sea_level_amplitude <- 0
sea_level_frequency <- 0
island_gradient_angle <- 0
island_ontogeny <- "beta"
sea_level <- "const"
extcutoff <- 1000
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
testthat::expect_silent(
DAISIE_sim_time_dep(
time = island_age,
M = n_mainland_species,
pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
replicates = 1,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
area_pars = create_area_pars(
max_area = max_area,
current_area = current_area,
proportional_peak_t = peak_time,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle),
hyper_pars = hyper_pars,
extcutoff = extcutoff,
plot_sims = FALSE,
verbose = FALSE
)
)
})
test_that("use CS split-rates with cond", {
set.seed(Sys.time()) # Always run a different sim
n_mainland_species <- 1000
island_age <- 0.4
clado_rate <- 0.001 # cladogenesis rate
ext_rate <- 0.5 # extinction rate
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.01 # immigration rate
ana_rate <- 0.1 # anagenesis rate
max_area <- 1000
current_area <- 500
peak_time <- 0.1
sharpness <- 1
total_island_age <- 10
sea_level_amplitude <- 0
sea_level_frequency <- 0
island_gradient_angle <- 0
island_ontogeny <- "beta"
sea_level <- "const"
extcutoff <- 1000
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
cond <- 5
testthat::expect_silent(
out <- DAISIE_sim_time_dep(
time = island_age,
M = n_mainland_species,
pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
replicates = 1,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
area_pars = create_area_pars(
max_area = max_area,
current_area = current_area,
proportional_peak_t = peak_time,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle),
hyper_pars = hyper_pars,
extcutoff = extcutoff,
plot_sims = FALSE,
verbose = FALSE,
cond = cond
)
)
testthat::expect_true(out[[1]][[1]]$stt_all[nrow(out[[1]][[1]]$stt_all), 5] >= cond)
})
test_that("CS split-rates with cond to without", {
set.seed(1) # Always run a different sim
n_mainland_species <- 1000
island_age <- 0.4
clado_rate <- 0.001 # cladogenesis rate
ext_rate <- 0.5 # extinction rate
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.01 # immigration rate
ana_rate <- 0.1 # anagenesis rate
max_area <- 1000
current_area <- 500
peak_time <- 0.1
sharpness <- 1
total_island_age <- 10
sea_level_amplitude <- 0
sea_level_frequency <- 0
island_gradient_angle <- 0
island_ontogeny <- "beta"
sea_level <- "const"
extcutoff <- 1000
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
cond <- 5
testthat::expect_silent(
out_cond <- DAISIE_sim_time_dep(
time = island_age,
M = n_mainland_species,
pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
replicates = 1,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
area_pars = create_area_pars(
max_area = max_area,
current_area = current_area,
proportional_peak_t = peak_time,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle),
hyper_pars = hyper_pars,
extcutoff = extcutoff,
plot_sims = FALSE,
verbose = FALSE,
cond = cond
)
)
testthat::expect_true(
out_cond[[1]][[1]]$stt_all[nrow(out_cond[[1]][[1]]$stt_all), 5] >= cond
)
set.seed(1)
testthat::expect_silent(
out_no_cond <- DAISIE_sim_time_dep(
time = island_age,
M = n_mainland_species,
pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
replicates = 1,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
area_pars = create_area_pars(
max_area = max_area,
current_area = current_area,
proportional_peak_t = peak_time,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle),
hyper_pars = hyper_pars,
extcutoff = extcutoff,
plot_sims = FALSE,
verbose = FALSE,
cond = 0
)
)
testthat::expect_true(
out_no_cond[[1]][[1]]$stt_all[nrow(out_no_cond[[1]][[1]]$stt_all), 5] < cond
)
})
test_that("A clean IW ontogeny run should produce no output", {
n_mainland_species <- 1000
island_age <- 0.4
clado_rate <- 0.0001 # cladogenesis rate
ext_rate <- 0.5 # extinction rate
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.001 # immigration rate
ana_rate <- 0.1 # anagenesis rate
divdepmodel <- "IW"
max_area <- 1000
current_area <- 500
peak_time <- 0.1
total_island_age <- 10
sea_level_amplitude <- 0
sea_level_frequency <- 0
island_gradient_angle <- 0
island_ontogeny <- "beta"
sea_level <- "const"
extcutoff <- 1000
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
nonoceanic_pars <- c(0, 0)
testthat::expect_silent(
DAISIE_sim_time_dep(
time = island_age,
M = n_mainland_species,
pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
replicates = 1,
divdepmodel = divdepmodel,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
area_pars = create_area_pars(
max_area = max_area,
current_area = current_area,
proportional_peak_t = peak_time,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle),
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars,
extcutoff = extcutoff,
plot_sims = FALSE,
verbose = FALSE
)
)
})
test_that("A clean GW ontogeny run should produce no output", {
n_mainland_species <- 1000
island_age <- 0.4
clado_rate <- 0.0001 # cladogenesis rate
ext_rate <- 0.5 # extinction rate
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.001 # immigration rate
ana_rate <- 0.1 # anagenesis rate
divdepmodel <- "GW"
num_guilds <- 10
max_area <- 1000
current_area <- 500
peak_time <- 0.1
total_island_age <- 10
sea_level_amplitude <- 0
sea_level_frequency <- 0
island_gradient_angle <- 0
island_ontogeny <- "beta"
sea_level <- "const"
extcutoff <- 1000
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
nonoceanic_pars <- c(0, 0)
testthat::expect_silent(
DAISIE_sim_time_dep(
time = island_age,
M = n_mainland_species,
pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
replicates = 1,
divdepmodel = divdepmodel,
num_guilds = num_guilds,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
area_pars = create_area_pars(
max_area = max_area,
current_area = current_area,
proportional_peak_t = peak_time,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle),
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars,
extcutoff = extcutoff,
plot_sims = FALSE,
verbose = FALSE
)
)
})
test_that("A clean sea_level run should produce no output", {
n_mainland_species <- 1000
island_age <- 5
clado_rate <- 0.0001 # cladogenesis rate
ext_rate <- 0.5 # extinction rate
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.001 # immigration rate
ana_rate <- 0.1 # anagenesis rate
max_area <- 1000
current_area <- 500
peak_time <- 0
total_island_age <- 10
sea_level_amplitude <- 50
sea_level_frequency <- 10
island_gradient_angle <- 45
island_ontogeny <- "const"
sea_level <- "sine"
extcutoff <- 1000
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
nonoceanic_pars <- c(0, 0)
testthat::expect_silent(
out <- DAISIE_sim_time_dep(
time = island_age,
M = n_mainland_species,
pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
replicates = 1,
island_ontogeny = island_ontogeny,
area_pars = create_area_pars(
max_area = max_area,
current_area = current_area,
proportional_peak_t = peak_time,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle),
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars,
extcutoff = extcutoff,
sea_level = sea_level,
plot_sims = FALSE,
verbose = FALSE
)
)
})
test_that("A clean CS ontogeny run with verbose should print to console", {
n_mainland_species <- 1000
island_age <- 0.4
clado_rate <- 0.0001 # cladogenesis rate
ext_rate <- 0.5 # extinction rate
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.001 # immigration rate
ana_rate <- 0.1 # anagenesis rate
max_area <- 1000
current_area <- 500
peak_time <- 0.1
sharpness <- 1
total_island_age <- 10
sea_level_amplitude <- 0
sea_level_frequency <- 0
island_gradient_angle <- 0
island_ontogeny <- "beta"
sea_level <- "const"
extcutoff <- 1000
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
testthat::expect_message(
DAISIE_sim_time_dep(
time = island_age,
M = n_mainland_species,
pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
replicates = 1,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
area_pars = create_area_pars(
max_area = max_area,
current_area = current_area,
proportional_peak_t = peak_time,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle),
hyper_pars = hyper_pars,
extcutoff = extcutoff,
plot_sims = FALSE,
verbose = TRUE
),
"Island replicate 1"
)
})
test_that("A clean IW ontogeny run should produce no output", {
n_mainland_species <- 1000
island_age <- 0.4
clado_rate <- 0.0001 # cladogenesis rate
ext_rate <- 0.5 # extinction rate
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.001 # immigration rate
ana_rate <- 0.1 # anagenesis rate
divdepmodel <- "IW"
max_area <- 1000
current_area <- 500
peak_time <- 0.1
total_island_age <- 10
sea_level_amplitude <- 0
sea_level_frequency <- 0
island_gradient_angle <- 0
island_ontogeny <- "beta"
sea_level <- "const"
extcutoff <- 1000
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
nonoceanic_pars <- c(0, 0)
testthat::expect_message(
DAISIE_sim_time_dep(
time = island_age,
M = n_mainland_species,
pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
replicates = 1,
divdepmodel = divdepmodel,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
area_pars = create_area_pars(
max_area = max_area,
current_area = current_area,
proportional_peak_t = peak_time,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle),
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars,
extcutoff = extcutoff,
plot_sims = FALSE,
verbose = TRUE
),
"Island replicate 1"
)
})
test_that("A clean GW ontogeny run should produce no output", {
n_mainland_species <- 1000
island_age <- 0.4
clado_rate <- 0.0001 # cladogenesis rate
ext_rate <- 0.5 # extinction rate
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.001 # immigration rate
ana_rate <- 0.1 # anagenesis rate
divdepmodel <- "GW"
num_guilds <- 10
max_area <- 1000
current_area <- 500
peak_time <- 0.1
total_island_age <- 10
sea_level_amplitude <- 0
sea_level_frequency <- 0
island_gradient_angle <- 0
island_ontogeny <- "beta"
sea_level <- "const"
extcutoff <- 1000
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
nonoceanic_pars <- c(0, 0)
testthat::expect_message(
DAISIE_sim_time_dep(
time = island_age,
M = n_mainland_species,
pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
replicates = 1,
divdepmodel = divdepmodel,
num_guilds = num_guilds,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
area_pars = create_area_pars(
max_area = max_area,
current_area = current_area,
proportional_peak_t = peak_time,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle),
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars,
extcutoff = extcutoff,
plot_sims = FALSE,
verbose = TRUE
),
"Island replicate 1"
)
})
test_that("A clean GW ontogeny run should produce no output", {
n_mainland_species <- 1000
island_age <- 0.4
clado_rate <- 0.0001 # cladogenesis rate
ext_rate <- 0.5 # extinction rate
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.001 # immigration rate
ana_rate <- 0.1 # anagenesis rate
divdepmodel <- "GW"
num_guilds <- "10"
max_area <- 1000
current_area <- 500
peak_time <- 0.1
total_island_age <- 10
sea_level_amplitude <- 0
sea_level_frequency <- 0
island_gradient_angle <- 0
island_ontogeny <- "beta"
sea_level <- "const"
extcutoff <- 1000
hyper_pars <- create_hyper_pars(d = 0.2, x = 0.1)
nonoceanic_pars <- c(0, 0)
testthat::expect_error(
DAISIE_sim_time_dep(
time = island_age,
M = n_mainland_species,
pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
replicates = 1,
divdepmodel = divdepmodel,
num_guilds = num_guilds,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
area_pars = create_area_pars(
max_area = max_area,
current_area = current_area,
proportional_peak_t = peak_time,
total_island_age = total_island_age,
sea_level_amplitude = sea_level_amplitude,
sea_level_frequency = sea_level_frequency,
island_gradient_angle = island_gradient_angle),
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars,
extcutoff = extcutoff,
plot_sims = FALSE,
verbose = TRUE
),
"num_guilds must be numeric"
)
})
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