Nothing
test_that("A clean CS two trait simulation run should produce no output", {
n_mainland_species <- 1000
island_age <- 0.4
clado_rate <- 0.0001 # cladogenesis rate
ext_rate <- 2.683454548 # extinction rate (not used)
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.001 # immigration rate
ana_rate <- 0.1 # anagenesis rate
trans_rate <- 0.5 # transition rate
trait_pars <- create_trait_pars(trans_rate = trans_rate,
immig_rate2 = imm_rate / 2,
ext_rate2 = ext_rate * 2,
ana_rate2 = ana_rate / 2,
clado_rate2 = clado_rate / 2,
trans_rate2 = trans_rate / 2,
M2 = n_mainland_species / 2)
island_ontogeny <- "const"
sea_level <- "const"
extcutoff <- 1000
testthat::expect_silent(
DAISIE_sim_trait_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,
trait_pars = trait_pars,
extcutoff = extcutoff,
plot_sims = FALSE,
verbose = FALSE
)
)
})
test_that("A divdepmodel = 'CS' two trait run with cond works as expected", {
set.seed(Sys.time()) # Always run a different sim
n_mainland_species <- 1000
island_age <- 0.4
clado_rate <- 0.0001 # cladogenesis rate
ext_rate <- 2.683454548 # extinction rate (not used)
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.01 # immigration rate
ana_rate <- 0.1 # anagenesis rate
trans_rate <- 0.5 # transition rate
cond <- 5
trait_pars <- create_trait_pars(trans_rate = trans_rate,
immig_rate2 = imm_rate / 2,
ext_rate2 = ext_rate * 2,
ana_rate2 = ana_rate / 2,
clado_rate2 = clado_rate / 2,
trans_rate2 = trans_rate / 2,
M2 = n_mainland_species / 2)
island_ontogeny <- "const"
sea_level <- "const"
extcutoff <- 1000
testthat::expect_silent(
out <- DAISIE_sim_trait_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,
trait_pars = trait_pars,
extcutoff = extcutoff,
plot_sims = FALSE,
verbose = FALSE,
cond = cond
)
)
testthat::expect_true(out[[1]][[1]]$stt_all[nrow(out[[1]][[1]]$stt_all), 8] >= cond)
})
test_that("A divdepmodel = 'CS' two trait run cond no cond work as expected", {
set.seed(1) # Always run the same sim
n_mainland_species <- 1000
island_age <- 0.4
clado_rate <- 0.0001 # cladogenesis rate
ext_rate <- 2.683454548 # extinction rate (not used)
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.01 # immigration rate
ana_rate <- 0.1 # anagenesis rate
trans_rate <- 0.5 # transition rate
cond <- 5
trait_pars <- create_trait_pars(trans_rate = trans_rate,
immig_rate2 = imm_rate / 2,
ext_rate2 = ext_rate * 2,
ana_rate2 = ana_rate / 2,
clado_rate2 = clado_rate / 2,
trans_rate2 = trans_rate / 2,
M2 = n_mainland_species / 2)
island_ontogeny <- "const"
sea_level <- "const"
extcutoff <- 1000
testthat::expect_silent(
out_cond <- DAISIE_sim_trait_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,
trait_pars = trait_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), 8] >= cond
)
set.seed(1)
testthat::expect_silent(
out_no_cond <- DAISIE_sim_trait_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,
trait_pars = trait_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), 8] < 5)
})
test_that("A clean IW two trait simulation run should produce no output", {
n_mainland_species <- 1000
island_age <- 0.4
clado_rate <- 0.0001 # cladogenesis rate
ext_rate <- 2.683454548 # extinction rate (not used)
clade_carr_cap <- 0.05 # clade-level carrying capacity
imm_rate <- 0.001 # immigration rate
ana_rate <- 0.1 # anagenesis rate
trans_rate <- 0.5 # transition rate
trait_pars <- create_trait_pars(trans_rate = trans_rate,
immig_rate2 = imm_rate / 2,
ext_rate2 = ext_rate * 2,
ana_rate2 = ana_rate / 2,
clado_rate2 = clado_rate / 2,
trans_rate2 = trans_rate / 2,
M2 = n_mainland_species / 2)
divdepmodel <- "IW"
island_ontogeny <- "const"
sea_level <- "const"
extcutoff <- 1000
testthat::expect_silent(
DAISIE_sim_trait_dep(
time = island_age,
M = n_mainland_species,
pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
trait_pars = trait_pars,
replicates = 1,
divdepmodel = divdepmodel,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
extcutoff = extcutoff,
plot_sims = FALSE,
verbose = FALSE
)
)
})
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