Nothing
tests/testthat/test-DAISIE_ONEcolonist.R
In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
test_that("DAISIE_ONEcolonist works on an oceanic DAISIE_sim_core", {
sim_time <- 10
n_mainland_species <- 1
clado_rate <- 1.0
ext_rate <- 0.1
carr_cap <- 4
imm_rate <- 1.0
ana_rate <- 1.0
set.seed(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)
sim <- 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)
stt_table <- sim$stt_table
island_spec <- matrix(nrow = 4, ncol = 7, data = "x")
island_spec[, 1] <- c("6", "10", "9", "11")
island_spec[, 2] <- c("1", "1", "1", "1")
island_spec[, 3] <- c("0.755181833128345",
"0.755181833128345",
"0.755181833128345",
"0.755181833128345")
island_spec[, 4] <- c("C", "C", "C", "C")
island_spec[, 5] <- c("AA", "ABA", "B", "ABB")
island_spec[, 6] <- c("0.755181833128345",
"2.66196121187029",
"0.808949241539306",
"9.7444563652974")
island_spec[, 7] <- c(NA, NA, NA, NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
init_nonend_spec <- sim$init_nonend_spec
init_end_spec <- sim$init_end_spec
carrying_capacity <- sim$carrying_capacity
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
testthat::expect_equal(result$stt_table, stt_table)
testthat::expect_true(
all.equal(
result$branching_times,
c(10.0000000, 9.7444564, 2.6619612, 0.8089492, 0.7551818),
tolerance = 1.0e-7
)
)
testthat::expect_equal(result$stac, sim$stac)
testthat::expect_equal(result$missing_species, sim$missing_species)
})
test_that("DAISIE_ONEcolonist works with >=2 cladogenetic with same ancestor", {
set.seed(42)
sim_time <- 10
n_mainland_species <- 1
clado_rate <- 1
ext_rate <- 0.00001
carr_cap <- 4
imm_rate <- 1
ana_rate <- 0.000001
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(out <- 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("DAISIE_ONEcolonist works with >=2 anagenetic with same ancestor", {
set.seed(42)
sim_time <- 10
n_mainland_species <- 1
clado_rate <- 0.0000001
ext_rate <- 0.00001
carr_cap <- 4
imm_rate <- 1
ana_rate <- 2
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(out <- 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("DAISIE_ONEcolonist works with >=2 nonendemic with same ancestor", {
set.seed(44)
sim_time <- 10
n_mainland_species <- 1
clado_rate <- 0.0000001
ext_rate <- 0.00001
carr_cap <- 4
imm_rate <- 3
ana_rate <- 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)
testthat::expect_silent(out <- 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("DAISIE_ONEcolonist stac and brts works for single colonist", {
sim_time <- 10
island_spec <- matrix(nrow = 4, ncol = 7, data = "x")
island_spec[, 1] <- c("6", "10", "9", "11")
island_spec[, 2] <- c("1", "1", "1", "1")
island_spec[, 3] <- c("0.755181833128345",
"0.755181833128345",
"0.755181833128345",
"0.755181833128345")
island_spec[, 4] <- c("C", "C", "C", "C")
island_spec[, 5] <- c("AA", "ABA", "B", "ABB")
island_spec[, 6] <- c("0.755181833128345",
"2.66196121187029",
"0.808949241539306",
"9.7444563652974")
island_spec[, 7] <- c(NA, NA, NA, NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
testthat::expect_equal(
result$branching_times,
c(sim_time, sort(as.numeric(island_spec[, 6]), decreasing = TRUE))
)
# Stac 2 for regular clade on island with no recolonization
testthat::expect_equal(result$stac, 2)
})
test_that("DAISIE_ONEcolonist stac and brts works for 1 nonendemic colonist", {
# With just 1 nonendemic recolonist, function works
sim_time <- 2
island_spec <- matrix(nrow = 2, ncol = 7, data = "x")
island_spec[, 1] <- c("1", "2")
island_spec[, 2] <- c("1", "1")
island_spec[, 3] <- c("0.7", "0.6")
island_spec[, 4] <- c("A", "I")
island_spec[, 5] <- c(NA, NA)
island_spec[, 6] <- c(NA, NA)
island_spec[, 7] <- c("Immig_parent", NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
testthat::expect_equal(
result$branching_times,
c(sim_time, max(as.numeric(island_spec[, 3])))
)
# Stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(2, 0.7))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(2, 0.6))
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "I")
})
test_that("DAISIE_ONEcolonist stac and brts works for 2 endemic colonists,
1 nonendemic", {
# With > 1 endemic recolonist, function works
sim_time <- 2
island_spec <- matrix(nrow = 3, ncol = 7, data = "x")
island_spec[, 1] <- c("1", "2", "3")
island_spec[, 2] <- c("1", "1", "1")
island_spec[, 3] <- c("0.7", "0.6", "0.5")
island_spec[, 4] <- c("A", "A", "I")
island_spec[, 5] <- c(NA, NA, NA)
island_spec[, 6] <- c(NA, NA, NA)
island_spec[, 7] <- c("Immig_parent", "Immig_parent", NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
# Only include oldest colonisation time time
testthat::expect_equal(
result$branching_times,
c(sim_time, as.numeric(island_spec[, 3])[1:2])
)
# stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(2, 0.7))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(2, 0.6))
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[3]]$event_times, c(2, 0.5))
testthat::expect_equal(result$all_colonisations[[3]]$species_type, "I")
})
test_that("DAISIE_ONEcolonist stac and brts works for 3 endemic colonists", {
# With > 1 endemic recolonist, function works
sim_time <- 2
island_spec <- matrix(nrow = 3, ncol = 7, data = "x")
island_spec[, 1] <- c("1", "2", "3")
island_spec[, 2] <- c("1", "1", "1")
island_spec[, 3] <- c("0.7", "0.6", "0.5")
island_spec[, 4] <- c("A", "A", "A")
island_spec[, 5] <- c(NA, NA, NA)
island_spec[, 6] <- c(NA, NA, NA)
island_spec[, 7] <- c("Immig_parent", "Immig_parent", "Immig_parent")
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
# Only include oldest colonisation time time
expect_equal(
result$branching_times,
c(sim_time, as.numeric(island_spec[, 3])[1:2])
)
# stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
testthat::expect_length(result$all_colonisations, 3)
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(2, 0.7))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(2, 0.6))
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[3]]$event_times, c(2, 0.5))
testthat::expect_equal(result$all_colonisations[[3]]$species_type, "A")
})
test_that("DAISIE_ONEcolonist stac and brts works for 2 endemic clades", {
# With > 1 endemic clades, function works
sim_time <- 2
# Species Mainland Ancestor Colonisation time (BP) Species type branch_code branching time (BP) Anagenetic_origin
# [1,] "4" "1" "1.13468671408026" "C" "AA" "1.13468671408026" NA
# [2,] "3" "1" "1.13468671408026" "C" "B" "0.96545899791969" NA
# [3,] "5" "1" "1.13468671408026" "C" "AB" "0.68696590746724" NA
# [4,] "6" "1" "0.67395467208331" "C" "A" "0.67395467208331" NA
# [5,] "7" "1" "0.67395467208331" "C" "B" "0.34198900695798" NA
island_spec <- matrix(nrow = 5, ncol = 7, data = "x")
island_spec[, 1] <- c("4", "3", "5", "6", "7")
island_spec[, 2] <- c("1", "1", "1", "1", "1")
island_spec[, 3] <-
c("1.13468671408026",
"1.13468671408026",
"1.13468671408026",
"0.67395467208331",
"0.67395467208331")
island_spec[, 4] <- c("C", "C", "C", "C", "C")
island_spec[, 5] <- c("AA", "B", "AB", "A", "B")
island_spec[, 6] <-
c(1.13468671408026,
0.96545899791969,
0.68696590746724,
0.67395467208331,
0.34198900695798)
island_spec[, 7] <- c(NA, NA, NA, NA, NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
btimes <- sort(as.numeric(island_spec[, 6]), decreasing = TRUE)
btimes_sans_yng_col <- btimes[-4]
testthat::expect_equal(
result$branching_times,
c(sim_time, btimes_sans_yng_col)
)
testthat::expect_length(result$all_colonisations, 2)
# stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
# all_colonisations
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(
2.0,
1.13468671408026,
0.96545899791969,
0.68696590746724
))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "C")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(
2.0,
0.67395467208331,
0.34198900695798
))
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "C")
})
test_that("DAISIE_ONEcolonist stac and brts works for 2 endemic clades,
1 nonendemic", {
# With > 1 endemic clades, function works
sim_time <- 2
# Species Mainland Ancestor Colonisation time (BP) Species type branch_code branching time (BP) Anagenetic_origin
# [1,] "4" "1" "1.13468671408026" "C" "AA" "1.13468671408026" NA
# [2,] "3" "1" "1.13468671408026" "C" "B" "0.96545899791969" NA
# [3,] "5" "1" "1.13468671408026" "C" "AB" "0.68696590746724" NA
# [4,] "6" "1" "0.67395467208331" "C" "A" "0.67395467208331" NA
# [5,] "7" "1" "0.67395467208331" "C" "B" "0.34198900695798" NA
# [6,] "8" "1" "0.47395467208331" "I" NA NA NA
island_spec <- matrix(nrow = 6, ncol = 7, data = "x")
island_spec[, 1] <- c("4", "3", "5", "6", "7", "8")
island_spec[, 2] <- c("1", "1", "1", "1", "1", "1")
island_spec[, 3] <-
c("1.13468671408026",
"1.13468671408026",
"1.13468671408026",
"0.67395467208331",
"0.67395467208331",
"0.47395467208331")
island_spec[, 4] <- c("C", "C", "C", "C", "C", "I")
island_spec[, 5] <- c("AA", "B", "AB", "A", "B", NA)
island_spec[, 6] <-
c(1.13468671408026,
0.96545899791969,
0.68696590746724,
0.67395467208331,
0.34198900695798,
NA)
island_spec[, 7] <- c(NA, NA, NA, NA, NA, NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
# Here, branching times already exclude youngest colononisation
btimes_sans_yng_col <- sort(as.numeric(island_spec[, 6]), decreasing = TRUE)
testthat::expect_equal(
result$branching_times,
c(sim_time, btimes_sans_yng_col)
)
testthat::expect_length(result$all_colonisations, 3)
# stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
# all_colonisations
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(
2.0,
1.13468671408026,
0.96545899791969,
0.68696590746724
))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "C")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(
2.0,
0.67395467208331,
0.34198900695798
))
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "C")
testthat::expect_equal(result$all_colonisations[[3]]$event_times, c(
2.0,
0.47395467208331
))
testthat::expect_equal(result$all_colonisations[[3]]$species_type, "I")
})
test_that("DAISIE_ONEcolonist stac and brts works for 2 endemic clades,
1 endemic singleton", {
# With > 1 endemic clades, function works
sim_time <- 2
# Species Mainland Ancestor Colonisation time (BP) Species type branch_code branching time (BP) Anagenetic_origin
# [1,] "4" "1" "1.13468671408026" "C" "AA" "1.13468671408026" NA
# [2,] "3" "1" "1.13468671408026" "C" "B" "0.96545899791969" NA
# [3,] "5" "1" "1.13468671408026" "C" "AB" "0.68696590746724" NA
# [4,] "6" "1" "0.7" "A" NA NA "Immig_parent"
# [5,] "7" "1" "0.67395467208331" "C" "A" "0.67395467208331" NA
# [6,] "8" "1" "0.67395467208331" "C" "B" "0.34198900695798" NA
island_spec <- matrix(nrow = 6, ncol = 7, data = "x")
island_spec[, 1] <- c("4", "3", "5", "6", "7", "8")
island_spec[, 2] <- c("1", "1", "1", "1", "1", "1")
island_spec[, 3] <-
c("1.13468671408026",
"1.13468671408026",
"1.13468671408026",
"0.7",
"0.67395467208331",
"0.67395467208331")
island_spec[, 4] <- c("C", "C", "C", "A", "C", "C")
island_spec[, 5] <- c("AA", "B", "AB", NA, "B", "C")
island_spec[, 6] <-
c(1.13468671408026,
0.96545899791969,
0.68696590746724,
NA,
0.67395467208331,
0.34198900695798)
island_spec[, 7] <- c(NA, NA, NA, "Immig_parent", NA, NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
btimes_sans_yng_col <- c(2.0, 1.1346867, 0.9654590, 0.7, 0.6869659, 0.3419890)
testthat::expect_equal(
result$branching_times,
c(btimes_sans_yng_col)
)
testthat::expect_length(result$all_colonisations, 3)
# stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
# all_colonisations
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(
2.0,
1.13468671408026,
0.96545899791969,
0.68696590746724
))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "C")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(2.0, 0.7))
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[3]]$event_times, c(
2.0,
0.67395467208331,
0.34198900695798
))
testthat::expect_equal(result$all_colonisations[[3]]$species_type, "C")
})
test_that("DAISIE_ONEcolonist stac and brts works for 1 anagenetic clade from
extinction of cladogenetic and 1 nonendemic recolonist ", {
sim_time <- 10.0
n_mainland_species <- 1
clado_rate <- 1.0
ext_rate <- 0.7
carr_cap <- 2
imm_rate <- 1.0
ana_rate <- 0
set.seed(3)
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)
result <- 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)
# Species Mainland Ancestor Colonisation time (BP) Species type branch_code branching time (BP) Anagenetic_origin
# island_spec "4" "1" "6.33541590408438" "A" NA NA "Clado_extinct"
# "1" "1" "0.643802977852591" "I" NA NA NA
testthat::expect_equal(
result$branching_times,
c(sim_time, 6.33541590408438)
)
testthat::expect_length(result$all_colonisations, 2)
# stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
# all_colonisations
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(
10.0,
6.33541590408438
))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(
10.0,
0.643802977852591)
)
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "I")
})
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test_that("DAISIE_ONEcolonist works on an oceanic DAISIE_sim_core", {
sim_time <- 10
n_mainland_species <- 1
clado_rate <- 1.0
ext_rate <- 0.1
carr_cap <- 4
imm_rate <- 1.0
ana_rate <- 1.0
set.seed(1)
area_pars <- create_area_pars(
max_area = 1,
current_area = 1,
proportional_peak_t = 0,
total_island_age = 0,
sea_level_amplitude = 0,
sea_level_frequency = 0,
island_gradient_angle = 0)
hyper_pars <- create_hyper_pars(d = 0, x = 0)
nonoceanic_pars <- c(0, 0)
sim <- DAISIE_sim_core_cr(
time = sim_time,
mainland_n = n_mainland_species,
pars = c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate),
area_pars = area_pars,
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars)
stt_table <- sim$stt_table
island_spec <- matrix(nrow = 4, ncol = 7, data = "x")
island_spec[, 1] <- c("6", "10", "9", "11")
island_spec[, 2] <- c("1", "1", "1", "1")
island_spec[, 3] <- c("0.755181833128345",
"0.755181833128345",
"0.755181833128345",
"0.755181833128345")
island_spec[, 4] <- c("C", "C", "C", "C")
island_spec[, 5] <- c("AA", "ABA", "B", "ABB")
island_spec[, 6] <- c("0.755181833128345",
"2.66196121187029",
"0.808949241539306",
"9.7444563652974")
island_spec[, 7] <- c(NA, NA, NA, NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
init_nonend_spec <- sim$init_nonend_spec
init_end_spec <- sim$init_end_spec
carrying_capacity <- sim$carrying_capacity
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
testthat::expect_equal(result$stt_table, stt_table)
testthat::expect_true(
all.equal(
result$branching_times,
c(10.0000000, 9.7444564, 2.6619612, 0.8089492, 0.7551818),
tolerance = 1.0e-7
)
)
testthat::expect_equal(result$stac, sim$stac)
testthat::expect_equal(result$missing_species, sim$missing_species)
})
test_that("DAISIE_ONEcolonist works with >=2 cladogenetic with same ancestor", {
set.seed(42)
sim_time <- 10
n_mainland_species <- 1
clado_rate <- 1
ext_rate <- 0.00001
carr_cap <- 4
imm_rate <- 1
ana_rate <- 0.000001
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(out <- 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("DAISIE_ONEcolonist works with >=2 anagenetic with same ancestor", {
set.seed(42)
sim_time <- 10
n_mainland_species <- 1
clado_rate <- 0.0000001
ext_rate <- 0.00001
carr_cap <- 4
imm_rate <- 1
ana_rate <- 2
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(out <- 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("DAISIE_ONEcolonist works with >=2 nonendemic with same ancestor", {
set.seed(44)
sim_time <- 10
n_mainland_species <- 1
clado_rate <- 0.0000001
ext_rate <- 0.00001
carr_cap <- 4
imm_rate <- 3
ana_rate <- 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)
testthat::expect_silent(out <- 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("DAISIE_ONEcolonist stac and brts works for single colonist", {
sim_time <- 10
island_spec <- matrix(nrow = 4, ncol = 7, data = "x")
island_spec[, 1] <- c("6", "10", "9", "11")
island_spec[, 2] <- c("1", "1", "1", "1")
island_spec[, 3] <- c("0.755181833128345",
"0.755181833128345",
"0.755181833128345",
"0.755181833128345")
island_spec[, 4] <- c("C", "C", "C", "C")
island_spec[, 5] <- c("AA", "ABA", "B", "ABB")
island_spec[, 6] <- c("0.755181833128345",
"2.66196121187029",
"0.808949241539306",
"9.7444563652974")
island_spec[, 7] <- c(NA, NA, NA, NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
testthat::expect_equal(
result$branching_times,
c(sim_time, sort(as.numeric(island_spec[, 6]), decreasing = TRUE))
)
# Stac 2 for regular clade on island with no recolonization
testthat::expect_equal(result$stac, 2)
})
test_that("DAISIE_ONEcolonist stac and brts works for 1 nonendemic colonist", {
# With just 1 nonendemic recolonist, function works
sim_time <- 2
island_spec <- matrix(nrow = 2, ncol = 7, data = "x")
island_spec[, 1] <- c("1", "2")
island_spec[, 2] <- c("1", "1")
island_spec[, 3] <- c("0.7", "0.6")
island_spec[, 4] <- c("A", "I")
island_spec[, 5] <- c(NA, NA)
island_spec[, 6] <- c(NA, NA)
island_spec[, 7] <- c("Immig_parent", NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
testthat::expect_equal(
result$branching_times,
c(sim_time, max(as.numeric(island_spec[, 3])))
)
# Stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(2, 0.7))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(2, 0.6))
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "I")
})
test_that("DAISIE_ONEcolonist stac and brts works for 2 endemic colonists,
1 nonendemic", {
# With > 1 endemic recolonist, function works
sim_time <- 2
island_spec <- matrix(nrow = 3, ncol = 7, data = "x")
island_spec[, 1] <- c("1", "2", "3")
island_spec[, 2] <- c("1", "1", "1")
island_spec[, 3] <- c("0.7", "0.6", "0.5")
island_spec[, 4] <- c("A", "A", "I")
island_spec[, 5] <- c(NA, NA, NA)
island_spec[, 6] <- c(NA, NA, NA)
island_spec[, 7] <- c("Immig_parent", "Immig_parent", NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
# Only include oldest colonisation time time
testthat::expect_equal(
result$branching_times,
c(sim_time, as.numeric(island_spec[, 3])[1:2])
)
# stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(2, 0.7))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(2, 0.6))
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[3]]$event_times, c(2, 0.5))
testthat::expect_equal(result$all_colonisations[[3]]$species_type, "I")
})
test_that("DAISIE_ONEcolonist stac and brts works for 3 endemic colonists", {
# With > 1 endemic recolonist, function works
sim_time <- 2
island_spec <- matrix(nrow = 3, ncol = 7, data = "x")
island_spec[, 1] <- c("1", "2", "3")
island_spec[, 2] <- c("1", "1", "1")
island_spec[, 3] <- c("0.7", "0.6", "0.5")
island_spec[, 4] <- c("A", "A", "A")
island_spec[, 5] <- c(NA, NA, NA)
island_spec[, 6] <- c(NA, NA, NA)
island_spec[, 7] <- c("Immig_parent", "Immig_parent", "Immig_parent")
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
# Only include oldest colonisation time time
expect_equal(
result$branching_times,
c(sim_time, as.numeric(island_spec[, 3])[1:2])
)
# stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
testthat::expect_length(result$all_colonisations, 3)
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(2, 0.7))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(2, 0.6))
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[3]]$event_times, c(2, 0.5))
testthat::expect_equal(result$all_colonisations[[3]]$species_type, "A")
})
test_that("DAISIE_ONEcolonist stac and brts works for 2 endemic clades", {
# With > 1 endemic clades, function works
sim_time <- 2
# Species Mainland Ancestor Colonisation time (BP) Species type branch_code branching time (BP) Anagenetic_origin
# [1,] "4" "1" "1.13468671408026" "C" "AA" "1.13468671408026" NA
# [2,] "3" "1" "1.13468671408026" "C" "B" "0.96545899791969" NA
# [3,] "5" "1" "1.13468671408026" "C" "AB" "0.68696590746724" NA
# [4,] "6" "1" "0.67395467208331" "C" "A" "0.67395467208331" NA
# [5,] "7" "1" "0.67395467208331" "C" "B" "0.34198900695798" NA
island_spec <- matrix(nrow = 5, ncol = 7, data = "x")
island_spec[, 1] <- c("4", "3", "5", "6", "7")
island_spec[, 2] <- c("1", "1", "1", "1", "1")
island_spec[, 3] <-
c("1.13468671408026",
"1.13468671408026",
"1.13468671408026",
"0.67395467208331",
"0.67395467208331")
island_spec[, 4] <- c("C", "C", "C", "C", "C")
island_spec[, 5] <- c("AA", "B", "AB", "A", "B")
island_spec[, 6] <-
c(1.13468671408026,
0.96545899791969,
0.68696590746724,
0.67395467208331,
0.34198900695798)
island_spec[, 7] <- c(NA, NA, NA, NA, NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
btimes <- sort(as.numeric(island_spec[, 6]), decreasing = TRUE)
btimes_sans_yng_col <- btimes[-4]
testthat::expect_equal(
result$branching_times,
c(sim_time, btimes_sans_yng_col)
)
testthat::expect_length(result$all_colonisations, 2)
# stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
# all_colonisations
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(
2.0,
1.13468671408026,
0.96545899791969,
0.68696590746724
))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "C")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(
2.0,
0.67395467208331,
0.34198900695798
))
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "C")
})
test_that("DAISIE_ONEcolonist stac and brts works for 2 endemic clades,
1 nonendemic", {
# With > 1 endemic clades, function works
sim_time <- 2
# Species Mainland Ancestor Colonisation time (BP) Species type branch_code branching time (BP) Anagenetic_origin
# [1,] "4" "1" "1.13468671408026" "C" "AA" "1.13468671408026" NA
# [2,] "3" "1" "1.13468671408026" "C" "B" "0.96545899791969" NA
# [3,] "5" "1" "1.13468671408026" "C" "AB" "0.68696590746724" NA
# [4,] "6" "1" "0.67395467208331" "C" "A" "0.67395467208331" NA
# [5,] "7" "1" "0.67395467208331" "C" "B" "0.34198900695798" NA
# [6,] "8" "1" "0.47395467208331" "I" NA NA NA
island_spec <- matrix(nrow = 6, ncol = 7, data = "x")
island_spec[, 1] <- c("4", "3", "5", "6", "7", "8")
island_spec[, 2] <- c("1", "1", "1", "1", "1", "1")
island_spec[, 3] <-
c("1.13468671408026",
"1.13468671408026",
"1.13468671408026",
"0.67395467208331",
"0.67395467208331",
"0.47395467208331")
island_spec[, 4] <- c("C", "C", "C", "C", "C", "I")
island_spec[, 5] <- c("AA", "B", "AB", "A", "B", NA)
island_spec[, 6] <-
c(1.13468671408026,
0.96545899791969,
0.68696590746724,
0.67395467208331,
0.34198900695798,
NA)
island_spec[, 7] <- c(NA, NA, NA, NA, NA, NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
# Here, branching times already exclude youngest colononisation
btimes_sans_yng_col <- sort(as.numeric(island_spec[, 6]), decreasing = TRUE)
testthat::expect_equal(
result$branching_times,
c(sim_time, btimes_sans_yng_col)
)
testthat::expect_length(result$all_colonisations, 3)
# stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
# all_colonisations
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(
2.0,
1.13468671408026,
0.96545899791969,
0.68696590746724
))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "C")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(
2.0,
0.67395467208331,
0.34198900695798
))
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "C")
testthat::expect_equal(result$all_colonisations[[3]]$event_times, c(
2.0,
0.47395467208331
))
testthat::expect_equal(result$all_colonisations[[3]]$species_type, "I")
})
test_that("DAISIE_ONEcolonist stac and brts works for 2 endemic clades,
1 endemic singleton", {
# With > 1 endemic clades, function works
sim_time <- 2
# Species Mainland Ancestor Colonisation time (BP) Species type branch_code branching time (BP) Anagenetic_origin
# [1,] "4" "1" "1.13468671408026" "C" "AA" "1.13468671408026" NA
# [2,] "3" "1" "1.13468671408026" "C" "B" "0.96545899791969" NA
# [3,] "5" "1" "1.13468671408026" "C" "AB" "0.68696590746724" NA
# [4,] "6" "1" "0.7" "A" NA NA "Immig_parent"
# [5,] "7" "1" "0.67395467208331" "C" "A" "0.67395467208331" NA
# [6,] "8" "1" "0.67395467208331" "C" "B" "0.34198900695798" NA
island_spec <- matrix(nrow = 6, ncol = 7, data = "x")
island_spec[, 1] <- c("4", "3", "5", "6", "7", "8")
island_spec[, 2] <- c("1", "1", "1", "1", "1", "1")
island_spec[, 3] <-
c("1.13468671408026",
"1.13468671408026",
"1.13468671408026",
"0.7",
"0.67395467208331",
"0.67395467208331")
island_spec[, 4] <- c("C", "C", "C", "A", "C", "C")
island_spec[, 5] <- c("AA", "B", "AB", NA, "B", "C")
island_spec[, 6] <-
c(1.13468671408026,
0.96545899791969,
0.68696590746724,
NA,
0.67395467208331,
0.34198900695798)
island_spec[, 7] <- c(NA, NA, NA, "Immig_parent", NA, NA)
colnames(island_spec) <- c(
"Species",
"Mainland Ancestor",
"Colonisation time (BP)",
"Species type",
"branch_code",
"branching time (BP)",
"Anagenetic_origin"
)
stt_table <- NULL
result <- DAISIE_ONEcolonist(
time = sim_time,
island_spec = island_spec,
stt_table = stt_table
)
btimes_sans_yng_col <- c(2.0, 1.1346867, 0.9654590, 0.7, 0.6869659, 0.3419890)
testthat::expect_equal(
result$branching_times,
c(btimes_sans_yng_col)
)
testthat::expect_length(result$all_colonisations, 3)
# stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
# all_colonisations
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(
2.0,
1.13468671408026,
0.96545899791969,
0.68696590746724
))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "C")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(2.0, 0.7))
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[3]]$event_times, c(
2.0,
0.67395467208331,
0.34198900695798
))
testthat::expect_equal(result$all_colonisations[[3]]$species_type, "C")
})
test_that("DAISIE_ONEcolonist stac and brts works for 1 anagenetic clade from
extinction of cladogenetic and 1 nonendemic recolonist ", {
sim_time <- 10.0
n_mainland_species <- 1
clado_rate <- 1.0
ext_rate <- 0.7
carr_cap <- 2
imm_rate <- 1.0
ana_rate <- 0
set.seed(3)
area_pars <- create_area_pars(
max_area = 1,
current_area = 1,
proportional_peak_t = 0,
total_island_age = 0,
sea_level_amplitude = 0,
sea_level_frequency = 0,
island_gradient_angle = 0)
hyper_pars <- create_hyper_pars(d = 0, x = 0)
nonoceanic_pars <- c(0, 0)
result <- DAISIE_sim_core_cr(
time = sim_time,
mainland_n = n_mainland_species,
pars = c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate),
area_pars = area_pars,
hyper_pars = hyper_pars,
nonoceanic_pars = nonoceanic_pars)
# Species Mainland Ancestor Colonisation time (BP) Species type branch_code branching time (BP) Anagenetic_origin
# island_spec "4" "1" "6.33541590408438" "A" NA NA "Clado_extinct"
# "1" "1" "0.643802977852591" "I" NA NA NA
testthat::expect_equal(
result$branching_times,
c(sim_time, 6.33541590408438)
)
testthat::expect_length(result$all_colonisations, 2)
# stac 3 for recolonisation cases
testthat::expect_equal(result$stac, 3)
# all_colonisations
testthat::expect_equal(result$all_colonisations[[1]]$event_times, c(
10.0,
6.33541590408438
))
testthat::expect_equal(result$all_colonisations[[1]]$species_type, "A")
testthat::expect_equal(result$all_colonisations[[2]]$event_times, c(
10.0,
0.643802977852591)
)
testthat::expect_equal(result$all_colonisations[[2]]$species_type, "I")
})
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