tests/testthat/test-DAISIE_sim_core.R

In xieshu95/Trait_dependent_TraiSIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

context("DAISIE_sim_core")

test_that("new and v1.4 should give same results", {

  sim_time <- 10
  n_mainland_species <- 1
  clado_rate <- 1.0
  ext_rate <- 0.5
  carr_cap <- 10
  imm_rate <- 1.0
  ana_rate <- 1.0
  pars <- c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate)
  rng_seed <- 42
  set.seed(rng_seed)
  new <- DAISIE:::DAISIE_sim_core(
    time = sim_time,
    mainland_n = n_mainland_species,
    pars = pars
  )
  set.seed(rng_seed)
  old <- DAISIE:::DAISIE_sim_core_1_4(
    time = sim_time,
    mainland_n = n_mainland_species,
    pars = pars
  )


  expect_true(all(names(new) == names(old)))
  # stt_table has different content
  expect_true(nrow(new$stt_table) == nrow(old$stt_table))
  # different branching times
  expect_equal(length(new$branching_times), length(old$branching_times))
  expect_true(new$stac == old$stac)
  expect_true(new$missing_species == old$missing_species)
  expect_true(length(new$other_clades_same_ancestor) == length(old$other_clades_same_ancestor))
  # expect_true(new$other_clades_same_ancestor[[1]]$species_type == old$other_clades_same_ancestor[[1]]$species_type)
  expect_true(all(new$stt_table == old$stt_table))
  expect_true(all(new$branching_times == old$branching_times))
  # expect_true(new$other_clades_same_ancestor[[1]]$brts_miss == old$other_clades_same_ancestor[[1]]$brts_miss)
})

test_that("Clean run should be silent", {

  set.seed(42)
  n_mainland_species <- 1
  sim_time <- 10
  clado_rate <- 0.1
  ext_rate <- 0.1
  carr_cap <- 10
  imm_rate <- 0.1
  ana_rate <- 0.2

  expect_silent(
    DAISIE:::DAISIE_sim_core(
      time = sim_time,
      mainland_n = n_mainland_species,
      island_type = "oceanic",
      pars = c(clado_rate, ext_rate, carr_cap, imm_rate, ana_rate)
    )
  )

})

test_that("Pedro's should run silent", {

  set.seed(234567890)
  DAISIE:::DAISIE_sim_core(
    time = 10,
    mainland_n = 1000,
    pars = c(0.0001, 2.2, 0.005, 0.001, 1),
    island_type = "oceanic",
    Apars = create_area_params(
      max_area = 5000,
      proportional_peak_t = 0.5,
      peak_sharpness = 1,
      total_island_age = 15
    ),
    Epars = c(1, 100),
    Tpars = NULL,
    island_ontogeny = "beta"
  )
  expect_silent(
    DAISIE:::DAISIE_sim_core(
      time = 10,
      mainland_n = 1,
      pars = c(2.5, 2.2, 0.009, 0.009, 1.01),
      Apars = create_area_params(5000, 0.2, 1, 15),
      Epars = c(1.7, 100),
      island_ontogeny = "beta"
    )
  )
})

test_that("all species extinct if island dead", {

  ontogeny_sim <- DAISIE:::DAISIE_sim_core(
                    time = 10,
                    mainland_n = 1000,
                    pars = c(0.0001, 2.2, 0.005, 0.001, 1),
                    island_type = "oceanic",
                    nonoceanic = NULL,
                    Apars = create_area_params(
                      max_area = 5000,
                      proportional_peak_t = 0.5,
                      peak_sharpness = 1,
                      total_island_age = 10
                    ),
                    Epars = c(1, 100),
                    Tpars = NULL,
                    keep_final_state = FALSE,
                    island_spec = NULL,
                    island_ontogeny = "beta"
  )
  last_entry <- ontogeny_sim$stt_table[nrow(ontogeny_sim$stt_table),]
  expect_true(last_entry[1] == 0)
  expect_true(last_entry[2] == 0)
  expect_true(last_entry[3] == 0)
  expect_true(last_entry[4] == 0)
})