tests/testthat/test-create_ideal_island.R

In joshwlambert/DAISIEmainland: Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

test_that("create_ideal_island is correct for singleton nonendemic (stac 4)", {
  island_tbl <- create_test_island_tbl(island_scenario = 48)
  ideal_island <- create_ideal_island(
    total_time = 1,
    island_tbl = island_tbl
  )
  expected_ideal_island <- list(
    branching_times = c(1.0, 0.5),
    stac = 4,
    missing_species = 0
  )
  expect_equal(ideal_island, expected_ideal_island)
})

test_that("create_ideal_island is correct for singleton endemic (stac 2)", {
  island_tbl <- create_test_island_tbl(island_scenario = 49)
  ideal_island <- create_ideal_island(
    total_time = 1,
    island_tbl = island_tbl
  )
  expected_ideal_island <- list(
    branching_times = c(1.0, 0.5),
    stac = 2,
    missing_species = 0
  )
  expect_equal(ideal_island, expected_ideal_island)
})

test_that("create_ideal_island is correct for endemic clade (stac 2)", {
  island_tbl <- create_test_island_tbl(island_scenario = 50)
  ideal_island <- create_ideal_island(
    total_time = 1,
    island_tbl = island_tbl
  )
  expected_ideal_island <- list(
    branching_times = c(1.0, 0.5, 0.25),
    stac = 2,
    missing_species = 0
  )
  expect_equal(ideal_island, expected_ideal_island)
})

test_that("create_ideal_island is correct for anagenetic and non-endemic
          recolonisation (stac 3)", {
  island_tbl <- create_test_island_tbl(island_scenario = 51)
  ideal_island <- create_ideal_island(
    total_time = 1,
    island_tbl = island_tbl
  )
  expected_ideal_island <- list(
    branching_times = c(1.0, 0.5),
    stac = 3,
    missing_species = 0,
    all_colonisations = list(
      list(
        event_times = c(1.0, 0.5),
        species_type = "A"
      ),
      list(
        event_times = c(1.0, 0.3),
        species_type = "I"
      )
    )
  )
  expect_equal(ideal_island, expected_ideal_island)
})

test_that("create_ideal_island is correct for cladogenetic and non-endemic
          recolonisation (stac 3)", {
  island_tbl <- create_test_island_tbl(island_scenario = 52)
  ideal_island <- create_ideal_island(
    total_time = 1,
    island_tbl = island_tbl
  )
  expected_ideal_island <- list(
    branching_times = c(1.0, 0.5, 0.4),
    stac = 3,
    missing_species = 0,
    all_colonisations = list(
      list(
        event_times = c(1.0, 0.5, 0.4),
        species_type = "C"
      ),
      list(
        event_times = c(1.0, 0.25),
        species_type = "I"
      )
    )
  )
  expect_equal(ideal_island, expected_ideal_island)
})

test_that("create_ideal_island is correct for anagenetic and anagenetic
          recolonisation (stac 3)", {
  island_tbl <- create_test_island_tbl(island_scenario = 53)
  ideal_island <- create_ideal_island(
    total_time = 1,
    island_tbl = island_tbl
  )
  expected_ideal_island <- list(
    branching_times = c(1.0, 0.5),
    stac = 3,
    missing_species = 0,
    all_colonisations = list(
      list(
        event_times = c(1.0, 0.5),
        species_type = "A"
      ),
      list(
        event_times = c(1.0, 0.25),
        species_type = "A"
      )
    )
  )
  expect_equal(ideal_island, expected_ideal_island)
})

test_that("create_ideal_island is correct for cladogenetic and anagenetic
          recolonisation (stac 3)", {
  island_tbl <- create_test_island_tbl(island_scenario = 54)
  ideal_island <- create_ideal_island(
    total_time = 1,
    island_tbl = island_tbl
  )
  expected_ideal_island <- list(
    branching_times = c(1.0, 0.5, 0.4),
    stac = 3,
    missing_species = 0,
    all_colonisations = list(
      list(
        event_times = c(1.0, 0.5, 0.4),
        species_type = "C"
      ),
      list(
        event_times = c(1.0, 0.25),
        species_type = "A"
      )
    )
  )
  expect_equal(ideal_island, expected_ideal_island)
})