tests/testthat/test-extract_island_species.R

In DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees

test_that("0 nonendemic, 2 species tree, min", {
  phylod <- create_test_phylod(test_scenario = 0)
  expect_error(
    extract_island_species(
      phylod = phylod,
      extraction_method = "min"
    ),
    regexp = "No species in the phylogeny are on the island"
  )
})

test_that("1 nonendemic, 2 species tree, min", {
  phylod <- create_test_phylod(test_scenario = 1)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "nonendemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.755181833128)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 nonendemic, 2 species tree, asr", {
  phylod <- create_test_phylod(test_scenario = 1)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "nonendemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.755181833128)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 nonendemic, 3 species tree, min, outgroup", {
  phylod <- create_test_phylod(test_scenario = 2)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_c")
  expect_equal(get_island_tbl(island_tbl)$status, "nonendemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 1.43337005682)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_c")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 nonendemic, 3 species tree, asr, outgroup", {
  phylod <- create_test_phylod(test_scenario = 2)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_c")
  expect_equal(get_island_tbl(island_tbl)$status, "nonendemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 1.43337005682)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_c")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 nonendemic, 3 species tree, min, non-outgroup", {
  phylod <- create_test_phylod(test_scenario = 3)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "nonendemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.251727277709)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 nonendemic, 3 species tree, asr, non-outgroup", {
  phylod <- create_test_phylod(test_scenario = 3)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "nonendemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.251727277709)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 nonendemic, 4 species tree, min, outgroup", {
  phylod <- create_test_phylod(test_scenario = 4)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_a")
  expect_equal(get_island_tbl(island_tbl)$status, "nonendemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.665451291928)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_a")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 nonendemic, 4 species tree, asr, outgroup", {
  phylod <- create_test_phylod(test_scenario = 4)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_a")
  expect_equal(get_island_tbl(island_tbl)$status, "nonendemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.665451291928)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_a")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 nonendemic, 4 species tree, min, non-outgroup", {
  phylod <- create_test_phylod(test_scenario = 5)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "nonendemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.519744565224)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 nonendemic, 4 species tree, asr, non-outgroup", {
  phylod <- create_test_phylod(test_scenario = 5)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "nonendemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.519744565224)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 endemic, 2 species tree, min", {
  phylod <- create_test_phylod(test_scenario = 6)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.755181833128)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 endemic, 2 species tree, asr", {
  phylod <- create_test_phylod(test_scenario = 6)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.755181833128)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 endemic, 3 species tree, min, outgroup", {
  phylod <- create_test_phylod(test_scenario = 7)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_c")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 1.43337005682)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_c")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 endemic, 3 species tree, asr, outgroup", {
  phylod <- create_test_phylod(test_scenario = 7)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_c")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 1.43337005682)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_c")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 endemic, 3 species tree, min, non-outgroup", {
  phylod <- create_test_phylod(test_scenario = 8)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.251727277709)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 endemic, 3 species tree, asr, non-outgroup", {
  phylod <- create_test_phylod(test_scenario = 8)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.251727277709)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 endemic, 4 species tree, min, outgroup", {
  phylod <- create_test_phylod(test_scenario = 9)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_a")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.665451291928)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_a")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 endemic, 4 species tree, asr, outgroup", {
  phylod <- create_test_phylod(test_scenario = 9)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_a")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.665451291928)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_a")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 endemic, 4 species tree, min, non-outgroup", {
  phylod <- create_test_phylod(test_scenario = 10)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.519744565224)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("1 endemic, 4 species tree, asr, non-outgroup", {
  phylod <- create_test_phylod(test_scenario = 10)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.519744565224)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_true(is.na(get_island_tbl(island_tbl)$branching_times))
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("2 nonendemics, 3 species tree, min, sisters", {
  phylod <- create_test_phylod(test_scenario = 11)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, c("bird_a", "bird_b"))
  expect_equal(get_island_tbl(island_tbl)$status, c("nonendemic", "nonendemic"))
  expect_equal(get_island_tbl(island_tbl)$missing_species, c(0, 0))
  expect_equal(
    get_island_tbl(island_tbl)$col_time,
    c(0.251727277709, 0.251727277709)
  )
  expect_equal(get_island_tbl(island_tbl)$col_max_age, c(FALSE, FALSE))
  expect_equal(
    get_island_tbl(island_tbl)$branching_times,
    I(list(NA_real_, NA_real_))
  )
  expect_equal(get_island_tbl(island_tbl)$min_age, c(NA_real_, NA_real_))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_a", "bird_b")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, c(1, 1))
})

test_that("2 nonendemics, 3 species tree, asr, sisters", {
  phylod <- create_test_phylod(test_scenario = 11)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_a")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, Inf)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_equal(
    get_island_tbl(island_tbl)$branching_times,
    I(list(0.251727277709))
  )
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(
    get_island_tbl(island_tbl)$species,
    I(list(c("bird_a", "bird_b")))
  )
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("2 nonendemics, 4 species tree, min, sister", {
  phylod <- create_test_phylod(test_scenario = 12)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, c("bird_c", "bird_d"))
  expect_equal(get_island_tbl(island_tbl)$status, c("nonendemic", "nonendemic"))
  expect_equal(get_island_tbl(island_tbl)$missing_species, c(0, 0))
  expect_equal(
    get_island_tbl(island_tbl)$col_time,
    c(0.125863638855, 0.125863638855)
  )
  expect_equal(get_island_tbl(island_tbl)$col_max_age, c(FALSE, FALSE))
  expect_equal(
    get_island_tbl(island_tbl)$branching_times,
    I(list(NA_real_, NA_real_))
  )
  expect_equal(get_island_tbl(island_tbl)$min_age, c(NA_real_, NA_real_))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_c", "bird_d")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, c(1, 1))
})

test_that("2 nonendemics, 4 species tree, asr, sister", {
  phylod <- create_test_phylod(test_scenario = 12)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_c")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.519744565224)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_equal(
    get_island_tbl(island_tbl)$branching_times,
    I(list(0.125863638855))
  )
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(
    get_island_tbl(island_tbl)$species,
    I(list(c("bird_c", "bird_d")))
  )
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("2 nonendemics, 4 species tree, min, non-sisters", {
  phylod <- create_test_phylod(test_scenario = 13)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, c("bird_b", "bird_d"))
  expect_equal(get_island_tbl(island_tbl)$status, c("nonendemic", "nonendemic"))
  expect_equal(get_island_tbl(island_tbl)$missing_species, c(0, 0))
  expect_equal(
    get_island_tbl(island_tbl)$col_time,
    c(0.519744565224, 0.125863638855)
  )
  expect_equal(get_island_tbl(island_tbl)$col_max_age, c(FALSE, FALSE))
  expect_equal(
    get_island_tbl(island_tbl)$branching_times,
    I(list(NA_real_, NA_real_))
  )
  expect_equal(get_island_tbl(island_tbl)$min_age, c(NA_real_, NA_real_))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b", "bird_d")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, c(1, 1))
})

test_that("2 nonendemics, 4 species tree, asr, non-sisters", {
  phylod <- create_test_phylod(test_scenario = 13)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, Inf)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_equal(
    get_island_tbl(island_tbl)$branching_times,
    I(list(0.519744565224))
  )
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(
    get_island_tbl(island_tbl)$species,
    I(list(c("bird_b", "bird_d")))
  )
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("2 endemics, 3 species tree, min, sisters", {
  phylod <- create_test_phylod(test_scenario = 14)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_a")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 1.433370056817)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_equal(
    get_island_tbl(island_tbl)$branching_times,
    I(list(0.251727277709))
  )
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(
    get_island_tbl(island_tbl)$species,
    I(list(c("bird_a", "bird_b")))
  )
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("2 endemics, 3 species tree, asr, sisters", {
  phylod <- create_test_phylod(test_scenario = 14)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_a")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, Inf)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_equal(
    get_island_tbl(island_tbl)$branching_times,
    I(list(0.251727277709))
  )
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(
    get_island_tbl(island_tbl)$species,
    I(list(c("bird_a", "bird_b")))
  )
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("2 endemics, 4 species tree, min, sisters", {
  phylod <- create_test_phylod(test_scenario = 15)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_c")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, 0.519744565224)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_equal(
    get_island_tbl(island_tbl)$branching_times,
    I(list(0.125863638855))
  )
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(
    get_island_tbl(island_tbl)$species,
    I(list(c("bird_c", "bird_d")))
  )
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("2 endemics, 4 species tree, asr, sisters", {
  phylod <- create_test_phylod(test_scenario = 15)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_c")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, Inf)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_equal(
    get_island_tbl(island_tbl)$branching_times,
    I(list(0.125863638855))
  )
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(
    get_island_tbl(island_tbl)$species,
    I(list(c("bird_c", "bird_d")))
  )
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("2 endemics, 4 species tree, min, non-sisters", {
  phylod <- create_test_phylod(test_scenario = 16)
  island_tbl <- extract_island_species(
    phylod = phylod,
    extraction_method = "min"
  )

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, c("bird_b", "bird_d"))
  expect_equal(get_island_tbl(island_tbl)$status, c("endemic", "endemic"))
  expect_equal(get_island_tbl(island_tbl)$missing_species, c(0, 0))
  expect_equal(
    get_island_tbl(island_tbl)$col_time,
    c(0.519744565224, 0.125863638855)
  )
  expect_equal(get_island_tbl(island_tbl)$col_max_age, c(FALSE, FALSE))
  expect_equal(
    get_island_tbl(island_tbl)$branching_times,
    I(list(NA_real_, NA_real_))
  )
  expect_equal(get_island_tbl(island_tbl)$min_age, c(NA_real_, NA_real_))
  expect_equal(get_island_tbl(island_tbl)$species, I(list("bird_b", "bird_d")))
  expect_equal(get_island_tbl(island_tbl)$clade_type, c(1, 1))
})

test_that("2 endemics, 4 species tree, asr, non-sisters", {
  phylod <- create_test_phylod(test_scenario = 16)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr"
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, Inf)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_equal(
    get_island_tbl(island_tbl)$branching_times,
    I(list(0.519744565224))
  )
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(
    get_island_tbl(island_tbl)$species,
    I(list(c("bird_b", "bird_d")))
  )
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})

test_that("2 endemics, 4 species tree, asr, non-sisters, include_not_present", {
  phylod <- create_test_phylod(test_scenario = 16)
  island_tbl <- suppressWarnings(extract_island_species(
    phylod = phylod,
    extraction_method = "asr",
    include_not_present = TRUE
  ))

  expect_s4_class(island_tbl, "Island_tbl")
  expect_true(is.data.frame(get_island_tbl(island_tbl)))
  expect_equal(
    colnames(get_island_tbl(island_tbl)),
    c("clade_name", "status", "missing_species", "col_time", "col_max_age",
      "branching_times", "min_age", "species", "clade_type")
  )
  expect_equal(get_island_tbl(island_tbl)$clade_name, "bird_b")
  expect_equal(get_island_tbl(island_tbl)$status, "endemic")
  expect_equal(get_island_tbl(island_tbl)$missing_species, 0)
  expect_equal(get_island_tbl(island_tbl)$col_time, Inf)
  expect_false(get_island_tbl(island_tbl)$col_max_age)
  expect_equal(
    get_island_tbl(island_tbl)$branching_times,
    I(list(c(0.665451291928, 0.519744565224, 0.125863638855)))
  )
  expect_true(is.na(get_island_tbl(island_tbl)$min_age))
  expect_equal(
    get_island_tbl(island_tbl)$species,
    I(list(c("bird_a", "bird_b", "bird_c", "bird_d")))
  )
  expect_equal(get_island_tbl(island_tbl)$clade_type, 1)
})