tests/testthat/test-plot_daisie_mainland_data.R

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

test_that("No extant colonists", {
  set.seed(
    2,
    kind = "Mersenne-Twister",
    normal.kind = "Inversion",
    sample.kind = "Rejection"
  )
  daisie_mainland_data <- sim_island_with_mainland(
    total_time = 1,
    m = 10,
    island_pars = c(1, 1, 10, 0.1, 1),
    mainland_ex = 1,
    mainland_sample_prob = 1,
    mainland_sample_type = "undiscovered",
    replicates = 10,
    verbose = FALSE
  )

  plot_daisie_mainland_data(daisie_mainland_data, replicate_index = 1)
})

test_that("One colonist clade", {
  set.seed(
    1,
    kind = "Mersenne-Twister",
    normal.kind = "Inversion",
    sample.kind = "Rejection"
  )
  daisie_mainland_data <- sim_island_with_mainland(
    total_time = 1,
    m = 10,
    island_pars = c(1, 1, 10, 0.1, 1),
    mainland_ex = 1,
    mainland_sample_prob = 1,
    mainland_sample_type = "undiscovered",
    replicates = 1,
    verbose = FALSE
  )
  plot_daisie_mainland_data(daisie_mainland_data, replicate_index = 1)
})

test_that("much branching", {
  set.seed(
    1018,
    kind = "Mersenne-Twister",
    normal.kind = "Inversion",
    sample.kind = "Rejection"
  )
  daisie_mainland_data <- sim_island_with_mainland(
    total_time = 1,
    m = 10,
    island_pars = c(1, 1, 10, 0.1, 1),
    mainland_ex = 1,
    mainland_sample_prob = 1,
    mainland_sample_type = "complete",
    replicates = 1,
    verbose = FALSE
  )
  plot_daisie_mainland_data(daisie_mainland_data, replicate_index = 1)
})

test_that("many clades", {
  set.seed(
    274,
    kind = "Mersenne-Twister",
    normal.kind = "Inversion",
    sample.kind = "Rejection"
  )
  daisie_mainland_data <- sim_island_with_mainland(
    total_time = 1,
    m = 10,
    island_pars = c(1, 1, 10, 0.1, 1),
    mainland_ex = 1,
    mainland_sample_prob = 1,
    mainland_sample_type = "complete",
    replicates = 1,
    verbose = FALSE
  )
  plot_daisie_mainland_data(daisie_mainland_data, replicate_index = 1)
})

test_that("Issue 64: use time before present", {

  # The Endemic_singleton_MaxAge island species are plotted near
  # the edge of the plot but they should have the longest line.
  # This makes me think that the plot_daisie_mainland_data function
  # should plot "Time before present" on the x-axis.
  set.seed(
    1,
    kind = "Mersenne-Twister",
    normal.kind = "Inversion",
    sample.kind = "Rejection"
  )

  daisie_mainland_data <- DAISIEmainland::sim_island_with_mainland(
    total_time = 1,
    m = 100,
    island_pars = c(1.0, 0.5, 10, 0.1, 0.5),
    mainland_ex = 2,
    mainland_sample_prob = 1,
    mainland_sample_type = "complete",
    replicates = 1,
    verbose = FALSE
  )

  DAISIEmainland::plot_daisie_mainland_data(
    daisie_mainland_data = daisie_mainland_data,
    replicate_index = 1
  )
})

test_that("Issue #68: plot all recolonisations", {
  set.seed(
    1,
    kind = "Mersenne-Twister",
    normal.kind = "Inversion",
    sample.kind = "Rejection"
  )

  daisie_mainland_data <- DAISIEmainland::sim_island_with_mainland(
    total_time = 1,
    m = 50,
    island_pars = c(1.0, 0.5, 10, 0.1, 0.5),
    mainland_ex = 2,
    mainland_sample_prob = 1,
    mainland_sample_type = "complete",
    replicates = 1,
    verbose = FALSE
  )
  DAISIEmainland::plot_daisie_mainland_data(
    daisie_mainland_data = daisie_mainland_data,
    replicate_index = 1
  )
})