tests/testthat/test-plot_daisie_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
  )
  ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]]
  empirical_daisie_data <- daisie_mainland_data$empirical_multi_daisie_data[[1]]
  expect_silent(plot_daisie_data(ideal_daisie_data))
  expect_silent(plot_daisie_data(empirical_daisie_data))
})

test_that("One colonist clade, stac = 4: Non_endemic", {
  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
  )
  ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]]
  empirical_daisie_data <- daisie_mainland_data$empirical_multi_daisie_data[[1]]
  expect_true(
    ideal_daisie_data[[2]]$stac == 4 || empirical_daisie_data[[2]]$stac == 4
  )
  plot_daisie_data(ideal_daisie_data)
  expect_silent(plot_daisie_data(ideal_daisie_data))
  expect_silent(plot_daisie_data(empirical_daisie_data))
})

test_that("stac == 2: Endemic (and Non_endemic)", {
  set.seed(
    4,
    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
  )
  ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]]
  empirical_daisie_data <- daisie_mainland_data$empirical_multi_daisie_data[[1]]
  expect_true(
    ideal_daisie_data[[2]]$stac == 2 || empirical_daisie_data[[2]]$stac == 2
  )
  expect_silent(plot_daisie_data(daisie_data = ideal_daisie_data))
  expect_silent(plot_daisie_data(empirical_daisie_data))
})

test_that("stac == 5: Endemic_singleton_MaxAge in empirical_daisie_data", {
  set.seed(
    7,
    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
  )
  ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]]
  empirical_daisie_data <- daisie_mainland_data$empirical_multi_daisie_data[[1]]
  expect_true(
    ideal_daisie_data[[2]]$stac == 5 || empirical_daisie_data[[2]]$stac == 5
  )
  expect_silent(plot_daisie_data(ideal_daisie_data))
  expect_silent(plot_daisie_data(empirical_daisie_data))
})

test_that("stace == 6: Endemic_clade_MaxAge, in empirical_daisie_data", {
  set.seed(
    40,
    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
  )
  ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]]
  empirical_daisie_data <- daisie_mainland_data$empirical_multi_daisie_data[[1]]
  expect_true(
    ideal_daisie_data[[2]]$stac == 6 || empirical_daisie_data[[2]]$stac == 6
  )
  plot_daisie_data(empirical_daisie_data)
  plot_daisie_data(ideal_daisie_data)

  # Simplify
  daisie_data <- ideal_daisie_data
  daisie_data[[3]] <- NULL
  daisie_data
  plot_daisie_data(daisie_data = daisie_data)

})

test_that("stac == 3: Endemic&Non_Endemic", {
  set.seed(
    179,
    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
  )
  ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]]
  empirical_daisie_data <- daisie_mainland_data$empirical_multi_daisie_data[[1]]
  expect_true(
    ideal_daisie_data[[2]]$stac == 3 || empirical_daisie_data[[2]]$stac == 3
  )
  expect_silent(plot_daisie_data(daisie_data = ideal_daisie_data))
  expect_silent(plot_daisie_data(empirical_daisie_data))
})

test_that("One colonist clade, with one branch", {
  set.seed(
    5,
    kind = "Mersenne-Twister",
    normal.kind = "Inversion",
    sample.kind = "Rejection"
  )
  total_time <- 1
  n_species_mainland <- 10
  daisie_mainland_data <- sim_island_with_mainland(
    total_time = total_time,
    m = n_species_mainland,
    island_pars = c(1, 1, 10, 0.1, 1),
    mainland_ex = 1,
    mainland_sample_prob = 1,
    mainland_sample_type = "undiscovered",
    replicates = 1,
    verbose = FALSE
  )
  ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]]
  expect_equal(length(ideal_daisie_data), 2)
  expect_equal(length(ideal_daisie_data[[2]]$branching_times), 3)
  expect_silent(plot_daisie_data(daisie_data = ideal_daisie_data))
})


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
  )
  ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]]
  empirical_daisie_data <- daisie_mainland_data$empirical_multi_daisie_data[[1]]
  expect_silent(plot_daisie_data(daisie_data = ideal_daisie_data))
  expect_silent(plot_daisie_data(empirical_daisie_data))
})

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
  )
  ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]]
  empirical_daisie_data <- daisie_mainland_data$empirical_multi_daisie_data[[1]]
  expect_silent(plot_daisie_data(daisie_data = ideal_daisie_data))
  expect_silent(plot_daisie_data(empirical_daisie_data))
})

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
  )
  ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]]
  empirical_daisie_data <- daisie_mainland_data$empirical_multi_daisie_data[[1]]

  expect_silent(plot_daisie_data(daisie_data = ideal_daisie_data))
  expect_silent(plot_daisie_data(empirical_daisie_data))
})


test_that("Issue #68: plot all recolonisations with many branches", {
  set.seed(
    631,
    kind = "Mersenne-Twister",
    normal.kind = "Inversion",
    sample.kind = "Rejection"
  )

  daisie_mainland_data <- DAISIEmainland::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
  )
  DAISIEmainland::plot_daisie_mainland_data(
    daisie_mainland_data = daisie_mainland_data,
    replicate_index = 1
  )
  ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]]
  empirical_daisie_data <- daisie_mainland_data$empirical_multi_daisie_data[[1]]

  expect_silent(plot_daisie_data(ideal_daisie_data))
  expect_silent(plot_daisie_data(empirical_daisie_data))
})

test_that("Multiple recolonisations", { # nolint indeed, this is complex :-)
  seed <- 1912
  set.seed(
    seed,
    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, 0.1, 30.0, 1.0, 5.0),
    mainland_ex = 1,
    mainland_sample_prob = 1,
    mainland_sample_type = "complete",
    replicates = 1,
    verbose = FALSE
  )
  ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]]
  clade_index <- 9
  n_colonisations <- length(ideal_daisie_data[[clade_index]]$all_colonisations) # nolint indeed a long line
  n_branches <- length(ideal_daisie_data[[clade_index]]$branching_times) - 1 # nolint indeed a long line
  expect_true(n_colonisations >= 3 && n_branches >= n_colonisations * 2)
  interesting_clade <- ideal_daisie_data[clade_index]

  expect_silent(plot_daisie_data(daisie_data = ideal_daisie_data))

  simplified_ideal_daisie_data <- list()
  simplified_ideal_daisie_data[[1]] <- ideal_daisie_data[[1]]
  simplified_ideal_daisie_data[[2]] <- ideal_daisie_data[[9]]
  daisie_data <- simplified_ideal_daisie_data
  expect_silent(plot_daisie_data(daisie_data = simplified_ideal_daisie_data))
})

test_that("Search for interesting scenarions", { # nolint indeed, this is complex :-)
  skip("Only run locally")
  seed <- 0
  while (1) {
    seed <- seed + 1
    message(seed)
    set.seed(
      seed,
      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, 0.1, 1.0, 1.0, 1.0),
      mainland_ex = 1,
      mainland_sample_prob = 1,
      mainland_sample_type = "complete",
      replicates = 1,
      verbose = FALSE
    )
    ideal_daisie_data <- daisie_mainland_data$ideal_multi_daisie_data[[1]]
    if (length(ideal_daisie_data) != 2) next
    if (length(ideal_daisie_data[[2]]$branching_times) == 3) {
      message(seed)
      stop("HIERO")
    }
  }
})