tests/testthat/test-DAISIE_format_CS.R

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

context("DAISIE_format_CS")

test_that("silent with empty island with correct output", {
  pars <- c(0.4, 0.2, 10, 0.0001, 0.5)
  time <- 1
  mainland_n <- 1
  verbose <- FALSE
  sample_freq <- 1
  set.seed(1)
  island_replicates <- list()
  out <- list()
  out[[1]] <- DAISIE:::DAISIE_sim_core_constant_rate(
    time = time,
    pars = pars,
    mainland_n = mainland_n
  )
  island_replicates[[1]] <- out
  expect_silent(
    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
    island_replicates = island_replicates,
    time = time,
    M = mainland_n,
    sample_freq = sample_freq,
    verbose = verbose
    )
  )
  expected_CS_format <- list()
  expected_CS_format[[1]] <- list()
  stt_all <- matrix(ncol = 5, nrow = 2)
  colnames(stt_all) <- c("Time", "nI", "nA", "nC", "present")
  stt_all[1, ] <- c(1, 0, 0, 0, 0)
  stt_all[2, ] <- c(0, 0, 0, 0, 0)
  expected_CS_format[[1]][[1]] <- list(island_age = 1,
                                  not_present = 1,
                                  stt_all = stt_all)
  expected_CS_format[[1]][[2]] <- list(branching_times = 1,
                                  stac = 0,
                                  missing_species = 0)
  expect_identical(formatted_CS_sim, expected_CS_format)
})

test_that("silent with non-empty island with correct output", {
  pars <- c(0.5, 0.1, 10, 1, 0.5)
  time <- 1
  mainland_n <- 1
  verbose <- FALSE
  sample_freq <- 1
  set.seed(1)
  island_replicates <- list()
  out <- list()
  out[[1]] <- DAISIE:::DAISIE_sim_core_constant_rate(
    time = time,
    pars = pars,
    mainland_n = mainland_n
  )
  island_replicates[[1]] <- out
  expect_silent(
    formatted_CS_sim <- DAISIE:::DAISIE_format_CS( # nolint
      island_replicates = island_replicates,
      time = time,
      M = mainland_n,
      sample_freq = sample_freq,
      verbose = verbose
    )
  )
  expected_CS_format <- list()
  expected_CS_format[[1]] <- list()
  stt_all <- matrix(ncol = 5, nrow = 2)
  colnames(stt_all) <- c("Time", "nI", "nA", "nC", "present")
  stt_all[1, ] <- c(1, 0, 0, 0, 0)
  stt_all[2, ] <- c(0, 0, 0, 3, 1)
  expected_CS_format[[1]][[1]] <- list(island_age = 1,
                                       not_present = 0,
                                       stt_all = stt_all)
  expected_CS_format[[1]][[2]] <- list(branching_times = c(1.000000000000000,
                                                           0.244818166871655,
                                                           0.173128288990374,
                                                           0.029668240213840),
                                       stac = 2,
                                       missing_species = 0)
  expect_equal(formatted_CS_sim, expected_CS_format)
})

test_that("output with empty island and verbose = TRUE", {
  pars <- c(0, 1, 1, 0.0001, 0)
  time <- 1
  mainland_n <- 1
  verbose <- TRUE
  sample_freq <- 1
  set.seed(1)
  island_replicates <- list()
  out <- list()
  out[[1]] <- DAISIE:::DAISIE_sim_core_constant_rate(
    time = time,
    pars = pars,
    mainland_n = mainland_n
  )
  island_replicates[[1]] <- out
  expect_output(
    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
      island_replicates = island_replicates,
      time = time,
      M = mainland_n,
      sample_freq = sample_freq,
      verbose = verbose
    )
  )
})

test_that("silent with empty 2 type island", {
  skip("this scenario can't run (min_type2 always produces species)")
  pars <- c(0, 10, 1, 0.0001, 0, 0, 10, 1, 0.0001, 0)
  totaltime <- 1
  M <- 1
  mainland_n <- M
  replicates <- 1
  prop_type2_pool <- 0.1
  verbose <- FALSE
  sample_freq <- 1
  set.seed(1)
  island_replicates <- list()
  island_replicates <- DAISIE:::DAISIE_sim_min_type2(
    time = totaltime,
    M = M,
    pars = pars,
    replicates = replicates,
    prop_type2_pool = prop_type2_pool,
    verbose = verbose
    )
  expect_silent(
    formatted_CS_sim <- DAISIE:::DAISIE_format_CS( # sim_min_type2 produces list with one extra element and fails
      island_replicates = island_replicates,
      time = totaltime,
      M = mainland_n,
      sample_freq = sample_freq,
      verbose = verbose
    )
  )
})

test_that("silent with non-empty 2 type island", {
  pars <- c(0.4, 0.1, 10, 1, 0.5, 0.4, 0.1, 10, 1, 0.5)
  totaltime <- 1
  M <- 10
  mainland_n <- M
  verbose <- FALSE
  replicates <- 1
  sample_freq <- 10
  set.seed(1)
  island_replicates <- list()
  prop_type2_pool <- 0.4
  island_replicates <- DAISIE:::DAISIE_sim_min_type2(
    time = totaltime,
    M = M,
    pars = pars,
    replicates = replicates,
    prop_type2_pool = prop_type2_pool,
    verbose = FALSE)
  expect_silent(
    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
      island_replicates = island_replicates,
      time = totaltime,
      M = mainland_n,
      sample_freq = sample_freq,
      verbose = verbose
    )
  )
})

test_that("silent with non-empty 2 type island full stt", {
  pars <- c(0.4, 0.1, 10, 1, 0.5, 0.4, 0.1, 10, 1, 0.5)
  totaltime <- 1
  M <- 10
  mainland_n <- M
  verbose <- FALSE
  replicates <- 1
  sample_freq <- Inf
  set.seed(1)
  island_replicates <- list()
  prop_type2_pool <- 0.4
  island_replicates <- DAISIE:::DAISIE_sim_min_type2(
    time = totaltime,
    M = M,
    pars = pars,
    replicates = replicates,
    prop_type2_pool = prop_type2_pool,
    verbose = FALSE)
  expect_silent(
    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
      island_replicates = island_replicates,
      time = totaltime,
      M = mainland_n,
      verbose = verbose
    )
  )
})

test_that("abuse", {
  expect_error(
    DAISIE:::DAISIE_format_CS(
      island_replicates = "nonsense",
      time = "nonsense",
      M = "nonsense",
      sample_freq = "nonsense",
      verbose = "nonsense"
    )
  )
})


test_that("use full stt", {
  pars <- c(0.4, 0.2, 10, 2, 0.5)
  time <- 5
  mainland_n <- 1
  verbose <- FALSE
  sample_freq <- Inf
  set.seed(1)
  island_replicates <- list()
  out <- list()
  out[[1]] <- DAISIE:::DAISIE_sim_core_constant_rate(
    time = time,
    pars = pars,
    mainland_n = mainland_n
  )
  island_replicates[[1]] <- out
  expect_silent(
    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
      island_replicates = island_replicates,
      time = time,
      M = mainland_n,
      sample_freq = sample_freq,
      verbose = verbose
    )
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$island_age,
    5
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$not_present,
    0
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$stt_all[2, ],
    c(Time = 4.62240908343582735, nI = 1.0, nA = 0.0, nC = 0.0, present = 1.0)
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$stt_all[5, ],
    c(Time = 3.81548257687248871, nI = 0.0, nA = 1.0, nC = 0.0, present = 1.0)
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$stt_all[11, ],
    c(Time = 2.22760715636035123, nI = 1.0, nA = 0.0, nC = 0.0, present = 1.0)
  )

  expect_equal(
    formatted_CS_sim[[1]][[2]]$branching_times,
    c(5.0000000000000000, 1.3487418169725700, 0.0921013811906803)
  )

  expect_equal(
    formatted_CS_sim[[1]][[2]]$stac,
    3
  )

  expect_equal(
    formatted_CS_sim[[1]][[2]]$other_clades_same_ancestor[[1]]$brts_miss,
    c(1.3487418169725700, 0.0921013811906803)
  )

  expect_equal(
    formatted_CS_sim[[1]][[2]]$other_clades_same_ancestor[[1]]$species_type,
    "C"
  )

  expect_equal(
    formatted_CS_sim[[1]][[2]]$other_clades_same_ancestor[[2]]$brts_miss,
    0.37899779115803
  )

  expect_equal(
    formatted_CS_sim[[1]][[2]]$other_clades_same_ancestor[[2]]$species_type,
    "I"
  )

  expect_equal(
    formatted_CS_sim[[1]][[2]]$missing_species,
    0
  )
})


test_that("use complete stt with ontogeny", {
  skip("passes on test but fails on check")
  totaltime <- 10
  mainland_n <- 1
  verbose <- FALSE
  sample_freq <- Inf
  set.seed(2)
  island_replicates <- list()
  out <- list()
  pars = c(0.0001, 2.2, 0.005, 1, 1)
  default_pars <- create_default_pars(
    island_ontogeny = 1,
    sea_level = 0,
    area_pars = create_area_pars(
      max_area = 5000,
      proportional_peak_t = 0.5,
      peak_sharpness = 1,
      total_island_age = 15,
      sea_level_amplitude = 0,
      sea_level_frequency = 0,
      island_gradient_angle = 0
    ),
    hyper_pars = NULL,
    dist_pars = NULL,
    ext_pars = c(1, 100),
    totaltime = totaltime,
    pars = pars
  )
  island_ontogeny = 1
  sea_level = "const"
  out[[1]] <- DAISIE:::DAISIE_sim_core_time_dependent(
    time = totaltime,
    pars = pars,
    mainland_n = mainland_n,
    island_ontogeny = island_ontogeny,
    area_pars = default_pars$area_pars,
    ext_pars = default_pars$ext_pars,
    sea_level = sea_level,
    hyper_pars = default_pars$hyper_pars,
    dist_pars = default_pars$dist_pars,
    extcutoff = 100
  )
  island_replicates[[1]] <- out
  expect_silent(
    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
      island_replicates = island_replicates,
      time = totaltime,
      M = mainland_n,
      sample_freq = sample_freq,
      verbose = verbose
    )
  )

  expect_equal(
    formatted_CS_sim[[1]][[1]]$island_age,
    10
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$not_present,
    0
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$stt_all[5, ],
    c(Time = 7.632397192069222, nI = 0.0, nA = 0.0, nC = 0.0, present = 0.0)
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$stt_all[12, ],
    c(Time = 5.239216044835945, nI = 1.0, nA = 1.0, nC = 0.0, present = 1.0)
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$stt_all[16, ],
    c(Time = 4.286111284371146, nI = 0.0, nA = 0.0, nC = 2.0, present = 1.0)
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$stt_all[35, ],
    c(Time = 2.331391545810463, nI = 1.0, nA = 0.0, nC = 7.0, present = 1.0)
  )
  expect_equal(
    formatted_CS_sim[[1]][[2]]$branching_times,
    c(10.00000000000000, 2.71523396955941, 2.10054941925337, 0.26839096300775)
  )

  expect_equal(
    formatted_CS_sim[[1]][[2]]$stac,
    2
  )

  expect_equal(
    formatted_CS_sim[[1]][[2]]$missing_species,
    0
  )
})

test_that("full stt works with multiple replicates", {
  pars <- c(0.4, 0.2, 10, 2, 0.5)
  time <- 5
  mainland_n <- 1
  verbose <- FALSE
  sample_freq <- Inf
  set.seed(1)
  island_replicates <- list()
  island_replicates[[1]] <- island_replicates
  out <- list()
  out[[1]] <- DAISIE:::DAISIE_sim_core_constant_rate(
    time = time,
    pars = pars,
    mainland_n = mainland_n
  )
  out[[2]] <- DAISIE:::DAISIE_sim_core_constant_rate(
    time = time,
    pars = pars,
    mainland_n = mainland_n
  )
  island_replicates[[1]] <- out
  expect_silent(
    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
      island_replicates = island_replicates,
      time = time,
      M = mainland_n,
      sample_freq = sample_freq,
      verbose = verbose
    )
  )
})

test_that("full stt works with empty island", {
  pars <- c(0.4, 0.2, 10, 0.0000001, 0.5)
  totaltime <- 1
  mainland_n <- 1
  verbose <- FALSE
  sample_freq <- Inf
  set.seed(1)
  replicates <- 2
  island_replicates <- list()
  for (rep in 1:replicates) {
    island_replicates[[rep]] <- list()
    full_list <- list()
    out <- list()
    for (m_spec in 1:mainland_n) {
      out$branching_times <- c(10)
        out <- DAISIE:::DAISIE_sim_core_constant_rate(
          time = totaltime,
          mainland_n = 1,
          pars = pars
        )
      full_list[[m_spec]] <- out
    }
    island_replicates[[rep]] <- full_list
  }
  expect_silent(
    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
      island_replicates = island_replicates,
      time = totaltime,
      M = mainland_n,
      sample_freq = sample_freq,
      verbose = verbose
    )
  )
})

test_that("full stt with two trait states", {
  pars <- c(0.4, 0.2, 20, 2, 0.5)
  time <- 5
  mainland_n <- 0
  verbose <- FALSE
  sample_freq <- Inf
  trait_pars = create_trait_pars(
    trans_rate = 0,
    immig_rate2 = 1,
    ext_rate2 = 0.4,
    ana_rate2 = 0.8,
    clado_rate2 = 0.4,
    trans_rate2 = 0,
    M2 = 1)
  set.seed(1)
  island_replicates <- list()
  out <- list()
  out[[1]] <- DAISIE:::DAISIE_sim_core_trait_dependent(
    time = time,
    pars = pars,
    mainland_n = mainland_n,
    trait_pars = trait_pars
  )
  island_replicates[[1]] <- out
  expect_silent(
    formatted_CS_sim <- DAISIE:::DAISIE_format_CS(
      island_replicates = island_replicates,
      time = time,
      M = mainland_n,
      sample_freq = sample_freq,
      verbose = verbose,
      trait_pars = trait_pars
    )
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$island_age,
    5
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$not_present,
    0
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$stt_all[2, ],
    c(Time = 4.24481817, nI = 0.0, nA = 0.0, nC = 0.0, nI2 = 1.0, nA2 = 0.0, nC2 = 0.0, present = 1.0)
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$stt_all[5, ],
    c(Time = 3.61806444, nI = 0.0, nA = 0.0, nC = 0.0, nI2 = 1.0, nA2 = 0.0, nC2 = 2.0, present = 1.0)
  )
  expect_equal(
    formatted_CS_sim[[1]][[1]]$stt_all[11, ],
    c(Time = 1.17170697, nI = 0.0, nA = 0.0, nC = 0.0, nI2 = 0.0, nA2 = 3.0, nC2 = 0.0, present = 1.0)
  )
  
  expect_equal(
    formatted_CS_sim[[1]][[2]]$branching_times,
    c(5.00000000, 4.24481817, 0.01277218)
  )
  
  expect_equal(
    formatted_CS_sim[[1]][[2]]$stac,
    3
  )
  
  expect_equal(
    formatted_CS_sim[[1]][[2]]$missing_species,
    0
  )
})