tests/testthat/test-extract_param_set.R

In Neves-P/DAISIErobustness: Test the Robustness of DAISIE to Geodynamics and Traits

test_that("test extract_param_set extracts correct param set from
          oceanic_ontogeny", {
  param_space <- load_param_space("oceanic_ontogeny_cs")
  sim_pars <- extract_param_set(
    param_space_name = "oceanic_ontogeny_cs",
    param_space = param_space,
    param_set = 1)
  expect_equal(sim_pars$time, 2.55)
  expect_equal(sim_pars$M, 1000)
  expect_equal(sim_pars$pars, c(0.02000, 0.97500, 0.00100, 0.03363, 0.02950))
  expect_equal(sim_pars$nonoceanic_pars, c(0, 0))
  expect_equal(sim_pars$island_ontogeny, "beta")
  expect_equal(sim_pars$sea_level, "const")
  expect_equal(sim_pars$area_pars, list(max_area = 13500,
                                        current_area = 3155,
                                        proportional_peak_t = 0.53,
                                        total_island_age = 2.864,
                                        sea_level_amplitude = 0,
                                        sea_level_frequency = 0,
                                        island_gradient_angle = 0))
  expect_equal(sim_pars$hyper_pars, list(d = 0.1108, x = 0.075))
  expect_equal(sim_pars$extcutoff, 1000)
})

test_that("test extract_param_set extracts correct param set from
          oceanic_sea_level", {
  param_space <- load_param_space("oceanic_sea_level_cs")
  sim_pars <- extract_param_set(
    param_space_name = "oceanic_sea_level_cs",
    param_space = param_space,
    param_set = 1)
  expect_equal(sim_pars$time, 2.55)
  expect_equal(sim_pars$M, 1000)
  expect_equal(sim_pars$pars, c(0.02000, 0.97500, 0.00100, 0.03363, 0.02950))
  expect_equal(sim_pars$nonoceanic_pars, c(0, 0))
  expect_equal(sim_pars$island_ontogeny, "const")
  expect_equal(sim_pars$sea_level, "sine")
  expect_equal(sim_pars$area_pars, list(max_area = 13500,
                                        current_area = 3155,
                                        proportional_peak_t = 0,
                                        total_island_age = 2.55,
                                        sea_level_amplitude = 60,
                                        sea_level_frequency = 25.5,
                                        island_gradient_angle = 80))
  expect_equal(sim_pars$hyper_pars, list(d = 0.1108, x = 0.075))
  expect_equal(sim_pars$extcutoff, 1000)
})

test_that("test extract_param_set extracts correct param set from
          oceanic_ontogeny_sea_level", {
  param_space <- load_param_space("oceanic_ontogeny_sea_level_cs")
  sim_pars <- extract_param_set(
    param_space_name = "oceanic_ontogeny_sea_level_cs",
    param_space = param_space,
    param_set = 1)
  expect_equal(sim_pars$time, 2.55)
  expect_equal(sim_pars$M, 1000)
  expect_equal(sim_pars$pars, c(0.02000, 0.97500, 0.00100, 0.03363, 0.02950))
  expect_equal(sim_pars$nonoceanic_pars, c(0, 0))
  expect_equal(sim_pars$island_ontogeny, "beta")
  expect_equal(sim_pars$sea_level, "sine")
  expect_equal(sim_pars$area_pars, list(max_area = 13500,
                                        current_area = 3155,
                                        proportional_peak_t = 0.53,
                                        total_island_age = 2.864,
                                        sea_level_amplitude = 60,
                                        sea_level_frequency = 25.5,
                                        island_gradient_angle = 80))
  expect_equal(sim_pars$hyper_pars, list(d = 0.1108, x = 0.075))
  expect_equal(sim_pars$extcutoff, 1000)
})

test_that("test extract_param_set extracts correct param set from
          continental", {
  param_space <- load_param_space("continental_cs")
  sim_pars <- extract_param_set(
    param_space_name = "continental_cs",
    param_space = param_space,
    param_set = 1)
  expect_equal(sim_pars$time, 2.55)
  expect_equal(sim_pars$M, 1000)
  expect_equal(sim_pars$pars, c(0.25, 0.25, 5, 0.01, 0.25))
  expect_equal(sim_pars$nonoceanic_pars, c(0.01, 0.10))
})

test_that("test extract_param_set extracts correct param set from
          continental_land_bridge_cs", {
  param_space <- load_param_space("continental_land_bridge_cs")
  sim_pars <- extract_param_set(
    param_space_name = "continental_land_bridge_cs",
    param_space = param_space,
    param_set = 1)
  expect_equal(sim_pars$time, 2.55)
  expect_equal(sim_pars$M, 1000)
  expect_equal(sim_pars$pars, c(0.5, 0.5, 10, 0.01, 1, 0.5, 0.5, 10, 0.02, 0))
  expect_equal(sim_pars$nonoceanic_pars, c(0.01, 0.1))
  expect_equal(sim_pars$shift_times, c(1.225, 1.325))
})

test_that("test extract_param_set extracts correct param set from
          trait", {
  param_space <- load_param_space("trait_CES")
  sim_pars <- extract_param_set(
    param_space_name = "trait_CES",
    param_space = param_space,
    param_set = 1)
  expect_equal(sim_pars$time, 5)
  expect_equal(sim_pars$M, 500)
  expect_equal(sim_pars$pars, c(0.2, 0.1, 20, 0.008, 0.4))
  expect_equal(sim_pars$trait_pars, list(trans_rate = 0.02,
                                         immig_rate2 = 0.008,
                                         ext_rate2 = 0.1,
                                         ana_rate2 = 0.4,
                                         clado_rate2 = 0.2,
                                         trans_rate2 = 0.02,
                                         M2 = 500))
})

test_that("test extract_param_set extracts correct param set from
          trait with 2 Ks", {
            param_space <- load_param_space("trait_CES_2K")
            sim_pars <- extract_param_set(
              param_space_name = "trait_CES_2K",
              param_space = param_space,
              param_set = 1)
            expect_equal(sim_pars$time, 5)
            expect_equal(sim_pars$M, 500)
            expect_equal(sim_pars$pars, c(0.2, 0.1, 2, 0.008, 0.2))
            expect_equal(sim_pars$trait_pars, list(trans_rate = 0.02,
                                                   immig_rate2 = 0.008,
                                                   ext_rate2 = 0.1,
                                                   ana_rate2 = 0.2,
                                                   clado_rate2 = 0.2,
                                                   trans_rate2 = 0.02,
                                                   M2 = 500,
                                                   K2 = 18))
})

test_that("test extract_param_set extracts correct param set from
          trait without transitions between states", {
            param_space <- load_param_space("trait_no_trans")
            sim_pars <- extract_param_set(
              param_space_name = "trait_no_trans",
              param_space = param_space,
              param_set = 1)
            expect_equal(sim_pars$time, 5)
            expect_equal(sim_pars$M, 500)
            expect_equal(sim_pars$pars, c(0.2, 0.1, 20, 0.008, 0.2))
            expect_equal(sim_pars$trait_pars, list(trans_rate = 0,
                                                   immig_rate2 = 0.008,
                                                   ext_rate2 = 0.1,
                                                   ana_rate2 = 0.2,
                                                   clado_rate2 = 0.2,
                                                   trans_rate2 = 0,
                                                   M2 = 500))
})

test_that("test extract_param_set extracts correct param set from
          trait-independent DAISIE", {
            param_space <- load_param_space("oceanic")
            sim_pars <- extract_param_set(
              param_space_name = "oceanic",
              param_space = param_space,
              param_set = 1)
            expect_equal(sim_pars$time, 5)
            expect_equal(sim_pars$M, 1000)
            expect_equal(sim_pars$pars, c(0.2, 0.1, 20, 0.008, 0.2))
            expect_equal(sim_pars$nonoceanic_pars, c(0, 0))
})