tests/testthat/test-2-print-anisotropy.R

In pbs-assess/sdmTMB: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

test_that("Print anisotropy prints correctly", {
  skip_on_cran()
  skip_on_ci() # slow

  # No anisotropy
  fit1 <- sdmTMB(
    data = pcod_2011,
    formula = density ~ 1,
    mesh = pcod_mesh_2011,
    family = tweedie(),
    anisotropy = FALSE
  )

  expect_output(print(fit1), regexp = "range: 33.23")
  # expect_null(plot_anisotropy(fit1))
  # expect_null(plot_anisotropy2(fit1))

  # -------------------
  # Anisotropy with spatial only
  fit_sp_only <- sdmTMB(
    data = pcod_2011,
    formula = density ~ 1,
    mesh = pcod_mesh_2011,
    family = tweedie(),
    spatial = "on",
    spatiotemporal = "off",
    anisotropy = TRUE
  )

  plot_anisotropy(fit_sp_only)
  plot_anisotropy2(fit_sp_only)
  expect_output(print(fit_sp_only), regexp = "\\(spatial\\): 6.1 to 86.0 at 126")

  # Anisotropy with only spatiotemporal random field
  test_mesh <- make_mesh(data = pcod, xy_cols = c("X", "Y"), cutoff = 20)
  fit_st_only <- sdmTMB(
    data = pcod,
    formula = density ~ 1,
    mesh = test_mesh,
    family = tweedie(),
    spatial = "off",
    spatiotemporal = "iid",
    time = "year",
    anisotropy = TRUE,
    control = sdmTMBcontrol(newton_loops = 1)
  )

  expect_output(print(fit_st_only), regexp = "\\(spatiotemporal\\): 16.5 to 29.1 at 54")
# -------------------

  # Anisotropy when not shared across random fields
  fit2 <- sdmTMB(
    data = pcod,
    formula = density ~ 1,
    mesh = test_mesh,
    family = tweedie(),
    share_range = FALSE,
    time = "year",
    anisotropy = TRUE,
    control = sdmTMBcontrol(newton_loops = 2)
  )

  expect_output(cat(print_anisotropy(fit2)), regexp = "\\(spatial\\): ")
  expect_output(cat(print_anisotropy(fit2)), regexp = "\\(spatiotemporal\\): ")

  # Anisotropy when shared across random fields in delta model
  fit_dg_shared <- sdmTMB(
    data = pcod_2011,
    formula = density ~ 1,
    mesh = pcod_mesh_2011,
    family = delta_gamma(),
    share_range = TRUE,
    time = "year",
    anisotropy = TRUE,
    control = sdmTMBcontrol(newton_loops = 1L)
  )

  expect_output(cat(print_anisotropy(fit_dg_shared, m = 1)), regexp = "\\(spatial\\): 36")
  expect_output(cat(print_anisotropy(fit_dg_shared, m = 2)), regexp = "\\(spatial\\): 2")

  # Anisotropy when not shared across random fields in delta model
  fit_dg_not_shared <- sdmTMB(
    data = pcod,
    formula = density ~ 1,
    mesh = test_mesh,
    family = delta_gamma(),
    share_range = FALSE,
    time = "year",
    anisotropy = TRUE,
    control = sdmTMBcontrol(newton_loops = 1L)
  )

  expect_output(cat(print_anisotropy(fit_dg_not_shared, m = 1)), regexp = "\\(spatial\\): 19")
  expect_output(cat(print_anisotropy(fit_dg_not_shared, m = 1)), regexp = "\\(spatiotemporal\\): 12")
  expect_output(cat(print_anisotropy(fit_dg_not_shared, m = 2)), regexp = "\\(spatial\\): 0")
  expect_output(cat(print_anisotropy(fit_dg_not_shared, m = 2)), regexp = "\\(spatiotemporal\\): 9")
})