tests/testthat/test-deprecated-args.R

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

test_that("Depreciated args work/throw warnings/stops", {
  skip_on_cran()

  # fields
  expect_error(m1 <- sdmTMB(
    formula = density ~ 1,
    data = pcod_2011,
    fields = "AR1",
    time = "year",
    mesh = pcod_mesh_2011,
    do_fit = FALSE
  ), regexp = "fields")

  expect_error(m3 <- sdmTMB(
    formula = density ~ 1,
    data = pcod_2011,
    ar1_fields = TRUE,
    time = "year",
    mesh = pcod_mesh_2011,
    do_fit = FALSE
  ), "ar1_fields")

  # spatial_only
  expect_error(m1 <- sdmTMB(
    formula = density ~ 1,
    data = pcod_2011,
    spatial_only = TRUE,
    time = "year",
    mesh = pcod_mesh_2011,
    do_fit = FALSE
  ), regexp = "spatial_only")

  # include_spatial
  expect_error(m1 <- sdmTMB(
    formula = density ~ 1,
    data = pcod_2011,
    include_spatial = FALSE,
    time = "year",
    mesh = pcod_mesh_2011,
    do_fit = FALSE
  ), regexp = "include_spatial")

})

# test_that("spatial = off and spatiotemporal = off triggers map_rf", {
#   skip_on_cran()
#   skip_if_not_installed("INLA")
#   m1 <- sdmTMB(
#     formula = density ~ 1,
#     data = pcod_2011,
#     spatial = "off",
#     spatiotemporal = "off",
#     mesh = pcod_mesh_2011
#   )
#   m2 <- sdmTMB(
#     formula = density ~ 1,
#     data = pcod_2011,
#     control = sdmTMBcontrol(map_rf = TRUE),
#     mesh = pcod_mesh_2011
#   )
#   expect_equal(m1$model$par, m2$model$par)
# })

test_that("spde/mesh args work", {
  skip_on_cran()
  expect_error(
    m1 <- sdmTMB(density ~ 1, data = pcod_2011, spde = pcod_mesh_2011, do_fit = FALSE),
    "mesh"
  )
  m2 <- sdmTMB(density ~ 1, data = pcod_2011, mesh = pcod_mesh_2011, do_fit = FALSE)
})