tests/testthat/test-offset.R

In inlabru: Bayesian Latent Gaussian Modelling using INLA and Extensions

test_that("Linear predictor offset", {
  skip_on_cran()
  local_bru_safe_inla()

  dat <- data.frame(
    id = c(1:8),
    deaths = c(5, 30, 2, 4, 5, 4, 7, 10),
    pop = c(1000, 2300, 300, 400, 500, 700, 1000, 700)
  )

  # Used to fail
  m1 <- bru(
    deaths ~ 1 + myoffset(log(pop), model = "offset"),
    data = dat,
    family = "poisson"
  )
  m2 <- bru(
    ~ 1 + myoffset(log(pop), model = "offset"),
    formula = deaths ~ Intercept + myoffset,
    data = dat,
    family = "poisson"
  )

  expect_equal(
    m1$summary.fixed$mean,
    m2$summary.fixed$mean,
    ignore_attr = TRUE,
    tolerance = lowtol
  )
  expect_equal(
    m1$summary.fixed$sd,
    m2$summary.fixed$sd,
    ignore_attr = TRUE,
    tolerance = midtol
  )

  # Ignore option option but give error. Note the need to make the
  # Intercept have the right length for a non-linear model
  expect_error(
    m3 <- bru(
      ~ Intercept(rep(1, NROW(.data.))),
      formula = deaths ~ Intercept,
      data = dat,
      family = "poisson",
      options = list(offset = log(dat$pop))
    )
  )
})