tests/testthat/test-latent_ar1.R

In inlabru: Bayesian Latent Gaussian Modelling using INLA and Extensions

latent_ar1_testdata <- function() {
  data1 <- data.frame(
    time = c(1, 2, 3, 5, 4),
    obs = c(1, 2, 1, 4, 2)
  )
  data1 <- data.frame(
    time = c(1, 2, 3.5, 5, 4),
    obs = c(1, 2, 1, 4, 2)
  )
  data2 <- data1[5:1, , drop = FALSE]
  data3 <- data1[c(2, 5, 4, 3, 1), , drop = FALSE]

  cmp <- obs ~ time(time, model = "ar1") - Intercept
  fit1 <- bru(cmp,
    data = data1, family = "gaussian"
  )
  fit2 <- bru(cmp,
    data = data2, family = "gaussian"
  )
  fit3 <- bru(cmp,
    data = data3, family = "gaussian"
  )

  list(
    data = list(data1 = data1, data2 = data2, data3 = data3),
    cmp = cmp,
    fit = list(fit1 = fit1, fit2 = fit2, fit3 = fit3)
  )
}

old <- function() {
  fit <- latent_ar1_testdata()

  cbind(
    fit$fit[[1]]$summary.random$time$mean,
    fit$fit[[2]]$summary.random$time$mean,
    fit$fit[[3]]$summary.random$time$mean
  )
  cbind(
    fit$fit[[1]]$summary.random$time$sd,
    fit$fit[[2]]$summary.random$time$sd,
    fit$fit[[3]]$summary.random$time$sd
  )
  cbind(
    fit$fit[[1]]$summary.hyperpar[, "mean"],
    fit$fit[[2]]$summary.hyperpar[, "mean"],
    fit$fit[[3]]$summary.hyperpar[, "mean"]
  )

  fit$fit_inla <- list(
    INLA::inla(obs ~ f(time, model = "ar1") - 1,
      data = fit$data[[1]], family = "gaussian"
    ),
    INLA::inla(obs ~ f(time, model = "ar1") - 1,
      data = fit$data[[2]], family = "gaussian"
    ),
    INLA::inla(obs ~ f(time, model = "ar1") - 1,
      data = fit$data[[3]], family = "gaussian"
    )
  )

  cbind(
    fit$fit_inla[[1]]$summary.hyperpar[, "mean"],
    fit$fit_inla[[2]]$summary.hyperpar[, "mean"],
    fit$fit_inla[[3]]$summary.hyperpar[, "mean"]
  )
  cbind(
    fit$fit_inla[[1]]$summary.random$time$mean,
    fit$fit_inla[[2]]$summary.random$time$mean,
    fit$fit_inla[[3]]$summary.random$time$mean
  )
}

test_that("Latent models: AR1 bru ordering", {
  skip_on_cran()
  local_bru_safe_inla()
  data <- latent_ar1_testdata()

  # Check AR1
  expect_equal(
    data$fit[[1]]$summary.random$time$mean,
    c(1, 2, 1, 2, 4),
    tolerance = midtol
  )
  expect_equal(
    data$fit[[2]]$summary.random$time$mean,
    c(1, 2, 1, 2, 4),
    tolerance = midtol
  )
  expect_equal(
    data$fit[[3]]$summary.random$time$mean,
    c(1, 2, 1, 2, 4),
    tolerance = midtol
  )
})