tests/testthat/test-offset.R

In nicholasjclark/mvgam: Multivariate (Dynamic) Generalized Additive Models

context("offsets")

skip_on_cran()

test_that("offset incorporated into link-level linpred for beta", {
  beta_data$data_train$pop <- as.numeric(beta_data$data_train$series) + 0.5
  beta_data$data_test$pop <- as.numeric(beta_data$data_test$series) + 0.5
  testmod <- mvgam(
    y ~
      s(season, bs = 'cc') +
        offset(pop) +
        s(series, bs = 're'),
    trend_model = 'GP',
    data = beta_data$data_train,
    family = betar(),
    run_model = FALSE
  )
  stancode <- testmod$model_file

  # Offset should be recorded in the mgcv model
  expect_true(!is.null(attr(testmod$mgcv_model$terms, 'offset')))

  # Offset should be in the linpred calculation
  expect_true(expect_match2(stancode, 'eta = X * b + off_set;'))

  # Offset should be inv_logit in the model declaration
  expect_true(expect_match2(
    stancode,
    '* append_row(b, 1.0) + off_set[obs_ind])'
  ))

  # Offset should be provided in 'data'
  expect_true(expect_match2(stancode, 'vector[total_obs] off_set;'))

  # Data for the offset vector should also be incorporated
  # in model_data
  expect_true(!is.null(testmod$model_data$off_set))
})

test_that("offset incorporated into link-level linpred for NB", {
  data = data.frame(
    out = rpois(100, lambda = 5),
    pop = rnorm(100),
    time = 1:100
  )
  testmod <- mvgam(
    out ~
      1 +
        offset(pop),
    trend_model = 'GP',
    data = data,
    family = nb(),
    run_model = FALSE
  )
  stancode <- testmod$model_file

  # Offset should be recorded in the mgcv model
  expect_true(!is.null(attr(testmod$mgcv_model$terms, 'offset')))

  # Offset should be in the linpred calculation
  expect_true(expect_match2(stancode, 'eta = X * b + off_set;'))

  # Offset should be exponentiated in the model declaration
  expect_true(expect_match2(
    stancode,
    '* append_row(b, 1.0) + off_set[obs_ind])'
  ))

  # Offset should be provided in 'data'
  expect_true(expect_match2(stancode, 'vector[total_obs] off_set;'))

  # Data for the offset vector should also be incorporated
  # in model_data
  expect_true(!is.null(testmod$model_data$off_set))
})


test_that("offset not allowed in trend_formula", {
  data = data.frame(
    out = rpois(100, lambda = 5),
    x = rnorm(100),
    pop = rnorm(100),
    time = 1:100
  )
  expect_error(
    mvgam(
      out ~ 1,
      trend_formula = ~ x + offset(pop),
      trend_model = 'AR1',
      data = data,
      family = nb(),
      run_model = FALSE
    ),
    'Offsets not allowed in argument "trend_formula"'
  )
})

test_that("offset works when no intercept is provided", {
  simdat <- sim_mvgam()
  simdat$data_train$offset <- rep(log(100), NROW(simdat$data_train))
  mod <- mvgam(
    formula = y ~ offset(offset) - 1,
    trend_formula = ~ s(season),
    trend_model = RW(),
    data = simdat$data_train,
    run_model = FALSE
  )
  stancode <- mod$model_file

  # Offset should be recorded in the mgcv model
  expect_true(!is.null(attr(mod$mgcv_model$terms, 'offset')))

  # Offset should be in the linpred calculation
  expect_true(expect_match2(stancode, 'eta = X * b + off_set;'))

  # Offset should be provided in 'data'
  expect_true(expect_match2(stancode, 'vector[total_obs] off_set;'))

  # Offset should be in model_data
  expect_true(!is.null(mod$model_data$off_set))
})