tests/testthat/test-delays.R

In epiforecasts/EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

test_stan_delays <- function(generation_time = generation_time_opts(Fixed(1)),
                             delays = delay_opts(),
                             truncation = trunc_opts(),
                             params = c()) {
  data <- EpiNow2:::create_stan_delays(
    generation_time = generation_time,
    delays = delays,
    truncation = truncation,
    time_points = 10
  )
  return(unlist(unname(data[params])))
}

delay_params <-
  c("delay_params_mean", "delay_params_sd", "delay_max", "delay_np_pmf")

test_that("generation times can be specified in different ways", {
  expect_equal(
    test_stan_delays(params = delay_params),
    c(0, 1, 1, 1)
  )
  expect_equal(
    test_stan_delays(
      generation_time = generation_time_opts(Fixed(value = 3)),
      params = delay_params
    ),
    c(0, 0, 0, 1, 1, 1)
  )
  expect_equal(
    round(test_stan_delays(
      generation_time = generation_time_opts(
        LogNormal(meanlog = 3, sdlog = 1, max = 4)
      ),
      params = delay_params
    ), digits = 2),
    c(0.01, 0.08, 0.20, 0.32, 0.40, 1.00, 1.00)
  )
})

test_that("delay parameters can be specified in different ways", {
  expect_equal(
    tail(test_stan_delays(
      delays = delay_opts(Fixed(value = 3)),
      params = delay_params
    ), n = -2),
    c(0, 0, 0, 1, 1)
  )
  expect_equal(
    tail(round(test_stan_delays(
      delays = delay_opts(
        LogNormal(meanlog = 3, sdlog = 1, max = 4)
      ),
      params = delay_params
    ), digits = 2), n = -2),
    c(0.01, 0.08, 0.20, 0.32, 0.40, 1.00)
  )
})

test_that("truncation parameters can be specified in different ways", {
  expect_equal(
    tail(round(test_stan_delays(
      truncation = trunc_opts(
        dist = LogNormal(meanlog = 3, sdlog = 1, max = 4)
      ),
      params = delay_params
    ), digits = 2), n = -2),
    c(1.00, 0.01, 0.08, 0.20, 0.32, 0.40)
  )
})

test_that("distributions incompatible with stan models are caught", {
  expect_error(generation_time_opts(
    Gamma(2, 2)
  ), "maximum")
  expect_error(delay_opts(
    Normal(2, 2, max = 10)
  ), "lognormal")
})