tests/testthat/test-stan-infections.R

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

skip_on_cran()
skip_on_os("windows")

# test update_infectiousness
test_that("update_infectiousness works as expected with default settings", {
  expect_equal(
    update_infectiousness(rep(1, 20), rep(0.1, 10), 5, 10),
    1
  )
  expect_equal(
    update_infectiousness(rep(1, 20), rep(0.1, 5), 5, 10),
    0.5
  )
  expect_error(update_infectiousness(rep(1, 20), rep(0.1, 5), 5, 10, 10))
})

pmf <- discretised_pmf(c(2.25, 0.75), 15, 1)
gt_rev_pmf <- get_delay_rev_pmf(
  1L, 15L, array(0L), array(1L),
  array(c(1L, 2L)), array(15L), pmf,
  array(c(1L, 16L)), numeric(0), 1L, 0L,
  1L, 1L, 0L
)

# test generate infections
test_that("generate_infections works as expected", {
  expect_equal(
    round(generate_infections(c(1, rep(1, 9)), 10, gt_rev_pmf, log(1000), 0, 0, 0), 0),
    c(rep(1000, 10), 995, 996, rep(997, 8))
  )
  expect_equal(
    round(generate_infections(c(1, rep(1.1, 9)), 10, gt_rev_pmf, log(20), 0.03, 0, 0), 0),
    c(20, 21, 21, 22, 23, 23, 24, 25, 25, 26, 24, 27, 28, 29, 30, 30, 31, 32, 33, 34)
  )
  expect_equal(
    round(generate_infections(c(1, rep(1.1, 9)), 10, gt_rev_pmf, log(100), 0, 0, 0), 0),
    c(rep(100, 10), 99, 110, 112, 115, 119, 122, 126, 130, 134, 138)
  )
  expect_equal(
    round(generate_infections(c(1, rep(1, 9)), 4, gt_rev_pmf, log(500), -0.02, 0, 0), 0),
    c(500, 490, 480, 471, 382, 403, 408, rep(409, 7))
  )
  expect_equal(
    round(generate_infections(c(1, rep(1.1, 9)), 4, gt_rev_pmf, log(500), 0, 0, 0), 0),
    c(rep(500, 4), 394, 460, 475, 489, 505, 520, 536, 553, 570, 588)
  )
  expect_equal(
    round(generate_infections(c(1, rep(1, 9)), 1, gt_rev_pmf, log(40), numeric(0), 0, 0), 0),
    c(40, 8, 11, 12, 12, rep(13, 6))
  )
  expect_equal(
    round(generate_infections(c(1, rep(1.1, 9)), 1, gt_rev_pmf, log(100), 0.01, 0, 0), 0),
    c(100, 20, 31, 35, 36, 37, 38, 39, 41, 42, 43)
  )
  expect_equal(
    round(generate_infections(c(1, rep(1, 9)), 10, gt_rev_pmf, log(1000), 0, 100000, 4), 0),
    c(rep(1000, 10), 995, 996, rep(997, 4), 980, 965, 947, 926)
  )
})