tests/testthat/test-stan-infections.R

In 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(3, 2, 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), numeric(0), 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), 996, rep(997, 3), rep(998, 6))
  )
  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, 25, 27, 28, 29, 30, 31, 32, 33, 35, 36)
  )
  expect_equal(
    round(generate_infections(c(1, rep(1.1, 9)), 10, gt_rev_pmf, log(100), 0, 0, 0), 0),
    c(rep(100, 11), 110, 113, 116, 120, 125, 129, 133, 138, 143)
  )
  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, 402, 413, 417, 417, rep(418, 6))
  )
  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), 417, 473, 490, 507, 525, 543, 562, 581, 601, 622)
  )
  expect_equal(
    round(generate_infections(c(1, rep(1, 9)), 1, gt_rev_pmf, log(40), numeric(0), 0, 0), 0),
    c(40, 11, 13, rep(14, 8))
  )
  expect_equal(
    round(generate_infections(c(1, rep(1.1, 9)), 1, gt_rev_pmf, log(100), 0.01, 0, 0), 0),
    c(100, 28, 36, 39, 41, 42, 44, 45, 47, 48, 50)
  )
  expect_equal(
    round(generate_infections(c(1, rep(1, 9)), 10, gt_rev_pmf, log(1000), 0, 100000, 4), 0),
    c(rep(1000, 10), 996, rep(997, 3), rep(998, 2), 980, 964, 944, 921)
  )
})