tests/testthat/test-adjust_infection_to_report.R

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

# define example cases
cases <- data.table::copy(example_confirmed)[, cases := as.integer(confirm)]

# define a single report delay distribution
delay <- LogNormal(
  meanlog = Normal(1.4, 0.3), sdlog = Normal(0.6, 0.2), max = 30
)

test_that("adjust_infection_to_report can correctly handle a simple mapping", {
  reports <- suppressWarnings(adjust_infection_to_report(
    cases,
    delay_defs = example_incubation_period + delay
  ))
  expect_true(nrow(reports) > 80)
  expect_true(all(!is.infinite(reports$cases)))
  expect_true(all(!is.na(reports$cases)))
})

test_that("adjust_infection_to_report can correctly handle a mapping with a day
           of the week effect", {
  reports <- suppressWarnings(adjust_infection_to_report(
    cases,
    delay_defs = example_incubation_period + delay,
    reporting_effect = c(1.1, rep(1, 4), 0.95, 0.95)
  ))
  expect_true(nrow(reports) > 80)
  expect_true(all(!is.infinite(reports$cases)))
  expect_true(all(!is.na(reports$cases)))
})

test_that("deprecated functions are deprecated", {
  # define example cases
  cases <- data.table::copy(example_confirmed)[, cases := as.integer(confirm)]
  expect_deprecated(
    adjust_infection_to_report(
      cases,
      delay_defs = example_incubation_period + delay,
    )
  )
})