tests/testthat/test-adjust_infection_to_report.R

In 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_def <- lognorm_dist_def(
  mean = 5, mean_sd = 1, sd = 3, sd_sd = 1,
  max_value = 30, samples = 1, to_log = TRUE
)

# define a single incubation period
incubation_def <- lognorm_dist_def(
  mean = incubation_periods[1, ]$mean,
  mean_sd = incubation_periods[1, ]$mean_sd,
  sd = incubation_periods[1, ]$sd,
  sd_sd = incubation_periods[1, ]$sd_sd,
  max_value = 30, samples = 1
)

test_that("adjust_infection_to_report can correctly handle a simple mapping", {
  reports <- adjust_infection_to_report(
    cases,
    delay_defs = list(incubation_def, delay_def)
  )
  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 <- adjust_infection_to_report(
    cases,
    delay_defs = list(incubation_def, delay_def),
    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)))
})