tests/testthat/test-utils-nowcast.R

In covid-19-Re/estimateR: Reproductive number estimation from delayed observations of infections

test_that("nowcast() is correct on a simple example", {
  toy_incidence <- c(9, 3, 4, 7, 8, 0, 2, 1, 0)
  toy_delay <- c(0.05, 0.05, 0.3, 0.2, 0.1, 0.3)

  corrected_result <- nowcast(toy_incidence, toy_delay, cutoff_observation_probability = 0.11)

  ref_values <- c(9, 3, 4, 7, 11.429, 0, 5)
  expect_equal(corrected_result$values, ref_values, tolerance = 0.01)
})


test_that("nowcast() is correct with large gap_to_present", {
  toy_incidence <- c(9, 3, 4, 7, 8, 0, 2, 1, 0)
  toy_delay <- c(0.05, 0.05, 0.3, 0.2, 0.1, 0.3)

  corrected_result <- nowcast(toy_incidence, toy_delay, cutoff_observation_probability = 0.11, gap_to_present = 10)

  expect_equal(corrected_result$values, toy_incidence, tolerance = 0.01)
})