tests/testthat/test-stan-rt.R

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

skip_on_cran()
skip_on_os("windows")

# Test update_Rt
test_that("update_Rt works to produce multiple Rt estimates with a static gaussian process", {
  expect_equal(
    update_Rt(10, log(1.2), rep(0, 9), rep(10, 0), numeric(0), 0),
    rep(1.2, 10)
  )
})
test_that("update_Rt works to produce multiple Rt estimates with a non-static gaussian process", {
  expect_equal(
    round(update_Rt(10, log(1.2), rep(0.1, 9), rep(10, 0), numeric(0), 0), 2),
    c(1.20, 1.33, 1.47, 1.62, 1.79, 1.98, 2.19, 2.42, 2.67, 2.95)
  )
})
test_that("update_Rt works to produce multiple Rt estimates with a non-static stationary gaussian process", {
  expect_equal(
    round(update_Rt(10, log(1.2), rep(0.1, 10), rep(10, 0), numeric(0), 1), 3),
    c(1.326, 1.326, 1.326, 1.326, 1.326, 1.326, 1.326, 1.326, 1.326, 1.326)
  )
})
test_that("update_Rt works when Rt is fixed", {
  expect_equal(
    round(update_Rt(10, log(1.2), numeric(0), rep(10, 0), numeric(0), 0), 2),
    rep(1.2, 10)
  )
  expect_equal(
    round(update_Rt(10, log(1.2), numeric(0), rep(10, 0), numeric(0), 1), 2),
    rep(1.2, 10)
  )
})
test_that("update_Rt works when Rt is fixed but a breakpoint is present", {
  expect_equal(
    round(update_Rt(5, log(1.2), numeric(0), c(0, 0, 1, 0, 0), 0.1, 0), 2),
    c(1.2, 1.2, rep(1.33, 3))
  )
  expect_equal(
    round(update_Rt(5, log(1.2), numeric(0), c(0, 0, 1, 0, 0), 0.1, 1), 2),
    c(1.2, 1.2, rep(1.33, 3))
  )
  expect_equal(
    round(update_Rt(5, log(1.2), numeric(0), c(0, 1, 1, 0, 0), rep(0.1, 2), 0), 2),
    c(1.2, 1.33, rep(1.47, 3))
  )
})
test_that("update_Rt works when Rt is variable and a breakpoint is present", {
  expect_equal(
    round(update_Rt(5, log(1.2), rep(0, 4), c(0, 0, 1, 0, 0), 0.1, 0), 2),
    c(1.2, 1.2, rep(1.33, 3))
  )
  expect_equal(
    round(update_Rt(5, log(1.2), rep(0, 5), c(0, 0, 1, 0, 0), 0.1, 1), 2),
    c(1.2, 1.2, rep(1.33, 3))
  )
  expect_equal(
    round(update_Rt(5, log(1.2), rep(0.1, 4), c(0, 0, 1, 0, 0), 0.1, 0), 2),
    c(1.20, 1.33, 1.62, 1.79, 1.98)
  )
})