tests/testthat/test-reff.R

In grattan/covidReff: Simulate Covid

# check:
# devtools::load_all()

zero_vac_sim_R5 <- simulate_covid(
  R = 5,
  n_iterations = 2,
  run_simulations = 10,
  vaccination_levels = 0,
  n_start_infected = 1,
  n_population = 26000,
  quiet = TRUE
  )

# 85% w kids
vacc85_kids <- c(
  "0-10"  = 0.80,
  "11-20" = 0.80,
  "21-30" = 0.75,
  "31-40" = 0.85,
  "41-50" = 0.90,
  "51-60" = 0.90,
  "61-70" = 0.90,
  "71-80" = 0.95,
  "81-90" = 0.95,
  "91+"   = 0.95)

high_vac_sim_R5 <- simulate_covid(
  R = 5,
  n_iterations = 5,
  run_simulations = 5,
  vaccination_levels = vacc85_kids,
  vac_transmission_reduction = 0.5,
  n_start_infected = 5,
  n_population = 26000,
  quiet = TRUE
  )



test_that("simulation returns sensible results", {

  # reff
  expect_equal(max(zero_vac_sim_R5$rt_i, na.rm = TRUE), 5)
  expect_lt(high_vac_sim_R5$rt_i[3], 2)
  expect_equal(nrow(zero_vac_sim_R5), 30)
  expect_equal(ncol(zero_vac_sim_R5), 28)
  expect_equal(zero_vac_sim_R5$new_cases_i[1], 1)
})


test_that("get population rate works", {

  expect_gte(
      get_population_rate(
        age_rate = c("0-10"  = 0.00,
                     "11-20" = 0.20,
                     "21-30" = 0.40,
                     "31-40" = 0.50,
                     "41-50" = 0.60,
                     "51-60" = 0.70,
                     "61-70" = 0.90,
                     "71-80" = 0.90,
                     "81-90" = 0.95,
                     "91+"   = 0.95)),
      0.5 # 0.502982
    )

  expect_equal(get_population_rate(age_rate = rep(0.7, 10)),  0.7)

  expect_error(simulate_covid(vaccination_levels = c(0.1, 0.2)))

})


test_that("hospital and death probabilities are as expected", {

  expect_equal(get_covid_hospitalisation(60, .vaccine = "none", .dose = 0),
               0.221)

  expect_equal(get_covid_hospitalisation(60, .vaccine = "pf", .dose = 2),
               0.221 * (1 - pf_2_poh) / (1 - pf_2_poi))

  expect_equal(get_covid_hospitalisation(80, .vaccine = "none", .dose = 0, type = "icu_rate"),
               0.027)

  expect_equal(get_covid_hospitalisation(80, .vaccine = "az", .dose = 2, type = "icu_rate"),
               0.027 * (1 - az_2_poh) / (1 - az_2_poi))

  expect_lt(get_covid_death(90, .vaccine = "az", .dose = 2, .treatment_improvement = 0.2),
            0.0068)

  expect_lt(get_covid_death(90, .vaccine = "pf", .dose = 2),
            get_covid_death(90, .vaccine = "pf", .dose = 1))


})