tests/testthat/test-sim_contacts.R

In simulist: Simulate Disease Outbreak Line List and Contacts Data

test_that("sim_contacts works as expected with defaults", {
  set.seed(1)
  expect_snapshot(sim_contacts())
})

contact_distribution <- function(x) stats::dpois(x = x, lambda = 2)
infectious_period <- function(x) stats::rgamma(n = x, shape = 1, scale = 1)

test_that("sim_contacts works as expected", {
  set.seed(1)
  expect_snapshot(
    sim_contacts(
      contact_distribution = contact_distribution,
      infectious_period = infectious_period,
      prob_infection = 0.5
    )
  )
})

test_that("sim_contacts works as expected with modified config", {
  set.seed(1)
  expect_snapshot(
    sim_contacts(
      contact_distribution = contact_distribution,
      infectious_period = infectious_period,
      prob_infection = 0.5,
      config = create_config(
        last_contact_distribution = function(x) stats::rgeom(n = x, prob = 0.5)
      )
    )
  )
})

test_that("sim_contacts works as expected with modified config parameters", {
  set.seed(1)
  expect_snapshot(
    sim_contacts(
      contact_distribution = contact_distribution,
      infectious_period = infectious_period,
      prob_infection = 0.5,
      config = create_config(
        last_contact_distribution = function(x) stats::rpois(n = x, lambda = 5)
      )
    )
  )
})

test_that("sim_contacts fails as expected with modified config", {
  expect_error(
    sim_contacts(
      contact_distribution = contact_distribution,
      infectious_period = infectious_period,
      prob_infection = 0.5,
      config = create_config(
        last_contact_distribution = function(x) stats::rgeom(n = x, lambda = 1)
      )
    ),
    regexp = "(used argument)*(lambda = 1)"
  )
})

test_that("sim_contacts fails as expected with empty config", {
  expect_error(
    sim_contacts(
      contact_distribution = contact_distribution,
      infectious_period = infectious_period,
      prob_infection = 0.5,
      config = list()
    ),
    regexp = "Network incorrectly specified, check config"
  )
})

test_that("sim_contacts works as expected with age structure", {
  age_struct <- data.frame(
    age_limit = c(1, 5, 80, 90),
    proportion = c(0.1, 0.7, 0.2, 0)
  )
  set.seed(1)
  expect_snapshot(
    sim_contacts(
      contact_distribution = contact_distribution,
      infectious_period = infectious_period,
      prob_infection = 0.5,
      population_age = age_struct
    )
  )
})