tests/testthat/test-estimate_R.R

In EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves

data("Flu2009")

# The following examples are from EpiEstim's documentation.
# set.seed(1)

test_that("Example 1 matches saved output", {
  out <- estimate_R(Flu2009$incidence, method = "non_parametric_si",
                    config = list(t_start = 2:26, t_end = 8:32,
                                  si_distr = Flu2009$si_distr, 
                                  seed = 1))
  expect_equal_to_reference(out, "../expected_output/Example1.rda", update = FALSE)
})

test_that("Example 2 matches saved output", {

  data <- c(0, 1, 1, 2, 1, 3, 4, 5, 5, 5, 5, 4, 4, 26, 6, 7, 9)
  location <- c("imported", "local", "imported", "imported", "local",
                "imported", "imported", "imported", "imported",
                "local", "local", "local", "imported", "local",
                "imported", "local", "imported")
  # get incidence per group (location)
  incid <- incidence::incidence(data, groups = location)
  out <- estimate_R(incid, method = "parametric_si",
                    config = list(t_start = 2:21, 
                                  t_end = 8:27,
                                  mean_si = 2.6, 
                                  std_si = 1.5, 
                                  seed = 1)
                    )
  expect_equal_to_reference(out, "../expected_output/Example2.rda", update = FALSE)
})

test_that("Example 3 matches saved output", {
  ## estimate the reproduction number (method "parametric_si")
  out <- estimate_R(Flu2009$incidence, method = "parametric_si",
                    config = list(t_start = 2:26, 
                                  t_end = 8:32,
                                  mean_si = 2.6, 
                                  std_si = 1.5, 
                                  seed = 1)
                    )
  expect_equal_to_reference(out, "../expected_output/Example3.rda", update = FALSE)
})

test_that("Example 4 matches saved output", {
  ## estimate the reproduction number (method "uncertain_si")
  out <- estimate_R(Flu2009$incidence, method = "uncertain_si",
                    config = list(t_start = 2:26, 
                                  t_end = 8:32,
                                  mean_si = 2.6, 
                                  std_mean_si = 1,
                                  min_mean_si = 1,
                                  max_mean_si = 4.2,
                                  std_si = 1.5,
                                  std_std_si = 0.5,
                                  min_std_si = 0.5, 
                                  max_std_si = 2.5,
                                  n1 = 100, 
                                  n2 = 100, 
                                  seed = 1)
                    )
  expect_equal_to_reference(out, "../expected_output/Example4.rda", update = FALSE)
})