tests/testthat/test-summarise_tb_burden.R

In getTBinR: Access and Summarise World Health Organization Tuberculosis Data

context("summarise_tb_burden")

test_countries <- c("Brazil", "Australia", "Croatia", "France")
test_year <- 2000


test_that("summarise_tb_burden can summarise a variable
          without confidence intervals for a group of countries", {
  sum_tab <- summarise_tb_burden(
    metric = "e_inc_num",
    stat = "mean",
    countries = test_countries,
    years = test_year,
    conf = NULL
  )
  skip_on_cran()
  expect_known_output(sum_tab, file = "../../tests/test-files/summarise_tb_burden/test-01.rds")
})


test_that("summarise_tb_burden can summarise a variable
          with confidence intervals for a group of countries", {
  sum_tab <- summarise_tb_burden(
    metric = "e_inc_num",
    stat = "mean",
    countries = test_countries,
    years = test_year,
    conf = c("_lo", "_hi")
  )
  skip_on_cran()
  expect_known_output(sum_tab, file = "../../tests/test-files/summarise_tb_burden/test-13.rds")
})

test_that("summarise_tb_burden can summarise a variable
          without confidence intervals for a group of countries, comparing within regions", {
  sum_tab <- summarise_tb_burden(
    metric = "e_inc_num",
    stat = "mean",
    countries = test_countries,
    compare_to_region = TRUE,
    years = test_year + 1,
    conf = NULL
  )
  skip_on_cran()
  expect_known_output(sum_tab, file = "../../tests/test-files/summarise_tb_burden/test-02.rds")
})


test_that("summarise_tb_burden can summarise a variable
          across to all regions", {
  sum_tab <- summarise_tb_burden(
    metric = "e_inc_num",
    stat = "mean",
    countries = NULL,
    compare_all_regions = TRUE,
    years = test_year + 2,
    conf = NULL
  )
  skip_on_cran()
  expect_known_output(sum_tab, file = "../../tests/test-files/summarise_tb_burden/test-03.rds")
})


test_that("summarise_tb_burden can summarise a variable
          for a custom group of countries", {
  sum_tab <- summarise_tb_burden(
    metric = "e_inc_num",
    countries = NULL,
    custom_compare = list(
      low = c("Germany", "Spain"),
      hi = c("Nigeria", "India")
    ),
    years = test_year + 3,
    conf = NULL
  )
  skip_on_cran()
  expect_known_output(sum_tab, file = "../../tests/test-files/summarise_tb_burden/test-04.rds")
  expect_error(
    summarise_tb_burden(
      metric = "e_inc_num",
      countries = NULL,
      custom_compare = c(
        low = c("Germany", "Spain"),
        hi = c("Nigeria", "India")
      ),
      years = test_year + 2,
      conf = NULL
    )
  )
  expect_error(
    summarise_tb_burden(
      metric = "e_inc_num",
      countries = NULL,
      custom_compare = c(c("Germany", "Spain"),
        hi = c("Nigeria", "India")
      ),
      years = test_year + 2,
      conf = NULL
    )
  )
})


test_that("summarise_tb_burden can summarise a variable
          globally", {
  sum_tab <- summarise_tb_burden(
    metric = "e_inc_num",
    countries = NULL,
    compare_to_world = TRUE,
    years = test_year + 4,
    conf = NULL
  )
  skip_on_cran()
  expect_known_output(sum_tab, file = "../../tests/test-files/summarise_tb_burden/test-05.rds")
})


test_that("summarise_tb_burden can summarise a variable
          for all regions, and globally without truncating zero", {
  sum_tab <- summarise_tb_burden(
    metric = "e_inc_num",
    countries = NULL,
    compare_all_regions = TRUE,
    compare_to_world = TRUE,
    truncate_at_zero = FALSE,
    years = test_year + 4,
    conf = NULL
  )
  skip_on_cran()
  expect_known_output(sum_tab, file = "../../tests/test-files/summarise_tb_burden/test-06.rds")
})



test_that("summarise_tb_burden can summarise a variable
          with confidence intervals for all regions and globally", {
  sum_tab <- summarise_tb_burden(
    metric = "e_inc_num",
    samples = 1000,
    countries = NULL,
    compare_all_regions = TRUE,
    compare_to_world = TRUE,
    years = test_year + 4
  )
  skip_on_cran()
  expect_known_output(sum_tab,
    file = "../../tests/test-files/summarise_tb_burden/test-07.rds",
    tolerance = 10
  )
})


test_that("summarise_tb_burden can summarise a variable
          with confidence intervals for all regions and globally then compare to a
          shortlist of countries", {
  sum_tab <- summarise_tb_burden(
    metric = "e_inc_num",
    samples = 1000,
    countries = test_countries,
    compare_all_regions = TRUE,
    compare_to_world = TRUE,
    years = test_year + 4
  )
  skip_on_cran()
  expect_known_output(sum_tab,
    file = "../../tests/test-files/summarise_tb_burden/test-08.rds",
    tolerance = 10
  )
})


test_that("summarise_tb_burden can summarise a variable using the median", {
  sum_tab <- summarise_tb_burden(
    metric = "e_inc_num",
    countries = NULL,
    stat = "median",
    conf = NULL,
    compare_all_regions = TRUE,
    compare_to_world = TRUE,
    years = test_year + 4
  )
  skip_on_cran()
  expect_known_output(sum_tab,
    file = "../../tests/test-files/summarise_tb_burden/test-09.rds"
  )
})



test_that("summarise_tb_burden can summarise the annual change of a variable
          with confidence intervals for all regions and globally then compare to a
          shortlist of countries", {
  sum_tab <- summarise_tb_burden(
    metric = "e_inc_100k",
    samples = 1000,
    countries = test_countries,
    compare_all_regions = TRUE,
    compare_to_world = TRUE,
    annual_change = TRUE
  )
  skip_on_cran()
  expect_known_output(sum_tab,
    file = "../../tests/test-files/summarise_tb_burden/test-10.rds"
  )
})


test_that("summarise_tb_burden can generate summarised incidence rates for regions and globally", {
  sum_tab <- summarise_tb_burden(
    metric = "e_inc_num",
    stat = "rate",
    countries = test_countries,
    compare_all_regions = TRUE,
    compare_to_world = TRUE,
    annual_change = FALSE
  )
  skip_on_cran()
  expect_known_output(sum_tab,
    file = "../../tests/test-files/summarise_tb_burden/test-11.rds"
  )
})

test_that("summarise_tb_burden can generate summarised proportions for regions and globally", {
  sum_tab <- summarise_tb_burden(
    metric = "e_mort_exc_tbhiv_num",
    stat = "prop",
    denom = "e_inc_num",
    countries = test_countries,
    compare_all_regions = TRUE,
    compare_to_world = TRUE,
    annual_change = FALSE
  )
  skip_on_cran()
  expect_known_output(sum_tab,
    file = "../../tests/test-files/summarise_tb_burden/test-12.rds"
  )
})



test_that("summarise_tb_burden works as expected when no confidence intervals are given and a country is specified", {
  sum_tab <- summarise_tb_burden(
    countries = test_countries,
    compare_all_regions = TRUE,
    compare_to_world = TRUE,
    conf = TRUE
  )
  skip_on_cran()
  expect_known_output(sum_tab,
    file = "../../tests/test-files/summarise_tb_burden/test-13.rds"
  )
})