Nothing
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"
)
})
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