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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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114
tests/testthat/test-age.R
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@ -27,69 +27,71 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_equal(
age(
test_that("age works", {
expect_equal(
age(
x = c("1980-01-01", "1985-01-01", "1990-01-01"),
reference = "2019-01-01"
),
c(39, 34, 29)
)
expect_equal(
age(
x = c("2019-01-01", "2019-04-01", "2019-07-01"),
reference = "2019-09-01",
exact = TRUE
),
c(0.6656393, 0.4191781, 0.1698630),
tolerance = 0.001
)
expect_error(age(
x = c("1980-01-01", "1985-01-01", "1990-01-01"),
reference = "2019-01-01"
),
c(39, 34, 29)
)
reference = c("2019-01-01", "2019-01-01")
))
expect_equal(
age(
x = c("2019-01-01", "2019-04-01", "2019-07-01"),
reference = "2019-09-01",
exact = TRUE
),
c(0.6656393, 0.4191781, 0.1698630),
tolerance = 0.001
)
# expect_warning(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"), reference = "1975-01-01"))
# expect_warning(age(x = c("1800-01-01", "1805-01-01", "1810-01-01"), reference = "2019-01-01"))
expect_error(age(
x = c("1980-01-01", "1985-01-01", "1990-01-01"),
reference = c("2019-01-01", "2019-01-01")
))
# expect_warning(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"), reference = "1975-01-01"))
# expect_warning(age(x = c("1800-01-01", "1805-01-01", "1810-01-01"), reference = "2019-01-01"))
expect_equal(
length(age(x = c("2019-01-01", NA), na.rm = TRUE)),
1
)
expect_equal(
length(age(x = c("2019-01-01", NA), na.rm = TRUE)),
1
)
ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
expect_equal(
length(unique(age_groups(ages, 50))),
2
)
expect_equal(
length(unique(age_groups(ages, c(50, 60)))),
3
)
expect_identical(
class(age_groups(ages, "child")),
c("ordered", "factor")
)
expect_equal(
length(unique(age_groups(ages, 50))),
2
)
expect_equal(
length(unique(age_groups(ages, c(50, 60)))),
3
)
expect_identical(
class(age_groups(ages, "child")),
c("ordered", "factor")
)
expect_identical(
class(age_groups(ages, "elderly")),
c("ordered", "factor")
)
expect_identical(
class(age_groups(ages, "elderly")),
c("ordered", "factor")
)
expect_identical(
class(age_groups(ages, "tens")),
c("ordered", "factor")
)
expect_identical(
class(age_groups(ages, "tens")),
c("ordered", "factor")
)
expect_identical(
class(age_groups(ages, "fives")),
c("ordered", "factor")
)
expect_identical(
class(age_groups(ages, "fives")),
c("ordered", "factor")
)
expect_equal(
length(age_groups(c(10, 20, 30, NA), na.rm = TRUE)),
3
)
expect_equal(
length(age_groups(c(10, 20, 30, NA), na.rm = TRUE)),
3
)
})