1
0
mirror of https://github.com/msberends/AMR.git synced 2025-07-11 05:41:53 +02:00

(v2.1.1.9186) replace antibiotics with antimicrobials!

This commit is contained in:
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions

View File

@ -27,72 +27,74 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
ab_reset_session()
test_that("ab_property works", {
ab_reset_session()
expect_identical(ab_name("AMX", language = NULL), "Amoxicillin")
expect_identical(ab_atc("AMX"), "J01CA04")
expect_identical(ab_cid("AMX"), as.integer(33613))
expect_identical(ab_name("AMX", language = NULL), "Amoxicillin")
expect_identical(ab_atc("AMX"), "J01CA04")
expect_identical(ab_cid("AMX"), as.integer(33613))
expect_inherits(ab_tradenames("AMX"), "character")
expect_inherits(ab_tradenames(c("AMX", "AMX")), "list")
expect_inherits(ab_tradenames("AMX"), "character")
expect_inherits(ab_tradenames(c("AMX", "AMX")), "list")
expect_identical(ab_group("AMX", language = NULL), "Beta-lactams/penicillins")
expect_identical(ab_atc_group1("AMX", language = NULL), "Beta-lactam antibacterials, penicillins")
expect_identical(ab_atc_group2("AMX", language = NULL), "Penicillins with extended spectrum")
expect_identical(ab_group("AMX", language = NULL), "Beta-lactams/penicillins")
expect_identical(ab_atc_group1("AMX", language = NULL), "Beta-lactam antibacterials, penicillins")
expect_identical(ab_atc_group2("AMX", language = NULL), "Penicillins with extended spectrum")
expect_identical(ab_name("Fluclox", language = NULL), "Flucloxacillin")
expect_identical(ab_name("fluklox", language = NULL), "Flucloxacillin")
expect_identical(ab_name("floxapen", language = NULL), "Flucloxacillin")
expect_identical(ab_name(21319, language = NULL), "Flucloxacillin")
expect_identical(ab_name("J01CF05", language = NULL), "Flucloxacillin")
expect_identical(ab_name("Fluclox", language = NULL), "Flucloxacillin")
expect_identical(ab_name("fluklox", language = NULL), "Flucloxacillin")
expect_identical(ab_name("floxapen", language = NULL), "Flucloxacillin")
expect_identical(ab_name(21319, language = NULL), "Flucloxacillin")
expect_identical(ab_name("J01CF05", language = NULL), "Flucloxacillin")
expect_identical(ab_ddd("AMX", "oral"), 1.5)
expect_identical(ab_ddd_units("AMX", "iv"), "g")
expect_identical(ab_ddd("AMX", "iv"), 3)
expect_identical(ab_ddd("AMX", "oral"), 1.5)
expect_identical(ab_ddd_units("AMX", "iv"), "g")
expect_identical(ab_ddd("AMX", "iv"), 3)
expect_identical(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B"))
expect_identical(
ab_name(x = c("AMC", "PLB"), tolower = TRUE, language = NULL),
c("amoxicillin/clavulanic acid", "polymyxin B")
)
expect_inherits(ab_info("AMX"), "list")
expect_error(ab_property("amox", "invalid property"))
expect_error(ab_name("amox", language = "INVALID"))
expect_stdout(print(ab_name("amox", language = NULL)))
expect_equal(ab_name("21066-6", language = NULL), "Ampicillin")
expect_equal(
ab_loinc("ampicillin"),
c("101477-8", "101478-6", "18864-9", "18865-6", "20374-5", "21066-6", "23618-2", "27-3", "28-1", "29-9", "30-7", "31-5", "32-3", "33-1", "3355-5", "33562-0", "33919-2", "34-9", "43883-8", "43884-6", "6979-9", "6980-7", "87604-5")
)
expect_true(ab_url("AMX") %like% "fhi[.]no")
expect_identical(
colnames(set_ab_names(example_isolates[, 17:22])),
c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin")
)
expect_identical(
colnames(set_ab_names(example_isolates[, 17:22], language = "nl", snake_case = FALSE)),
c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine")
)
expect_identical(
colnames(set_ab_names(example_isolates[, 17:22], property = "atc")),
c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")
)
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
expect_identical(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B"))
expect_identical(
example_isolates %>% set_ab_names(),
example_isolates %>% rename_with(set_ab_names)
ab_name(x = c("AMC", "PLB"), tolower = TRUE, language = NULL),
c("amoxicillin/clavulanic acid", "polymyxin B")
)
expect_true(all(c(
"SXT", "nitrofurantoin", "fosfomycin", "linezolid", "ciprofloxacin",
"moxifloxacin", "vancomycin", "TEC"
) %in%
(example_isolates %>%
set_ab_names(NIT:VAN) %>%
colnames())))
}
expect_inherits(ab_info("AMX"), "list")
expect_error(ab_property("amox", "invalid property"))
expect_error(ab_name("amox", language = "INVALID"))
expect_output(print(ab_name("amox", language = NULL)))
expect_equal(ab_name("21066-6", language = NULL), "Ampicillin")
expect_equal(
ab_loinc("ampicillin"),
c("101477-8", "101478-6", "18864-9", "18865-6", "20374-5", "21066-6", "23618-2", "27-3", "28-1", "29-9", "30-7", "31-5", "32-3", "33-1", "3355-5", "33562-0", "33919-2", "34-9", "43883-8", "43884-6", "6979-9", "6980-7", "87604-5")
)
expect_true(ab_url("AMX") %like% "fhi[.]no")
expect_identical(
colnames(set_ab_names(example_isolates[, 17:22])),
c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin")
)
expect_identical(
colnames(set_ab_names(example_isolates[, 17:22], language = "nl", snake_case = FALSE)),
c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine")
)
expect_identical(
colnames(set_ab_names(example_isolates[, 17:22], property = "atc")),
c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")
)
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
expect_identical(
example_isolates %>% set_ab_names(),
example_isolates %>% rename_with(set_ab_names)
)
expect_true(all(c(
"SXT", "nitrofurantoin", "fosfomycin", "linezolid", "ciprofloxacin",
"moxifloxacin", "vancomycin", "TEC"
) %in%
(example_isolates %>%
set_ab_names(NIT:VAN) %>%
colnames())))
}
})