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(v2.1.1.9186) replace antibiotics with antimicrobials!
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@ -27,72 +27,74 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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ab_reset_session()
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test_that("ab_property works", {
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ab_reset_session()
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expect_identical(ab_name("AMX", language = NULL), "Amoxicillin")
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expect_identical(ab_atc("AMX"), "J01CA04")
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expect_identical(ab_cid("AMX"), as.integer(33613))
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expect_identical(ab_name("AMX", language = NULL), "Amoxicillin")
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expect_identical(ab_atc("AMX"), "J01CA04")
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expect_identical(ab_cid("AMX"), as.integer(33613))
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expect_inherits(ab_tradenames("AMX"), "character")
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expect_inherits(ab_tradenames(c("AMX", "AMX")), "list")
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expect_inherits(ab_tradenames("AMX"), "character")
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expect_inherits(ab_tradenames(c("AMX", "AMX")), "list")
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expect_identical(ab_group("AMX", language = NULL), "Beta-lactams/penicillins")
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expect_identical(ab_atc_group1("AMX", language = NULL), "Beta-lactam antibacterials, penicillins")
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expect_identical(ab_atc_group2("AMX", language = NULL), "Penicillins with extended spectrum")
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expect_identical(ab_group("AMX", language = NULL), "Beta-lactams/penicillins")
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expect_identical(ab_atc_group1("AMX", language = NULL), "Beta-lactam antibacterials, penicillins")
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expect_identical(ab_atc_group2("AMX", language = NULL), "Penicillins with extended spectrum")
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expect_identical(ab_name("Fluclox", language = NULL), "Flucloxacillin")
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expect_identical(ab_name("fluklox", language = NULL), "Flucloxacillin")
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expect_identical(ab_name("floxapen", language = NULL), "Flucloxacillin")
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expect_identical(ab_name(21319, language = NULL), "Flucloxacillin")
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expect_identical(ab_name("J01CF05", language = NULL), "Flucloxacillin")
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expect_identical(ab_name("Fluclox", language = NULL), "Flucloxacillin")
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expect_identical(ab_name("fluklox", language = NULL), "Flucloxacillin")
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expect_identical(ab_name("floxapen", language = NULL), "Flucloxacillin")
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expect_identical(ab_name(21319, language = NULL), "Flucloxacillin")
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expect_identical(ab_name("J01CF05", language = NULL), "Flucloxacillin")
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expect_identical(ab_ddd("AMX", "oral"), 1.5)
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expect_identical(ab_ddd_units("AMX", "iv"), "g")
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expect_identical(ab_ddd("AMX", "iv"), 3)
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expect_identical(ab_ddd("AMX", "oral"), 1.5)
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expect_identical(ab_ddd_units("AMX", "iv"), "g")
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expect_identical(ab_ddd("AMX", "iv"), 3)
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expect_identical(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B"))
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expect_identical(
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ab_name(x = c("AMC", "PLB"), tolower = TRUE, language = NULL),
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c("amoxicillin/clavulanic acid", "polymyxin B")
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)
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expect_inherits(ab_info("AMX"), "list")
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expect_error(ab_property("amox", "invalid property"))
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expect_error(ab_name("amox", language = "INVALID"))
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expect_stdout(print(ab_name("amox", language = NULL)))
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expect_equal(ab_name("21066-6", language = NULL), "Ampicillin")
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expect_equal(
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ab_loinc("ampicillin"),
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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")
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)
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expect_true(ab_url("AMX") %like% "fhi[.]no")
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expect_identical(
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colnames(set_ab_names(example_isolates[, 17:22])),
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c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin")
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)
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expect_identical(
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colnames(set_ab_names(example_isolates[, 17:22], language = "nl", snake_case = FALSE)),
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c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine")
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)
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expect_identical(
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colnames(set_ab_names(example_isolates[, 17:22], property = "atc")),
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c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")
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)
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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expect_identical(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B"))
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expect_identical(
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example_isolates %>% set_ab_names(),
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example_isolates %>% rename_with(set_ab_names)
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ab_name(x = c("AMC", "PLB"), tolower = TRUE, language = NULL),
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c("amoxicillin/clavulanic acid", "polymyxin B")
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)
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expect_true(all(c(
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"SXT", "nitrofurantoin", "fosfomycin", "linezolid", "ciprofloxacin",
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"moxifloxacin", "vancomycin", "TEC"
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) %in%
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(example_isolates %>%
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set_ab_names(NIT:VAN) %>%
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colnames())))
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}
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expect_inherits(ab_info("AMX"), "list")
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expect_error(ab_property("amox", "invalid property"))
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expect_error(ab_name("amox", language = "INVALID"))
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expect_output(print(ab_name("amox", language = NULL)))
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expect_equal(ab_name("21066-6", language = NULL), "Ampicillin")
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expect_equal(
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ab_loinc("ampicillin"),
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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")
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)
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expect_true(ab_url("AMX") %like% "fhi[.]no")
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expect_identical(
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colnames(set_ab_names(example_isolates[, 17:22])),
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c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin")
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)
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expect_identical(
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colnames(set_ab_names(example_isolates[, 17:22], language = "nl", snake_case = FALSE)),
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c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine")
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)
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expect_identical(
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colnames(set_ab_names(example_isolates[, 17:22], property = "atc")),
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c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")
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)
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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expect_identical(
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example_isolates %>% set_ab_names(),
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example_isolates %>% rename_with(set_ab_names)
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)
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expect_true(all(c(
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"SXT", "nitrofurantoin", "fosfomycin", "linezolid", "ciprofloxacin",
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"moxifloxacin", "vancomycin", "TEC"
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) %in%
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(example_isolates %>%
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set_ab_names(NIT:VAN) %>%
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colnames())))
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}
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})
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