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75 lines
4.3 KiB
75 lines
4.3 KiB
# ==================================================================== # |
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# TITLE # |
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# Antimicrobial Resistance (AMR) Data Analysis for R # |
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# # |
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# SOURCE # |
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# https://github.com/msberends/AMR # |
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# # |
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# LICENCE # |
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# (c) 2018-2021 Berends MS, Luz CF et al. # |
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# Developed at the University of Groningen, the Netherlands, in # |
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# collaboration with non-profit organisations Certe Medical # |
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# Diagnostics & Advice, and University Medical Center Groningen. # |
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# # |
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# This R package is free software; you can freely use and distribute # |
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# it for both personal and commercial purposes under the terms of the # |
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# GNU General Public License version 2.0 (GNU GPL-2), as published by # |
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# the Free Software Foundation. # |
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# We created this package for both routine data analysis and academic # |
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# research and it was publicly released in the hope that it will be # |
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # |
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# # |
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# Visit our website for the full manual and a complete tutorial about # |
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # |
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# ==================================================================== # |
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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_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_ddd("AMX", "oral"), 1.5) |
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expect_warning(ab_ddd("AMX", "oral", units = TRUE)) # old behaviour |
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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_units("AMX", "iv"), "g") |
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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(ab_name(x = c("AMC", "PLB"), tolower = TRUE, language = NULL), |
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c("amoxicillin/clavulanic acid", "polymyxin B")) |
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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(ab_loinc("ampicillin"), |
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c("21066-6", "3355-5", "33562-0", "33919-2", "43883-8", "43884-6", "87604-5")) |
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expect_true(ab_url("AMX") %like% "whocc.no") |
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expect_warning(ab_url("ASP")) |
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expect_identical(colnames(set_ab_names(example_isolates[, 20:25])), |
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c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin")) |
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expect_identical(colnames(set_ab_names(example_isolates[, 20:25], language = "nl", snake_case = FALSE)), |
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c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine")) |
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expect_identical(colnames(set_ab_names(example_isolates[, 20:25], "atc")), |
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c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")) |
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) { |
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expect_identical(example_isolates %>% set_ab_names(), |
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example_isolates %>% rename_with(set_ab_names)) |
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}
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