mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 20:06:11 +01:00
82 lines
4.6 KiB
R
82 lines
4.6 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2018-2022 Berends MS, Luz CF et al. #
|
|
# Developed at the University of Groningen, the Netherlands, in #
|
|
# collaboration with non-profit organisations Certe Medical #
|
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# We created this package for both routine data analysis and academic #
|
|
# research and it was publicly released in the hope that it will be #
|
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
|
# #
|
|
# Visit our website for the full manual and a complete tutorial about #
|
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
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_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_ddd("AMX", "oral"), 1.5)
|
|
expect_warning(ab_ddd("AMX", "oral", units = TRUE)) # old behaviour
|
|
expect_identical(ab_ddd_units("AMX", "iv"), "g")
|
|
expect_identical(ab_ddd("AMX", "iv"), 3)
|
|
expect_identical(ab_ddd_units("AMX", "iv"), "g")
|
|
|
|
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("21066-6", "3355-5", "33562-0", "33919-2", "43883-8", "43884-6", "87604-5"))
|
|
|
|
expect_true(ab_url("AMX") %like% "whocc.no")
|
|
expect_warning(ab_url("ASP"))
|
|
|
|
expect_identical(colnames(set_ab_names(example_isolates[, 20:25])),
|
|
c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin"))
|
|
expect_identical(colnames(set_ab_names(example_isolates[, 20:25], language = "nl", snake_case = FALSE)),
|
|
c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine"))
|
|
expect_identical(colnames(set_ab_names(example_isolates[, 20:25], property = "atc")),
|
|
c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01"))
|
|
|
|
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
|
|
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())))
|
|
}
|