mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 18:06:12 +01:00
37 lines
2.5 KiB
R
37 lines
2.5 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_equal(length(key_antimicrobials(example_isolates, antifungal = NULL)), nrow(example_isolates))
|
|
expect_false(all(is.na(key_antimicrobials(example_isolates, antifungal = NULL))))
|
|
expect_true(antimicrobials_equal("SSS", "SSS", type = "points"))
|
|
expect_false(antimicrobials_equal("SSS", "SRS", type = "keyantimicrobials"))
|
|
expect_true(antimicrobials_equal("SSS", "SRS", type = "points"))
|
|
expect_true(antimicrobials_equal("SSS", "SIS", ignore_I = TRUE, type = "keyantimicrobials"))
|
|
expect_false(antimicrobials_equal("SSS", "SIS", ignore_I = FALSE, type = "keyantimicrobials"))
|
|
expect_true(antimicrobials_equal(".SS", "SI.", ignore_I = TRUE, type = "keyantimicrobials"))
|
|
expect_false(antimicrobials_equal(".SS", "SI.", ignore_I = FALSE, type = "keyantimicrobials"))
|
|
|
|
expect_warning(key_antimicrobials(example_isolates[rep(1, 10), ]))
|