2021-01-22 10:20:41 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
# TITLE #
|
2021-02-02 23:57:35 +01:00
|
|
|
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
2021-01-22 10:20:41 +01:00
|
|
|
# #
|
|
|
|
|
# SOURCE #
|
|
|
|
|
# https://github.com/msberends/AMR #
|
|
|
|
|
# #
|
|
|
|
|
# LICENCE #
|
|
|
|
|
# (c) 2018-2021 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 #
|
2021-02-02 23:57:35 +01:00
|
|
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
2021-01-22 10:20:41 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
|
|
|
|
|
context("isolate_identifier.R")
|
|
|
|
|
|
|
|
|
|
test_that("isolate_identifier works", {
|
|
|
|
|
x <- suppressMessages(isolate_identifier(example_isolates))
|
|
|
|
|
expect_s3_class(x, "isolate_identifier")
|
|
|
|
|
expect_s3_class(x, "character")
|
|
|
|
|
|
|
|
|
|
expect_equal(suppressMessages(
|
|
|
|
|
unique(nchar(isolate_identifier(example_isolates, cols_ab = carbapenems(), col_mo = FALSE)))),
|
|
|
|
|
2)
|
|
|
|
|
|
|
|
|
|
expect_warning(isolate_identifier(example_isolates[, 1:3, drop = FALSE])) # without mo and without rsi
|
|
|
|
|
expect_warning(isolate_identifier(example_isolates[, 1:9, drop = FALSE])) # only without rsi
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
expect_output(print(x))
|
|
|
|
|
expect_s3_class(unique(c(x, x)), "isolate_identifier")
|
|
|
|
|
|
|
|
|
|
})
|
