2018-12-16 22:45:12 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
# TITLE #
|
2021-02-02 23:57:35 +01:00
|
|
|
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
2018-12-16 22:45:12 +01:00
|
|
|
# #
|
2019-01-02 23:24:07 +01:00
|
|
|
# SOURCE #
|
2020-07-08 14:48:06 +02:00
|
|
|
# https://github.com/msberends/AMR #
|
2018-12-16 22:45:12 +01:00
|
|
|
# #
|
|
|
|
|
# LICENCE #
|
2020-12-27 00:30:28 +01:00
|
|
|
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
2020-10-08 11:16:03 +02:00
|
|
|
# Developed at the University of Groningen, the Netherlands, in #
|
|
|
|
|
# collaboration with non-profit organisations Certe Medical #
|
|
|
|
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
2018-12-16 22:45:12 +01:00
|
|
|
# #
|
2019-01-02 23:24:07 +01:00
|
|
|
# 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. #
|
2020-01-05 17:22:09 +01:00
|
|
|
# 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. #
|
2020-10-08 11:16:03 +02:00
|
|
|
# #
|
|
|
|
|
# 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/ #
|
2018-12-16 22:45:12 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
|
2021-04-26 23:57:37 +02:00
|
|
|
context("key_antimcrobials.R")
|
2018-07-23 10:35:39 +02:00
|
|
|
|
2021-04-26 23:57:37 +02:00
|
|
|
test_that("key_antimcrobials work", {
|
2020-07-31 10:50:08 +02:00
|
|
|
skip_on_cran()
|
2021-04-26 23:57:37 +02:00
|
|
|
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"))
|
|
|
|
|
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"))
|
2019-09-12 15:08:53 +02:00
|
|
|
|
2020-09-26 16:26:01 +02:00
|
|
|
library(dplyr, warn.conflicts = FALSE)
|
2021-04-26 23:57:37 +02:00
|
|
|
expect_warning(key_antimicrobials(example_isolates %>% slice(rep(1, 10))))
|
2018-07-23 10:35:39 +02:00
|
|
|
})
|
