2018-12-16 22:45:12 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
# TITLE #
|
2020-10-08 11:16:03 +02:00
|
|
|
# Antimicrobial Resistance (AMR) 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 #
|
2020-01-05 17:22:09 +01:00
|
|
|
# (c) 2018-2020 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 #
|
|
|
|
|
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
|
2018-12-16 22:45:12 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
|
2018-08-25 22:01:14 +02:00
|
|
|
context("mic.R")
|
2018-03-27 17:43:42 +02:00
|
|
|
|
|
|
|
|
test_that("mic works", {
|
2020-07-31 10:50:08 +02:00
|
|
|
skip_on_cran()
|
2018-03-27 17:43:42 +02:00
|
|
|
expect_true(as.mic(8) == as.mic("8"))
|
|
|
|
|
expect_true(as.mic("1") > as.mic("<=0.0625"))
|
|
|
|
|
expect_true(as.mic("1") < as.mic(">=32"))
|
|
|
|
|
expect_true(is.mic(as.mic(8)))
|
2018-04-02 16:05:09 +02:00
|
|
|
|
2018-03-27 17:43:42 +02:00
|
|
|
expect_equal(as.double(as.mic(">=32")), 32)
|
2018-08-24 11:08:20 +02:00
|
|
|
expect_equal(as.numeric(as.mic(">=32")), 32)
|
2018-03-27 17:43:42 +02:00
|
|
|
expect_equal(as.integer(as.mic(">=32")), 32)
|
|
|
|
|
expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA)
|
2018-04-02 16:05:09 +02:00
|
|
|
|
2018-08-24 11:08:20 +02:00
|
|
|
# all levels should be valid MICs
|
2020-09-25 14:44:50 +02:00
|
|
|
x <- as.mic(c(2, 4))
|
|
|
|
|
expect_s3_class(x[1], "mic")
|
|
|
|
|
expect_s3_class(x[[1]], "mic")
|
|
|
|
|
expect_s3_class(c(x[1], x[9]), "mic")
|
|
|
|
|
expect_s3_class(unique(x[1], x[9]), "mic")
|
2018-08-24 11:08:20 +02:00
|
|
|
expect_warning(as.mic("INVALID VALUE"))
|
2020-09-30 10:24:53 +02:00
|
|
|
|
2018-08-24 11:08:20 +02:00
|
|
|
|
2020-09-19 15:15:57 +02:00
|
|
|
pdf(NULL) # prevent Rplots.pdf being created
|
|
|
|
|
expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
|
|
|
|
|
expect_silent(plot(as.mic(c(1, 2, 4, 8))))
|
|
|
|
|
expect_output(print(as.mic(c(1, 2, 4, 8))))
|
2020-09-18 16:05:53 +02:00
|
|
|
|
|
|
|
|
expect_equal(summary(as.mic(c(2, 8))),
|
|
|
|
|
structure(c("Class" = "mic",
|
|
|
|
|
"<NA>" = "0",
|
|
|
|
|
"Min." = "2",
|
|
|
|
|
"Max." = "8"), class = c("summaryDefault", "table")))
|
2018-03-27 17:43:42 +02:00
|
|
|
})
|
