mirror of https://github.com/msberends/AMR.git
50 lines
2.6 KiB
R
Executable File
50 lines
2.6 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# 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. #
|
|
# #
|
|
# This R package was created for academic research and was publicly #
|
|
# released in the hope that it will be useful, but it comes WITHOUT #
|
|
# ANY WARRANTY OR LIABILITY. #
|
|
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
context("misc.R")
|
|
|
|
test_that("percentages works", {
|
|
expect_equal(percent(0.25), "25%")
|
|
expect_equal(percent(0.5), "50%")
|
|
expect_equal(percent(0.500, force_zero = TRUE), "50.0%")
|
|
expect_equal(percent(0.1234), "12.3%")
|
|
# round up 0.5
|
|
expect_equal(percent(0.0054), "0.5%")
|
|
expect_equal(percent(0.0055), "0.6%")
|
|
})
|
|
|
|
test_that("functions missing in older R versions work", {
|
|
expect_equal(strrep("A", 5), "AAAAA")
|
|
expect_equal(strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
|
|
expect_equal(trimws(" test "), "test")
|
|
expect_equal(trimws(" test ", "l"), "test ")
|
|
expect_equal(trimws(" test ", "r"), " test")
|
|
})
|
|
|
|
test_that("looking up ab columns works", {
|
|
expect_warning(generate_warning_abs_missing(c("AMP", "AMX")))
|
|
expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
|
|
expect_warning(get_column_abx(example_isolates, hard_dependencies = "FUS"))
|
|
expect_message(get_column_abx(example_isolates, soft_dependencies = "FUS"))
|
|
expect_message(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
|
|
expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
|
|
})
|