AMR/tests/testthat/test-_misc.R

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R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# 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 #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
context("aa_helper_functions.R")
test_that("percentages works", {
skip_on_cran()
expect_equal(percentage(0.25), "25%")
expect_equal(percentage(0.5), "50%")
expect_equal(percentage(0.500, digits = 1), "50.0%")
expect_equal(percentage(0.1234), "12.3%")
# round up 0.5
expect_equal(percentage(0.0054), "0.5%")
expect_equal(percentage(0.0055), "0.6%")
})
test_that("functions missing in older R versions work", {
skip_on_cran()
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", {
skip_on_cran()
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_warning(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))
})
test_that("looking up ab columns works", {
skip_on_cran()
# we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
if (require("dplyr")) {
expect_true(is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id)))
}
})