AMR/inst/tinytest/test-bug_drug_combinations.R

# ==================================================================== #
# TITLE:                                                               #
# AMR: An R Package for Working with Antimicrobial Resistance Data     #
#                                                                      #
# SOURCE CODE:                                                         #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# PLEASE CITE THIS SOFTWARE AS:                                        #
# Berends MS, Luz CF, Friedrich AW, et al. (2022).                     #
# AMR: An R Package for Working with Antimicrobial Resistance Data.    #
# Journal of Statistical Software, 104(3), 1-31.                       #
# https://doi.org/10.18637/jss.v104.i03                                #
#                                                                      #
# Developed at the University of Groningen and the University Medical  #
# Center Groningen in The Netherlands, in collaboration with many      #
# colleagues from around the world, see our website.                   #
#                                                                      #
# 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/   #
# ==================================================================== #

b <- suppressWarnings(bug_drug_combinations(example_isolates))
expect_inherits(b, "bug_drug_combinations")
expect_stdout(suppressMessages(print(b)))
expect_true(is.data.frame(format(b)))
expect_true(is.data.frame(format(b, add_ab_group = FALSE)))
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
  expect_true(example_isolates %>%
    group_by(ward) %>%
    bug_drug_combinations(FUN = mo_gramstain) %>%
    is.data.frame())
}