AMR/inst/tinytest/test-disk.R

# ==================================================================== #
# TITLE:                                                               #
# Antidiskrobial Resistance (AMR) Analysis                              #
#                                                                      #
# SOURCE CODE:                                                         #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# PLEASE CITE THIS SOFTWARE AS:                                        #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C    #
# (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/   #
# ==================================================================== #

expect_true(as.disk(8) == as.disk("8"))
expect_true(is.disk(as.disk(8)))

expect_equal(suppressWarnings(as.logical(as.disk("INVALID VALUE"))), NA)

# all levels should be valid disks
x <- as.disk(c(20, 40))
expect_inherits(x[1], "disk")
expect_inherits(x[[1]], "disk")
expect_inherits(c(x[1], x[9]), "disk")
expect_inherits(unique(x[1], x[9]), "disk")
# expect_warning(as.disk("INVALID VALUE"))
x[2] <- 32
expect_inherits(x, "disk")

pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.disk(c(10, 20, 40))))
expect_silent(plot(as.disk(c(10, 20, 40))))
expect_silent(plot(as.disk(c(10, 20, 40)), expand = FALSE))
expect_silent(plot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"))
if (AMR:::pkg_is_available("ggplot2")) {
  expect_inherits(ggplot2::autoplot(as.disk(c(10, 20, 40))), "gg")
  expect_inherits(ggplot2::autoplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
  expect_inherits(ggplot2::autoplot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"), "gg")
}
expect_stdout(print(as.disk(12)))

if (AMR:::pkg_is_available("tibble")) {
  expect_stdout(print(tibble::tibble(d = as.disk(12))))
}