AMR/inst/tinytest/test-vctrs.R

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R
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# ==================================================================== #
# TITLE #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# CITE 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. #
# doi: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/ #
# ==================================================================== #
# extra tests for {vctrs} pkg support
if (AMR:::pkg_is_available("dplyr", also_load = FALSE)) {
test <- dplyr::tibble(ab = as.ab("CIP"),
mo = as.mo("Escherichia coli"),
mic = as.mic(2),
disk = as.disk(20),
rsi = as.rsi("S"))
check1 <- lapply(test, class)
test[1, "ab"] <- "GEN"
test[1, "mo"] <- "B_KLBSL_PNMN"
test[1, "mic"] <- ">=32"
test[1, "mic"] <- 32
test[1, "disk"] <- "35"
test[1, "disk"] <- 25
test[1, "disk"] <- 26L
test[1, "rsi"] <- "R"
check2 <- lapply(test, class)
expect_identical(check1, check2)
test <- dplyr::tibble(cipro = as.rsi("S"),
variable = "test")
expect_equal(nrow(test[quinolones() == "S", ]), 1)
expect_equal(nrow(test[quinolones() == "R", ]), 0)
}