AMR/inst/tinytest/test-av.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. #
# 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_equal(
as.character(as.av(c(
"J05AB01",
"J 05 AB 01",
"Aciclovir",
"aciclo",
" aciclo 123",
"ACICL",
"ACI",
"Virorax",
"Zovirax"
))),
rep("ACI", 9)
)
expect_identical(class(as.av("acic")), c("av", "character"))
expect_identical(class(antivirals$av), c("av", "character"))
expect_true(is.av(as.av("acic")))
expect_stdout(print(as.av("acic")))
expect_stdout(print(data.frame(a = as.av("acic"))))
# expect_warning(as.av("J00AA00")) # ATC not yet available in data set
# expect_warning(as.av("UNKNOWN"))
expect_stdout(print(as.av("acic")))
expect_equal(
as.character(as.av("zovirax")),
"ACI"
)
expect_equal(
as.character(as.av(c("Abacaivr", "Celvudine"))),
c("ABA", "CLE")
)
# expect_warning(as.av("Abacavir Clevudine"))
# based on Levenshtein distance
expect_identical(av_name("adevofir dypifo", language = NULL), "Adefovir dipivoxil")
# assigning and subsetting
x <- antivirals$av
expect_inherits(x[1], "av")
expect_inherits(x[[1]], "av")
expect_inherits(c(x[1], x[9]), "av")
expect_inherits(unique(x[1], x[9]), "av")
expect_inherits(rep(x[1], 2), "av")
# expect_warning(x[1] <- "invalid code")
# expect_warning(x[[1]] <- "invalid code")
# expect_warning(c(x[1], "test"))