AMR/inst/tinytest/test-ab.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, 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/ #
# ==================================================================== #
expect_equal(
as.character(as.ab(c(
"J01FA01",
"J 01 FA 01",
"Erythromycin",
"eryt",
" eryt 123",
"ERYT",
"ERY",
"erytromicine",
"Erythrocin",
"Romycin"
))),
rep("ERY", 10)
)
expect_identical(class(as.ab("amox")), c("ab", "character"))
expect_identical(class(antibiotics$ab), c("ab", "character"))
expect_true(is.ab(as.ab("amox")))
expect_stdout(print(as.ab("amox")))
expect_stdout(print(data.frame(a = as.ab("amox"))))
expect_warning(as.ab("J00AA00")) # ATC not yet available in data set
expect_warning(as.ab("UNKNOWN"))
expect_stdout(print(as.ab("amox")))
expect_equal(
as.character(as.ab("Phloxapen")),
"FLC"
)
expect_equal(
suppressWarnings(as.character(as.ab(c("Bacteria", "Bacterial")))),
c(NA, "TMP")
)
expect_equal(
as.character(as.ab("Amoxy + clavulaanzuur")),
"AMC"
)
expect_equal(
as.character(as.ab(c("mreopenem", "co-maoxiclav"))),
c("MEM", "AMC")
)
expect_warning(as.ab("cipro mero"))
# based on Levenshtein distance
expect_identical(ab_name("ceftazidim/avibactam", language = NULL), "Ceftazidime/avibactam")
# assigning and subsetting
x <- antibiotics$ab
expect_inherits(x[1], "ab")
expect_inherits(x[[1]], "ab")
expect_inherits(c(x[1], x[9]), "ab")
expect_inherits(unique(x[1], x[9]), "ab")
expect_inherits(rep(x[1], 2), "ab")
expect_warning(x[1] <- "invalid code")
expect_warning(x[[1]] <- "invalid code")
expect_warning(c(x[1], "test"))