mirror of https://github.com/msberends/AMR.git
92 lines
3.4 KiB
R
Executable File
92 lines
3.4 KiB
R
Executable File
# ==================================================================== #
|
|
# 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/ #
|
|
# ==================================================================== #
|
|
|
|
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"))
|