mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 10:46:12 +01:00
81 lines
3.2 KiB
R
Executable File
81 lines
3.2 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE: #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE CODE: #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# PLEASE CITE THIS SOFTWARE AS: #
|
|
# Berends MS, Luz CF, Friedrich AW, et al. (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"))
|