mirror of https://github.com/msberends/AMR.git
67 lines
2.9 KiB
R
Executable File
67 lines
2.9 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# AUTHORS #
|
|
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# LICENCE #
|
|
# This package is free software; you can redistribute it and/or modify #
|
|
# it under the terms of the GNU General Public License version 2.0, #
|
|
# as published by the Free Software Foundation. #
|
|
# #
|
|
# This R package is distributed in the hope that it will be useful, #
|
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
|
# GNU General Public License version 2.0 for more details. #
|
|
# ==================================================================== #
|
|
|
|
context("atc.R")
|
|
|
|
# test_that("atc_property works", {
|
|
# skip_on_cran() # relies on internet connection of server, don't test
|
|
# skip_on_appveyor() # security error on AppVeyor
|
|
#
|
|
# if (!is.null(curl::nslookup("www.whocc.no", error = FALSE))) {
|
|
# expect_equal(tolower(atc_property("J01CA04", property = "Name")), "amoxicillin")
|
|
# expect_equal(atc_property("J01CA04", property = "unit"), "g")
|
|
# expect_equal(atc_property("J01CA04", property = "DDD"),
|
|
# atc_ddd("J01CA04"))
|
|
#
|
|
# expect_identical(atc_property("J01CA04", property = "Groups"),
|
|
# atc_groups("J01CA04"))
|
|
#
|
|
# expect_warning(atc_property("ABCDEFG", property = "DDD"))
|
|
#
|
|
# expect_error(atc_property("J01CA04", property = c(1:5)))
|
|
# expect_error(atc_property("J01CA04", property = "test"))
|
|
# expect_error(atc_property("J01CA04", property = "test", administration = c(1:5)))
|
|
# }
|
|
# })
|
|
|
|
test_that("guess_atc works", {
|
|
expect_equal(as.character(guess_atc(c("J01FA01",
|
|
"Erythromycin",
|
|
"eryt",
|
|
"ERYT",
|
|
"ERY",
|
|
"Erythrocin",
|
|
"Eryzole",
|
|
"Pediamycin"))),
|
|
rep("J01FA01", 8))
|
|
|
|
expect_identical(class(as.atc("amox")), "atc")
|
|
expect_identical(class(pull(antibiotics, atc)), "atc")
|
|
expect_identical(ab_trivial_nl("Cefmenoxim"), "Cefmenoxim")
|
|
|
|
expect_warning(as.atc("Z00ZZ00")) # not yet available in data set
|
|
expect_warning(as.atc("UNKNOWN"))
|
|
|
|
expect_output(print(as.atc("amox")))
|
|
|
|
# first 5 chars of official name
|
|
expect_equal(as.character(as.atc(c("nitro", "cipro"))),
|
|
c("J01XE01", "J01MA02"))
|
|
|
|
})
|