AMR/tests/testthat/test-ab.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
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# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
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# 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. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
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context("ab.R")
test_that("as.ab works", {
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")), "ab")
expect_identical(class(pull(antibiotics, ab)), "ab")
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expect_true(is.ab(as.ab("amox")))
expect_output(print(as.ab("amox")))
expect_output(print(data.frame(a = as.ab("amox"))))
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expect_warning(as.ab("Z00ZZ00")) # not yet available in data set
expect_warning(as.ab("UNKNOWN"))
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expect_warning(as.ab(""))
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expect_output(print(as.ab("amox")))
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expect_identical(class(pull(antibiotics, ab)), "ab")
# first 5 chars of official name
expect_equal(as.character(as.atc(c("nitro", "cipro"))),
c("J01XE01", "J01MA02"))
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# EARS-Net
expect_equal(as.character(as.atc("AMX")),
"J01CA04")
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expect_equal(as.character(as.ab("Phloxapen")),
"FLC")
expect_equal(suppressWarnings(as.character(as.ab(c("Bacteria", "Bacterial")))),
c(NA, "TMP"))
})