AMR/tests/testthat/test-ab.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
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# SOURCE #
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# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
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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. #
# #
# 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. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
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context("ab.R")
test_that("as.ab works", {
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skip_on_cran()
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expect_equal(as.character(as.ab(c("J01FA01",
"J 01 FA 01",
"Erythromycin",
"eryt",
" eryt 123",
"ERYT",
"ERY",
"erytromicine",
"Erythrocin",
"Romycin"))),
rep("ERY", 10))
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expect_identical(class(as.ab("amox")), c("ab", "character"))
expect_identical(class(antibiotics$ab), c("ab", "character"))
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expect_true(is.ab(as.ab("amox")))
expect_output(print(as.ab("amox")))
expect_output(print(data.frame(a = as.ab("amox"))))
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expect_warning(as.ab("J00AA00")) # ATC not yet available in data set
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expect_warning(as.ab("UNKNOWN"))
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expect_warning(as.ab(""))
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expect_output(print(as.ab("amox")))
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expect_equal(as.character(as.ab("Phloxapen")),
"FLC")
expect_equal(suppressWarnings(as.character(as.ab(c("Bacteria", "Bacterial")))),
c(NA, "TMP"))
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expect_equal(as.character(as.ab("Amoxy + clavulaanzuur")),
"AMC")
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expect_equal(as.character(as.ab(c("mreopenem", "co-maoxiclav"))),
c("MEM", "AMC"))
expect_message(as.ab("cipro mero"))
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# assigning and subsetting
x <- antibiotics$ab
expect_s3_class(x[1], "ab")
expect_s3_class(x[[1]], "ab")
expect_s3_class(c(x[1], x[9]), "ab")
expect_warning(x[1] <- "invalid code")
expect_warning(x[[1]] <- "invalid code")
expect_warning(c(x[1], "test"))
})