AMR/tests/testthat/test-ab.R

67 lines
2.9 KiB
R
Raw Normal View History

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
2019-01-02 23:24:07 +01:00
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
2019-01-02 23:24:07 +01:00
# 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. #
2019-04-05 18:47:39 +02:00
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
2019-05-10 16:44:59 +02:00
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))
2020-05-19 12:08:49 +02:00
expect_identical(class(as.ab("amox")), c("ab", "character"))
expect_identical(class(pull(antibiotics, ab)), c("ab", "character"))
2019-05-13 10:10:16 +02:00
expect_true(is.ab(as.ab("amox")))
expect_output(print(as.ab("amox")))
expect_output(print(data.frame(a = as.ab("amox"))))
2019-05-10 16:44:59 +02:00
expect_warning(as.ab("Z00ZZ00")) # not yet available in data set
expect_warning(as.ab("UNKNOWN"))
2019-05-13 14:56:23 +02:00
expect_warning(as.ab(""))
2019-05-10 16:44:59 +02:00
expect_output(print(as.ab("amox")))
2019-05-13 14:56:23 +02:00
expect_equal(as.character(as.ab("Phloxapen")),
"FLC")
expect_equal(suppressWarnings(as.character(as.ab(c("Bacteria", "Bacterial")))),
c(NA, "TMP"))
2019-10-04 15:36:12 +02:00
expect_equal(as.character(as.ab("Amoxy + clavulaanzuur")),
"AMC")
# 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"))
})