AMR/inst/tinytest/test-ab.R

# ==================================================================== #
# 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, Sinha BNM, Albers CJ, Glasner C    #
# (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.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")), c("ab", "character"))
expect_identical(class(antibiotics$ab), c("ab", "character"))
expect_true(is.ab(as.ab("amox")))
expect_stdout(print(as.ab("amox")))
expect_stdout(print(data.frame(a = as.ab("amox"))))

# expect_warning(as.ab("J00AA00")) # ATC not yet available in data set
# expect_warning(as.ab("UNKNOWN"))

expect_stdout(print(as.ab("amox")))

expect_equal(
  as.character(as.ab("Phloxapen")),
  "FLC"
)

expect_equal(
  suppressWarnings(as.character(as.ab(c("Bacteria", "Bacterial")))),
  c(NA, "TMP")
)

expect_equal(
  as.character(as.ab("Amoxy + clavulaanzuur")),
  "AMC"
)

expect_equal(
  as.character(as.ab(c("mreopenem", "co-maoxiclav"))),
  c("MEM", "AMC")
)

# expect_warning(as.ab("cipro mero"))

# based on Levenshtein distance
expect_identical(ab_name("ceftazidim/avibactam", language = NULL), "Ceftazidime/avibactam")

expect_identical(as.character(as.ab(c("gentamicine High Level",
                                      "gentamicine High",
                                      "gentamicine (High Level)",
                                      "gentamicine (High)",
                                      "gentamicine HL",
                                      "gentamicine H-L",
                                      "gentamicine (HL)",
                                      "gentamicine (H-L)"))),
                 rep("GEH", 8))

# assigning and subsetting
x <- antibiotics$ab
expect_inherits(x[1], "ab")
expect_inherits(x[[1]], "ab")
expect_inherits(c(x[1], x[9]), "ab")
expect_inherits(unique(x[1], x[9]), "ab")
expect_inherits(rep(x[1], 2), "ab")
# expect_warning(x[1] <- "invalid code")
# expect_warning(x[[1]] <- "invalid code")
# expect_warning(c(x[1], "test"))