AMR/inst/tinytest/test-ab.R

# ==================================================================== #
# TITLE                                                                #
# AMR: An R Package for Working with Antimicrobial Resistance Data     #
#                                                                      #
# SOURCE                                                               #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# CITE 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.                 #
# doi:10.18637/jss.v104.i03                                            #
#                                                                      #
# Developed at the University of Groningen, the Netherlands, in        #
# collaboration with non-profit organisations Certe Medical            #
# Diagnostics & Advice, and University Medical Center Groningen.       #
#                                                                      #
# 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_warning(as.ab(""))

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_message(as.ab("cipro mero"))

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

# 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_warning(x[1] <- "invalid code")
expect_warning(x[[1]] <- "invalid code")
expect_warning(c(x[1], "test"))