AMR/inst/tinytest/test-mo.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 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/   #
# ==================================================================== #

MOs <- subset(microorganisms, !is.na(mo) & nchar(mo) > 3)
expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))

expect_identical(
  as.character(as.mo(c("E. coli", "H. influenzae"), keep_synonyms = FALSE)),
  c("B_ESCHR_COLI", "B_HMPHL_INFL")
)

expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("Escherichia  coli")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo(112283007)), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("Escherichia  species")), "B_ESCHR")
expect_equal(as.character(as.mo("Escherichia")), "B_ESCHR")
expect_equal(as.character(as.mo("Eschr spp.")), "B_ESCHR")
expect_equal(as.character(as.mo(" B_ESCHR_COLI ")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COLI") # not Campylobacter
expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNMN")
expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
expect_equal(as.character(as.mo("K. pneumo rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
expect_equal(as.character(as.mo("C. difficile")), "B_CRDDS_DFFC")
expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNMP")
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")

expect_equal(as.character(as.mo(c("GAS", "GBS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_HAEM"))


expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes

# GLIMS
expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRGL")

expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPDR")
expect_equal(as.character(as.mo("VRE")), "B_ENTRC")
expect_equal(as.character(as.mo("MRPA")), "B_PSDMN_AERG")
expect_equal(as.character(as.mo("PISP")), "B_STRPT_PNMN")
expect_equal(as.character(as.mo("PRSP")), "B_STRPT_PNMN")
expect_equal(as.character(as.mo("VISP")), "B_STRPT_PNMN")
expect_equal(as.character(as.mo("VRSP")), "B_STRPT_PNMN")

expect_equal(as.character(as.mo("CNS")), "B_STPHY_CONS")
expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CONS")
expect_equal(as.character(as.mo("CPS")), "B_STPHY_COPS")
expect_equal(as.character(as.mo("CoPS")), "B_STPHY_COPS")
expect_equal(as.character(as.mo("VGS")), "B_STRPT_VIRI")
expect_equal(as.character(as.mo("streptococcus milleri")), "B_STRPT_MILL")


expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP"))

expect_warning(as.mo("Acinetobacter calcoaceticus/baumannii complex"))

# prevalent MO
expect_identical(
  suppressWarnings(as.character(
    as.mo(c(
      "stau", # WHONET code
      "STAU",
      "staaur",
      "S. aureus",
      "S aureus",
      "Sthafilokkockus aureus", # handles incorrect spelling
      "Staphylococcus aureus (MRSA)",
      "MRSA", # Methicillin Resistant S. aureus
      "VISA", # Vancomycin Intermediate S. aureus
      "VRSA", # Vancomycin Resistant S. aureus
      115329001 # SNOMED CT code
    ))
  )),
  rep("B_STPHY_AURS", 11)
)
expect_identical(
  as.character(
    as.mo(c("EHEC", "EPEC", "EIEC", "STEC", "ATEC", "UPEC"))
  ),
  rep("B_ESCHR_COLI", 6)
)
# unprevalent MO
expect_identical(
  as.character(
    as.mo(c(
      "parnod",
      "Paraburkholderia nodosa"
    ))
  ),
  rep("B_PRBRK_NODS", 2)
)

# empty values
expect_identical(as.character(as.mo(c("", "  ", NA, NaN))), rep(NA_character_, 4))
expect_identical(as.character(as.mo("  ")), NA_character_)
# too few characters
expect_warning(as.mo("ab"))

expect_identical(
  suppressWarnings(as.character(as.mo(c("Qq species", "MRSA", "K. pneu rhino", "esco")))),
  c("UNKNOWN", "B_STPHY_AURS", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI")
)

# check for Becker classification
expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
expect_identical(as.character(as.mo("Sta intermedius", Becker = FALSE)), "B_STPHY_INTR")
expect_identical(as.character(as.mo("Sta intermedius", Becker = TRUE)), "B_STPHY_COPS")
expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
# aureus must only be influenced if Becker = "all"
expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AURS")
expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AURS")
expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_COPS")

# check for Lancefield classification
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPT_PYGN")
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPT_GRPA")
expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRPA") # group A
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGLC")
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRPB") # group B
expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRPB")
expect_identical(as.character(as.mo("S. equi", Lancefield = FALSE)), "B_STRPT_EQUI")
expect_identical(as.character(as.mo("S. equi", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
# Enterococci must only be influenced if Lancefield = "all"
expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_FACM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_FACM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPT_GRPD") # group D
expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPT_ANGN")
expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPT_GRPF") # group F
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPT_SNGN")
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPT_GRPH") # group H
expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SLVR")
expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRPK") # group K

if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
  # select with one column
  expect_identical(
    example_isolates %>%
      slice(1:10) %>%
      left_join_microorganisms() %>%
      select(genus) %>%
      as.mo() %>%
      as.character(),
    c(
      "B_ESCHR", "B_ESCHR", "B_STPHY", "B_STPHY", "B_STPHY",
      "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY", "B_STPHY"
    )
  )

  # select with two columns
  expect_identical(
    example_isolates %>%
      slice(1:10) %>%
      pull(mo),
    example_isolates %>%
      slice(1:10) %>%
      left_join_microorganisms() %>%
      select(genus, species) %>%
      as.mo()
  )

  # too many columns
  expect_error(example_isolates %>% select(1:3) %>% as.mo())

  # test pull
  expect_equal(
    nrow(example_isolates %>% mutate(mo = as.mo(mo))),
    2000
  )
  expect_true(example_isolates %>% pull(mo) %>% is.mo())
}

# print
expect_stdout(print(as.mo(c("B_ESCHR_COLI", NA))))

# test data.frame
expect_equal(
  nrow(data.frame(test = as.mo("B_ESCHR_COLI"))),
  1
)

# check empty values
expect_equal(
  as.character(as.mo("")),
  NA_character_
)

# check less prevalent MOs
expect_equal(as.character(as.mo("Actinosynnema pretiosum auranticum")), "B_ANNMA_PRTS_ARNT")
# expect_equal(as.character(as.mo("Actinosynnema preti aura")), "B_ANNMA_PRTS_ARNT")
# expect_equal(as.character(as.mo("A pre aur")), "B_ANNMA_PRTS_ARNT")
expect_equal(as.character(as.mo("Actinosynnema  pretiosum")), "B_ANNMA_PRTS")
expect_equal(as.character(as.mo("Actinosynnema")), "B_ANNMA")
expect_equal(as.character(as.mo(" B_ANNMA_PRTS ")), "B_ANNMA_PRTS")

# check old names
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT"))
expect_equal(suppressMessages(mo_name("eubcom")), "Clostridium combesii")

# predefined reference_df
expect_equal(
  as.character(as.mo("TestingOwnID",
    reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI")
  )),
  "B_ESCHR_COLI"
)
expect_equal(
  as.character(as.mo(c("TestingOwnID", "E. coli"),
    reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI")
  )),
  c("B_ESCHR_COLI", "B_ESCHR_COLI")
)
# expect_warning(as.mo("TestingOwnID", reference_df = NULL))
expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))

# combination of existing mo and other code
expect_identical(
  suppressWarnings(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL")))),
  c("B_ESCHR_COLI", "B_ESCHR_COLI")
)

# from different sources
expect_equal(
  as.character(as.mo(
    c("PRTMIR", "bclcer", "B_ESCHR_COLI")
  )),
  c("B_PROTS_MRBL", "B_BCLLS_CERS", "B_ESCHR_COLI")
)

# hard to find
expect_equal(
  as.character(suppressMessages(as.mo(
    c(
      "Microbacterium paraoxidans",
      "Streptococcus suis (bovis gr)",
      "Raoultella (here some text) terrigena"
    )
  ))),
  c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG")
)
expect_stdout(print(mo_uncertainties()))
x <- as.mo("Sta. aur")
# many hits
expect_stdout(print(mo_uncertainties()))

# no viruses
expect_equal(suppressWarnings(as.mo("Virus")), as.mo("UNKNOWN"))

# summary
expect_equal(length(summary(example_isolates$mo)), 6)

# WHONET codes and NA/NaN
expect_equal(
  as.character(as.mo(c("xxx", "na", "nan"), debug = TRUE)),
  rep(NA_character_, 3)
)
expect_equal(as.character(as.mo("con")), "UNKNOWN")
expect_equal(as.character(as.mo("xxx")), NA_character_)
expect_equal(as.character(as.mo(c("xxx", "con", "eco"))), c(NA_character_, "UNKNOWN", "B_ESCHR_COLI"))
expect_equal(
  as.character(suppressWarnings(as.mo(c("other", "none", "unknown")))),
  rep("UNKNOWN", 3)
)

# ..coccus
expect_equal(
  as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
  c("B_NESSR_MNNG", "B_NESSR_GNRR", "B_STRPT_PNMN")
)
# yeasts and fungi
expect_equal(
  suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))),
  c("F_YEAST", "F_FUNGUS")
)

if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
  # print tibble
  expect_stdout(print(tibble(mo = as.mo("B_ESCHR_COLI"))))
}

# assigning and subsetting
x <- example_isolates$mo
expect_inherits(x[1], "mo")
expect_inherits(x[[1]], "mo")
expect_inherits(c(x[1], x[9]), "mo")
expect_warning(x[1] <- "invalid code")
expect_warning(x[[1]] <- "invalid code")
expect_warning(c(x[1], "test"))

# ignoring patterns
expect_true(is.na(as.mo("E. coli ignorethis", ignore_pattern = "this")))

# frequency tables
if (AMR:::pkg_is_available("cleaner")) {
  expect_inherits(cleaner::freq(example_isolates$mo), "freq")
}