AMR/inst/tinytest/test-mo.R

# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Data Analysis for R                   #
#                                                                      #
# SOURCE                                                               #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# LICENCE                                                              #
# (c) 2018-2021 Berends MS, Luz CF et al.                              #
# 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/   #
# ==================================================================== #

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"))),
  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("Esch 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. pneu 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("Strepto")), "B_STRPT")
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("mycobacterie", "mycobakterium"))), c("B_MYCBC", "B_MYCBC"))

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

# prevalent MO
expect_identical(
  suppressWarnings(as.character(
    as.mo(c("stau",
            "STAU",
            "staaur",
            "S. aureus",
            "S aureus",
            "Sthafilokkockus aureeuzz",
            "Staphylococcus aureus",
            "MRSA",
            "VISA")))),
  rep("B_STPHY_AURS", 9))
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",
            "P. nodosa",
            "P nodosa",
            "Paraburkholderia nodosa"))),
  rep("B_PRBRK_NODS", 4))

# 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_equal(suppressWarnings(as.character(as.mo(c("Qq species", "", "CRSM", "K. pneu rhino", "esco")))),
             c("UNKNOWN", NA_character_, "B_STNTR_MLTP", "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. equisimilis", Lancefield = FALSE)), "B_STRPT_DYSG_EQSM")
expect_identical(as.character(as.mo("S. equisimilis", 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")) {
  # select with one column
  expect_identical(
    example_isolates[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[1:10, ] %>%
      pull(mo),
    example_isolates[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())
}

# unknown results
expect_warning(as.mo(c("INVALID", "Yeah, unknown")))

# 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(suppressWarnings(as.mo(""))),
             NA_character_)

# check less prevalent MOs
expect_equal(as.character(as.mo("Gomphosphaeria aponina delicatula")), "B_GMPHS_APNN_DLCT")
expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APNN_DLCT")
expect_equal(as.character(as.mo("G apo deli")), "B_GMPHS_APNN_DLCT")
expect_equal(as.character(as.mo("Gomphosphaeria  aponina")), "B_GMPHS_APNN")
expect_equal(as.character(as.mo("Gomphosphaeria  species")), "B_GMPHS")
expect_equal(as.character(as.mo("Gomphosphaeria")), "B_GMPHS")
expect_equal(as.character(as.mo(" B_GMPHS_APNN ")), "B_GMPHS_APNN")
expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APNN")

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

# check uncertain names
expect_equal(suppressMessages(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
expect_message(as.mo("e coli extra_text", allow_uncertain = TRUE))
expect_equal(suppressMessages(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY_COPS")
expect_equal(suppressMessages(as.character(as.mo(c("s aur THISISATEST", "Staphylococcus aureus unexisting"), allow_uncertain = 3))), c("B_STPHY_AURS_ANRB", "B_STPHY_AURS_ANRB"))

# 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(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("S. aur")
# many hits
expect_stdout(print(mo_uncertainties()))

# Salmonella (City) are all actually Salmonella enterica spp (City)
expect_equal(suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
             as.mo(c("Salmonella enterica", "Salmonella enterica", "Salmonella")))

# no virusses
expect_equal(as.character(as.mo("Virus")), NA_character_)

# 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(as.mo(c("other", "none", "unknown"))),
             rep("UNKNOWN", 3))

expect_null(mo_failures())

expect_error(translate_allow_uncertain(5))

# debug mode
expect_stdout(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 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")) {
  # 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_equal(as.character(as.mo(c("E. coli", "E. coli ignorethis"), ignore_pattern = "this")),
             c("B_ESCHR_COLI", NA))

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