AMR/tests/testthat/test-mo.R

context("mo.R")

test_that("as.mo works", {

  library(dplyr)
  MOs <- AMR::microorganisms %>% filter(!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("ESCCOL", "HAEINF"))

  expect_equal(as.character(as.mo("Escherichia coli")), "ESCCOL")
  expect_equal(as.character(as.mo("Escherichia  coli")), "ESCCOL")
  expect_equal(as.character(as.mo("Escherichia  species")), "ESCSPP")
  expect_equal(as.character(as.mo("Escherichia")), "ESCSPP")
  expect_equal(as.character(as.mo(" ESCCOL ")), "ESCCOL")
  expect_equal(as.character(as.mo("coli")), "ESCCOL") # not Campylobacter
  expect_equal(as.character(as.mo("klpn")), "KLEPNE")
  expect_equal(as.character(as.mo("Klebsiella")), "KLESPP")
  expect_equal(as.character(as.mo("K. pneu rhino")), "KLEPNERH") # K. pneumoniae subspp. rhinoscleromatis
  expect_equal(as.character(as.mo("Bartonella")), "BARSPP")
  expect_equal(as.character(as.mo("C. difficile")), "CLODIF")
  expect_equal(as.character(as.mo("L. pneumophila")), "LEGPNE")
  expect_equal(as.character(as.mo("L. non pneumophila")), "LEGNON")
  expect_equal(as.character(as.mo("S. beta-haemolytic")), "STCHAE")
  expect_equal(as.character(as.mo("Strepto")), "STCSPP")
  expect_equal(as.character(as.mo("Streptococcus")), "STCSPP") # not Peptostreptoccus

  expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("STCGRA", "STCGRB"))


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

  expect_equal(as.character(as.mo("P. aer")), "PSEAER") # not Pasteurella aerogenes

  expect_equal(as.character(as.mo("Negative rods")), "GNR")
  expect_equal(as.character(as.mo("Gram negative rods")), "GNR")

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

  expect_equal(as.character(as.mo("MRSE")), "STAEPI")
  expect_equal(as.character(as.mo("VRE")), "ENCSPP")
  expect_equal(as.character(as.mo("MRPA")), "PSEAER")
  expect_equal(as.character(as.mo("PISP")), "STCPNE")
  expect_equal(as.character(as.mo("PRSP")), "STCPNE")
  expect_equal(as.character(as.mo("VISP")), "STCPNE")
  expect_equal(as.character(as.mo("VRSP")), "STCPNE")

  expect_equal(as.character(as.mo("CNS")), "STACNS")
  expect_equal(as.character(as.mo("CoNS")), "STACNS")
  expect_equal(as.character(as.mo("CPS")), "STACPS")
  expect_equal(as.character(as.mo("CoPS")), "STACPS")

  expect_identical(
    as.character(
      as.mo(c("stau",
              "STAU",
              "staaur",
              "S. aureus",
              "S aureus",
              "Staphylococcus aureus",
              "MRSA",
              "VISA"))),
    rep("STAAUR", 8))

  # check for Becker classification
  expect_identical(as.character(guess_mo("S. epidermidis", Becker = FALSE)), "STAEPI")
  expect_identical(as.character(guess_mo("S. epidermidis", Becker = TRUE)),  "STACNS")
  expect_identical(as.character(guess_mo("STAEPI",         Becker = TRUE)),  "STACNS")
  expect_identical(as.character(guess_mo("S. intermedius", Becker = FALSE)), "STCINT") # Strep (!) intermedius
  expect_identical(as.character(guess_mo("Sta intermedius",Becker = FALSE)), "STAINT")
  expect_identical(as.character(guess_mo("Sta intermedius",Becker = TRUE)),  "STACPS")
  expect_identical(as.character(guess_mo("STAINT",         Becker = TRUE)),  "STACPS")
  # aureus must only be influenced if Becker = "all"
  expect_identical(as.character(guess_mo("STAAUR", Becker = FALSE)), "STAAUR")
  expect_identical(as.character(guess_mo("STAAUR", Becker = TRUE)),  "STAAUR")
  expect_identical(as.character(guess_mo("STAAUR", Becker = "all")), "STACPS")

  # check for Lancefield classification
  expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = FALSE)),    "STCPYO")
  expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = TRUE)),     "STCGRA")
  expect_identical(as.character(guess_mo("STCPYO",      Lancefield = TRUE)),     "STCGRA") # group A
  expect_identical(as.character(guess_mo("S. agalactiae",  Lancefield = FALSE)), "STCAGA")
  expect_identical(as.character(guess_mo("S. agalactiae",  Lancefield = TRUE)),  "STCGRB") # group B
  expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = FALSE)), "STCEQS")
  expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = TRUE)),  "STCGRC") # group C
  # Enterococci must only be influenced if Lancefield = "all"
  expect_identical(as.character(guess_mo("E. faecium", Lancefield = FALSE)),     "ENCFAC")
  expect_identical(as.character(guess_mo("E. faecium", Lancefield = TRUE)),      "ENCFAC")
  expect_identical(as.character(guess_mo("E. faecium", Lancefield = "all")),     "STCGRD") # group D
  expect_identical(as.character(guess_mo("S. anginosus",   Lancefield = FALSE)), "STCANG")
  expect_identical(as.character(guess_mo("S. anginosus",   Lancefield = TRUE)),  "STCGRF") # group F
  expect_identical(as.character(guess_mo("S. sanguis",     Lancefield = FALSE)), "STCSAN")
  expect_identical(as.character(guess_mo("S. sanguis",     Lancefield = TRUE)),  "STCGRH") # group H
  expect_identical(as.character(guess_mo("S. salivarius",  Lancefield = FALSE)), "STCSAL")
  expect_identical(as.character(guess_mo("S. salivarius",  Lancefield = TRUE)),  "STCGRK") # group K

  library(dplyr)

  # select with one column
  expect_identical(
    septic_patients[1:10,] %>%
      left_join_microorganisms() %>%
      select(genus) %>%
      as.mo() %>%
      as.character(),
    paste0(c("ESC", "ESC", "STA", "STA", "STA",
             "STA", "STA", "STA", "STA", "STA"),
           "SPP"))

  # select with two columns
  expect_identical(
    septic_patients[1:10,] %>%
      pull(mo),
    septic_patients[1:10,] %>%
      left_join_microorganisms() %>%
      select(genus, species) %>%
      as.mo() %>%
      as.character())

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

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

  # print
  expect_output(print(as.mo(c("ESCCOL", NA))))

  # helper function
  expect_identical(as.mo("ESCCOL"),
                   guess_mo("ESCCOL"))

  # test pull
  expect_equal(nrow(septic_patients %>% mutate(mo = as.mo(mo))),
               2000)

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

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

})