AMR/tests/testthat/test-bactid.R

111 lines
4.6 KiB
R

context("bactid.R")
test_that("as.bactid works", {
expect_identical(
as.character(as.bactid(c("E. coli", "H. influenzae"))),
c("ESCCOL", "HAEINF"))
expect_equal(as.character(as.bactid("Escherichia coli")), "ESCCOL")
expect_equal(as.character(as.bactid("Escherichia coli")), "ESCCOL")
expect_equal(as.character(as.bactid("Escherichia species")), "ESC")
expect_equal(as.character(as.bactid(" ESCCOL ")), "ESCCOL")
expect_equal(as.character(as.bactid("klpn")), "KLEPNE")
expect_equal(as.character(as.bactid("P. aer")), "PSEAER") # not Pasteurella aerogenes
expect_equal(as.character(as.bactid("Negative rods")), "GNR")
# GLIMS
expect_equal(as.character(as.bactid("shiboy")), "SHIBOY")
expect_equal(as.character(as.bactid("MRSE")), "STAEPI")
expect_equal(as.character(as.bactid("VRE")), "ENC")
expect_equal(as.character(as.bactid("MRPA")), "PSEAER")
expect_equal(as.character(as.bactid("PISP")), "STCPNE")
expect_equal(as.character(as.bactid("PRSP")), "STCPNE")
expect_equal(as.character(as.bactid("VISP")), "STCPNE")
expect_equal(as.character(as.bactid("VRSP")), "STCPNE")
expect_identical(
as.character(
as.bactid(c("stau",
"STAU",
"staaur",
"S. aureus",
"S aureus",
"Staphylococcus aureus",
"MRSA",
"VISA"))),
rep("STAAUR", 8))
# check for Becker classification
expect_identical(as.character(guess_bactid("S. epidermidis", Becker = FALSE)), "STAEPI")
expect_identical(as.character(guess_bactid("S. epidermidis", Becker = TRUE)), "STACNS")
expect_identical(as.character(guess_bactid("STAEPI", Becker = TRUE)), "STACNS")
expect_identical(as.character(guess_bactid("S. intermedius", Becker = FALSE)), "STAINT")
expect_identical(as.character(guess_bactid("S. intermedius", Becker = TRUE)), "STACPS")
expect_identical(as.character(guess_bactid("STAINT", Becker = TRUE)), "STACPS")
# aureus must only be influenced if Becker = "all"
expect_identical(as.character(guess_bactid("STAAUR", Becker = FALSE)), "STAAUR")
expect_identical(as.character(guess_bactid("STAAUR", Becker = TRUE)), "STAAUR")
expect_identical(as.character(guess_bactid("STAAUR", Becker = "all")), "STACPS")
# check for Lancefield classification
expect_identical(as.character(guess_bactid("S. pyogenes", Lancefield = FALSE)), "STCPYO")
expect_identical(as.character(guess_bactid("S. pyogenes", Lancefield = TRUE)), "STCGRA")
expect_identical(as.character(guess_bactid("STCPYO", Lancefield = TRUE)), "STCGRA")
expect_identical(as.character(guess_bactid("S. agalactiae", Lancefield = FALSE)), "STCAGA")
expect_identical(as.character(guess_bactid("S. agalactiae", Lancefield = TRUE)), "STCGRB") # group B
expect_identical(as.character(guess_bactid("S. equisimilis", Lancefield = FALSE)), "STCEQS")
expect_identical(as.character(guess_bactid("S. equisimilis", Lancefield = TRUE)), "STCGRC") # group C
expect_identical(as.character(guess_bactid("S. anginosus", Lancefield = FALSE)), "STCANG")
expect_identical(as.character(guess_bactid("S. anginosus", Lancefield = TRUE)), "STCGRF") # group F
expect_identical(as.character(guess_bactid("S. sanguis", Lancefield = FALSE)), "STCSAN")
expect_identical(as.character(guess_bactid("S. sanguis", Lancefield = TRUE)), "STCGRH") # group H
expect_identical(as.character(guess_bactid("S. salivarius", Lancefield = FALSE)), "STCSAL")
expect_identical(as.character(guess_bactid("S. salivarius", Lancefield = TRUE)), "STCGRK") # group K
# select with one column
expect_identical(
septic_patients[1:10,] %>%
left_join_microorganisms() %>%
select(genus) %>%
as.bactid() %>%
as.character(),
c("ESC", "ESC", "STA", "STA", "STA",
"STA", "STA", "STA", "STA", "STA"))
# select with two columns
expect_identical(
septic_patients[1:10,] %>%
pull(bactid),
septic_patients[1:10,] %>%
left_join_microorganisms() %>%
select(genus, species) %>%
as.bactid() %>%
as.character())
# unknown results
expect_warning(as.bactid(c("INVALID", "Yeah, unknown")))
# print
expect_output(print(as.bactid(c("ESCCOL", NA))))
# helper function
expect_identical(as.bactid("ESCCOL"),
guess_bactid("ESCCOL"))
# test pull
expect_equal(nrow(septic_patients %>% mutate(bactid = as.bactid(bactid))),
2000)
# test data.frame
expect_equal(nrow(data.frame(test = as.bactid("ESCCOL"))),
1)
# check empty values
expect_equal(as.character(suppressWarnings(as.bactid(""))),
NA_character_)
})