AMR/tests/testthat/test-mo.R

132 lines
5.5 KiB
R

context("mo.R")
test_that("as.mo works", {
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")), "ESC")
expect_equal(as.character(as.mo(" ESCCOL ")), "ESCCOL")
expect_equal(as.character(as.mo("klpn")), "KLEPNE")
expect_equal(as.character(as.mo("Klebsiella")), "KLE")
expect_equal(as.character(as.mo("K. pneu rhino")), "KLEPNERH") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("Bartonella")), "BAR")
expect_equal(as.character(as.mo("C. difficile")), "CLODIF")
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("shiboy")), "SHIBOY")
expect_equal(as.character(as.mo("MRSE")), "STAEPI")
expect_equal(as.character(as.mo("VRE")), "ENC")
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)), "STAINT")
expect_identical(as.character(guess_mo("S. 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(),
c("ESC", "ESC", "STA", "STA", "STA",
"STA", "STA", "STA", "STA", "STA"))
# 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_)
})