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("coagulase negative")), "STACNS") 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_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") 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 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_) })