# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # # AUTHORS # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # # # LICENCE # # This package is free software; you can redistribute it and/or modify # # it under the terms of the GNU General Public License version 2.0, # # as published by the Free Software Foundation. # # # # This R package is distributed in the hope that it will be useful, # # but WITHOUT ANY WARRANTY; without even the implied warranty of # # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # GNU General Public License version 2.0 for more details. # # ==================================================================== # 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("B_ESCHR_COL", "B_HMPHL_INF")) expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COL") expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COL") 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(" B_ESCHR_COL ")), "B_ESCHR_COL") expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COL") # not Campylobacter expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNE") expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL") expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNE_RHI") # K. pneumoniae subspp. rhinoscleromatis expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL") expect_equal(as.character(as.mo("C. difficile")), "B_CTRDM_DIF") expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNE") expect_equal(as.character(as.mo("Strepto")), "B_STRPTC") expect_equal(as.character(as.mo("Streptococcus")), "B_STRPTC") # not Peptostreptoccus expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("B_STRPTC_GRA", "B_STRPTC_GRB")) expect_equal(as.character(as.mo("S. pyo")), "B_STRPTC_PYO") # not Actinomyces pyogenes expect_equal(as.character(as.mo("P. aer")), "B_PDMNS_AER") # not Pasteurella aerogenes # GLIMS expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRA") expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPI") expect_equal(as.character(as.mo("VRE")), "B_ENTRC") expect_equal(as.character(as.mo("MRPA")), "B_PDMNS_AER") expect_equal(as.character(as.mo("PISP")), "B_STRPTC_PNE") expect_equal(as.character(as.mo("PRSP")), "B_STRPTC_PNE") expect_equal(as.character(as.mo("VISP")), "B_STRPTC_PNE") expect_equal(as.character(as.mo("VRSP")), "B_STRPTC_PNE") expect_equal(as.character(as.mo("CNS")), "B_STPHY_CNS") expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CNS") expect_equal(as.character(as.mo("CPS")), "B_STPHY_CPS") expect_equal(as.character(as.mo("CoPS")), "B_STPHY_CPS") expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP")) # prevalent MO expect_identical( as.character( as.mo(c("stau", "STAU", "staaur", "S. aureus", "S aureus", "Staphylococcus aureus", "MRSA", "VISA"))), rep("B_STPHY_AUR", 8)) # unprevalent MO expect_identical( as.character( as.mo(c("buno", "BUNO", "burnod", "B. nodosa", "B nodosa", "Burkholderia nodosa"))), rep("B_BRKHL_NOD", 6)) # empty values expect_identical(as.character(as.mo(c("", NA, NaN))), rep(NA_character_, 3)) # too few characters expect_warning(as.mo("ab")) expect_equal(suppressWarnings(as.character(as.mo(c("Qq species", "", "CRS", "K. pneu rhino", "esco")))), c(NA_character_, NA_character_, "B_STNTR_MAL", "B_KLBSL_PNE_RHI", "B_ESCHR_COL")) # check for Becker classification expect_identical(as.character(guess_mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPI") expect_identical(as.character(guess_mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CNS") expect_identical(as.character(guess_mo("STAEPI", Becker = TRUE)), "B_STPHY_CNS") expect_identical(as.character(guess_mo("S. intermedius", Becker = FALSE)), "B_STRPTC_INT") # Strep (!) intermedius expect_identical(as.character(guess_mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INT") expect_identical(as.character(guess_mo("Sta intermedius",Becker = TRUE)), "B_STPHY_CPS") expect_identical(as.character(guess_mo("STAINT", Becker = TRUE)), "B_STPHY_CPS") # aureus must only be influenced if Becker = "all" expect_identical(as.character(guess_mo("STAAUR", Becker = FALSE)), "B_STPHY_AUR") expect_identical(as.character(guess_mo("STAAUR", Becker = TRUE)), "B_STPHY_AUR") expect_identical(as.character(guess_mo("STAAUR", Becker = "all")), "B_STPHY_CPS") # check for Lancefield classification expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = FALSE)), "B_STRPTC_PYO") expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = TRUE)), "B_STRPTC_GRA") expect_identical(as.character(guess_mo("STCPYO", Lancefield = TRUE)), "B_STRPTC_GRA") # group A expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = FALSE)), "B_STRPTC_AGA") expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = TRUE)), "B_STRPTC_GRB") # group B expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = FALSE)), "B_STRPTC_DYS_EQU") expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = TRUE)), "B_STRPTC_GRC") # group C # Enterococci must only be influenced if Lancefield = "all" expect_identical(as.character(guess_mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_IUM") expect_identical(as.character(guess_mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_IUM") expect_identical(as.character(guess_mo("E. faecium", Lancefield = "all")), "B_STRPTC_GRD") # group D expect_identical(as.character(guess_mo("S. anginosus", Lancefield = FALSE)), "B_STRPTC_ANG") expect_identical(as.character(guess_mo("S. anginosus", Lancefield = TRUE)), "B_STRPTC_GRF") # group F expect_identical(as.character(guess_mo("S. sanguinis", Lancefield = FALSE)), "B_STRPTC_SAN") expect_identical(as.character(guess_mo("S. sanguinis", Lancefield = TRUE)), "B_STRPTC_GRH") # group H expect_identical(as.character(guess_mo("S. salivarius", Lancefield = FALSE)), "B_STRPTC_SAL") expect_identical(as.character(guess_mo("S. salivarius", Lancefield = TRUE)), "B_STRPTC_GRK") # group K library(dplyr) # select with one column expect_identical( septic_patients[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( 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("B_ESCHR_COL", NA)))) # helper function expect_identical(as.mo("B_ESCHR_COL"), guess_mo("B_ESCHR_COL")) # test pull expect_equal(nrow(septic_patients %>% mutate(mo = as.mo(mo))), 2000) # test data.frame expect_equal(nrow(data.frame(test = as.mo("B_ESCHR_COL"))), 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_APO_DEL") expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APO_DEL") expect_equal(as.character(as.mo("G apo deli")), "B_GMPHS_APO_DEL") expect_equal(as.character(as.mo("Gomphosphaeria aponina")), "B_GMPHS_APO") 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_APO ")), "B_GMPHS_APO") expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APO") # check old names expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLA") # - Didymosphaeria spartinae (unprevalent) expect_warning(suppressMessages(as.mo("D spartin", allow_uncertain = TRUE))) # - was renames to Leptosphaeria obiones expect_equal(suppressWarnings(suppressMessages(as.character(as.mo("D spartin", allow_uncertain = TRUE)))), "F_LPTSP_OBI") # check uncertain names expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = FALSE))), NA_character_) expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = TRUE))), "B_ESCHR_COL") expect_warning(as.mo("esco extra_text", allow_uncertain = TRUE)) # predefined reference_df expect_equal(as.character(as.mo("TestingOwnID", reference_df = data.frame(a = "TestingOwnID", b = "B_ESCHR_COL"))), "B_ESCHR_COL") expect_equal(as.character(as.mo(c("TestingOwnID", "E. coli"), reference_df = data.frame(a = "TestingOwnID", b = "B_ESCHR_COL"))), c("B_ESCHR_COL", "B_ESCHR_COL")) expect_warning(as.mo("TestingOwnID", reference_df = NULL)) expect_error(as.mo("E. coli", reference_df = data.frame(a = "TestingOwnID"))) # combination of existing mo and certe expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))), c("B_ESCHR_COL", "B_ESCHR_COL")) # TSN of prevalent and non prevalent ones expect_equal(mo_TSN(c("Gomphosphaeria aponina delicatula", "Escherichia coli")), c(717, 285)) expect_equal(mo_fullname(c("E. spp.", "E. spp", "E. species")), rep("Escherichia species", 3)) # from different sources expect_equal(as.character(as.mo( c("PRTMIR", "bclcer", "B_ESCHR_COL"))), c("B_PROTS_MIR", "B_BCLLS_CER", "B_ESCHR_COL")) # hard to find expect_equal(as.character(suppressWarnings(as.mo( c("Microbacterium paraoxidans", "Streptococcus suis (bovis gr)", "Raoultella (here some text) terrigena")))), c("B_MCRBC", "B_STRPTC_SUI", "B_RLTLL_TER")) # Salmonella (City) are all actually Salmonella enterica spp (City) expect_equal(as.character(suppressMessages(as.mo("Salmonella Goettingen"))), "B_SLMNL_ENT") })