# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Data Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2021 Berends MS, Luz CF et al. # # Developed at the University of Groningen, the Netherlands, in # # collaboration with non-profit organisations Certe Medical # # Diagnostics & Advice, and University Medical Center Groningen. # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # MOs <- subset(microorganisms, !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_COLI", "B_HMPHL_INFL")) expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI") expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI") expect_equal(as.character(as.mo(112283007)), "B_ESCHR_COLI") 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("Esch spp.")), "B_ESCHR") expect_equal(as.character(as.mo(" B_ESCHR_COLI ")), "B_ESCHR_COLI") expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COLI") # not Campylobacter expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNMN") expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL") expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL") expect_equal(as.character(as.mo("C. difficile")), "B_CRDDS_DFFC") expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNMP") expect_equal(as.character(as.mo("Strepto")), "B_STRPT") expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB") expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB") expect_equal(as.character(as.mo(c("mycobacterie", "mycobakterium"))), c("B_MYCBC", "B_MYCBC")) expect_equal(as.character(as.mo(c("GAS", "GBS", "a MGS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_MILL", "B_STRPT_HAEM")) expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes # GLIMS expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRGL") expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPDR") expect_equal(as.character(as.mo("VRE")), "B_ENTRC") expect_equal(as.character(as.mo("MRPA")), "B_PSDMN_AERG") expect_equal(as.character(as.mo("PISP")), "B_STRPT_PNMN") expect_equal(as.character(as.mo("PRSP")), "B_STRPT_PNMN") expect_equal(as.character(as.mo("VISP")), "B_STRPT_PNMN") expect_equal(as.character(as.mo("VRSP")), "B_STRPT_PNMN") expect_equal(as.character(as.mo("CNS")), "B_STPHY_CONS") expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CONS") expect_equal(as.character(as.mo("CPS")), "B_STPHY_COPS") expect_equal(as.character(as.mo("CoPS")), "B_STPHY_COPS") expect_equal(as.character(as.mo("VGS")), "B_STRPT_VIRI") expect_equal(as.character(as.mo("streptococcus milleri")), "B_STRPT_MILL") expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP")) # prevalent MO expect_identical( suppressWarnings(as.character( as.mo(c("stau", "STAU", "staaur", "S. aureus", "S aureus", "Sthafilokkockus aureeuzz", "Staphylococcus aureus", "MRSA", "VISA")))), rep("B_STPHY_AURS", 9)) expect_identical( as.character( as.mo(c("EHEC", "EPEC", "EIEC", "STEC", "ATEC", "UPEC"))), rep("B_ESCHR_COLI", 6)) # unprevalent MO expect_identical( as.character( as.mo(c("parnod", "P. nodosa", "P nodosa", "Paraburkholderia nodosa"))), rep("B_PRBRK_NODS", 4)) # empty values expect_identical(as.character(as.mo(c("", " ", NA, NaN))), rep(NA_character_, 4)) expect_identical(as.character(as.mo(" ")), NA_character_) # too few characters expect_warning(as.mo("ab")) expect_equal(suppressWarnings(as.character(as.mo(c("Qq species", "", "CRSM", "K. pneu rhino", "esco")))), c("UNKNOWN", NA_character_, "B_STNTR_MLTP", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI")) # check for Becker classification expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR") expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS") expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS") expect_identical(as.character(as.mo("Sta intermedius", Becker = FALSE)), "B_STPHY_INTR") expect_identical(as.character(as.mo("Sta intermedius", Becker = TRUE)), "B_STPHY_COPS") expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS") # aureus must only be influenced if Becker = "all" expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AURS") expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AURS") expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_COPS") # check for Lancefield classification expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPT_PYGN") expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPT_GRPA") expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRPA") # group A expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGLC") expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRPB") # group B expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRPB") expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPT_DYSG_EQSM") expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPT_GRPC") # group C # Enterococci must only be influenced if Lancefield = "all" expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_FACM") expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_FACM") expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPT_GRPD") # group D expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPT_ANGN") expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPT_GRPF") # group F expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPT_SNGN") expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPT_GRPH") # group H expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SLVR") expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRPK") # group K if (AMR:::pkg_is_available("dplyr")) { # select with one column expect_identical( example_isolates[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( example_isolates[1:10, ] %>% pull(mo), example_isolates[1:10, ] %>% left_join_microorganisms() %>% select(genus, species) %>% as.mo()) # too many columns expect_error(example_isolates %>% select(1:3) %>% as.mo()) # test pull expect_equal(nrow(example_isolates %>% mutate(mo = as.mo(mo))), 2000) expect_true(example_isolates %>% pull(mo) %>% is.mo()) } # unknown results expect_warning(as.mo(c("INVALID", "Yeah, unknown"))) # print expect_stdout(print(as.mo(c("B_ESCHR_COLI", NA)))) # test data.frame expect_equal(nrow(data.frame(test = as.mo("B_ESCHR_COLI"))), 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_APNN_DLCT") expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APNN_DLCT") expect_equal(as.character(as.mo("G apo deli")), "B_GMPHS_APNN_DLCT") expect_equal(as.character(as.mo("Gomphosphaeria aponina")), "B_GMPHS_APNN") 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_APNN ")), "B_GMPHS_APNN") expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APNN") # check old names expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT") print(mo_renamed()) expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT")) # check uncertain names expect_equal(suppressMessages(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS") expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN") expect_message(as.mo("e coli extra_text", allow_uncertain = TRUE)) expect_equal(suppressMessages(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS") expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY_COPS") expect_equal(suppressMessages(as.character(as.mo(c("s aur THISISATEST", "Staphylococcus aureus unexisting"), allow_uncertain = 3))), c("B_STPHY_AURS_ANRB", "B_STPHY_AURS_ANRB")) # predefined reference_df expect_equal(as.character(as.mo("TestingOwnID", reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI"))), "B_ESCHR_COLI") expect_equal(as.character(as.mo(c("TestingOwnID", "E. coli"), reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI"))), c("B_ESCHR_COLI", "B_ESCHR_COLI")) expect_warning(as.mo("TestingOwnID", reference_df = NULL)) expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID"))) # combination of existing mo and other code expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))), c("B_ESCHR_COLI", "B_ESCHR_COLI")) # from different sources expect_equal(as.character(as.mo( c("PRTMIR", "bclcer", "B_ESCHR_COLI"))), c("B_PROTS_MRBL", "B_BCLLS_CERS", "B_ESCHR_COLI")) # hard to find expect_equal(as.character(suppressMessages(as.mo( c("Microbacterium paraoxidans", "Streptococcus suis (bovis gr)", "Raoultella (here some text) terrigena")))), c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG")) expect_stdout(print(mo_uncertainties())) x <- as.mo("S. aur") # many hits expect_stdout(print(mo_uncertainties())) # Salmonella (City) are all actually Salmonella enterica spp (City) expect_equal(suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))), as.mo(c("Salmonella enterica", "Salmonella enterica", "Salmonella"))) # no virusses expect_equal(as.character(as.mo("Virus")), NA_character_) # summary expect_equal(length(summary(example_isolates$mo)), 6) # WHONET codes and NA/NaN expect_equal(as.character(as.mo(c("xxx", "na", "nan"), debug = TRUE)), rep(NA_character_, 3)) expect_equal(as.character(as.mo("con")), "UNKNOWN") expect_equal(as.character(as.mo("xxx")), NA_character_) expect_equal(as.character(as.mo(c("xxx", "con", "eco"))), c(NA_character_, "UNKNOWN", "B_ESCHR_COLI")) expect_equal(as.character(as.mo(c("other", "none", "unknown"))), rep("UNKNOWN", 3)) expect_null(mo_failures()) expect_error(translate_allow_uncertain(5)) # debug mode expect_stdout(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3))))) # ..coccus expect_equal(as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))), c("B_NESSR_MNNG", "B_NESSR_GNRR", "B_STRPT_PNMN")) # yeasts and fungi expect_equal(suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))), c("F_YEAST", "F_FUNGUS")) if (AMR:::pkg_is_available("dplyr")) { # print tibble expect_stdout(print(tibble(mo = as.mo("B_ESCHR_COLI")))) } # assigning and subsetting x <- example_isolates$mo expect_inherits(x[1], "mo") expect_inherits(x[[1]], "mo") expect_inherits(c(x[1], x[9]), "mo") expect_warning(x[1] <- "invalid code") expect_warning(x[[1]] <- "invalid code") expect_warning(c(x[1], "test")) # ignoring patterns expect_equal(as.character(as.mo(c("E. coli", "E. coli ignorethis"), ignore_pattern = "this")), c("B_ESCHR_COLI", NA)) # frequency tables if (AMR:::pkg_is_available("cleaner")) { expect_inherits(cleaner::freq(example_isolates$mo), "freq") }