# ==================================================================== # # TITLE # # AMR: An R Package for Working with Antimicrobial Resistance Data # # # # SOURCE # # https://github.com/msberends/AMR # # # # CITE AS # # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # # (2022). AMR: An R Package for Working with Antimicrobial Resistance # # Data. Journal of Statistical Software, 104(3), 1-31. # # doi:10.18637/jss.v104.i03 # # # # Developed at the University of Groningen and the University Medical # # Center Groningen in The Netherlands, in collaboration with many # # colleagues from around the world, see our website. # # # # 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"), keep_synonyms = FALSE)), 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("Eschr 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. pneumo 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("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("GAS", "GBS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "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")) # expect_warning(as.mo("Acinetobacter calcoaceticus/baumannii complex")) # prevalent MO expect_identical( suppressWarnings(as.character( as.mo(c( "stau", # WHONET code "STAU", "staaur", "S. aureus", "S aureus", "Sthafilokkockus aureus", # handles incorrect spelling "Staphylococcus aureus (MRSA)", "MRSA", # Methicillin Resistant S. aureus "VISA", # Vancomycin Intermediate S. aureus "VRSA", # Vancomycin Resistant S. aureus 115329001 # SNOMED CT code )) )), rep("B_STPHY_AURS", 11) ) 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", "Paraburkholderia nodosa" )) ), rep("B_PRBRK_NODS", 2) ) # 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_identical( suppressWarnings(as.character(as.mo(c("Qq species", "MRSA", "K. pneu rhino", "esco")))), c("UNKNOWN", "B_STPHY_AURS", "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. equi", Lancefield = FALSE)), "B_STRPT_EQUI") expect_identical(as.character(as.mo("S. equi", 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", min_version = "1.0.0", also_load = TRUE)) { # select with one column expect_identical( example_isolates %>% slice(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 %>% slice(1:10) %>% pull(mo), example_isolates %>% slice(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()) } # 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(as.mo("")), NA_character_ ) # check less prevalent MOs expect_equal(as.character(as.mo("Actinosynnema pretiosum auranticum")), "B_ANNMA_PRTS_ARNT") # expect_equal(as.character(as.mo("Actinosynnema preti aura")), "B_ANNMA_PRTS_ARNT") # expect_equal(as.character(as.mo("A pre aur")), "B_ANNMA_PRTS_ARNT") expect_equal(as.character(as.mo("Actinosynnema pretiosum")), "B_ANNMA_PRTS") expect_equal(as.character(as.mo("Actinosynnema")), "B_ANNMA") expect_equal(as.character(as.mo(" B_ANNMA_PRTS ")), "B_ANNMA_PRTS") # check old names expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT") expect_equal(suppressMessages(as.character(as.mo(c("E. coli", "Chlamydo psittaci")))), c("B_ESCHR_COLI", "B_CHLMY_PSTT")) expect_equal(suppressMessages(mo_name("eubcom")), "Clostridium combesii") # 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( suppressWarnings(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("Sta. aur") # many hits expect_stdout(print(mo_uncertainties())) # no viruses expect_equal(suppressWarnings(as.mo("Virus")), as.mo("UNKNOWN")) # summary expect_equal(length(summary(example_isolates$mo)), 6) # WHONET codes and NA/NaN expect_equal( as.character(as.mo(c("xxx", "na", "nan"), debug = TRUE)), rep(NA_character_, 3) ) expect_equal(as.character(as.mo("con")), "UNKNOWN") expect_equal(as.character(as.mo("xxx")), NA_character_) expect_equal(as.character(as.mo(c("xxx", "con", "eco"))), c(NA_character_, "UNKNOWN", "B_ESCHR_COLI")) expect_equal( as.character(suppressWarnings(as.mo(c("other", "none", "unknown")))), rep("UNKNOWN", 3) ) # ..coccus expect_equal( as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))), c("B_NESSR_MNNG", "B_NESSR_GNRR", "B_STRPT_PNMN") ) # yeasts and fungi expect_equal( suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))), c("F_YEAST", "F_FUNGUS") ) if (AMR:::pkg_is_available("tibble")) { # print tibble expect_stdout(print(tibble::tibble(mo = as.mo("B_ESCHR_COLI")))) } # assigning and subsetting x <- example_isolates$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_true(is.na(as.mo("E. coli ignorethis", ignore_pattern = "this"))) # frequency tables if (AMR:::pkg_is_available("cleaner")) { expect_inherits(cleaner::freq(example_isolates$mo), "freq") }