# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # # SOURCE # # https://gitlab.com/msberends/AMR # # # # LICENCE # # (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # # # 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. # # # # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # # Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # # global variables EUCAST_RULES_FILE_LOCATION <- system.file("eucast/eucast_rules.tsv", package = "AMR") EUCAST_VERSION_BREAKPOINTS <- "9.0, 2019" EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016" #' EUCAST rules #' #' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables. #' @param x data with antibiotic columns, like e.g. \code{amox} and \code{amcl} #' @param info print progress #' @param rules a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")} #' @param verbose a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected. It runs all EUCAST rules, but will not be applied to an output - only an informative \code{data.frame} with changes will be returned as output. #' @param amcl,amik,amox,ampi,azit,azlo,aztr,cefa,cfep,cfot,cfox,cfra,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mezl,mino,moxi,nali,neom,neti,nitr,norf,novo,oflo,oxac,peni,pipe,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic, see Antibiotics #' @param ... parameters that are passed on to \code{eucast_rules} #' @inheritParams first_isolate #' @details #' The file used for applying all EUCAST rules can be retrieved with \code{\link{eucast_rules_file}()}. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by this function can be found when running this command: \cr #' \code{AMR::EUCAST_RULES_FILE_LOCATION} (without brackets). #' #' In the source code it is located under \href{https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv}{\code{./inst/eucast/eucast_rules.tsv}}. #' #' \strong{Note:} When ampicillin (J01CA01) is not available but amoxicillin (J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. #' @section Antibiotics: #' To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning. #' #' Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code}) #' #' \strong{amcl}: amoxicillin+clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}), #' \strong{amik}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}), #' \strong{amox}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}), #' \strong{ampi}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}), #' \strong{azit}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}), #' \strong{azlo}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}), #' \strong{aztr}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}), #' \strong{cefa}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}), #' \strong{cfep}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}), #' \strong{cfot}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}), #' \strong{cfox}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}), #' \strong{cfra}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}), #' \strong{cfta}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}), #' \strong{cftr}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}), #' \strong{cfur}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}), #' \strong{chlo}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}), #' \strong{cipr}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}), #' \strong{clar}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}), #' \strong{clin}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}), #' \strong{clox}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}), #' \strong{coli}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}), #' \strong{czol}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}), #' \strong{dapt}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}), #' \strong{doxy}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}), #' \strong{erta}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}), #' \strong{eryt}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}), #' \strong{fosf}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}), #' \strong{fusi}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}), #' \strong{gent}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}), #' \strong{imip}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}), #' \strong{kana}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}), #' \strong{levo}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}), #' \strong{linc}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}), #' \strong{line}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}), #' \strong{mero}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}), #' \strong{mezl}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}), #' \strong{mino}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}), #' \strong{moxi}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}), #' \strong{nali}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}), #' \strong{neom}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}), #' \strong{neti}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}), #' \strong{nitr}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}), #' \strong{norf}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}), #' \strong{novo}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}), #' \strong{oflo}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}), #' \strong{peni}: (benzyl)penicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}), #' \strong{pipe}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}), #' \strong{pita}: piperacillin+tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}), #' \strong{poly}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}), #' \strong{pris}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}), #' \strong{qida}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}), #' \strong{rifa}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}), #' \strong{roxi}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}), #' \strong{siso}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}), #' \strong{teic}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}), #' \strong{tetr}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}), #' \strong{tica}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}), #' \strong{tige}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}), #' \strong{tobr}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}), #' \strong{trim}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}), #' \strong{trsu}: sulfamethoxazole and trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}), #' \strong{vanc}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{J01XA01}). #' @keywords interpretive eucast reading resistance #' @rdname eucast_rules #' @export #' @importFrom dplyr %>% select pull mutate_at vars group_by summarise n #' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic strip_style #' @return The input of \code{tbl_}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with all original and new values of the affected bug-drug combinations. #' @source #' \itemize{ #' \item{ #' EUCAST Expert Rules. Version 2.0, 2012. \cr #' Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60. \cr #' \url{https://doi.org/10.1111/j.1469-0691.2011.03703.x} #' } #' \item{ #' EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \cr #' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf} #' } #' \item{ #' EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \cr #' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx} #' } #' } #' #' For editing the reference file (which is available with \code{\link{eucast_rules_file}}), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like amcl. They can be separated by comma: \code{"amcl, fluoroquinolones"}. The mo_property can be any column name from the \code{\link{microorganisms}} data set, or \code{genus_species} or \code{gramstain}. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180). #' @inheritSection AMR Read more on our website! #' @examples #' a <- eucast_rules(septic_patients) #' #' a <- data.frame(mo = c("Staphylococcus aureus", #' "Enterococcus faecalis", #' "Escherichia coli", #' "Klebsiella pneumoniae", #' "Pseudomonas aeruginosa"), #' vanc = "-", # Vancomycin #' amox = "-", # Amoxicillin #' coli = "-", # Colistin #' cfta = "-", # Ceftazidime #' cfur = "-", # Cefuroxime #' peni = "S", # Benzylpenicillin #' cfox = "S", # Cefoxitin #' stringsAsFactors = FALSE) #' #' a #' # mo vanc amox coli cfta cfur peni cfox #' # 1 Staphylococcus aureus - - - - - S S #' # 2 Enterococcus faecalis - - - - - S S #' # 3 Escherichia coli - - - - - S S #' # 4 Klebsiella pneumoniae - - - - - S S #' # 5 Pseudomonas aeruginosa - - - - - S S #' #' #' # apply EUCAST rules: 18 results are forced as R or S #' b <- eucast_rules(a) #' #' b #' # mo vanc amox coli cfta cfur peni cfox #' # 1 Staphylococcus aureus - S R R S S S #' # 2 Enterococcus faecalis - - R R R S R #' # 3 Escherichia coli R - - - - R S #' # 4 Klebsiella pneumoniae R R - - - R S #' # 5 Pseudomonas aeruginosa R R - - R R R #' #' #' # do not apply EUCAST rules, but rather get a a data.frame #' # with 18 rows, containing all details about the transformations: #' c <- eucast_rules(a, verbose = TRUE) eucast_rules <- function(x, col_mo = NULL, info = TRUE, rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE, amcl = guess_ab_col(), amik = guess_ab_col(), amox = guess_ab_col(), ampi = guess_ab_col(), azit = guess_ab_col(), azlo = guess_ab_col(), aztr = guess_ab_col(), cefa = guess_ab_col(), cfep = guess_ab_col(), cfot = guess_ab_col(), cfox = guess_ab_col(), cfra = guess_ab_col(), cfta = guess_ab_col(), cftr = guess_ab_col(), cfur = guess_ab_col(), chlo = guess_ab_col(), cipr = guess_ab_col(), clar = guess_ab_col(), clin = guess_ab_col(), clox = guess_ab_col(), coli = guess_ab_col(), czol = guess_ab_col(), dapt = guess_ab_col(), doxy = guess_ab_col(), erta = guess_ab_col(), eryt = guess_ab_col(), fosf = guess_ab_col(), fusi = guess_ab_col(), gent = guess_ab_col(), imip = guess_ab_col(), kana = guess_ab_col(), levo = guess_ab_col(), linc = guess_ab_col(), line = guess_ab_col(), mero = guess_ab_col(), mezl = guess_ab_col(), mino = guess_ab_col(), moxi = guess_ab_col(), nali = guess_ab_col(), neom = guess_ab_col(), neti = guess_ab_col(), nitr = guess_ab_col(), norf = guess_ab_col(), novo = guess_ab_col(), oflo = guess_ab_col(), oxac = guess_ab_col(), peni = guess_ab_col(), pipe = guess_ab_col(), pita = guess_ab_col(), poly = guess_ab_col(), pris = guess_ab_col(), qida = guess_ab_col(), rifa = guess_ab_col(), roxi = guess_ab_col(), siso = guess_ab_col(), teic = guess_ab_col(), tetr = guess_ab_col(), tica = guess_ab_col(), tige = guess_ab_col(), tobr = guess_ab_col(), trim = guess_ab_col(), trsu = guess_ab_col(), vanc = guess_ab_col(), ...) { # support old `tbl` parameter if ("tbl" %in% names(list(...))) { x <- list(...)$tbl } tbl_ <- x if (!is.data.frame(tbl_)) { stop("`tbl_` must be a data frame.", call. = FALSE) } # try to find columns based on type # -- mo if (is.null(col_mo)) { col_mo <- search_type_in_df(tbl = tbl_, type = "mo") } if (is.null(col_mo)) { stop("`col_mo` must be set.", call. = FALSE) } if (!all(rules %in% c("breakpoints", "expert", "other", "all"))) { stop("`rules` must be one or more of: 'breakpoints', 'expert', 'other', 'all'.") } if (is.null(col_mo)) { stop("`col_mo` must be set") } warned <- FALSE txt_error <- function() { cat("", bgRed(black(" ERROR ")), "\n") } txt_warning <- function() { if (warned == FALSE) { cat("", bgYellow(black(" WARNING ")), "\n") }; warned <<- TRUE } txt_ok <- function(no_of_changes) { if (warned == FALSE) { if (no_of_changes > 0) { if (no_of_changes == 1) { cat(blue(" (1 new change)\n")) } else { cat(blue(paste0(" (", no_of_changes, " new changes)\n"))) } } else { cat(green(" (no new changes)\n")) } warned <<- FALSE } } # check columns if (identical(amcl, as.name("guess_ab_col"))) { amcl <- guess_ab_col(tbl_, "amcl", verbose = verbose) } if (identical(amik, as.name("guess_ab_col"))) { amik <- guess_ab_col(tbl_, "amik", verbose = verbose) } if (identical(amox, as.name("guess_ab_col"))) { amox <- guess_ab_col(tbl_, "amox", verbose = verbose) } if (identical(ampi, as.name("guess_ab_col"))) { ampi <- guess_ab_col(tbl_, "ampi", verbose = verbose) } if (identical(azit, as.name("guess_ab_col"))) { azit <- guess_ab_col(tbl_, "azit", verbose = verbose) } if (identical(azlo, as.name("guess_ab_col"))) { azlo <- guess_ab_col(tbl_, "azlo", verbose = verbose) } if (identical(aztr, as.name("guess_ab_col"))) { aztr <- guess_ab_col(tbl_, "aztr", verbose = verbose) } if (identical(cefa, as.name("guess_ab_col"))) { cefa <- guess_ab_col(tbl_, "cefa", verbose = verbose) } if (identical(cfep, as.name("guess_ab_col"))) { cfep <- guess_ab_col(tbl_, "cfep", verbose = verbose) } if (identical(cfot, as.name("guess_ab_col"))) { cfot <- guess_ab_col(tbl_, "cfot", verbose = verbose) } if (identical(cfox, as.name("guess_ab_col"))) { cfox <- guess_ab_col(tbl_, "cfox", verbose = verbose) } if (identical(cfra, as.name("guess_ab_col"))) { cfra <- guess_ab_col(tbl_, "cfra", verbose = verbose) } if (identical(cfta, as.name("guess_ab_col"))) { cfta <- guess_ab_col(tbl_, "cfta", verbose = verbose) } if (identical(cftr, as.name("guess_ab_col"))) { cftr <- guess_ab_col(tbl_, "cftr", verbose = verbose) } if (identical(cfur, as.name("guess_ab_col"))) { cfur <- guess_ab_col(tbl_, "cfur", verbose = verbose) } if (identical(chlo, as.name("guess_ab_col"))) { chlo <- guess_ab_col(tbl_, "chlo", verbose = verbose) } if (identical(cipr, as.name("guess_ab_col"))) { cipr <- guess_ab_col(tbl_, "cipr", verbose = verbose) } if (identical(clar, as.name("guess_ab_col"))) { clar <- guess_ab_col(tbl_, "clar", verbose = verbose) } if (identical(clin, as.name("guess_ab_col"))) { clin <- guess_ab_col(tbl_, "clin", verbose = verbose) } if (identical(clox, as.name("guess_ab_col"))) { clox <- guess_ab_col(tbl_, "clox", verbose = verbose) } if (identical(coli, as.name("guess_ab_col"))) { coli <- guess_ab_col(tbl_, "coli", verbose = verbose) } if (identical(czol, as.name("guess_ab_col"))) { czol <- guess_ab_col(tbl_, "czol", verbose = verbose) } if (identical(dapt, as.name("guess_ab_col"))) { dapt <- guess_ab_col(tbl_, "dapt", verbose = verbose) } if (identical(doxy, as.name("guess_ab_col"))) { doxy <- guess_ab_col(tbl_, "doxy", verbose = verbose) } if (identical(erta, as.name("guess_ab_col"))) { erta <- guess_ab_col(tbl_, "erta", verbose = verbose) } if (identical(eryt, as.name("guess_ab_col"))) { eryt <- guess_ab_col(tbl_, "eryt", verbose = verbose) } if (identical(fosf, as.name("guess_ab_col"))) { fosf <- guess_ab_col(tbl_, "fosf", verbose = verbose) } if (identical(fusi, as.name("guess_ab_col"))) { fusi <- guess_ab_col(tbl_, "fusi", verbose = verbose) } if (identical(gent, as.name("guess_ab_col"))) { gent <- guess_ab_col(tbl_, "gent", verbose = verbose) } if (identical(imip, as.name("guess_ab_col"))) { imip <- guess_ab_col(tbl_, "imip", verbose = verbose) } if (identical(kana, as.name("guess_ab_col"))) { kana <- guess_ab_col(tbl_, "kana", verbose = verbose) } if (identical(levo, as.name("guess_ab_col"))) { levo <- guess_ab_col(tbl_, "levo", verbose = verbose) } if (identical(linc, as.name("guess_ab_col"))) { linc <- guess_ab_col(tbl_, "linc", verbose = verbose) } if (identical(line, as.name("guess_ab_col"))) { line <- guess_ab_col(tbl_, "line", verbose = verbose) } if (identical(mero, as.name("guess_ab_col"))) { mero <- guess_ab_col(tbl_, "mero", verbose = verbose) } if (identical(mezl, as.name("guess_ab_col"))) { mezl <- guess_ab_col(tbl_, "mezl", verbose = verbose) } if (identical(mino, as.name("guess_ab_col"))) { mino <- guess_ab_col(tbl_, "mino", verbose = verbose) } if (identical(moxi, as.name("guess_ab_col"))) { moxi <- guess_ab_col(tbl_, "moxi", verbose = verbose) } if (identical(nali, as.name("guess_ab_col"))) { nali <- guess_ab_col(tbl_, "nali", verbose = verbose) } if (identical(neom, as.name("guess_ab_col"))) { neom <- guess_ab_col(tbl_, "neom", verbose = verbose) } if (identical(neti, as.name("guess_ab_col"))) { neti <- guess_ab_col(tbl_, "neti", verbose = verbose) } if (identical(nitr, as.name("guess_ab_col"))) { nitr <- guess_ab_col(tbl_, "nitr", verbose = verbose) } if (identical(norf, as.name("guess_ab_col"))) { norf <- guess_ab_col(tbl_, "norf", verbose = verbose) } if (identical(novo, as.name("guess_ab_col"))) { novo <- guess_ab_col(tbl_, "novo", verbose = verbose) } if (identical(oflo, as.name("guess_ab_col"))) { oflo <- guess_ab_col(tbl_, "oflo", verbose = verbose) } if (identical(oxac, as.name("guess_ab_col"))) { oxac <- guess_ab_col(tbl_, "oxac", verbose = verbose) } if (identical(peni, as.name("guess_ab_col"))) { peni <- guess_ab_col(tbl_, "peni", verbose = verbose) } if (identical(pipe, as.name("guess_ab_col"))) { pipe <- guess_ab_col(tbl_, "pipe", verbose = verbose) } if (identical(pita, as.name("guess_ab_col"))) { pita <- guess_ab_col(tbl_, "pita", verbose = verbose) } if (identical(poly, as.name("guess_ab_col"))) { poly <- guess_ab_col(tbl_, "poly", verbose = verbose) } if (identical(pris, as.name("guess_ab_col"))) { pris <- guess_ab_col(tbl_, "pris", verbose = verbose) } if (identical(qida, as.name("guess_ab_col"))) { qida <- guess_ab_col(tbl_, "qida", verbose = verbose) } if (identical(rifa, as.name("guess_ab_col"))) { rifa <- guess_ab_col(tbl_, "rifa", verbose = verbose) } if (identical(roxi, as.name("guess_ab_col"))) { roxi <- guess_ab_col(tbl_, "roxi", verbose = verbose) } if (identical(siso, as.name("guess_ab_col"))) { siso <- guess_ab_col(tbl_, "siso", verbose = verbose) } if (identical(teic, as.name("guess_ab_col"))) { teic <- guess_ab_col(tbl_, "teic", verbose = verbose) } if (identical(tetr, as.name("guess_ab_col"))) { tetr <- guess_ab_col(tbl_, "tetr", verbose = verbose) } if (identical(tica, as.name("guess_ab_col"))) { tica <- guess_ab_col(tbl_, "tica", verbose = verbose) } if (identical(tige, as.name("guess_ab_col"))) { tige <- guess_ab_col(tbl_, "tige", verbose = verbose) } if (identical(tobr, as.name("guess_ab_col"))) { tobr <- guess_ab_col(tbl_, "tobr", verbose = verbose) } if (identical(trim, as.name("guess_ab_col"))) { trim <- guess_ab_col(tbl_, "trim", verbose = verbose) } if (identical(trsu, as.name("guess_ab_col"))) { trsu <- guess_ab_col(tbl_, "trsu", verbose = verbose) } if (identical(vanc, as.name("guess_ab_col"))) { vanc <- guess_ab_col(tbl_, "vanc", verbose = verbose) } col.list <- c(amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfra, cfep, cfot, cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, novo, norf, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc) if (length(col.list) < 63) { warning('Some columns do not exist -- THIS MAY STRONGLY INFLUENCE THE OUTCOME.', immediate. = TRUE, call. = FALSE) } col.list <- check_available_columns(tbl = tbl_, col.list = col.list, info = info) amcl <- col.list[amcl] amik <- col.list[amik] amox <- col.list[amox] ampi <- col.list[ampi] azit <- col.list[azit] azlo <- col.list[azlo] aztr <- col.list[aztr] cefa <- col.list[cefa] cfep <- col.list[cfep] cfot <- col.list[cfot] cfox <- col.list[cfox] cfra <- col.list[cfra] cfta <- col.list[cfta] cftr <- col.list[cftr] cfur <- col.list[cfur] chlo <- col.list[chlo] cipr <- col.list[cipr] clar <- col.list[clar] clin <- col.list[clin] clox <- col.list[clox] coli <- col.list[coli] czol <- col.list[czol] dapt <- col.list[dapt] doxy <- col.list[doxy] erta <- col.list[erta] eryt <- col.list[eryt] fosf <- col.list[fosf] fusi <- col.list[fusi] gent <- col.list[gent] imip <- col.list[imip] kana <- col.list[kana] levo <- col.list[levo] linc <- col.list[linc] line <- col.list[line] mero <- col.list[mero] mezl <- col.list[mezl] mino <- col.list[mino] moxi <- col.list[moxi] nali <- col.list[nali] neom <- col.list[neom] neti <- col.list[neti] nitr <- col.list[nitr] norf <- col.list[norf] novo <- col.list[novo] oflo <- col.list[oflo] oxac <- col.list[oxac] peni <- col.list[peni] pipe <- col.list[pipe] pita <- col.list[pita] poly <- col.list[poly] pris <- col.list[pris] qida <- col.list[qida] rifa <- col.list[rifa] roxi <- col.list[roxi] siso <- col.list[siso] teic <- col.list[teic] tetr <- col.list[tetr] tica <- col.list[tica] tige <- col.list[tige] tobr <- col.list[tobr] trim <- col.list[trim] trsu <- col.list[trsu] vanc <- col.list[vanc] ab_missing <- function(ab) { all(ab %in% c(NULL, NA)) } verbose_info <- data.frame(row = integer(0), col = character(0), mo_fullname = character(0), old = character(0), new = character(0), rule = character(0), rule_group = character(0), rule_name = character(0), stringsAsFactors = FALSE) # helper function for editing the table edit_rsi <- function(to, rule, rows, cols) { cols <- unique(cols[!is.na(cols) & !is.null(cols)]) if (length(rows) > 0 & length(cols) > 0) { before_df <- tbl_original before <- as.character(unlist(as.list(tbl_original[rows, cols]))) tryCatch( # insert into original table tbl_original[rows, cols] <<- to, warning = function(w) { if (w$message %like% 'invalid factor level') { warning('Value "', to, '" could not be applied to column(s) `', paste(cols, collapse = '`, `'), '` because this value is not an existing factor level.', call. = FALSE) } else { warning(w$message, call. = FALSE) } txt_warning() }, error = function(e) { txt_error() stop(e, call. = FALSE) } ) tbl_[rows, cols] <<- tbl_original[rows, cols] after <- as.character(unlist(as.list(tbl_original[rows, cols]))) # before_df might not be a data.frame, but a tibble of data.table instead old <- as.data.frame(before_df, stringsAsFactors = FALSE)[rows,] no_of_changes_this_run <- 0 for (i in 1:length(cols)) { verbose_new <- data.frame(row = rows, col = cols[i], mo_fullname = tbl_[rows, "fullname"], old = as.character(old[, cols[i]]), new = as.character(tbl_[rows, cols[i]]), rule = strip_style(rule[1]), rule_group = strip_style(rule[2]), rule_name = strip_style(rule[3]), stringsAsFactors = FALSE) colnames(verbose_new) <- c("row", "col", "mo_fullname", "old", "new", "rule", "rule_group", "rule_name") verbose_new <- verbose_new %>% filter(old != new | is.na(old)) verbose_info <<- rbind(verbose_info, verbose_new) no_of_changes_this_run <- no_of_changes_this_run + nrow(verbose_new) } # return number of (new) changes return(no_of_changes_this_run) } # return number of (new) changes: none. return(0) } # save original table tbl_original <- tbl_ # join to microorganisms data set suppressWarnings( tbl_ <- tbl_ %>% mutate_at(vars(col_mo), as.mo) %>% left_join_microorganisms(by = col_mo, suffix = c("_oldcols", "")) %>% mutate(gramstain = mo_gramstain(pull(., col_mo), language = "en"), genus_species = paste(genus, species)) %>% as.data.frame(stringsAsFactors = FALSE) ) if (info == TRUE) { cat(paste0( "\nRules by the ", bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"), "\n", blue("http://eucast.org/"), "\n")) } # since ampicillin ^= amoxicillin, get the first from the latter (not in original EUCAST table) if (!ab_missing(ampi) & !ab_missing(amox)) { if (verbose == TRUE) { cat("\n VERBOSE: transforming", length(which(tbl_[, amox] == "S" & !tbl_[, ampi] %in% c("S", "I", "R"))), "empty ampicillin fields to 'S' based on amoxicillin. ") cat("\n VERBOSE: transforming", length(which(tbl_[, amox] == "I" & !tbl_[, ampi] %in% c("S", "I", "R"))), "empty ampicillin fields to 'I' based on amoxicillin. ") cat("\n VERBOSE: transforming", length(which(tbl_[, amox] == "R" & !tbl_[, ampi] %in% c("S", "I", "R"))), "empty ampicillin fields to 'R' based on amoxicillin. \n") } tbl_[which(tbl_[, amox] == "S" & !tbl_[, ampi] %in% c("S", "I", "R")), ampi] <- "S" tbl_[which(tbl_[, amox] == "I" & !tbl_[, ampi] %in% c("S", "I", "R")), ampi] <- "I" tbl_[which(tbl_[, amox] == "R" & !tbl_[, ampi] %in% c("S", "I", "R")), ampi] <- "R" } else if (ab_missing(ampi) & !ab_missing(amox)) { # ampicillin column is missing, but amoxicillin is available message(blue(paste0("NOTE: Using column `", bold(amox), "` as input for ampicillin (J01CA01) since many EUCAST rules depend on it."))) ampi <- amox } # antibiotic classes aminoglycosides <- c(tobr, gent, kana, neom, neti, siso) tetracyclines <- c(doxy, mino, tetr) # since EUCAST v3.1 tige(cycline) is set apart polymyxins <- c(poly, coli) macrolides <- c(eryt, azit, roxi, clar) # since EUCAST v3.1 clinda is set apart glycopeptides <- c(vanc, teic) streptogramins <- c(qida, pris) # should officially also be quinupristin/dalfopristin cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol) cephalosporins_without_cfta <- cephalosporins[cephalosporins != ifelse(is.null(cfta), "", cfta)] carbapenems <- c(erta, imip, mero) aminopenicillins <- c(ampi, amox) ureidopenicillins <- c(pipe, pita, azlo, mezl) fluoroquinolones <- c(oflo, cipr, norf, levo, moxi) all_betalactams <- c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, amcl, oxac, clox, peni) # Help function to get available antibiotic column names ------------------ get_antibiotic_columns <- function(x, df) { x <- trimws(unlist(strsplit(x, ",", fixed = TRUE))) y <- character(0) for (i in 1:length(x)) { y <- c(y, tryCatch(get(x[i]), error = function(e) "")) } y[y != "" & y %in% colnames(df)] } eucast_rules_df <- eucast_rules_file() no_of_changes <- 0 for (i in 1:nrow(eucast_rules_df)) { rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule"] rule_current <- eucast_rules_df[i, "reference.rule"] rule_next <- eucast_rules_df[min(nrow(eucast_rules_df), i + 1), "reference.rule"] rule_group_previous <- eucast_rules_df[max(1, i - 1), "reference.rule_group"] rule_group_current <- eucast_rules_df[i, "reference.rule_group"] rule_group_next <- eucast_rules_df[min(nrow(eucast_rules_df), i + 1), "reference.rule_group"] if (is.na(eucast_rules_df[i, 4])) { rule_text <- paste(eucast_rules_df[i, 6], "=", eucast_rules_df[i, 7]) } else { rule_text <- paste("if", eucast_rules_df[i, 4], "=", eucast_rules_df[i, 5], "then", eucast_rules_df[i, 6], "=", eucast_rules_df[i, 7]) } if (i == 1) { rule_previous <- "" rule_group_previous <- "" } if (i == nrow(eucast_rules_df)) { rule_next <- "" rule_group_next <- "" } # don't apply rules if user doesn't want to apply them if (rule_group_current %like% "breakpoint" & !any(c("all", "breakpoints") %in% rules)) { next } if (rule_group_current %like% "expert" & !any(c("all", "expert") %in% rules)) { next } if (rule_group_current %like% "other" & !any(c("all", "other") %in% rules)) { next } if (info == TRUE) { # Print rule (group) ------------------------------------------------------ if (rule_group_current != rule_group_previous) { # is new rule group, one of Breakpoints, Expert Rules and Other cat(bold( case_when( rule_group_current %like% "breakpoint" ~ paste0("\nEUCAST Clinical Breakpoints (v", EUCAST_VERSION_BREAKPOINTS, ")\n"), rule_group_current %like% "expert" ~ paste0("\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v", EUCAST_VERSION_EXPERT_RULES, ")\n"), TRUE ~ "\nOther rules\n" ) )) } # Print rule ------------------------------------------------------------- if (rule_current != rule_previous) { # is new rule within group, print its name if (rule_current %in% c(AMR::microorganisms$family, AMR::microorganisms$fullname)) { cat(italic(rule_current)) } else { cat(rule_current) } warned <- FALSE } } # Get rule from file ------------------------------------------------------ col_mo_property <- eucast_rules_df[i, 1] like_is_one_of <- eucast_rules_df[i, 2] # be sure to comprise all coagulase-negative/-positive Staphylococci when they are mentioned if (eucast_rules_df[i, 3] %like% "coagulase-") { suppressWarnings( all_staph <- AMR::microorganisms %>% filter(genus == "Staphylococcus") %>% mutate(CNS_CPS = mo_fullname(mo, Becker = "all")) ) if (eucast_rules_df[i, 3] %like% "coagulase-") { eucast_rules_df[i, 3] <- paste0("^(", paste0(all_staph %>% filter(CNS_CPS %like% "coagulase-negative") %>% pull(fullname), collapse = "|"), ")$") } else { eucast_rules_df[i, 3] <- paste0("^(", paste0(all_staph %>% filter(CNS_CPS %like% "coagulase-positive") %>% pull(fullname), collapse = "|"), ")$") } like_is_one_of <- "like" } if (like_is_one_of == "is") { mo_value <- paste0("^", eucast_rules_df[i, 3], "$") } else if (like_is_one_of == "one_of") { # "Clostridium, Actinomyces, ..." -> "^(Clostridium|Actinomyces|...)$" mo_value <- paste0("^(", paste(trimws(unlist(strsplit(eucast_rules_df[i, 3], ",", fixed = TRUE))), collapse = "|"), ")$") } else if (like_is_one_of == "like") { mo_value <- eucast_rules_df[i, 3] } else { stop("invalid like_is_one_of", call. = FALSE) } source_antibiotics <- eucast_rules_df[i, 4] source_value <- trimws(unlist(strsplit(eucast_rules_df[i, 5], ",", fixed = TRUE))) target_antibiotics <- eucast_rules_df[i, 6] target_value <- eucast_rules_df[i, 7] if (is.na(source_antibiotics)) { rows <- tryCatch(which(tbl_[, col_mo_property] %like% mo_value), error = function(e) integer(0)) } else { source_antibiotics <- get_antibiotic_columns(source_antibiotics, tbl_) if (length(source_value) == 1 & length(source_antibiotics) > 1) { source_value <- rep(source_value, length(source_antibiotics)) } if (length(source_antibiotics) == 0) { rows <- integer(0) } else if (length(source_antibiotics) == 1) { rows <- tryCatch(which(tbl_[, col_mo_property] %like% mo_value & tbl_[, source_antibiotics[1L]] == source_value[1L]), error = function(e) integer(0)) } else if (length(source_antibiotics) == 2) { rows <- tryCatch(which(tbl_[, col_mo_property] %like% mo_value & tbl_[, source_antibiotics[1L]] == source_value[1L] & tbl_[, source_antibiotics[2L]] == source_value[2L]), error = function(e) integer(0)) } else if (length(source_antibiotics) == 3) { rows <- tryCatch(which(tbl_[, col_mo_property] %like% mo_value & tbl_[, source_antibiotics[1L]] == source_value[1L] & tbl_[, source_antibiotics[2L]] == source_value[2L] & tbl_[, source_antibiotics[3L]] == source_value[3L]), error = function(e) integer(0)) } else { stop("only 3 antibiotics supported for source_antibiotics ", call. = FALSE) } } cols <- get_antibiotic_columns(target_antibiotics, tbl_) # Apply rule on data ------------------------------------------------------ # this will return the unique number of changes no_of_changes <- no_of_changes + edit_rsi(to = target_value, rule = c(rule_text, rule_group_current, rule_current), rows = rows, cols = cols) # Print number of new changes --------------------------------------------- if (info == TRUE & rule_next != rule_current) { # print only on last one of rules in this group txt_ok(no_of_changes = no_of_changes) no_of_changes <- 0 } } # Print overview ---------------------------------------------------------- if (info == TRUE) { if (verbose == TRUE) { wouldve <- "would have " } else { wouldve <- "" } verbose_info <- verbose_info %>% arrange(row, rule_group, rule_name, col) decimal.mark <- getOption("OutDec") big.mark <- ifelse(decimal.mark != ",", ",", ".") formatnr <- function(x) { trimws(format(x, big.mark = big.mark, decimal.mark = decimal.mark)) } cat(paste0("\n", silver(strrep("-", options()$width - 1)), "\n")) cat(bold(paste('EUCAST rules', paste0(wouldve, 'affected'), formatnr(n_distinct(verbose_info$row)), 'out of', formatnr(nrow(tbl_original)), 'rows, making a total of', formatnr(nrow(verbose_info)), 'edits\n'))) # print added values ---- if (verbose_info %>% filter(is.na(old)) %>% nrow() == 0) { colour <- cat # is function } else { colour <- blue # is function } cat(colour(paste0("=> ", wouldve, "added ", bold(formatnr(verbose_info %>% filter(is.na(old)) %>% nrow()), "test results"), "\n"))) if (verbose_info %>% filter(is.na(old)) %>% nrow() > 0) { verbose_info %>% filter(is.na(old)) %>% # sort it well: S < I < R mutate(new = as.rsi(new)) %>% group_by(new) %>% summarise(n = n()) %>% mutate(plural = ifelse(n > 1, "s", ""), txt = paste0(formatnr(n), " test result", plural, " added as ", new)) %>% pull(txt) %>% paste(" -", ., collapse = "\n") %>% cat() } # print changed values ---- if (verbose_info %>% filter(!is.na(old)) %>% nrow() == 0) { colour <- cat # is function } else { colour <- blue # is function } cat(colour(paste0("\n=> ", wouldve, "changed ", bold(formatnr(verbose_info %>% filter(!is.na(old)) %>% nrow()), "test results"), "\n"))) if (verbose_info %>% filter(!is.na(old)) %>% nrow() > 0) { verbose_info %>% filter(!is.na(old)) %>% # sort it well: S < I < R mutate(old = as.rsi(old), new = as.rsi(new)) %>% group_by(old, new) %>% summarise(n = n()) %>% mutate(plural = ifelse(n > 1, "s", ""), txt = paste0(formatnr(n), " test result", plural, " changed from ", old, " to ", new)) %>% pull(txt) %>% paste(" -", ., collapse = "\n") %>% cat() cat("\n") } cat(paste0(silver(strrep("-", options()$width - 1)), "\n")) if (verbose == FALSE & nrow(verbose_info) > 0) { cat(paste("\nUse", bold("verbose = TRUE"), "to get a data.frame with all specified edits instead.\n")) } } # Return data set --------------------------------------------------------- if (verbose == TRUE) { verbose_info } else { tbl_original } } #' @rdname eucast_rules #' @importFrom dplyr %>% arrange #' @export eucast_rules_file <- function() { utils::read.delim(file = EUCAST_RULES_FILE_LOCATION, sep = "\t", stringsAsFactors = FALSE, header = TRUE, strip.white = TRUE, na = c(NA, "", NULL)) %>% arrange(reference.rule_group, reference.rule) }