# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2020 Berends MS, Luz CF et al. # # # # 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 more info: https://msberends.github.io/AMR. # # ==================================================================== # # add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" # (running "data-raw/internals.R" will process that TSV file) EUCAST_VERSION_BREAKPOINTS <- list("10.0" = list(version_txt = "v10.0", year = 2020, title = "EUCAST Clinical Breakpoints")) EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1", year = 2016, title = "EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes"), "3.2" = list(version_txt = "v3.2", year = 2020, title = "EUCAST Expert Rules / EUCAST Intrinsic Resistance and Unusual Phenotypes")) #' Apply EUCAST rules #' #' @description #' Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, ), see *Source*. #' #' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details. #' @inheritSection lifecycle Stable lifecycle #' @param x data with antibiotic columns, such as `amox`, `AMX` and `AMC` #' @param info print progress #' @param rules a character vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value, e.g. using `options(AMR_eucastrules = "all")`. #' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time. #' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Currently supported: `r paste0(names(EUCAST_VERSION_BREAKPOINTS), collapse = ", ")`. #' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Currently supported: `r paste0(names(EUCAST_VERSION_EXPERT_RULES), collapse = ", ")`. #' @param ... column name of an antibiotic, please see section *Antibiotics* below #' @inheritParams first_isolate #' @details #' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] for that. \cr #' **Note:** When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, 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. #' #' The file containing all EUCAST rules is located here: . #' #' ## 'Other' rules #' #' Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are: #' #' 1. A drug **with** enzyme inhibitor will be set to S if the same drug **without** enzyme inhibitor is S #' 2. A drug **without** enzyme inhibitor will be set to R if the same drug **with** enzyme inhibitor is R #' #' Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set. #' #' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` parameter, or use `eucast_rules(..., rules = "all")`. #' @section Antibiotics: #' To define antibiotics column names, leave as it is to determine it automatically with [guess_ab_col()] or input a text (case-insensitive), or use `NULL` to skip a column (e.g. `TIC = NULL` to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning. #' #' The following antibiotics are used for the functions [eucast_rules()] and [mdro()]. These are shown below in the format 'name (`antimicrobial ID`, [ATC code](https://www.whocc.no/atc/structure_and_principles/))', sorted alphabetically: #' #' `r create_ab_documentation(c("AMC", "AMK", "AMP", "AMX", "ATM", "AVO", "AZL", "AZM", "BAM", "BPR", "CAC", "CAP", "CAT", "CAZ", "CCV", "CDR", "CDZ", "CEC", "CED", "CEI", "CEP", "CFM", "CFM1", "CFP", "CFR", "CFS", "CHL", "CID", "CIP", "CLI", "CLR", "CMX", "CMZ", "CND", "COL", "CPD", "CPM", "CPO", "CPR", "CPT", "CRB", "CRD", "CRN", "CRO", "CSL", "CTB", "CTF", "CTL", "CTT", "CTX", "CTZ", "CXM", "CYC", "CZD", "CZO", "CZX", "DAL", "DAP", "DIR", "DIT", "DIZ", "DKB", "DOR", "DOX", "ENX", "EPC", "ERY", "ETH", "ETP", "FEP", "FLC", "FLE", "FLR1", "FOS", "FOX", "FOX1", "FUS", "GAT", "GEH", "GEM", "GEN", "GRX", "HAP", "HET", "INH", "IPM", "ISE", "JOS", "KAN", "LEX", "LIN", "LNZ", "LOM", "LOR", "LTM", "LVX", "MAN", "MCM", "MEC", "MEM", "MEV", "MEZ", "MFX", "MID", "MNO", "MTM", "NAL", "NEO", "NET", "NIT", "NOR", "NOV", "NVA", "OFX", "OLE", "ORI", "OXA", "PAZ", "PEF", "PEN", "PHN", "PIP", "PLB", "PME", "PRI", "PRL", "PRU", "PVM", "PZA", "QDA", "RAM", "RFL", "RFP", "RIB", "RID", "RIF", "ROK", "RST", "RXT", "SAM", "SBC", "SDI", "SDM", "SIS", "SLF", "SLF1", "SLF10", "SLF11", "SLF12", "SLF13", "SLF2", "SLF3", "SLF4", "SLF5", "SLF6", "SLF7", "SLF8", "SLF9", "SLT1", "SLT2", "SLT3", "SLT4", "SLT5", "SMX", "SPI", "SPX", "STH", "STR", "STR1", "SUD", "SUT", "SXT", "SZO", "TAL", "TCC", "TCM", "TCY", "TEC", "TEM", "TGC", "THA", "TIC", "TLT", "TLV", "TMP", "TMX", "TOB", "TRL", "TVA", "TZD", "TZP", "VAN"))` #' @aliases EUCAST #' @rdname eucast_rules #' @export #' @return The input of `x`, possibly with edited values of antibiotics. Or, if `verbose = TRUE`, a [data.frame] with all original and new values of the affected bug-drug combinations. #' @source #' - EUCAST Expert Rules. Version 2.0, 2012. \cr #' Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility testing.** *Clin Microbiol Infect.* 2013;19(2):141-60. \cr #' #' - EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \cr #' #' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. \cr #' #' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \cr #' #' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. \cr #' #' @inheritSection AMR Reference data publicly available #' @inheritSection AMR Read more on our website! #' @examples #' \donttest{ #' a <- data.frame(mo = c("Staphylococcus aureus", #' "Enterococcus faecalis", #' "Escherichia coli", #' "Klebsiella pneumoniae", #' "Pseudomonas aeruginosa"), #' VAN = "-", # Vancomycin #' AMX = "-", # Amoxicillin #' COL = "-", # Colistin #' CAZ = "-", # Ceftazidime #' CXM = "-", # Cefuroxime #' PEN = "S", # Benzylpenicillin #' FOX = "S", # Cefoxitin #' stringsAsFactors = FALSE) #' #' a #' # mo VAN AMX COL CAZ CXM PEN FOX #' # 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: some results wil be changed #' b <- eucast_rules(a) #' #' b #' # mo VAN AMX COL CAZ CXM PEN FOX #' # 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 data.frame #' # containing all details about the transformations: #' c <- eucast_rules(a, verbose = TRUE) #' } eucast_rules <- function(x, col_mo = NULL, info = interactive(), rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")), verbose = FALSE, version_breakpoints = 10.0, version_expertrules = 3.2, ...) { x_deparsed <- deparse(substitute(x)) if (length(x_deparsed) > 0 || !all(x_deparsed %like% "[a-z]")) { x_deparsed <- "your_data" } check_dataset_integrity() version_breakpoints <- as.double(gsub("[^0-9.]+", "", version_breakpoints)) version_expertrules <- as.double(gsub("[^0-9.]+", "", version_expertrules)) stop_ifnot(version_breakpoints %in% as.double(names(EUCAST_VERSION_BREAKPOINTS)), "EUCAST version ", version_breakpoints, " for clinical breakpoints not found") stop_ifnot(version_expertrules %in% as.double(names(EUCAST_VERSION_EXPERT_RULES)), "EUCAST version ", version_expertrules, " for expert rules/intrinsic resistance not found") breakpoints_info <- EUCAST_VERSION_BREAKPOINTS[[which(as.double(names(EUCAST_VERSION_BREAKPOINTS)) == version_breakpoints)]] expertrules_info <- EUCAST_VERSION_EXPERT_RULES[[which(as.double(names(EUCAST_VERSION_EXPERT_RULES)) == version_expertrules)]] # support old setting (until AMR v1.3.0) if (missing(rules) & !is.null(getOption("AMR.eucast_rules", default = NULL))) { rules <- getOption("AMR.eucast_rules") } if (interactive() & verbose == TRUE & info == TRUE) { txt <- paste0("WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.", "\n\nThis may overwrite your existing data if you use e.g.:", "\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?") showQuestion <- import_fn("showQuestion", "rstudioapi", error_on_fail = FALSE) if (!is.null(showQuestion)) { q_continue <- showQuestion("Using verbose = TRUE with eucast_rules()", txt) } else { q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt) } if (q_continue %in% c(FALSE, 2)) { message("Cancelled, returning original data") return(x) } } stop_ifnot(is.data.frame(x), "`x` must be a data frame") # try to find columns based on type # -- mo if (is.null(col_mo)) { col_mo <- search_type_in_df(x = x, type = "mo", info = info) } stop_if(is.null(col_mo), "`col_mo` must be set") stop_ifnot(col_mo %in% colnames(x), "column '", col_mo, "' (`col_mo`) not found") stop_ifnot(all(rules %in% c("breakpoints", "expert", "other", "all")), '`rules` must be one or more of: "breakpoints", "expert", "other", "all".') decimal.mark <- getOption("OutDec") big.mark <- ifelse(decimal.mark != ",", ",", ".") formatnr <- function(x, big = big.mark, dec = decimal.mark) { trimws(format(x, big.mark = big, decimal.mark = dec)) } warned <- FALSE warn_lacking_rsi_class <- FALSE txt_ok <- function(n_added, n_changed, warned = FALSE) { if (warned == FALSE) { if (n_added + n_changed == 0) { cat(font_subtle(" (no changes)\n")) } else { # opening cat(font_grey(" (")) # additions if (n_added > 0) { if (n_added == 1) { cat(font_green("1 value added")) } else { cat(font_green(formatnr(n_added), "values added")) } } # separator if (n_added > 0 & n_changed > 0) { cat(font_grey(", ")) } # changes if (n_changed > 0) { if (n_changed == 1) { cat(font_blue("1 value changed")) } else { cat(font_blue(formatnr(n_changed), "values changed")) } } # closing cat(font_grey(")\n")) } warned <<- FALSE } } cols_ab <- get_column_abx(x = x, soft_dependencies = c("AMC", "AMP", "AMX", "CIP", "ERY", "FOX1", "GEN", "MFX", "NAL", "NOR", "PEN", "PIP", "TCY", "TIC", "TOB"), hard_dependencies = NULL, verbose = verbose, info = info, ...) AMC <- cols_ab["AMC"] AMK <- cols_ab["AMK"] AMP <- cols_ab["AMP"] AMX <- cols_ab["AMX"] ATM <- cols_ab["ATM"] AVO <- cols_ab["AVO"] AZL <- cols_ab["AZL"] AZM <- cols_ab["AZM"] BAM <- cols_ab["BAM"] BPR <- cols_ab["BPR"] CAC <- cols_ab["CAC"] CAT <- cols_ab["CAT"] CAZ <- cols_ab["CAZ"] CCV <- cols_ab["CCV"] CDR <- cols_ab["CDR"] CDZ <- cols_ab["CDZ"] CEC <- cols_ab["CEC"] CED <- cols_ab["CED"] CEI <- cols_ab["CEI"] CEP <- cols_ab["CEP"] CFM <- cols_ab["CFM"] CFM1 <- cols_ab["CFM1"] CFP <- cols_ab["CFP"] CFR <- cols_ab["CFR"] CFS <- cols_ab["CFS"] CHL <- cols_ab["CHL"] CID <- cols_ab["CID"] CIP <- cols_ab["CIP"] CLI <- cols_ab["CLI"] CLI <- cols_ab["CLI"] CLR <- cols_ab["CLR"] CMX <- cols_ab["CMX"] CMZ <- cols_ab["CMZ"] CND <- cols_ab["CND"] COL <- cols_ab["COL"] CPD <- cols_ab["CPD"] CPM <- cols_ab["CPM"] CPO <- cols_ab["CPO"] CPR <- cols_ab["CPR"] CPT <- cols_ab["CPT"] CRB <- cols_ab["CRB"] CRD <- cols_ab["CRD"] CRN <- cols_ab["CRN"] CRO <- cols_ab["CRO"] CSL <- cols_ab["CSL"] CTB <- cols_ab["CTB"] CTF <- cols_ab["CTF"] CTL <- cols_ab["CTL"] CTT <- cols_ab["CTT"] CTX <- cols_ab["CTX"] CTZ <- cols_ab["CTZ"] CXM <- cols_ab["CXM"] CYC <- cols_ab["CYC"] CZD <- cols_ab["CZD"] CZO <- cols_ab["CZO"] CZX <- cols_ab["CZX"] DAL <- cols_ab["DAL"] DAP <- cols_ab["DAP"] DIR <- cols_ab["DIR"] DIT <- cols_ab["DIT"] DIZ <- cols_ab["DIZ"] DKB <- cols_ab["DKB"] DOR <- cols_ab["DOR"] DOX <- cols_ab["DOX"] ENX <- cols_ab["ENX"] EPC <- cols_ab["EPC"] ERY <- cols_ab["ERY"] ETP <- cols_ab["ETP"] FEP <- cols_ab["FEP"] FLC <- cols_ab["FLC"] FLE <- cols_ab["FLE"] FLR1 <- cols_ab["FLR1"] FOS <- cols_ab["FOS"] FOX <- cols_ab["FOX"] FOX1 <- cols_ab["FOX1"] FUS <- cols_ab["FUS"] GAT <- cols_ab["GAT"] GEM <- cols_ab["GEM"] GEN <- cols_ab["GEN"] GRX <- cols_ab["GRX"] HAP <- cols_ab["HAP"] HET <- cols_ab["HET"] IPM <- cols_ab["IPM"] ISE <- cols_ab["ISE"] JOS <- cols_ab["JOS"] KAN <- cols_ab["KAN"] LEX <- cols_ab["LEX"] LIN <- cols_ab["LIN"] LNZ <- cols_ab["LNZ"] LOM <- cols_ab["LOM"] LOR <- cols_ab["LOR"] LTM <- cols_ab["LTM"] LVX <- cols_ab["LVX"] MAN <- cols_ab["MAN"] MCM <- cols_ab["MCM"] MEC <- cols_ab["MEC"] MEM <- cols_ab["MEM"] MEV <- cols_ab["MEV"] MEZ <- cols_ab["MEZ"] MFX <- cols_ab["MFX"] MID <- cols_ab["MID"] MNO <- cols_ab["MNO"] MTM <- cols_ab["MTM"] NAL <- cols_ab["NAL"] NEO <- cols_ab["NEO"] NET <- cols_ab["NET"] NIT <- cols_ab["NIT"] NOR <- cols_ab["NOR"] NOV <- cols_ab["NOV"] NVA <- cols_ab["NVA"] OFX <- cols_ab["OFX"] OLE <- cols_ab["OLE"] ORI <- cols_ab["ORI"] OXA <- cols_ab["OXA"] PAZ <- cols_ab["PAZ"] PEF <- cols_ab["PEF"] PEN <- cols_ab["PEN"] PHN <- cols_ab["PHN"] PIP <- cols_ab["PIP"] PLB <- cols_ab["PLB"] PME <- cols_ab["PME"] PRI <- cols_ab["PRI"] PRL <- cols_ab["PRL"] PRU <- cols_ab["PRU"] PVM <- cols_ab["PVM"] QDA <- cols_ab["QDA"] QDA <- cols_ab["QDA"] RAM <- cols_ab["RAM"] RFL <- cols_ab["RFL"] RID <- cols_ab["RID"] RIF <- cols_ab["RIF"] ROK <- cols_ab["ROK"] RST <- cols_ab["RST"] RXT <- cols_ab["RXT"] SAM <- cols_ab["SAM"] SBC <- cols_ab["SBC"] SDI <- cols_ab["SDI"] SDM <- cols_ab["SDM"] SIS <- cols_ab["SIS"] SLF <- cols_ab["SLF"] SLF1 <- cols_ab["SLF1"] SLF10 <- cols_ab["SLF10"] SLF11 <- cols_ab["SLF11"] SLF12 <- cols_ab["SLF12"] SLF13 <- cols_ab["SLF13"] SLF2 <- cols_ab["SLF2"] SLF3 <- cols_ab["SLF3"] SLF4 <- cols_ab["SLF4"] SLF5 <- cols_ab["SLF5"] SLF6 <- cols_ab["SLF6"] SLF7 <- cols_ab["SLF7"] SLF8 <- cols_ab["SLF8"] SLF9 <- cols_ab["SLF9"] SLT1 <- cols_ab["SLT1"] SLT2 <- cols_ab["SLT2"] SLT3 <- cols_ab["SLT3"] SLT4 <- cols_ab["SLT4"] SLT5 <- cols_ab["SLT5"] SMX <- cols_ab["SMX"] SPI <- cols_ab["SPI"] SPX <- cols_ab["SPX"] STR <- cols_ab["STR"] STR1 <- cols_ab["STR1"] SUD <- cols_ab["SUD"] SUT <- cols_ab["SUT"] SXT <- cols_ab["SXT"] SZO <- cols_ab["SZO"] TAL <- cols_ab["TAL"] TCC <- cols_ab["TCC"] TCM <- cols_ab["TCM"] TCY <- cols_ab["TCY"] TEC <- cols_ab["TEC"] TEM <- cols_ab["TEM"] TGC <- cols_ab["TGC"] THA <- cols_ab["THA"] TIC <- cols_ab["TIC"] TLT <- cols_ab["TLT"] TLV <- cols_ab["TLV"] TMP <- cols_ab["TMP"] TMX <- cols_ab["TMX"] TOB <- cols_ab["TOB"] TRL <- cols_ab["TRL"] TVA <- cols_ab["TVA"] TZD <- cols_ab["TZD"] TZP <- cols_ab["TZP"] VAN <- cols_ab["VAN"] ab_missing <- function(ab) { all(ab %in% c(NULL, NA)) } if (ab_missing(AMP) & !ab_missing(AMX)) { # ampicillin column is missing, but amoxicillin is available if (info == TRUE) { message(font_blue(paste0("NOTE: Using column `", font_bold(AMX), "` as input for ampicillin since many EUCAST rules depend on it."))) } AMP <- AMX } # data preparation ---- if (info == TRUE & NROW(x) > 10000) { message(font_blue("NOTE: Preparing data..."), appendLF = FALSE) } # nolint start # antibiotic classes ---- aminoglycosides <- c(AMK, DKB, GEN, ISE, KAN, NEO, NET, RST, SIS, STR, STR1, TOB) aminopenicillins <- c(AMP, AMX) carbapenems <- c(DOR, ETP, IPM, MEM, MEV) cephalosporins <- c(CDZ, CAC, CEC, CFR, RID, MAN, CTZ, CZD, CZO, CDR, DIT, FEP, CAT, CFM, CMX, CMZ, DIZ, CID, CFP, CSL, CND, CTX, CTT, CTF, FOX, CPM, CPO, CPD, CPR, CRD, CFS, CPT, CAZ, CCV, CTL, CTB, CZX, BPR, CFM1, CEI, CRO, CXM, LEX, CEP, HAP, CED, LTM, LOR) cephalosporins_1st <- c(CAC, CFR, RID, CTZ, CZD, CZO, CRD, CTL, LEX, CEP, HAP, CED) cephalosporins_2nd <- c(CEC, MAN, CMZ, CID, CND, CTT, CTF, FOX, CPR, CXM, LOR) cephalosporins_except_CAZ <- cephalosporins[cephalosporins != ifelse(is.null(CAZ), "", CAZ)] fluoroquinolones <- c(CIP, ENX, FLE, GAT, GEM, GRX, LVX, LOM, MFX, NOR, OFX, PAZ, PEF, PRU, RFL, SPX, TMX, TVA) glycopeptides <- c(AVO, NVA, RAM, TEC, TCM, VAN) # dalba/orita/tela are in lipoglycopeptides lincosamides <- c(CLI, LIN, PRL) lipoglycopeptides <- c(DAL, ORI, TLV) macrolides <- c(AZM, CLR, DIR, ERY, FLR1, JOS, MID, MCM, OLE, ROK, RXT, SPI, TLT, TRL) oxazolidinones <- c(CYC, LNZ, THA, TZD) polymyxins <- c(PLB, COL) streptogramins <- c(QDA, PRI) tetracyclines <- c(DOX, MNO, TCY) # since EUCAST v3.1 tigecycline (TGC) is set apart ureidopenicillins <- c(PIP, TZP, AZL, MEZ) all_betalactams <- c(aminopenicillins, cephalosporins, carbapenems, ureidopenicillins, AMC, OXA, FLC, PEN) # nolint end # Some helper functions --------------------------------------------------- get_antibiotic_columns <- function(x, df) { x <- trimws(unlist(strsplit(x, ",", fixed = TRUE))) y <- character(0) for (i in seq_len(length(x))) { if (is.function(get(x[i]))) { stop("Column ", x[i], " is also a function. Please create an issue on github.com/msberends/AMR/issues.") } y <- c(y, tryCatch(get(x[i]), error = function(e) "")) } y[y != "" & y %in% colnames(df)] } markup_italics_where_needed <- function(x) { # returns names found in family, genus or species as italics if (!has_colour()) { return(x) } x <- unlist(strsplit(x, " ")) ind <- gsub("[)(:]", "", x) %in% c(MO_lookup[which(MO_lookup$rank %in% c("family", "genus")), ]$fullname, MO_lookup[which(MO_lookup$rank == "species"), ]$species) x[ind] <- font_italic(x[ind], collapse = NULL) paste(x, collapse = " ") } get_antibiotic_names <- function(x) { x <- x %pm>% strsplit(",") %pm>% unlist() %pm>% trimws() %pm>% sapply(function(x) if (x %in% antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE) else x) %pm>% sort() %pm>% paste(collapse = ", ") x <- gsub("_", " ", x, fixed = TRUE) x <- gsub("except CAZ", paste("except", ab_name("CAZ", language = NULL, tolower = TRUE)), x, fixed = TRUE) x <- gsub("cephalosporins (1st|2nd|3rd|4th|5th)", "cephalosporins (\\1 gen.)", x) x } format_antibiotic_names <- function(ab_names, ab_results) { ab_names <- trimws(unlist(strsplit(ab_names, ","))) ab_results <- trimws(unlist(strsplit(ab_results, ","))) if (length(ab_results) == 1) { if (length(ab_names) == 1) { # like FOX S x <- paste(ab_names, "is") } else if (length(ab_names) == 2) { # like PEN,FOX S x <- paste(paste0(ab_names, collapse = " and "), "are both") } else { # like PEN,FOX,GEN S (although dependency on > 2 ABx does not exist at the moment) x <- paste(paste0(ab_names, collapse = " and "), "are all") } return(paste0(x, " '", ab_results, "'")) } else { if (length(ab_names) == 2) { # like PEN,FOX S,R paste0(ab_names[1], " is '", ab_results[1], "' and ", ab_names[2], " is '", ab_results[2], "'") } else { # like PEN,FOX,GEN S,R,R (although dependency on > 2 ABx does not exist at the moment) paste0(ab_names[1], " is '", ab_results[1], "' and ", ab_names[2], " is '", ab_results[2], "' and ", ab_names[3], " is '", ab_results[3], "'") } } } as.rsi_no_warning <- function(x) { if (is.rsi(x)) { return(x) } suppressWarnings(as.rsi(x)) } verbose_info <- data.frame(rowid = character(0), col = character(0), mo_fullname = character(0), old = as.rsi(character(0)), new = as.rsi(character(0)), rule = character(0), rule_group = character(0), rule_name = character(0), rule_source = character(0), stringsAsFactors = FALSE) old_cols <- colnames(x) old_attributes <- attributes(x) x <- as.data.frame(x, stringsAsFactors = FALSE) # no tibbles, data.tables, etc. rownames(x) <- NULL # will later be restored with old_attributes # create unique row IDs - combination of the MO and all ABx columns (so they will only run once per unique combination) x$`.rowid` <- sapply(as.list(as.data.frame(t(x[, c(col_mo, cols_ab), drop = FALSE]))), function(x) { x[is.na(x)] <- "." paste0(x, collapse = "") }) # save original table, with the new .rowid column x.bak <- x # keep only unique rows for MO and ABx x <- x %pm>% pm_arrange(`.rowid`) %pm>% # big speed gain! only analyse unique rows: pm_distinct(`.rowid`, .keep_all = TRUE) %pm>% as.data.frame(stringsAsFactors = FALSE) x[, col_mo] <- as.mo(x[, col_mo, drop = TRUE]) x <- x %pm>% left_join_microorganisms(by = col_mo, suffix = c("_oldcols", "")) x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL) x$genus_species <- paste(x$genus, x$species) if (info == TRUE & NROW(x) > 10000) { message(font_blue("OK.")) } if (any(x$genus == "Staphylococcus", na.rm = TRUE)) { all_staph <- MO_lookup[which(MO_lookup$genus == "Staphylococcus"), ] all_staph$CNS_CPS <- suppressWarnings(mo_name(all_staph$mo, Becker = "all", language = NULL)) } if (any(x$genus == "Streptococcus", na.rm = TRUE)) { all_strep <- MO_lookup[which(MO_lookup$genus == "Streptococcus"), ] all_strep$Lancefield <- suppressWarnings(mo_name(all_strep$mo, Lancefield = TRUE, language = NULL)) } n_added <- 0 n_changed <- 0 # Other rules: enzyme inhibitors ------------------------------------------ if (any(c("all", "other") %in% rules)) { if (info == TRUE) { cat(font_bold(paste0("\nRules by this AMR package (", font_red(paste0("v", utils::packageVersion("AMR"), ", ", format(utils::packageDate("AMR"), "%Y"))), "), see ?eucast_rules\n"))) } ab_enzyme <- subset(antibiotics, name %like% "/")[, c("ab", "name")] ab_enzyme$base_name <- gsub("^([a-zA-Z0-9]+).*", "\\1", ab_enzyme$name) ab_enzyme$base_ab <- as.ab(ab_enzyme$base_name) for (i in seq_len(nrow(ab_enzyme))) { if (all(c(ab_enzyme[i, ]$ab, ab_enzyme[i, ]$base_ab) %in% names(cols_ab), na.rm = TRUE)) { ab_name_base <- ab_name(cols_ab[ab_enzyme[i, ]$base_ab], language = NULL, tolower = TRUE) ab_name_enzyme <- ab_name(cols_ab[ab_enzyme[i, ]$ab], language = NULL, tolower = TRUE) # Set base to R where base + enzyme inhibitor is R rule_current <- paste0("Set ", ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = R where ", ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = R") if (info == TRUE) { cat(rule_current) } run_changes <- edit_rsi(x = x, col_mo = col_mo, to = "R", rule = c(rule_current, "Other rules", "", paste0("Non-EUCAST: AMR package v", utils::packageVersion("AMR"))), rows = which(as.rsi_no_warning(x[, cols_ab[ab_enzyme[i, ]$ab]]) == "R"), cols = cols_ab[ab_enzyme[i, ]$base_ab], last_verbose_info = verbose_info, original_data = x.bak, warned = warned, info = info) n_added <- n_added + run_changes$added n_changed <- n_changed + run_changes$changed verbose_info <- run_changes$verbose_info x <- run_changes$output warn_lacking_rsi_class <- warn_lacking_rsi_class | run_changes$rsi_warn # Print number of new changes if (info == TRUE) { # print only on last one of rules in this group txt_ok(n_added = n_added, n_changed = n_changed, warned = warned) # and reset counters n_added <- 0 n_changed <- 0 } # Set base + enzyme inhibitor to S where base is S rule_current <- paste0("Set ", ab_name_enzyme, " (", cols_ab[ab_enzyme[i, ]$ab], ") = S where ", ab_name_base, " (", cols_ab[ab_enzyme[i, ]$base_ab], ") = S") if (info == TRUE) { cat(rule_current) } run_changes <- edit_rsi(x = x, col_mo = col_mo, to = "S", rule = c(rule_current, "Other rules", "", paste0("Non-EUCAST: AMR package v", utils::packageVersion("AMR"))), rows = which(as.rsi_no_warning(x[, cols_ab[ab_enzyme[i, ]$base_ab]]) == "S"), cols = cols_ab[ab_enzyme[i, ]$ab], last_verbose_info = verbose_info, original_data = x.bak, warned = warned, info = info) n_added <- n_added + run_changes$added n_changed <- n_changed + run_changes$changed verbose_info <- run_changes$verbose_info x <- run_changes$output warn_lacking_rsi_class <- warn_lacking_rsi_class | run_changes$rsi_warn # Print number of new changes if (info == TRUE) { # print only on last one of rules in this group txt_ok(n_added = n_added, n_changed = n_changed, warned = warned) # and reset counters n_added <- 0 n_changed <- 0 } } } } else { if (info == TRUE) { cat(font_red("\nSkipping inheritance rules defined by this package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R.\nUse eucast_rules(..., rules = \"all\") to also apply those rules.\n")) } } # Official EUCAST rules --------------------------------------------------- eucast_notification_shown <- FALSE if (!is.null(list(...)$eucast_rules_df)) { # this allows: eucast_rules(x, eucast_rules_df = AMR:::eucast_rules_file %pm>% filter(is.na(have_these_values))) eucast_rules_df <- list(...)$eucast_rules_df } else { # otherwise internal data file, created in data-raw/internals.R eucast_rules_df <- eucast_rules_file } # filter on user-set guideline versions ---- if (any(c("all", "breakpoints") %in% rules)) { eucast_rules_df <- subset(eucast_rules_df, !reference.rule_group %like% "breakpoint" | (reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints)) } if (any(c("all", "expert") %in% rules)) { eucast_rules_df <- subset(eucast_rules_df, !reference.rule_group %like% "expert" | (reference.rule_group %like% "expert" & reference.version == version_expertrules)) } for (i in seq_len(nrow(eucast_rules_df))) { rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule", drop = TRUE] rule_current <- eucast_rules_df[i, "reference.rule", drop = TRUE] rule_next <- eucast_rules_df[min(nrow(eucast_rules_df), i + 1), "reference.rule", drop = TRUE] rule_group_previous <- eucast_rules_df[max(1, i - 1), "reference.rule_group", drop = TRUE] rule_group_current <- eucast_rules_df[i, "reference.rule_group", drop = TRUE] if (isFALSE(info) | isFALSE(verbose)) { rule_text <- "" } else { if (is.na(eucast_rules_df[i, "and_these_antibiotics", drop = TRUE])) { rule_text <- paste0("always report as '", eucast_rules_df[i, "to_value", drop = TRUE], "': ", get_antibiotic_names(eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE])) } else { rule_text <- paste0("report as '", eucast_rules_df[i, "to_value", drop = TRUE], "' when ", format_antibiotic_names(ab_names = get_antibiotic_names(eucast_rules_df[i, "and_these_antibiotics", drop = TRUE]), ab_results = eucast_rules_df[i, "have_these_values", drop = TRUE]), ": ", get_antibiotic_names(eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE])) } } if (i == 1) { rule_previous <- "" rule_group_previous <- "" } if (i == nrow(eucast_rules_df)) { rule_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 (info == TRUE) { # Print EUCAST intro ------------------------------------------------------ if (!rule_group_current %like% "other" & eucast_notification_shown == FALSE) { cat(paste0("\n", font_grey(strrep("-", 0.95 * options()$width)), "\nRules by the ", font_bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"), "\n", font_blue("https://eucast.org/"), "\n")) eucast_notification_shown <- TRUE } # Print rule (group) ------------------------------------------------------ if (rule_group_current != rule_group_previous) { # is new rule group, one of Breakpoints, Expert Rules and Other cat(font_bold( ifelse( rule_group_current %like% "breakpoint", paste0("\n", breakpoints_info$title, " (", font_red(paste0(breakpoints_info$version_txt, ", ", breakpoints_info$year)), ")\n"), ifelse( rule_group_current %like% "expert", paste0("\n", expertrules_info$title, " (", font_red(paste0(expertrules_info$version_txt, ", ", expertrules_info$year)), ")\n"), "")))) } # Print rule ------------------------------------------------------------- if (rule_current != rule_previous) { # is new rule within group, print its name cat(markup_italics_where_needed(rule_current)) warned <- FALSE } } # Get rule from file ------------------------------------------------------ if_mo_property <- trimws(eucast_rules_df[i, "if_mo_property", drop = TRUE]) like_is_one_of <- trimws(eucast_rules_df[i, "like.is.one_of", drop = TRUE]) mo_value <- trimws(eucast_rules_df[i, "this_value", drop = TRUE]) # be sure to comprise all coagulase-negative/-positive Staphylococci when they are mentioned if (mo_value %like% "coagulase" && any(x$genus == "Staphylococcus", na.rm = TRUE)) { if (mo_value %like% "negative") { eucast_rules_df[i, "this_value"] <- paste0("^(", paste0(all_staph[which(all_staph$CNS_CPS %like% "negative"), "fullname", drop = TRUE], collapse = "|"), ")$") } else { eucast_rules_df[i, "this_value"] <- paste0("^(", paste0(all_staph[which(all_staph$CNS_CPS %like% "positive"), "fullname", drop = TRUE], collapse = "|"), ")$") } like_is_one_of <- "like" } # be sure to comprise all beta-haemolytic Streptococci (Lancefield groups A, B, C and G) when they are mentioned if (mo_value %like% "group [ABCG]" && any(x$genus == "Streptococcus", na.rm = TRUE)) { eucast_rules_df[i, "this_value"] <- paste0("^(", paste0(all_strep[which(all_strep$Lancefield %like% "group [ABCG]"), "fullname", drop = TRUE], collapse = "|"), ")$") like_is_one_of <- "like" } if (like_is_one_of == "is") { # so e.g. 'Enterococcus' will turn into '^Enterococcus$' mo_value <- paste0("^", mo_value, "$") } else if (like_is_one_of == "one_of") { # so 'Clostridium, Actinomyces, ...' will turn into '^(Clostridium|Actinomyces|...)$' mo_value <- paste0("^(", paste(trimws(unlist(strsplit(mo_value, ",", fixed = TRUE))), collapse = "|"), ")$") } else if (like_is_one_of != "like") { stop("invalid value for column 'like.is.one_of'", call. = FALSE) } source_antibiotics <- eucast_rules_df[i, "and_these_antibiotics", drop = TRUE] source_value <- trimws(unlist(strsplit(eucast_rules_df[i, "have_these_values", drop = TRUE], ",", fixed = TRUE))) target_antibiotics <- eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE] target_value <- eucast_rules_df[i, "to_value", drop = TRUE] if (is.na(source_antibiotics)) { rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like_perl% mo_value), error = function(e) integer(0)) } else { source_antibiotics <- get_antibiotic_columns(source_antibiotics, x) 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(x[, if_mo_property, drop = TRUE] %like_perl% mo_value & as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L]), error = function(e) integer(0)) } else if (length(source_antibiotics) == 2) { rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like_perl% mo_value & as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L] & as.rsi_no_warning(x[, source_antibiotics[2L]]) == source_value[2L]), error = function(e) integer(0)) } else if (length(source_antibiotics) == 3) { rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like_perl% mo_value & as.rsi_no_warning(x[, source_antibiotics[1L]]) == source_value[1L] & as.rsi_no_warning(x[, source_antibiotics[2L]]) == source_value[2L] & as.rsi_no_warning(x[, source_antibiotics[3L]]) == source_value[3L]), error = function(e) integer(0)) } else { stop_("only 3 antibiotics supported for source_antibiotics") } } cols <- get_antibiotic_columns(target_antibiotics, x) # Apply rule on data ------------------------------------------------------ # this will return the unique number of changes run_changes <- edit_rsi(x = x, col_mo = col_mo, to = target_value, rule = c(rule_text, rule_group_current, rule_current, ifelse(rule_group_current %like% "breakpoint", paste0(breakpoints_info$title, " ", breakpoints_info$version_txt, ", ", breakpoints_info$year), paste0(expertrules_info$title, " ", expertrules_info$version_txt, ", ", expertrules_info$year))), rows = rows, cols = cols, last_verbose_info = verbose_info, original_data = x.bak, warned = warned, info = info) n_added <- n_added + run_changes$added n_changed <- n_changed + run_changes$changed verbose_info <- run_changes$verbose_info x <- run_changes$output warn_lacking_rsi_class <- warn_lacking_rsi_class | run_changes$rsi_warn # Print number of new changes --------------------------------------------- if (info == TRUE & rule_next != rule_current) { # print only on last one of rules in this group txt_ok(n_added = n_added, n_changed = n_changed, warned = warned) # and reset counters n_added <- 0 n_changed <- 0 } } # Print overview ---------------------------------------------------------- if (info == TRUE) { rownames(verbose_info) <- NULL affected <- x.bak[which(x.bak$`.rowid` %in% x$`.rowid`), , drop = FALSE] rows_affected <- as.integer(rownames(affected)) verbose_info <- verbose_info %pm>% pm_left_join(data.frame(row = rows_affected, rowid = affected[, ".rowid", drop = TRUE], stringsAsFactors = FALSE), by = "rowid") %pm>% pm_select(-rowid) %pm>% pm_select(row, pm_everything()) %pm>% pm_filter(!is.na(new)) %pm>% pm_arrange(row, rule_group, rule_name, col) if (verbose == TRUE) { wouldve <- "would have " } else { wouldve <- "" } cat(paste0("\n", font_grey(strrep("-", 0.95 * options()$width)), "\n")) cat(font_bold(paste("The rules", paste0(wouldve, "affected"), formatnr(pm_n_distinct(verbose_info$row)), "out of", formatnr(nrow(x.bak)), "rows, making a total of", formatnr(nrow(verbose_info)), "edits\n"))) total_n_added <- verbose_info %pm>% pm_filter(is.na(old)) %pm>% nrow() total_n_changed <- verbose_info %pm>% pm_filter(!is.na(old)) %pm>% nrow() # print added values if (total_n_added == 0) { colour <- cat # is function } else { colour <- font_green # is function } cat(colour(paste0("=> ", wouldve, "added ", font_bold(formatnr(verbose_info %pm>% pm_filter(is.na(old)) %pm>% nrow()), "test results"), "\n"))) if (total_n_added > 0) { added_summary <- verbose_info %pm>% pm_filter(is.na(old)) %pm>% pm_count(new, name = "n") cat(paste(" -", paste0(formatnr(added_summary$n), " test result", ifelse(added_summary$n > 1, "s", ""), " added as ", paste0('"', added_summary$new, '"')), collapse = "\n")) } # print changed values if (total_n_changed == 0) { colour <- cat # is function } else { colour <- font_blue # is function } if (total_n_added + total_n_changed > 0) { cat("\n") } cat(colour(paste0("=> ", wouldve, "changed ", font_bold(formatnr(verbose_info %pm>% pm_filter(!is.na(old)) %pm>% nrow()), "test results"), "\n"))) if (total_n_changed > 0) { changed_summary <- verbose_info %pm>% pm_filter(!is.na(old)) %pm>% pm_count(old, new, name = "n") cat(paste(" -", paste0(formatnr(changed_summary$n), " test result", ifelse(changed_summary$n > 1, "s", ""), " changed from ", paste0('"', changed_summary$old, '"'), " to ", paste0('"', changed_summary$new, '"')), collapse = "\n")) cat("\n") } cat(paste0(font_grey(strrep("-", 0.95 * options()$width)), "\n")) if (verbose == FALSE & total_n_added + total_n_changed > 0) { cat(paste("\nUse", font_bold("eucast_rules(..., verbose = TRUE)"), "(on your original data) to get a data.frame with all specified edits instead.\n\n")) } else if (verbose == TRUE) { cat(paste0("\nUsed 'Verbose mode' (", font_bold("verbose = TRUE"), "), which returns a data.frame with all specified edits.\nUse ", font_bold("verbose = FALSE"), " to apply the rules on your data.\n\n")) } } if (isTRUE(warn_lacking_rsi_class)) { unique_cols <- colnames(x.bak)[colnames(x.bak) %in% verbose_info$col] warning("Not all columns with antimicrobial results are of class . Transform them on beforehand, with e.g.:\n", " ", x_deparsed, " %>% mutate_if(is.rsi.eligible, as.rsi)\n", " ", x_deparsed, " %>% as.rsi(", unique_cols[1], ":", unique_cols[length(unique_cols)], ")", call. = FALSE) } # Return data set --------------------------------------------------------- if (verbose == TRUE) { verbose_info } else { # x was analysed with only unique rows, so join everything together again x <- x[, c(cols_ab, ".rowid"), drop = FALSE] x.bak <- x.bak[, setdiff(colnames(x.bak), cols_ab), drop = FALSE] x.bak <- x.bak %pm>% pm_left_join(x, by = ".rowid") x.bak <- x.bak[, old_cols, drop = FALSE] # reset original attributes attributes(x.bak) <- old_attributes x.bak } } # helper function for editing the table ---- edit_rsi <- function(x, col_mo, to, rule, rows, cols, last_verbose_info, original_data, warned, info) { cols <- unique(cols[!is.na(cols) & !is.null(cols)]) # for Verbose Mode, keep track of all changes and return them track_changes <- list(added = 0, changed = 0, output = x, verbose_info = last_verbose_info, rsi_warn = FALSE) txt_error <- function() { if (info == TRUE) cat("", font_red_bg(font_white(" ERROR ")), "\n\n") } txt_warning <- function() { if (warned == FALSE) { if (info == TRUE) cat("", font_yellow_bg(font_black(" WARNING "))) } warned <<- TRUE } if (length(rows) > 0 & length(cols) > 0) { new_edits <- x if (any(!sapply(x[, cols, drop = FALSE], is.rsi), na.rm = TRUE)) { track_changes$rsi_warn <- TRUE } tryCatch( # insert into original table new_edits[rows, cols] <- to, warning = function(w) { if (w$message %like% "invalid factor level") { xyz <- sapply(cols, function(col) { new_edits[, col] <- factor(x = as.character(pm_pull(new_edits, col)), levels = c(to, levels(pm_pull(new_edits, col)))) # x[, col] <<- factor(x = as.character(pm_pull(x, col)), levels = c(to, levels(pm_pull(x, col)))) invisible() }) new_edits[rows, cols] <- to warning('Value "', to, '" added to the factor levels of column(s) `', paste(cols, collapse = "`, `"), "` because this value was not an existing factor level.\nA better way is to use as.rsi() on beforehand on antimicrobial columns to guarantee the right structure.", call. = FALSE) txt_warning() warned <- FALSE } else { warning(w$message, call. = FALSE) txt_warning() cat("\n") # txt_warning() does not append a "\n" on itself } }, error = function(e) { txt_error() stop(paste0("In row(s) ", paste(rows[1:min(length(rows), 10)], collapse = ","), ifelse(length(rows) > 10, "...", ""), " while writing value '", to, "' to column(s) `", paste(cols, collapse = "`, `"), "`:\n", e$message), call. = FALSE) } ) track_changes$output <- new_edits if (isTRUE(info) && !isTRUE(all.equal(x, track_changes$output))) { get_original_rows <- function(rowids) { as.integer(rownames(original_data[which(original_data$.rowid %in% rowids), , drop = FALSE])) } for (i in seq_len(length(cols))) { verbose_new <- data.frame(rowid = new_edits[rows, ".rowid", drop = TRUE], col = cols[i], mo_fullname = new_edits[rows, "fullname", drop = TRUE], old = x[rows, cols[i], drop = TRUE], new = to, rule = font_stripstyle(rule[1]), rule_group = font_stripstyle(rule[2]), rule_name = font_stripstyle(rule[3]), rule_source = font_stripstyle(rule[4]), stringsAsFactors = FALSE) colnames(verbose_new) <- c("rowid", "col", "mo_fullname", "old", "new", "rule", "rule_group", "rule_name", "rule_source") verbose_new <- verbose_new %pm>% pm_filter(old != new | is.na(old)) # save changes to data set 'verbose_info' track_changes$verbose_info <- rbind(track_changes$verbose_info, verbose_new) # count adds and changes track_changes$added <- track_changes$added + verbose_new %pm>% pm_filter(is.na(old)) %pm>% pm_pull(rowid) %pm>% get_original_rows() %pm>% length() track_changes$changed <- track_changes$changed + verbose_new %pm>% pm_filter(!is.na(old)) %pm>% pm_pull(rowid) %pm>% get_original_rows() %pm>% length() } } } return(track_changes) }