# ==================================================================== # # 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/ # # ==================================================================== # format_eucast_version_nr <- function(version, markdown = TRUE) { # for documentation - adds title, version number, year and url in markdown language lst <- c(EUCAST_VERSION_BREAKPOINTS, EUCAST_VERSION_EXPERT_RULES) version <- format(unique(version), nsmall = 1) txt <- character(0) for (i in seq_len(length(version))) { v <- version[i] if (markdown == TRUE) { txt <- c(txt, paste0("[", lst[[v]]$title, " ", lst[[v]]$version_txt, "](", lst[[v]]$url, ")", " (", lst[[v]]$year, ")")) } else { txt <- c(txt, paste0(lst[[version]]$title, " ", lst[[v]]$version_txt, " (", lst[[v]]$year, ")")) } } vector_and(txt, quotes = FALSE) } #' 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*. Use [eucast_dosage()] to get a [data.frame] with advised dosages of a certain bug-drug combination, which is based on the [dosage] data set. #' #' 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 a [logical] to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions #' @param rules a [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value, e.g. using `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()]. #' @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. Can be either `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`. #' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`. #' @param ampc_cephalosporin_resistance a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to `NA`. Currently only works when `version_expertrules` is `3.2`; '*EUCAST Expert Rules v3.2 on Enterobacterales*' states that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of `NA` (the default) for this argument will remove results for these three agents, while e.g. a value of `"R"` will make the results for these agents resistant. Use `NULL` or `FALSE` to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(EUCAST_RULES_DF[which(EUCAST_RULES_DF$reference.version == 3.2 & EUCAST_RULES_DF$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`. #' @param ... column name of an antibiotic, see section *Antibiotics* below #' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()] #' @param administration route of administration, either `r vector_or(dosage$administration)` #' @param only_rsi_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `` (see [as.rsi()]) on beforehand (defaults to `FALSE`) #' @param custom_rules custom rules to apply, created with [custom_eucast_rules()] #' @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. \cr #' #' The file containing all EUCAST rules is located here: . **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this `AMR` package contains the taxonomy updated until [`r CATALOGUE_OF_LIFE$yearmonth_LPSN`][catalogue_of_life()]. #' #' ## Custom Rules #' #' Custom rules can be created using [custom_eucast_rules()], e.g.: #' #' ``` #' x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R", #' AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I") #' #' eucast_rules(example_isolates, rules = "custom", custom_rules = x) #' ``` #' #' #' ## '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` argument, or use `eucast_rules(..., rules = "all")`. You can also set the option `AMR_eucastrules`, i.e. run `options(AMR_eucastrules = "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 eligible 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_eucast_ab_documentation()` #' @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; \doi{https://doi.org/10.1111/j.1469-0691.2011.03703.x} #' - EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf) #' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf) #' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx) #' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx) #' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx) #' @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_dosage(c("tobra", "genta", "cipro"), "iv") eucast_rules <- function(x, col_mo = NULL, info = interactive(), rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")), verbose = FALSE, version_breakpoints = 11.0, version_expertrules = 3.2, ampc_cephalosporin_resistance = NA, only_rsi_columns = FALSE, custom_rules = NULL, ...) { meet_criteria(x, allow_class = "data.frame") meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE) meet_criteria(info, allow_class = "logical", has_length = 1) meet_criteria(rules, allow_class = "character", has_length = c(1, 2, 3, 4, 5), is_in = c("breakpoints", "expert", "other", "all", "custom")) meet_criteria(verbose, allow_class = "logical", has_length = 1) meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS))) meet_criteria(version_expertrules, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_EXPERT_RULES))) meet_criteria(ampc_cephalosporin_resistance, allow_class = c("logical", "character", "rsi"), has_length = 1, allow_NA = TRUE, allow_NULL = TRUE) meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1) meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE) if ("custom" %in% rules & is.null(custom_rules)) { warning_("No custom rules were set with the `custom_rules` argument", call = FALSE, immediate = TRUE) rules <- rules[rules != "custom"] if (length(rules) == 0) { if (info == TRUE) { message_("No other rules were set, returning original data", add_fn = font_red, as_note = FALSE) } return(x) } } x_deparsed <- deparse(substitute(x)) if (length(x_deparsed) > 1 || any(x_deparsed %unlike% "[a-z]+")) { x_deparsed <- "your_data" } check_dataset_integrity() 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", add_fn = font_red, as_note = FALSE) return(x) } } # 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") } 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 <- character(0) 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 if (n_added > 0 & n_changed == 0) { cat(font_green(" (")) } else if (n_added == 0 & n_changed > 0) { cat(font_blue(" (")) } else { 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 if (n_added > 0 & n_changed == 0) { cat(font_green(")\n")) } else if (n_added == 0 & n_changed > 0) { cat(font_blue(")\n")) } else { 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, only_rsi_columns = only_rsi_columns, ...) if (!"AMP" %in% names(cols_ab) & "AMX" %in% names(cols_ab)) { # ampicillin column is missing, but amoxicillin is available if (info == TRUE) { message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many EUCAST rules depend on it.") } cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"]))) } # data preparation ---- if (info == TRUE & NROW(x) > 10000) { message_("Preparing data...", appendLF = FALSE, as_note = FALSE) } # Some helper functions --------------------------------------------------- get_antibiotic_columns <- function(x, cols_ab) { x <- trimws(unique(toupper(unlist(strsplit(x, ","))))) x_new <- character() for (val in x) { if (val %in% ls(envir = asNamespace("AMR"))) { # antibiotic group names, as defined in data-raw/_internals.R, such as `CARBAPENEMS` val <- eval(parse(text = val), envir = asNamespace("AMR")) } else if (val %in% AB_lookup$ab) { # separate drugs, such as `AMX` val <- as.ab(val) } else { stop_("unknown antimicrobial agent (group) in EUCAST rules file: ", val, call = FALSE) } x_new <- c(x_new, val) } x_new <- unique(x_new) out <- cols_ab[match(x_new, names(cols_ab))] out[!is.na(out)] } get_antibiotic_names <- function(x) { x <- x %pm>% strsplit(",") %pm>% unlist() %pm>% trimws() %pm>% vapply(FUN.VALUE = character(1), function(x) if (x %in% antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE, fast_mode = 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("except TGC", paste("except", ab_name("TGC", 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) # nolint start # x <- paste(paste0(ab_names, collapse = " and "), "are all") # nolint end } 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)) } # Preparing the data ------------------------------------------------------ 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` <- vapply(FUN.VALUE = character(1), as.list(as.data.frame(t(x[, c(col_mo, cols_ab), drop = FALSE]), stringsAsFactors = 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(as.character(x[, col_mo, drop = TRUE])) # rename col_mo to prevent interference with joined columns colnames(x)[colnames(x) == col_mo] <- ".col_mo" col_mo <- ".col_mo" # join to microorganisms data set x <- left_join_microorganisms(x, by = col_mo, suffix = c("_oldcols", "")) x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL) x$genus_species <- trimws(paste(x$genus, x$species)) if (info == TRUE & NROW(x) > 10000) { message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE) } 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("\n") cat(word_wrap( font_bold(paste0("Rules by this AMR package (", font_red(paste0("v", utils::packageDescription("AMR")$Version, ", ", format(as.Date(utils::packageDescription("AMR")$Date), format = "%Y"))), "), see ?eucast_rules\n")))) } ab_enzyme <- subset(antibiotics, name %like% "/")[, c("ab", "name")] colnames(ab_enzyme) <- c("enzyme_ab", "enzyme_name") ab_enzyme$base_name <- gsub("^([a-zA-Z0-9]+).*", "\\1", ab_enzyme$enzyme_name) ab_enzyme$base_ab <- antibiotics[match(ab_enzyme$base_name, antibiotics$name), "ab", drop = TRUE] ab_enzyme <- subset(ab_enzyme, !is.na(base_ab)) # make ampicillin and amoxicillin interchangable ampi <- subset(ab_enzyme, base_ab == "AMX") ampi$base_ab <- "AMP" ampi$base_name <- ab_name("AMP", language = NULL) amox <- subset(ab_enzyme, base_ab == "AMP") amox$base_ab <- "AMX" amox$base_name <- ab_name("AMX", language = NULL) # merge and sort ab_enzyme <- rbind(ab_enzyme, ampi, amox) ab_enzyme <- ab_enzyme[order(ab_enzyme$enzyme_name), ] for (i in seq_len(nrow(ab_enzyme))) { # check if both base and base + enzyme inhibitor are part of the data set if (all(c(ab_enzyme$base_ab[i], ab_enzyme$enzyme_ab[i]) %in% names(cols_ab), na.rm = TRUE)) { col_base <- unname(cols_ab[ab_enzyme$base_ab[i]]) col_enzyme <- unname(cols_ab[ab_enzyme$enzyme_ab[i]]) # Set base to R where base + enzyme inhibitor is R ---- rule_current <- paste0(ab_enzyme$base_name[i], " ('", font_bold(col_base), "') = R if ", tolower(ab_enzyme$enzyme_name[i]), " ('", font_bold(col_enzyme), "') = R") if (info == TRUE) { cat(word_wrap(rule_current, width = getOption("width") - 30, extra_indent = 6)) } run_changes <- edit_rsi(x = x, to = "R", rule = c(rule_current, "Other rules", "", paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)), rows = which(as.rsi_no_warning(x[, col_enzyme, drop = TRUE]) == "R"), cols = col_base, last_verbose_info = verbose_info, original_data = x.bak, warned = warned, info = info, verbose = verbose) n_added <- n_added + run_changes$added n_changed <- n_changed + run_changes$changed verbose_info <- run_changes$verbose_info x <- run_changes$output warn_lacking_rsi_class <- c(warn_lacking_rsi_class, run_changes$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(ab_enzyme$enzyme_name[i], " ('", font_bold(col_enzyme), "') = S if ", tolower(ab_enzyme$base_name[i]), " ('", font_bold(col_base), "') = S") if (info == TRUE) { cat(word_wrap(rule_current, width = getOption("width") - 30, extra_indent = 6)) } run_changes <- edit_rsi(x = x, to = "S", rule = c(rule_current, "Other rules", "", paste0("Non-EUCAST: AMR package v", utils::packageDescription("AMR")$Version)), rows = which(as.rsi_no_warning(x[, col_base, drop = TRUE]) == "S"), cols = col_enzyme, last_verbose_info = verbose_info, original_data = x.bak, warned = warned, info = info, verbose = verbose) n_added <- n_added + run_changes$added n_changed <- n_changed + run_changes$changed verbose_info <- run_changes$verbose_info x <- run_changes$output warn_lacking_rsi_class <- c(warn_lacking_rsi_class, run_changes$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("\n") message_("Skipping inheritance rules defined by this AMR package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R. Add \"other\" or \"all\" to the `rules` argument to apply those rules.") } } if (!any(c("all", "custom") %in% rules) & !is.null(custom_rules)) { if (info == TRUE) { message_("Skipping custom EUCAST rules, since the `rules` argument does not contain \"custom\".") } custom_rules <- NULL } # Official EUCAST rules --------------------------------------------------- eucast_notification_shown <- FALSE if (!is.null(list(...)$eucast_rules_df)) { # this allows: eucast_rules(x, eucast_rules_df = AMR:::EUCAST_RULES_DF %>% filter(is.na(have_these_values))) eucast_rules_df <- list(...)$eucast_rules_df } else { # otherwise internal data file, created in data-raw/_internals.R eucast_rules_df <- EUCAST_RULES_DF } # filter on user-set guideline versions ---- if (any(c("all", "breakpoints") %in% rules)) { eucast_rules_df <- subset(eucast_rules_df, reference.rule_group %unlike% "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 %unlike% "expert" | (reference.rule_group %like% "expert" & reference.version == version_expertrules)) } # filter out AmpC de-repressed cephalosporin-resistant mutants ---- # cefotaxime, ceftriaxone, ceftazidime if (is.null(ampc_cephalosporin_resistance) || isFALSE(ampc_cephalosporin_resistance)) { eucast_rules_df <- subset(eucast_rules_df, reference.rule %unlike% "ampc") } else { if (isTRUE(ampc_cephalosporin_resistance)) { ampc_cephalosporin_resistance <- "R" } eucast_rules_df[which(eucast_rules_df$reference.rule %like% "ampc"), "to_value"] <- as.character(ampc_cephalosporin_resistance) } # Go over all rules and apply them ---- for (i in seq_len(nrow(eucast_rules_df))) { rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule", drop = TRUE] rule_current <- eucast_rules_df[i, "reference.rule", drop = TRUE] rule_next <- eucast_rules_df[min(nrow(eucast_rules_df), i + 1), "reference.rule", drop = TRUE] rule_group_previous <- eucast_rules_df[max(1, i - 1), "reference.rule_group", drop = TRUE] rule_group_current <- eucast_rules_df[i, "reference.rule_group", drop = TRUE] # don't apply rules if user doesn't want to apply them if (rule_group_current %like% "breakpoint" & !any(c("all", "breakpoints") %in% rules)) { next } if (rule_group_current %like% "expert" & !any(c("all", "expert") %in% rules)) { next } if (isFALSE(info) | isFALSE(verbose)) { rule_text <- "" } else { if (is.na(eucast_rules_df[i, "and_these_antibiotics", drop = TRUE])) { rule_text <- paste0("always report as '", eucast_rules_df[i, "to_value", drop = TRUE], "': ", get_antibiotic_names(eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE])) } else { rule_text <- paste0("report as '", eucast_rules_df[i, "to_value", drop = TRUE], "' when ", format_antibiotic_names(ab_names = get_antibiotic_names(eucast_rules_df[i, "and_these_antibiotics", drop = TRUE]), ab_results = eucast_rules_df[i, "have_these_values", drop = TRUE]), ": ", get_antibiotic_names(eucast_rules_df[i, "then_change_these_antibiotics", drop = TRUE])) } } if (i == 1) { rule_previous <- "" rule_group_previous <- "" } if (i == nrow(eucast_rules_df)) { rule_next <- "" } if (info == TRUE) { # Print EUCAST intro ------------------------------------------------------ if (rule_group_current %unlike% "other" & eucast_notification_shown == FALSE) { cat( paste0("\n", font_grey(strrep("-", 0.95 * options()$width)), "\n", word_wrap("Rules 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", word_wrap( breakpoints_info$title, " (", font_red(paste0(breakpoints_info$version_txt, ", ", breakpoints_info$year)), ")\n")), ifelse( rule_group_current %like% "expert", paste0("\n", word_wrap( expertrules_info$title, " (", font_red(paste0(expertrules_info$version_txt, ", ", expertrules_info$year)), ")\n")), ""))), "\n") } # Print rule ------------------------------------------------------------- if (rule_current != rule_previous) { # is new rule within group, print its name cat(italicise_taxonomy(word_wrap(rule_current, width = getOption("width") - 30, extra_indent = 6), type = "ansi")) 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% mo_value), error = function(e) integer(0)) } else { source_antibiotics <- get_antibiotic_columns(source_antibiotics, cols_ab) 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% 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% 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)) # nolint start # } else if (length(source_antibiotics) == 3) { # rows <- tryCatch(which(x[, if_mo_property, drop = TRUE] %like% 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)) # nolint end } else { stop_("only 2 antibiotics supported for source_antibiotics") } } cols <- get_antibiotic_columns(target_antibiotics, cols_ab) # Apply rule on data ------------------------------------------------------ # this will return the unique number of changes run_changes <- edit_rsi(x = x, 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, verbose = verbose) 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 <- c(warn_lacking_rsi_class, run_changes$rsi_warn) # Print number of new changes --------------------------------------------- if (info == TRUE & rule_next != rule_current) { # print only on last one of rules in this group txt_ok(n_added = n_added, n_changed = n_changed, warned = warned) # and reset counters n_added <- 0 n_changed <- 0 } } # end of going over all rules # Apply custom rules ---- if (!is.null(custom_rules)) { if (info == TRUE) { cat("\n") cat(font_bold("Custom EUCAST rules, set by user"), "\n") } for (i in seq_len(length(custom_rules))) { rule <- custom_rules[[i]] rows <- which(eval(parse(text = rule$query), envir = x)) cols <- as.character(rule$result_group) cols <- c(cols[cols %in% colnames(x)], # direct column names unname(cols_ab[names(cols_ab) %in% cols])) # based on previous cols_ab finding cols <- unique(cols) target_value <- as.character(rule$result_value) rule_text <- paste0("report as '", target_value, "' when ", format_custom_query_rule(rule$query, colours = FALSE), ": ", get_antibiotic_names(cols)) if (info == TRUE) { # print rule cat(italicise_taxonomy(word_wrap(format_custom_query_rule(rule$query, colours = FALSE), width = getOption("width") - 30, extra_indent = 6), type = "ansi")) warned <- FALSE } run_changes <- edit_rsi(x = x, to = target_value, rule = c(rule_text, "Custom EUCAST rules", paste0("Custom EUCAST rule ", i), paste0("Object '", deparse(substitute(custom_rules)), "' consisting of ", length(custom_rules), " custom rules")), rows = rows, cols = cols, last_verbose_info = verbose_info, original_data = x.bak, warned = warned, info = info, verbose = verbose) 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 <- c(warn_lacking_rsi_class, run_changes$rsi_warn) # Print number of new changes --------------------------------------------- if (info == TRUE & rule_next != rule_current) { # print only on last one of rules in this group txt_ok(n_added = n_added, n_changed = n_changed, warned = warned) # and reset counters n_added <- 0 n_changed <- 0 } } } # Print overview ---------------------------------------------------------- if (info == TRUE | verbose == TRUE) { verbose_info <- x.bak %pm>% pm_mutate(row = pm_row_number()) %pm>% pm_select(`.rowid`, row) %pm>% pm_right_join(verbose_info, by = c(".rowid" = "rowid")) %pm>% pm_select(-`.rowid`) %pm>% pm_select(row, pm_everything()) %pm>% pm_filter(!is.na(new) | is.na(new) & !is.na(old)) %pm>% pm_arrange(row, rule_group, rule_name, col) rownames(verbose_info) <- NULL } if (info == TRUE) { if (verbose == TRUE) { wouldve <- "would have " } else { wouldve <- "" } cat(paste0("\n", font_grey(strrep("-", 0.95 * options()$width)), "\n")) cat(word_wrap(paste0("The rules ", paste0(wouldve, "affected "), font_bold(formatnr(pm_n_distinct(verbose_info$row)), "out of", formatnr(nrow(x.bak)), "rows"), ", making a total of ", font_bold(formatnr(nrow(verbose_info)), "edits\n")))) total_n_added <- verbose_info %pm>% pm_filter(is.na(old)) %pm>% nrow() total_n_changed <- verbose_info %pm>% pm_filter(!is.na(old)) %pm>% nrow() # print added values if (total_n_added == 0) { colour <- cat # is function } else { colour <- font_green # is function } cat(colour(paste0("=> ", wouldve, "added ", font_bold(formatnr(verbose_info %pm>% pm_filter(is.na(old)) %pm>% nrow()), "test results"), "\n"))) if (total_n_added > 0) { added_summary <- verbose_info %pm>% pm_filter(is.na(old)) %pm>% pm_count(new, name = "n") cat(paste(" -", paste0(formatnr(added_summary$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_mutate(new = ifelse(is.na(new), "NA", new)) %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("\n", word_wrap("Use ", font_bold("eucast_rules(..., verbose = TRUE)"), " (on your original data) to get a data.frame with all specified edits instead."), "\n\n", sep = "") } else if (verbose == TRUE) { cat("\n", word_wrap("Used '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", sep = "") } } if (length(warn_lacking_rsi_class) > 0) { warn_lacking_rsi_class <- unique(warn_lacking_rsi_class) # take order from original data set warn_lacking_rsi_class <- warn_lacking_rsi_class[order(colnames(x.bak))] warn_lacking_rsi_class <- warn_lacking_rsi_class[!is.na(warn_lacking_rsi_class)] warning_("Not all columns with antimicrobial results are of class . Transform them on beforehand, with e.g.:\n", " - ", x_deparsed, " %>% as.rsi(", ifelse(length(warn_lacking_rsi_class) == 1, warn_lacking_rsi_class, paste0(warn_lacking_rsi_class[1], ":", warn_lacking_rsi_class[length(warn_lacking_rsi_class)])), ")\n", " - ", x_deparsed, " %>% mutate_if(is.rsi.eligible, as.rsi)\n", " - ", x_deparsed, " %>% mutate(across(where(is.rsi.eligible), as.rsi))", 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, to, rule, rows, cols, last_verbose_info, original_data, warned, info, verbose) { 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 = character(0)) 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_rsi_I_bg(" WARNING "), sep = "") } warned <<- TRUE } if (length(rows) > 0 & length(cols) > 0) { new_edits <- x if (any(!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.rsi), na.rm = TRUE)) { track_changes$rsi_warn <- cols[!vapply(FUN.VALUE = logical(1), x[, cols, drop = FALSE], is.rsi)] } tryCatch( # insert into original table new_edits[rows, cols] <- to, warning = function(w) { if (w$message %like% "invalid factor level") { xyz <- vapply(FUN.VALUE = logical(1), cols, function(col) { new_edits[, col] <<- factor(x = as.character(pm_pull(new_edits, col)), levels = unique(c(to, levels(pm_pull(new_edits, col))))) TRUE }) suppressWarnings(new_edits[rows, cols] <<- to) warning_("Value \"", to, "\" added to the factor levels of column", ifelse(length(cols) == 1, "", "s"), " ", vector_and(cols, quotes = "`", sort = FALSE), " because this value was not an existing factor level.", call = FALSE) txt_warning() warned <- FALSE } else { warning_(w$message, call = FALSE) txt_warning() } }, 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 ((info == TRUE | verbose == TRUE) && !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) | is.na(new) & !is.na(old)) # save changes to data set 'verbose_info' track_changes$verbose_info <- rbind(track_changes$verbose_info, verbose_new, stringsAsFactors = FALSE) # 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) } #' @rdname eucast_rules #' @export eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 11.0) { meet_criteria(ab, allow_class = c("character", "numeric", "integer", "factor")) meet_criteria(administration, allow_class = "character", is_in = dosage$administration[!is.na(dosage$administration)], has_length = 1) meet_criteria(version_breakpoints, allow_class = c("numeric", "integer"), has_length = 1, is_in = as.double(names(EUCAST_VERSION_BREAKPOINTS))) # show used version_breakpoints number once per session (pkg_env will reload every session) if (message_not_thrown_before(paste0("eucast_dosage_v", gsub("[^0-9]", "", version_breakpoints)), entire_session = TRUE)) { message_("Dosages for antimicrobial drugs, as meant for ", format_eucast_version_nr(version_breakpoints, markdown = FALSE), ". ", font_red("This note will be shown once per session.")) remember_thrown_message(paste0("eucast_dosage_v", gsub("[^0-9]", "", version_breakpoints)), entire_session = TRUE) } ab <- as.ab(ab) lst <- vector("list", length = length(ab)) for (i in seq_len(length(ab))) { df <- AMR::dosage[which(AMR::dosage$ab == ab[i] & AMR::dosage$administration == administration), , drop = FALSE] lst[[i]] <- list(ab = "", name = "", standard_dosage = ifelse("standard_dosage" %in% df$type, df[which(df$type == "standard_dosage"), ]$original_txt, NA_character_), high_dosage = ifelse("high_dosage" %in% df$type, df[which(df$type == "high_dosage"), ]$original_txt, NA_character_)) } out <- do.call("rbind", lapply(lst, as.data.frame, stringsAsFactors = FALSE)) rownames(out) <- NULL out$ab <- ab out$name <- ab_name(ab, language = NULL) out }