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AMR/R/eucast_rules.R

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# ==================================================================== #
# 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)
}
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