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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.gitab.io/AMR. #
# ==================================================================== #
#' 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 tbl table 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
#' @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
#' @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}
#' }
#' }
#' @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(tbl,
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()) {
EUCAST_VERSION_BREAKPOINTS <- "9.0, 2019"
EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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("Parameter `rules` must be one or more of: 'breakpoints', 'expert', 'other', 'all'.")
}
if (is.null(col_mo)) {
stop("Parameter `col_mo` must be set")
}
warned <- FALSE
changed_results <- 0
txt_error <- function() { cat("", bgRed(black(" ERROR ")), "\n") }
txt_warning <- function() { if (warned == FALSE) { cat("", bgYellow(black(" WARNING ")), "\n") }; warned <<- TRUE }
txt_ok <- function() {
if (warned == FALSE) {
if (changed_results > 0) {
if (changed_results == 1) {
cat(blue(" (1 change)\n"))
} else {
cat(blue(paste0(" (", changed_results, " changes)\n")))
}
} else {
cat(green(" (no 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]
number_added_S <- 0
number_added_I <- 0
number_added_R <- 0
number_changed_to_S <- 0
number_changed_to_I <- 0
number_changed_to_R <- 0
number_affected_rows <- integer(0)
verbose_info <- data.frame(row = integer(0),
col = character(0),
mo = character(0),
mo_fullname = character(0),
old = character(0),
new = character(0),
rule_source = character(0),
rule_group = 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)
}
)
# suppressMessages(
# suppressWarnings(
# tbl[rows, cols] <<- to
# ))
after <- as.character(unlist(as.list(tbl_original[rows, cols])))
tbl[rows, cols] <<- tbl_original[rows, cols]
number_newly_added_S <- sum(!before %in% c("S", "I", "R") & after == "S", na.rm = TRUE)
number_newly_added_I <- sum(!before %in% c("S", "I", "R") & after == "I", na.rm = TRUE)
number_newly_added_R <- sum(!before %in% c("S", "I", "R") & after == "R", na.rm = TRUE)
number_newly_changed_to_S <- sum(before %in% c("I", "R") & after == "S", na.rm = TRUE)
number_newly_changed_to_I <- sum(before %in% c("S", "R") & after == "I", na.rm = TRUE)
number_newly_changed_to_R <- sum(before %in% c("S", "I") & after == "R", na.rm = TRUE)
# totals
number_added_S <<- number_added_S + number_newly_added_S
number_added_I <<- number_added_I + number_newly_added_I
number_added_R <<- number_added_R + number_newly_added_R
number_changed_to_S <<- number_changed_to_S + number_newly_changed_to_S
number_changed_to_I <<- number_changed_to_I + number_newly_changed_to_I
number_changed_to_R <<- number_changed_to_R + number_newly_changed_to_R
number_affected_rows <<- unique(c(number_affected_rows, rows))
# will be reset at start of every rule
changed_results <<- changed_results +
number_newly_added_S +
number_newly_added_I +
number_newly_added_R +
number_newly_changed_to_S +
number_newly_changed_to_I +
number_newly_changed_to_R
if (verbose == TRUE) {
old <- as.data.frame(tbl_bak, stringsAsFactors = FALSE)[rows,]
new <- as.data.frame(tbl, stringsAsFactors = FALSE)[rows,]
MOs <- as.data.frame(tbl_original, stringsAsFactors = FALSE)[rows, col_mo][[1]]
for (i in 1:length(cols)) {
verbose_new <- data.frame(row = rows,
col = cols[i],
mo = MOs,
mo_fullname = "",
old = as.character(old[, cols[i]]),
new = as.character(new[, cols[i]]),
rule_source = strip_style(rule[1]),
rule_group = strip_style(rule[2]),
stringsAsFactors = FALSE)
colnames(verbose_new) <- c("row", "col", "mo", "mo_fullname", "old", "new", "rule_source", "rule_group")
verbose_info <<- rbind(verbose_info, verbose_new)
}
}
}
}
na.rm <- function(col) {
if (is.null(col)) {
""
} else {
col
}
}
# save original table
tbl_original <- tbl
tbl_bak <- tbl
# join to microorganisms data set
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))) %>%
as.data.frame(stringsAsFactors = FALSE)
if (info == TRUE) {
cat("\nRules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)\n")
}
# since ampicillin ^= amoxicillin, get the first from the latter (not in original EUCAST table)
if (!is.null(ampi) & !is.null(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 (is.null(ampi) & !is.null(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)
carbapenems <- c(erta, imip, mero)
aminopenicillins <- c(ampi, amox)
ureidopenicillins <- c(pipe, pita, azlo, mezl)
fluoroquinolones <- c(oflo, cipr, norf, levo, moxi)
all_betalactam <- c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, amcl, oxac, clox, peni)
if (any(c("all", "breakpoints") %in% rules)) {
# BREAKPOINTS -------------------------------------------------------------
if (info == TRUE) {
cat(bold(paste0('\nEUCAST Clinical Breakpoints (v', EUCAST_VERSION_BREAKPOINTS, ')\n')))
}
rule_group <- "Breakpoints"
# Enterobacteriales (Order) ----
rule <- 'Enterobacteriales (Order)'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$order == 'Enterobacteriales'
& tbl[, ampi] == 'S'),
cols = amox)
}
if (!is.null(ampi)) {
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$order == 'Enterobacteriales'
& tbl[, ampi] == 'I'),
cols = amox)
}
if (!is.null(ampi)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$order == 'Enterobacteriales'
& tbl[, ampi] == 'R'),
cols = amox)
}
if (info == TRUE) {
txt_ok()
}
# Staphylococcus ----
rule <- italic('Staphylococcus')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(peni) & !is.null(cfox)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, peni] == 'S'
& tbl[, cfox] == 'S'),
cols = c(ampi, amox, pipe, tica))
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, peni] == 'R'
& tbl[, cfox] == 'S'),
cols = c(oxac, clox))
}
if (!is.null(cfox)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, cfox] == 'R'),
cols = all_betalactam)
}
if (!is.null(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Staphylococcus saprophyticus"
& tbl[, ampi] == 'S'),
cols = c(amox, amcl, pipe, pita))
}
if (!is.null(cfox)) {
# inferred from cefoxitin
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, cfox] == 'S'),
cols = c(carbapenems, cephalosporins[cephalosporins != na.rm(cfta)]))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, cfox] == 'I'),
cols = c(carbapenems, cephalosporins[cephalosporins != na.rm(cfta)]))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, cfox] == 'R'),
cols = c(carbapenems, cephalosporins[cephalosporins != na.rm(cfta)]))
}
if (!is.null(norf)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, norf] == 'S'),
cols = c(cipr, levo, moxi, oflo))
}
if (!is.null(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, eryt] == 'S'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, eryt] == 'I'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, eryt] == 'R'),
cols = c(azit, clar, roxi))
}
if (!is.null(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
& tbl[, tetr] == 'S'),
cols = c(doxy, mino))
}
if (info == TRUE) {
txt_ok()
}
# Enterococcus ----
rule <- italic('Enterococcus')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(ampi)) { # penicillin group
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Enterococcus faecium"
& tbl[, ampi] == 'R'),
cols = all_betalactam)
}
if (!is.null(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, ampi] == 'S'),
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, ampi] == 'I'),
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, ampi] == 'R'),
cols = c(amox, amcl, pipe, pita))
}
if (!is.null(norf)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, norf] == 'S'),
cols = c(cipr, levo))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, norf] == 'I'),
cols = c(cipr, levo))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, norf] == 'R'),
cols = c(cipr, levo))
}
if (info == TRUE) {
txt_ok()
}
# Streptococcus groups A, B, C, G----
rule <- paste(italic('Streptococcus'), 'groups A, B, C, G')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, peni] == 'S'),
cols = c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, clox, amcl))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, peni] == 'I'),
cols = c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, clox, amcl))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, peni] == 'R'),
cols = c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, clox, amcl))
}
if (!is.null(norf)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, norf] == 'S'),
cols = c(levo, moxi))
}
if (!is.null(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, eryt] == 'S'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, eryt] == 'I'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, eryt] == 'R'),
cols = c(azit, clar, roxi))
}
if (!is.null(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
& tbl[, tetr] == 'S'),
cols = c(doxy, mino))
}
if (info == TRUE) {
txt_ok()
}
# Streptococcus pneumoniae ----
rule <- italic('Streptococcus pneumoniae')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, peni] == 'S'),
cols = c(ampi, amox, amcl, pipe, pita))
}
if (!is.null(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, ampi] == 'S'),
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, ampi] == 'I'),
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, ampi] == 'R'),
cols = c(amox, amcl, pipe, pita))
}
if (!is.null(norf)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, norf] == 'S'),
cols = c(levo, moxi))
}
if (!is.null(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, eryt] == 'S'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, eryt] == 'I'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, eryt] == 'R'),
cols = c(azit, clar, roxi))
}
if (!is.null(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, tetr] == 'S'),
cols = c(doxy, mino))
}
if (info == TRUE) {
txt_ok()
}
# Viridans group streptococci ----
rule <- 'Viridans group streptococci'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
viridans_group <- c("anginosus", "australis", "bovis", "constellatus", "cristatus",
"equinus", "gallolyticus", "gordonii", "infantarius", "infantis",
"intermedius", "mitis", "mutans", "oligofermentans", "oralis",
"parasanguinis", "peroris", "pseudopneumoniae", "salivarius",
"sanguinis", "sinensis", "sobrinus", "thermophilus", "vestibularis")
if (!is.null(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
& tbl[, peni] == 'S'),
cols = c(ampi, amox, amcl, pipe, pita))
}
if (!is.null(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
& tbl[, ampi] == 'S'),
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
& tbl[, ampi] == 'I'),
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
& tbl[, ampi] == 'R'),
cols = c(amox, amcl, pipe, pita))
}
if (info == TRUE) {
txt_ok()
}
# Haemophilus influenzae ----
rule <- italic('Haemophilus influenzae')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, ampi] == 'S'),
cols = c(amox, pipe))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, ampi] == 'I'),
cols = c(amox, pipe))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, ampi] == 'R'),
cols = c(amox, pipe))
}
if (!is.null(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, peni] == 'S'),
cols = c(ampi, amox, amcl, pipe, pita))
}
if (!is.null(amcl)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, amcl] == 'S'),
cols = pita)
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, amcl] == 'I'),
cols = pita)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, amcl] == 'R'),
cols = pita)
}
if (!is.null(nali)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, nali] == 'S'),
cols = c(cipr, levo, moxi, oflo))
}
if (!is.null(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, tetr] == 'S'),
cols = c(doxy, mino))
}
if (info == TRUE) {
txt_ok()
}
# Moraxella catarrhalis ----
rule <- italic('Moraxella catarrhalis')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(amcl)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, amcl] == 'S'),
cols = pita)
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, amcl] == 'I'),
cols = pita)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, amcl] == 'R'),
cols = pita)
}
if (!is.null(nali)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, nali] == 'S'),
cols = c(cipr, levo, moxi, oflo))
}
if (!is.null(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, eryt] == 'S'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, eryt] == 'I'),
cols = c(azit, clar, roxi))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, eryt] == 'R'),
cols = c(azit, clar, roxi))
}
if (!is.null(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
& tbl[, tetr] == 'S'),
cols = c(doxy, mino))
}
if (info == TRUE) {
txt_ok()
}
# Anaerobic Gram positives ----
rule <- 'Anaerobic Gram positives'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium",
"Cutibacterium", # new name of Propionibacterium
"Bifidobacterium", "Eggerthella", "Eubacterium",
"Lactobacillus ", "Actinomyces")
& tbl[, peni] == 'S'),
cols = c(ampi, amox, pipe, pita, tica))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium",
"Cutibacterium", # new name of Propionibacterium
"Bifidobacterium", "Eggerthella", "Eubacterium",
"Lactobacillus ", "Actinomyces")
& tbl[, peni] == 'I'),
cols = c(ampi, amox, pipe, pita, tica))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium",
"Cutibacterium", # new name of Propionibacterium
"Bifidobacterium", "Eggerthella", "Eubacterium",
"Lactobacillus ", "Actinomyces")
& tbl[, peni] == 'R'),
cols = c(ampi, amox, pipe, pita, tica))
}
if (info == TRUE) {
txt_ok()
}
# Anaerobic Gram negatives ----
rule <- 'Anaerobic Gram negatives'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas",
"Fusobacterium", "Bilophila ", "Mobiluncus")
& tbl[, peni] == 'S'),
cols = c(ampi, amox, pipe, pita, tica))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas",
"Fusobacterium", "Bilophila ", "Mobiluncus")
& tbl[, peni] == 'I'),
cols = c(ampi, amox, pipe, pita, tica))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas",
"Fusobacterium", "Bilophila ", "Mobiluncus")
& tbl[, peni] == 'R'),
cols = c(ampi, amox, pipe, pita, tica))
}
if (info == TRUE) {
txt_ok()
}
# Pasteurella multocida ----
rule <- italic('Pasteurella multocida')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Pasteurella multocida"
& tbl[, peni] == 'S'),
cols = c(ampi, amox))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Pasteurella multocida"
& tbl[, peni] == 'I'),
cols = c(ampi, amox))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Pasteurella multocida"
& tbl[, peni] == 'R'),
cols = c(ampi, amox))
}
if (info == TRUE) {
txt_ok()
}
# Campylobacter jejuni and coli ----
rule <- paste(italic('Campylobacter jejuni'), 'and', italic('C. coli'))
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, eryt] == 'S'),
cols = c(azit, clar))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, eryt] == 'I'),
cols = c(azit, clar))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, eryt] == 'R'),
cols = c(azit, clar))
}
if (!is.null(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, tetr] == 'S'),
cols = doxy)
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, tetr] == 'I'),
cols = doxy)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, tetr] == 'R'),
cols = doxy)
}
if (info == TRUE) {
txt_ok()
}
# Aerococcus sanguinicola/urinae ----
rule <- paste(italic('Aerococcus sanguinicola'), 'and', italic('A. urinae'))
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(norf)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, norf] == 'S'),
cols = fluoroquinolones)
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, norf] == 'I'),
cols = fluoroquinolones)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, norf] == 'R'),
cols = fluoroquinolones)
}
if (!is.null(cipr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, cipr] == 'S'),
cols = levo)
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, cipr] == 'I'),
cols = levo)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, cipr] == 'R'),
cols = levo)
}
if (info == TRUE) {
txt_ok()
}
# Kingella kingae ----
rule <- italic('Kingella kingae')
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, peni] == 'S'),
cols = c(ampi, amox))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, peni] == 'I'),
cols = c(ampi, amox))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, peni] == 'R'),
cols = c(ampi, amox))
}
if (!is.null(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, eryt] == 'S'),
cols = c(azit, clar))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, eryt] == 'I'),
cols = c(azit, clar))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, eryt] == 'R'),
cols = c(azit, clar))
}
if (!is.null(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, tetr] == 'S'),
cols = doxy)
}
if (info == TRUE) {
txt_ok()
}
} # end of breakpoints
if (any(c("all", "expert") %in% rules)) {
# EXPERT RULES AND INTRINSIC RESISTANCE -----------------------------------
if (info == TRUE) {
cat(bold(paste0('\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v', EUCAST_VERSION_EXPERT_RULES, ')\n')))
}
rule_group <- "Expert Rules"
# Table 1: Intrinsic resistance in Enterobacteriaceae ----
rule <- paste('Table 1: Intrinsic resistance in', italic('Enterobacteriaceae'))
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# Intrinsic R for this group
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$family == 'Enterobacteriaceae'),
cols = c(peni, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line))
# Citrobacter
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)'),
cols = c(aminopenicillins, tica))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)'),
cols = c(aminopenicillins, amcl, czol, cfox))
# Enterobacter
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Enterobacter cloacae'),
cols = c(aminopenicillins, amcl, czol, cfox))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Enterobacter aerogenes'),
cols = c(aminopenicillins, amcl, czol, cfox))
# Escherichia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Escherichia hermanni'),
cols = c(aminopenicillins, tica))
# Hafnia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Hafnia alvei'),
cols = c(aminopenicillins, amcl, czol, cfox))
# Klebsiella
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Klebsiella'),
cols = c(aminopenicillins, tica))
# Morganella / Proteus
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Morganella morganii'),
cols = c(aminopenicillins, amcl, czol, tetracyclines, polymyxins, nitr))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Proteus mirabilis'),
cols = c(tetracyclines, tige, polymyxins, nitr))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Proteus penneri'),
cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Proteus vulgaris'),
cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr))
# Providencia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Providencia rettgeri'),
cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Providencia stuartii'),
cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr))
# Raoultella
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Raoultella'),
cols = c(aminopenicillins, tica))
# Serratia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Serratia marcescens'),
cols = c(aminopenicillins, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != na.rm(mino)], polymyxins, nitr))
# Yersinia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Yersinia enterocolitica'),
cols = c(aminopenicillins, amcl, tica, czol, cfox))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Yersinia pseudotuberculosis'),
cols = c(poly, coli))
if (info == TRUE) {
txt_ok()
}
# Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria ----
rule <- 'Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# Intrinsic R for this group
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c('Achromobacter',
'Acinetobacter',
'Alcaligenes',
'Bordatella',
'Burkholderia',
'Elizabethkingia',
'Flavobacterium',
'Ochrobactrum',
'Pseudomonas',
'Stenotrophomonas')),
cols = c(peni, cfox, cfur, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line))
# Acinetobacter
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Acinetobacter (baumannii|pittii|nosocomialis|calcoaceticus)'),
cols = c(aminopenicillins, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, tetracyclines[tetracyclines != na.rm(mino)]))
# Achromobacter
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Achromobacter (xylosoxydans|xylosoxidans)'),
cols = c(aminopenicillins, czol, cfot, cftr, erta))
# Burkholderia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
# the 'Burkholderia cepacia complex' are all these species: (PMID 16217180)
rows = which(tbl$fullname %like% '^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis)'),
cols = c(aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosides, trim, fosf, polymyxins))
# Elizabethkingia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Elizabethkingia meningoseptic(a|um)'),
cols = c(aminopenicillins, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxins))
# Ochrobactrum
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Ochrobactrum anthropi'),
cols = c(aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
# Pseudomonas
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Pseudomonas aeruginosa'),
cols = c(aminopenicillins, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige))
# Stenotrophomonas
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
cols = c(aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosides, trim, fosf, tetr))
if (info == TRUE) {
txt_ok()
}
# Table 3: Intrinsic resistance in other Gram-negative bacteria ----
rule <- 'Table 3: Intrinsic resistance in other Gram-negative bacteria'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# Intrinsic R for this group
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c('Haemophilus',
'Moraxella',
'Neisseria',
'Campylobacter')),
cols = c(glycopeptides, linc, dapt, line))
# Haemophilus
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Haemophilus influenzae'),
cols = c(fusi, streptogramins))
# Moraxella
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Moraxella catarrhalis'),
cols = trim)
# Neisseria
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Neisseria'),
cols = trim)
# Campylobacter
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Campylobacter fetus'),
cols = c(fusi, streptogramins, trim, nali))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Campylobacter (jejuni|coli)'),
cols = c(fusi, streptogramins, trim))
if (info == TRUE) {
txt_ok()
}
# Table 4: Intrinsic resistance in Gram-positive bacteria ----
rule <- 'Table 4: Intrinsic resistance in Gram-positive bacteria'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# Intrinsic R for this group
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$gramstain == "Gram positive"),
cols = c(aztr, polymyxins, nali))
# Staphylococcus
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Staphylococcus saprophyticus'),
cols = c(fusi, cfta, fosf, novo))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Staphylococcus (cohnii|xylosus)'),
cols = c(cfta, novo))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Staphylococcus capitis'),
cols = c(cfta, fosf))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)'),
cols = cfta)
# Streptococcus
# rule 4.5
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Streptococcus'),
cols = c(fusi, aminoglycosides))
# Enterococcus
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Enterococcus faecalis'),
cols = c(fusi, cfta, cephalosporins[cephalosporins != na.rm(cfta)], aminoglycosides, macrolides, clin, qida, trim, trsu))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Enterococcus (gallinarum|casseliflavus)'),
cols = c(fusi, cfta, cephalosporins[cephalosporins != na.rm(cfta)], aminoglycosides, macrolides, clin, qida, vanc, trim, trsu))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Enterococcus faecium'),
cols = c(fusi, cfta, cephalosporins[cephalosporins != na.rm(cfta)], aminoglycosides, macrolides, trim, trsu))
# Corynebacterium
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Corynebacterium'),
cols = fosf)
# Listeria
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Listeria monocytogenes'),
cols = c(cfta, cephalosporins[cephalosporins != na.rm(cfta)]))
# other
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c('Leuconostoc', 'Pediococcus')),
cols = glycopeptides)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Lactobacillus'),
cols = glycopeptides)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Clostridium (ramosum|innocuum)'),
cols = vanc)
if (info == TRUE) {
txt_ok()
}
# Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci ----
rule <- 'Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# rule 8.3
if (!is.null(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)'
& tbl[, peni] == 'S'),
cols = c(aminopenicillins, cephalosporins, carbapenems))
}
# rule 8.6
if (!is.null(ampi)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Enterococcus'
& tbl[, ampi] == 'R'),
cols = c(ureidopenicillins, carbapenems))
}
if (!is.null(amox)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Enterococcus'
& tbl[, amox] == 'R'),
cols = c(ureidopenicillins, carbapenems))
}
if (info == TRUE) {
txt_ok()
}
# Table 9: Interpretive rules for B-lactam agents and Gram-negative rods ----
rule <- 'Table 9: Interpretive rules for B-lactam agents and Gram-negative rods'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# rule 9.3
if (!is.null(tica) & !is.null(pipe)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$family == 'Enterobacteriaceae'
& tbl[, tica] == 'R'
& tbl[, pipe] == 'S'),
cols = pipe)
}
if (info == TRUE) {
txt_ok()
}
# Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria ----
rule <- 'Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# rule 10.2
# if (!is.null(ampi)) {
# you should know first if the are B-lactamase positive, so do not run for now
# edit_rsi(to = 'R',
# rule = c(rule_group, rule),
# rows = which(tbl$fullname %like% '^Haemophilus influenza'
# & tbl[, ampi] == 'R'),
# cols = c(ampi, amox, amcl, pipe, pita, cfur))
# }
if (info == TRUE) {
txt_ok()
}
# Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins ----
rule <- 'Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# rule 11.1
if (!is.null(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl[, eryt] == 'S'),
cols = c(azit, clar))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl[, eryt] == 'I'),
cols = c(azit, clar))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl[, eryt] == 'R'),
cols = c(azit, clar))
}
if (info == TRUE) {
txt_ok()
}
# Table 12: Interpretive rules for aminoglycosides ----
rule <- 'Table 12: Interpretive rules for aminoglycosides'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# rule 12.2
if (!is.null(tobr)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Staphylococcus'
& tbl[, tobr] == 'R'),
cols = c(kana, amik))
}
# rule 12.3
if (!is.null(gent)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Staphylococcus'
& tbl[, gent] == 'R'),
cols = aminoglycosides)
}
# rule 12.8
if (!is.null(gent) & !is.null(tobr)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$family == 'Enterobacteriaceae'
& tbl[, gent] == 'I'
& tbl[, tobr] == 'S'),
cols = gent)
}
# rule 12.9
if (!is.null(gent) & !is.null(tobr)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$family == 'Enterobacteriaceae'
& tbl[, tobr] == 'I'
& tbl[, gent] == 'R'),
cols = tobr)
}
if (info == TRUE) {
txt_ok()
}
# Table 13: Interpretive rules for quinolones ----
rule <- 'Table 13: Interpretive rules for quinolones'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
# rule 13.2
if (!is.null(moxi)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == 'Staphylococcus'
& tbl[, moxi] == 'R'),
cols = fluoroquinolones)
}
# rule 13.4
if (!is.null(moxi)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Streptococcus pneumoniae'
& tbl[, moxi] == 'R'),
cols = fluoroquinolones)
}
# rule 13.5
if (!is.null(cipr)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$family == 'Enterobacteriaceae'
& tbl[, cipr] == 'R'),
cols = fluoroquinolones)
}
# rule 13.8
if (!is.null(cipr)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Neisseria gonorrhoeae'
& tbl[, cipr] == 'R'),
cols = fluoroquinolones)
}
if (info == TRUE) {
txt_ok()
}
} # end of expert rules
if (any(c("all", "other") %in% rules)) {
# OTHER RULES -------------------------------------------------------------
if (info == TRUE) {
cat(bold('\nOther rules\n'))
}
rule_group <- "Other rules"
rule <- 'Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(amcl)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl[, amcl] == 'R'),
cols = ampi)
}
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(pita)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl[, pita] == 'R'),
cols = pipe)
}
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(trsu)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl[, trsu] == 'R'),
cols = trim)
}
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl[, ampi] == 'S'),
cols = amcl)
}
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(pipe)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl[, pipe] == 'S'),
cols = pita)
}
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.null(trim)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl[, trim] == 'S'),
cols = trsu)
}
if (info == TRUE) {
txt_ok()
}
} # end of other rules
# restore old col_mo values if needed
# if (!is.null(col_mo_original)) {
# tbl_original[, col_mo] <- col_mo_original
# }
if (info == TRUE) {
if (verbose == TRUE) {
wouldve <- "would have "
} else {
wouldve <- ""
}
if (sum(number_added_S, number_added_I, number_added_R,
number_changed_to_S, number_changed_to_I, number_changed_to_R,
na.rm = TRUE) == 0) {
colour <- green # is function
} else {
colour <- blue # is function
}
decimal.mark <- getOption("OutDec")
big.mark <- ifelse(decimal.mark != ",", ",", ".")
formatnr <- function(x) {
format(x, big.mark = big.mark, decimal.mark = decimal.mark)
}
cat(bold(paste('\n=> EUCAST rules', paste0(wouldve, 'affected'),
number_affected_rows %>% length() %>% formatnr(),
'out of', nrow(tbl_original) %>% formatnr(),
'rows\n')))
total_added <- number_added_S + number_added_I + number_added_R
total_changed <- number_changed_to_S + number_changed_to_I + number_changed_to_R
cat(colour(paste0(" -> ", wouldve, "added ",
bold(formatnr(total_added), "test results"),
if(total_added > 0)
paste0(" (", formatnr(number_added_S), " as S; ",
formatnr(number_added_I), " as I; ",
formatnr(number_added_R), " as R)"),
"\n")))
cat(colour(paste0(" -> ", wouldve, "changed ",
bold(formatnr(total_changed), "test results"),
if(total_changed > 0)
paste0(" (", formatnr(number_changed_to_S), " to S; ",
formatnr(number_changed_to_I), " to I; ",
formatnr(number_changed_to_R), " to R)"),
"\n")))
if (verbose == FALSE) {
cat(paste("Use", bold("verbose = TRUE"), "to get a data.frame with all specified edits.\n"))
}
}
if (verbose == TRUE) {
suppressWarnings(
suppressMessages(
verbose_info$mo_fullname <- mo_fullname(verbose_info$mo)
)
)
verbose_info <- verbose_info %>%
filter(!is.na(new) & !identical(old, new)) %>%
arrange(row)
return(verbose_info)
}
tbl_original
}
#' @rdname eucast_rules
#' @export
EUCAST_rules <- function(...) {
.Deprecated("eucast_rules")
eucast_rules(...)
}
#' @rdname eucast_rules
#' @export
interpretive_reading <- function(...) {
.Deprecated("eucast_rules")
eucast_rules(...)
}
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