mirror of https://github.com/msberends/AMR.git
1843 lines
76 KiB
R
Executable File
1843 lines
76 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitab.io/AMR. #
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# ==================================================================== #
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#' EUCAST rules
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#'
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#' 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.
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#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
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#' @param info print progress
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#' @param rules a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}
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#' @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
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#' @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
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#' @param ... parameters that are passed on to \code{eucast_rules}
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#' @inheritParams first_isolate
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#' @section Antibiotics:
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#' To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab}} 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.
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#'
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#' Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
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#'
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#' \strong{amcl}: amoxicillin+clavulanic acid (\emph{J01CR02}),
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#' \strong{amik}: amikacin (\emph{J01GB06}),
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#' \strong{amox}: amoxicillin (\emph{J01CA04}),
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#' \strong{ampi}: ampicillin (\emph{J01CA01}),
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#' \strong{azit}: azithromycin (\emph{J01FA10}),
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#' \strong{azlo}: azlocillin (\emph{J01CA09}),
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#' \strong{aztr}: aztreonam (\emph{J01DF01}),
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#' \strong{cefa}: cefaloridine (\emph{J01DB02}),
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#' \strong{cfep}: cefepime (\emph{J01DE01}),
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#' \strong{cfot}: cefotaxime (\emph{J01DD01}),
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#' \strong{cfox}: cefoxitin (\emph{J01DC01}),
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#' \strong{cfra}: cefradine (\emph{J01DB09}),
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#' \strong{cfta}: ceftazidime (\emph{J01DD02}),
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#' \strong{cftr}: ceftriaxone (\emph{J01DD04}),
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#' \strong{cfur}: cefuroxime (\emph{J01DC02}),
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#' \strong{chlo}: chloramphenicol (\emph{J01BA01}),
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#' \strong{cipr}: ciprofloxacin (\emph{J01MA02}),
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#' \strong{clar}: clarithromycin (\emph{J01FA09}),
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#' \strong{clin}: clindamycin (\emph{J01FF01}),
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#' \strong{clox}: flucloxacillin (\emph{J01CF05}),
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#' \strong{coli}: colistin (\emph{J01XB01}),
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#' \strong{czol}: cefazolin (\emph{J01DB04}),
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#' \strong{dapt}: daptomycin (\emph{J01XX09}),
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#' \strong{doxy}: doxycycline (\emph{J01AA02}),
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#' \strong{erta}: ertapenem (\emph{J01DH03}),
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#' \strong{eryt}: erythromycin (\emph{J01FA01}),
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#' \strong{fosf}: fosfomycin (\emph{J01XX01}),
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#' \strong{fusi}: fusidic acid (\emph{J01XC01}),
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#' \strong{gent}: gentamicin (\emph{J01GB03}),
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#' \strong{imip}: imipenem (\emph{J01DH51}),
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#' \strong{kana}: kanamycin (\emph{J01GB04}),
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#' \strong{levo}: levofloxacin (\emph{J01MA12}),
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#' \strong{linc}: lincomycin (\emph{J01FF02}),
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#' \strong{line}: linezolid (\emph{J01XX08}),
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#' \strong{mero}: meropenem (\emph{J01DH02}),
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#' \strong{mezl}: mezlocillin (\emph{J01CA10}),
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#' \strong{mino}: minocycline (\emph{J01AA08}),
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#' \strong{moxi}: moxifloxacin (\emph{J01MA14}),
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#' \strong{nali}: nalidixic acid (\emph{J01MB02}),
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#' \strong{neom}: neomycin (\emph{J01GB05}),
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#' \strong{neti}: netilmicin (\emph{J01GB07}),
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#' \strong{nitr}: nitrofurantoin (\emph{J01XE01}),
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#' \strong{norf}: norfloxacin (\emph{J01MA06}),
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#' \strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
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#' \strong{oflo}: ofloxacin (\emph{J01MA01}),
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#' \strong{peni}: penicillin (\emph{J01RA01}),
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#' \strong{pipe}: piperacillin (\emph{J01CA12}),
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#' \strong{pita}: piperacillin+tazobactam (\emph{J01CR05}),
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#' \strong{poly}: polymyxin B (\emph{J01XB02}),
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#' \strong{pris}: pristinamycin (\emph{J01FG01}),
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#' \strong{qida}: quinupristin/dalfopristin (\emph{J01FG02}),
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#' \strong{rifa}: rifampicin (\emph{J04AB02}),
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#' \strong{roxi}: roxithromycin (\emph{J01FA06}),
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#' \strong{siso}: sisomicin (\emph{J01GB08}),
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#' \strong{teic}: teicoplanin (\emph{J01XA02}),
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#' \strong{tetr}: tetracycline (\emph{J01AA07}),
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#' \strong{tica}: ticarcillin (\emph{J01CA13}),
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#' \strong{tige}: tigecycline (\emph{J01AA12}),
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#' \strong{tobr}: tobramycin (\emph{J01GB01}),
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#' \strong{trim}: trimethoprim (\emph{J01EA01}),
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#' \strong{trsu}: sulfamethoxazole and trimethoprim (\emph{J01EE01}),
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#' \strong{vanc}: vancomycin (\emph{J01XA01}).
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#' @keywords interpretive eucast reading resistance
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#' @rdname eucast_rules
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#' @export
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#' @importFrom dplyr %>% select pull mutate_at vars
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#' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic strip_style
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#' @return The input of \code{tbl}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with verbose info.
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#' @source
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#' \itemize{
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#' \item{
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#' EUCAST Expert Rules. Version 2.0, 2012. \cr
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#' Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60. \cr
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#' \url{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
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#' }
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#' \item{
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#' EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \cr
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#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
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#' }
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#' \item{
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#' EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 8.1, 2018. \cr
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#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_8.1_Breakpoint_Tables.xlsx}
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#' }
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#' }
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' a <- eucast_rules(septic_patients)
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#'
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#' a <- data.frame(mo = c("Staphylococcus aureus",
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#' "Enterococcus faecalis",
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#' "Escherichia coli",
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#' "Klebsiella pneumoniae",
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#' "Pseudomonas aeruginosa"),
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#' vanc = "-", # Vancomycin
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#' amox = "-", # Amoxicillin
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#' coli = "-", # Colistin
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#' cfta = "-", # Ceftazidime
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#' cfur = "-", # Cefuroxime
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#' peni = "S", # Benzylpenicillin
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#' cfox = "S", # Cefoxitin
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#' stringsAsFactors = FALSE)
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#'
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#' a
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#' # mo vanc amox coli cfta cfur peni cfox
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#' # 1 Staphylococcus aureus - - - - - S S
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#' # 2 Enterococcus faecalis - - - - - S S
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#' # 3 Escherichia coli - - - - - S S
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#' # 4 Klebsiella pneumoniae - - - - - S S
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#' # 5 Pseudomonas aeruginosa - - - - - S S
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#'
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#' b <- eucast_rules(a, "mo") # 18 results are forced as R or S
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#'
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#' b
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#' # mo vanc amox coli cfta cfur peni cfox
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#' # 1 Staphylococcus aureus - S R R S S S
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#' # 2 Enterococcus faecalis - - R R R S R
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#' # 3 Escherichia coli R - - - - R S
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#' # 4 Klebsiella pneumoniae R R - - - R S
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#' # 5 Pseudomonas aeruginosa R R - - R R R
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eucast_rules <- function(tbl,
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col_mo = NULL,
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info = TRUE,
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rules = c("breakpoints", "expert", "other", "all"),
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verbose = FALSE,
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amcl = guess_ab(),
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amik = guess_ab(),
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amox = guess_ab(),
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ampi = guess_ab(),
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azit = guess_ab(),
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azlo = guess_ab(),
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aztr = guess_ab(),
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cefa = guess_ab(),
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cfep = guess_ab(),
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cfot = guess_ab(),
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cfox = guess_ab(),
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cfra = guess_ab(),
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cfta = guess_ab(),
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cftr = guess_ab(),
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cfur = guess_ab(),
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chlo = guess_ab(),
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cipr = guess_ab(),
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clar = guess_ab(),
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clin = guess_ab(),
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clox = guess_ab(),
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coli = guess_ab(),
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czol = guess_ab(),
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dapt = guess_ab(),
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doxy = guess_ab(),
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erta = guess_ab(),
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eryt = guess_ab(),
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fosf = guess_ab(),
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fusi = guess_ab(),
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gent = guess_ab(),
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imip = guess_ab(),
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kana = guess_ab(),
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levo = guess_ab(),
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linc = guess_ab(),
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line = guess_ab(),
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mero = guess_ab(),
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mezl = guess_ab(),
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mino = guess_ab(),
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moxi = guess_ab(),
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nali = guess_ab(),
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neom = guess_ab(),
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neti = guess_ab(),
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nitr = guess_ab(),
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norf = guess_ab(),
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novo = guess_ab(),
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oflo = guess_ab(),
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oxac = guess_ab(),
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peni = guess_ab(),
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pipe = guess_ab(),
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pita = guess_ab(),
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poly = guess_ab(),
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pris = guess_ab(),
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qida = guess_ab(),
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rifa = guess_ab(),
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roxi = guess_ab(),
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siso = guess_ab(),
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teic = guess_ab(),
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tetr = guess_ab(),
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tica = guess_ab(),
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tige = guess_ab(),
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tobr = guess_ab(),
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trim = guess_ab(),
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trsu = guess_ab(),
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vanc = guess_ab()) {
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EUCAST_VERSION_BREAKPOINTS <- "8.1, 2018"
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EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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if (!is.data.frame(tbl)) {
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stop("`tbl` must be a data frame.", call. = FALSE)
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}
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# try to find columns based on type
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# -- mo
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if (is.null(col_mo) & "mo" %in% lapply(tbl, class)) {
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col_mo <- colnames(tbl)[lapply(tbl, class) == "mo"][1]
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message(blue(paste0("NOTE: Using column `", bold(col_mo), "` as input for `col_mo`.")))
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}
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if (is.null(col_mo)) {
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stop("`col_mo` must be set.", call. = FALSE)
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}
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if (!all(rules %in% c("breakpoints", "expert", "other", "all"))) {
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stop("Parameter `rules` must be one or more of: 'breakpoints', 'expert', 'other', 'all'.")
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}
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if (is.null(col_mo)) {
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stop("Parameter `col_mo` must be set")
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}
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warned <- FALSE
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changed_results <- 0
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txt_error <- function() { cat("", bgRed(black(" ERROR ")), "\n") }
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txt_warning <- function() { if (warned == FALSE) { cat("", bgYellow(black(" WARNING ")), "\n") }; warned <<- TRUE }
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txt_ok <- function() {
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if (warned == FALSE) {
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if (changed_results > 0) {
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if (changed_results == 1) {
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cat(blue(" (1 change)\n"))
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} else {
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cat(blue(paste0(" (", changed_results, " changes)\n")))
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}
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} else {
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cat(green(" (no changes)\n"))
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}
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warned <<- FALSE
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}
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}
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# check columns
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if (identical(amcl, as.name("guess_ab"))) { amcl <- guess_ab(tbl, "amcl", verbose = verbose) }
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if (identical(amik, as.name("guess_ab"))) { amik <- guess_ab(tbl, "amik", verbose = verbose) }
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if (identical(amox, as.name("guess_ab"))) { amox <- guess_ab(tbl, "amox", verbose = verbose) }
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if (identical(ampi, as.name("guess_ab"))) { ampi <- guess_ab(tbl, "ampi", verbose = verbose) }
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if (identical(azit, as.name("guess_ab"))) { azit <- guess_ab(tbl, "azit", verbose = verbose) }
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if (identical(azlo, as.name("guess_ab"))) { azlo <- guess_ab(tbl, "azlo", verbose = verbose) }
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if (identical(aztr, as.name("guess_ab"))) { aztr <- guess_ab(tbl, "aztr", verbose = verbose) }
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if (identical(cefa, as.name("guess_ab"))) { cefa <- guess_ab(tbl, "cefa", verbose = verbose) }
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if (identical(cfep, as.name("guess_ab"))) { cfep <- guess_ab(tbl, "cfep", verbose = verbose) }
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if (identical(cfot, as.name("guess_ab"))) { cfot <- guess_ab(tbl, "cfot", verbose = verbose) }
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if (identical(cfox, as.name("guess_ab"))) { cfox <- guess_ab(tbl, "cfox", verbose = verbose) }
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if (identical(cfra, as.name("guess_ab"))) { cfra <- guess_ab(tbl, "cfra", verbose = verbose) }
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if (identical(cfta, as.name("guess_ab"))) { cfta <- guess_ab(tbl, "cfta", verbose = verbose) }
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if (identical(cftr, as.name("guess_ab"))) { cftr <- guess_ab(tbl, "cftr", verbose = verbose) }
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if (identical(cfur, as.name("guess_ab"))) { cfur <- guess_ab(tbl, "cfur", verbose = verbose) }
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if (identical(chlo, as.name("guess_ab"))) { chlo <- guess_ab(tbl, "chlo", verbose = verbose) }
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if (identical(cipr, as.name("guess_ab"))) { cipr <- guess_ab(tbl, "cipr", verbose = verbose) }
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if (identical(clar, as.name("guess_ab"))) { clar <- guess_ab(tbl, "clar", verbose = verbose) }
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if (identical(clin, as.name("guess_ab"))) { clin <- guess_ab(tbl, "clin", verbose = verbose) }
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if (identical(clox, as.name("guess_ab"))) { clox <- guess_ab(tbl, "clox", verbose = verbose) }
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if (identical(coli, as.name("guess_ab"))) { coli <- guess_ab(tbl, "coli", verbose = verbose) }
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if (identical(czol, as.name("guess_ab"))) { czol <- guess_ab(tbl, "czol", verbose = verbose) }
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if (identical(dapt, as.name("guess_ab"))) { dapt <- guess_ab(tbl, "dapt", verbose = verbose) }
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if (identical(doxy, as.name("guess_ab"))) { doxy <- guess_ab(tbl, "doxy", verbose = verbose) }
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if (identical(erta, as.name("guess_ab"))) { erta <- guess_ab(tbl, "erta", verbose = verbose) }
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if (identical(eryt, as.name("guess_ab"))) { eryt <- guess_ab(tbl, "eryt", verbose = verbose) }
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if (identical(fosf, as.name("guess_ab"))) { fosf <- guess_ab(tbl, "fosf", verbose = verbose) }
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if (identical(fusi, as.name("guess_ab"))) { fusi <- guess_ab(tbl, "fusi", verbose = verbose) }
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if (identical(gent, as.name("guess_ab"))) { gent <- guess_ab(tbl, "gent", verbose = verbose) }
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if (identical(imip, as.name("guess_ab"))) { imip <- guess_ab(tbl, "imip", verbose = verbose) }
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if (identical(kana, as.name("guess_ab"))) { kana <- guess_ab(tbl, "kana", verbose = verbose) }
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if (identical(levo, as.name("guess_ab"))) { levo <- guess_ab(tbl, "levo", verbose = verbose) }
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if (identical(linc, as.name("guess_ab"))) { linc <- guess_ab(tbl, "linc", verbose = verbose) }
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if (identical(line, as.name("guess_ab"))) { line <- guess_ab(tbl, "line", verbose = verbose) }
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if (identical(mero, as.name("guess_ab"))) { mero <- guess_ab(tbl, "mero", verbose = verbose) }
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if (identical(mezl, as.name("guess_ab"))) { mezl <- guess_ab(tbl, "mezl", verbose = verbose) }
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if (identical(mino, as.name("guess_ab"))) { mino <- guess_ab(tbl, "mino", verbose = verbose) }
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if (identical(moxi, as.name("guess_ab"))) { moxi <- guess_ab(tbl, "moxi", verbose = verbose) }
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if (identical(nali, as.name("guess_ab"))) { nali <- guess_ab(tbl, "nali", verbose = verbose) }
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if (identical(neom, as.name("guess_ab"))) { neom <- guess_ab(tbl, "neom", verbose = verbose) }
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if (identical(neti, as.name("guess_ab"))) { neti <- guess_ab(tbl, "neti", verbose = verbose) }
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if (identical(nitr, as.name("guess_ab"))) { nitr <- guess_ab(tbl, "nitr", verbose = verbose) }
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if (identical(norf, as.name("guess_ab"))) { norf <- guess_ab(tbl, "norf", verbose = verbose) }
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if (identical(novo, as.name("guess_ab"))) { novo <- guess_ab(tbl, "novo", verbose = verbose) }
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if (identical(oflo, as.name("guess_ab"))) { oflo <- guess_ab(tbl, "oflo", verbose = verbose) }
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if (identical(oxac, as.name("guess_ab"))) { oxac <- guess_ab(tbl, "oxac", verbose = verbose) }
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if (identical(peni, as.name("guess_ab"))) { peni <- guess_ab(tbl, "peni", verbose = verbose) }
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if (identical(pipe, as.name("guess_ab"))) { pipe <- guess_ab(tbl, "pipe", verbose = verbose) }
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if (identical(pita, as.name("guess_ab"))) { pita <- guess_ab(tbl, "pita", verbose = verbose) }
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if (identical(poly, as.name("guess_ab"))) { poly <- guess_ab(tbl, "poly", verbose = verbose) }
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if (identical(pris, as.name("guess_ab"))) { pris <- guess_ab(tbl, "pris", verbose = verbose) }
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if (identical(qida, as.name("guess_ab"))) { qida <- guess_ab(tbl, "qida", verbose = verbose) }
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if (identical(rifa, as.name("guess_ab"))) { rifa <- guess_ab(tbl, "rifa", verbose = verbose) }
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if (identical(roxi, as.name("guess_ab"))) { roxi <- guess_ab(tbl, "roxi", verbose = verbose) }
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if (identical(siso, as.name("guess_ab"))) { siso <- guess_ab(tbl, "siso", verbose = verbose) }
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|
if (identical(teic, as.name("guess_ab"))) { teic <- guess_ab(tbl, "teic", verbose = verbose) }
|
|
if (identical(tetr, as.name("guess_ab"))) { tetr <- guess_ab(tbl, "tetr", verbose = verbose) }
|
|
if (identical(tica, as.name("guess_ab"))) { tica <- guess_ab(tbl, "tica", verbose = verbose) }
|
|
if (identical(tige, as.name("guess_ab"))) { tige <- guess_ab(tbl, "tige", verbose = verbose) }
|
|
if (identical(tobr, as.name("guess_ab"))) { tobr <- guess_ab(tbl, "tobr", verbose = verbose) }
|
|
if (identical(trim, as.name("guess_ab"))) { trim <- guess_ab(tbl, "trim", verbose = verbose) }
|
|
if (identical(trsu, as.name("guess_ab"))) { trsu <- guess_ab(tbl, "trsu", verbose = verbose) }
|
|
if (identical(vanc, as.name("guess_ab"))) { vanc <- guess_ab(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_changed <- 0
|
|
number_affected_rows <- integer(0)
|
|
verbose_info <- data.frame(rule_type = character(0),
|
|
rule_set = character(0),
|
|
force_to = character(0),
|
|
found = integer(0),
|
|
changed = integer(0),
|
|
target_columns = integer(0),
|
|
target_rows = integer(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 <- 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])))
|
|
number_changed <<- number_changed + sum(before != after, na.rm = TRUE)
|
|
number_affected_rows <<- unique(c(number_affected_rows, rows))
|
|
changed_results <<- changed_results + sum(before != after, na.rm = TRUE) # will be reset at start of every rule
|
|
|
|
if (verbose == TRUE) {
|
|
for (i in 1:length(cols)) {
|
|
# add new row for every affected column
|
|
verbose_new <- data.frame(rule_type = strip_style(rule[1]),
|
|
rule_set = strip_style(rule[2]),
|
|
force_to = to,
|
|
found = length(before),
|
|
changed = sum(before != after, na.rm = TRUE),
|
|
target_column = cols[i],
|
|
stringsAsFactors = FALSE)
|
|
verbose_new$target_rows <- list(unname(rows))
|
|
rownames(verbose_new) <- NULL
|
|
verbose_info <<- rbind(verbose_info, verbose_new)
|
|
}
|
|
|
|
}
|
|
}
|
|
}
|
|
na.rm <- function(col) {
|
|
if (is.null(col)) {
|
|
""
|
|
} else {
|
|
col
|
|
}
|
|
}
|
|
|
|
# save original table
|
|
tbl_original <- tbl
|
|
|
|
# join to microorganisms data set
|
|
tbl <- tbl %>%
|
|
mutate_at(vars(col_mo), as.mo) %>%
|
|
left_join_microorganisms(by = col_mo, suffix = c("_oldcols", "")) %>%
|
|
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(bgGreen("\n VERBOSE: transforming",
|
|
length(which(tbl[, amox] == "S" & !tbl[, ampi] %in% c("S", "I", "R"))),
|
|
"empty ampicillin fields to 'S' based on amoxicillin. "))
|
|
cat(bgGreen("\n VERBOSE: transforming",
|
|
length(which(tbl[, amox] == "I" & !tbl[, ampi] %in% c("S", "I", "R"))),
|
|
"empty ampicillin fields to 'I' based on amoxicillin. "))
|
|
cat(bgGreen("\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 (number_changed == 0) {
|
|
colour <- green
|
|
} else {
|
|
colour <- blue
|
|
}
|
|
decimal.mark <- getOption("OutDec")
|
|
big.mark <- ifelse(decimal.mark != ",", ",", ".")
|
|
cat(bold(paste('\n=> EUCAST rules', paste0(wouldve, 'affected'),
|
|
number_affected_rows %>% length() %>% format(big.mark = big.mark, decimal.mark = decimal.mark),
|
|
'out of', nrow(tbl_original) %>% format(big.mark = big.mark, decimal.mark = decimal.mark),
|
|
'rows ->',
|
|
colour(paste0(wouldve, 'changed'),
|
|
number_changed %>% format(big.mark = big.mark, decimal.mark = decimal.mark), 'test results.\n\n'))))
|
|
}
|
|
|
|
if (verbose == TRUE) {
|
|
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(...)
|
|
}
|