mirror of https://github.com/msberends/AMR.git
1771 lines
69 KiB
R
Executable File
1771 lines
69 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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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This package is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This R package is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License version 2.0 for more details. #
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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, 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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#' @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 = 'amcl',
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amik = 'amik',
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amox = 'amox',
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ampi = 'ampi',
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azit = 'azit',
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azlo = 'azlo',
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aztr = 'aztr',
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cefa = 'cefa',
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cfep = 'cfep',
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cfot = 'cfot',
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cfox = 'cfox',
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cfra = 'cfra',
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cfta = 'cfta',
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cftr = 'cftr',
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cfur = 'cfur',
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chlo = 'chlo',
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cipr = 'cipr',
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clar = 'clar',
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clin = 'clin',
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clox = 'clox',
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coli = 'coli',
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czol = 'czol',
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dapt = 'dapt',
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doxy = 'doxy',
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erta = 'erta',
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eryt = 'eryt',
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fosf = 'fosf',
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fusi = 'fusi',
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gent = 'gent',
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imip = 'imip',
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kana = 'kana',
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levo = 'levo',
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linc = 'linc',
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line = 'line',
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mero = 'mero',
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mezl = 'mezl',
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mino = 'mino',
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moxi = 'moxi',
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nali = 'nali',
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neom = 'neom',
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neti = 'neti',
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nitr = 'nitr',
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norf = 'norf',
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novo = 'novo',
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oflo = 'oflo',
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oxac = 'oxac',
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peni = 'peni',
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pipe = 'pipe',
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pita = 'pita',
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poly = 'poly',
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pris = 'pris',
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qida = 'qida',
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rifa = 'rifa',
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roxi = 'roxi',
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siso = 'siso',
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teic = 'teic',
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tetr = 'tetr',
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tica = 'tica',
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tige = 'tige',
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tobr = 'tobr',
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trim = 'trim',
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trsu = 'trsu',
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vanc = 'vanc') {
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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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col.list <- c(amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfra, cfep, cfot,
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cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli,
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czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana,
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levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr,
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novo, norf, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa,
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roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc)
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col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
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amcl <- col.list[amcl]
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amik <- col.list[amik]
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amox <- col.list[amox]
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ampi <- col.list[ampi]
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azit <- col.list[azit]
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azlo <- col.list[azlo]
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aztr <- col.list[aztr]
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cefa <- col.list[cefa]
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cfep <- col.list[cfep]
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cfot <- col.list[cfot]
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cfox <- col.list[cfox]
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cfra <- col.list[cfra]
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cfta <- col.list[cfta]
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cftr <- col.list[cftr]
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cfur <- col.list[cfur]
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chlo <- col.list[chlo]
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cipr <- col.list[cipr]
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clar <- col.list[clar]
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clin <- col.list[clin]
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clox <- col.list[clox]
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coli <- col.list[coli]
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czol <- col.list[czol]
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dapt <- col.list[dapt]
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doxy <- col.list[doxy]
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erta <- col.list[erta]
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eryt <- col.list[eryt]
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fosf <- col.list[fosf]
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fusi <- col.list[fusi]
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gent <- col.list[gent]
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imip <- col.list[imip]
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kana <- col.list[kana]
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levo <- col.list[levo]
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linc <- col.list[linc]
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line <- col.list[line]
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mero <- col.list[mero]
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mezl <- col.list[mezl]
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mino <- col.list[mino]
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moxi <- col.list[moxi]
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nali <- col.list[nali]
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neom <- col.list[neom]
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neti <- col.list[neti]
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nitr <- col.list[nitr]
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norf <- col.list[norf]
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novo <- col.list[novo]
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oflo <- col.list[oflo]
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oxac <- col.list[oxac]
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peni <- col.list[peni]
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pipe <- col.list[pipe]
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pita <- col.list[pita]
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poly <- col.list[poly]
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pris <- col.list[pris]
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qida <- col.list[qida]
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rifa <- col.list[rifa]
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roxi <- col.list[roxi]
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siso <- col.list[siso]
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teic <- col.list[teic]
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tetr <- col.list[tetr]
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tica <- col.list[tica]
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tige <- col.list[tige]
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tobr <- col.list[tobr]
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trim <- col.list[trim]
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trsu <- col.list[trsu]
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vanc <- col.list[vanc]
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amount_changed <- 0
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amount_affected_rows <- integer(0)
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verbose_info <- data.frame(rule_type = character(0),
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rule_set = character(0),
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force_to = character(0),
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found = integer(0),
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changed = integer(0),
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target_columns = integer(0),
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target_rows = integer(0),
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stringsAsFactors = FALSE)
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# helper function for editing the table
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edit_rsi <- function(to, rule, rows, cols) {
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cols <- unique(cols[!is.na(cols)])
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if (length(rows) > 0 & length(cols) > 0) {
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before <- as.character(unlist(as.list(tbl_original[rows, cols])))
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tryCatch(
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# insert into original table
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tbl_original[rows, cols] <<- to,
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warning = function(w) {
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if (w$message %like% 'invalid factor level') {
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warning('Value "', to, '" could not be applied to column(s) `', paste(cols, collapse = '`, `'), '` because this value is not an existing factor level.', call. = FALSE)
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} else {
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warning(w$message, call. = FALSE)
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}
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txt_warning()
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},
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error = function(e) {
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txt_error()
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stop(e, call. = FALSE)
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}
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)
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suppressMessages(
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suppressWarnings(
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tbl[rows, cols] <<- to
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))
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after <- as.character(unlist(as.list(tbl_original[rows, cols])))
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amount_changed <<- amount_changed + sum(before != after, na.rm = TRUE)
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amount_affected_rows <<- unique(c(amount_affected_rows, rows))
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changed_results <<- changed_results + sum(before != after, na.rm = TRUE) # will be reset at start of every rule
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if (verbose == TRUE) {
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for (i in 1:length(cols)) {
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# add new row for every affected column
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verbose_new <- data.frame(rule_type = strip_style(rule[1]),
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rule_set = strip_style(rule[2]),
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force_to = to,
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found = length(before),
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changed = sum(before != after, na.rm = TRUE),
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target_column = cols[i],
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stringsAsFactors = FALSE)
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verbose_new$target_rows <- list(unname(rows))
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rownames(verbose_new) <- NULL
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verbose_info <<- rbind(verbose_info, verbose_new)
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}
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}
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}
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}
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na.rm <- function(col) {
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if (is.na(col)) {
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""
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} else {
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col
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}
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}
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# save original table
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tbl_original <- tbl
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# join to microorganisms data set
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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.na(ampi) & !is.na(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.na(ampi) & !is.na(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.na(ampi)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$order == 'Enterobacteriales'
|
|
& tbl[, ampi] == 'S'),
|
|
cols = amox)
|
|
}
|
|
if (!is.na(ampi)) {
|
|
edit_rsi(to = 'I',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$order == 'Enterobacteriales'
|
|
& tbl[, ampi] == 'I'),
|
|
cols = amox)
|
|
}
|
|
if (!is.na(ampi)) {
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(peni) & !is.na(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.na(cfox)) {
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$genus == "Staphylococcus"
|
|
& tbl[, cfox] == 'R'),
|
|
cols = all_betalactam)
|
|
}
|
|
if (!is.na(ampi)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$fullname %like% "^Staphylococcus saprophyticus"
|
|
& tbl[, ampi] == 'S'),
|
|
cols = c(amox, amcl, pipe, pita))
|
|
}
|
|
if (!is.na(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$genus == "Staphylococcus"
|
|
& tbl[, cfox] == 'R'),
|
|
cols = c(carbapenems, cephalosporins[cephalosporins != na.rm(cfta)]))
|
|
}
|
|
if (!is.na(norf)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$genus == "Staphylococcus"
|
|
& tbl[, norf] == 'S'),
|
|
cols = c(cipr, levo, moxi, oflo))
|
|
}
|
|
if (!is.na(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$genus == "Staphylococcus"
|
|
& tbl[, eryt] == 'R'),
|
|
cols = c(azit, clar, roxi))
|
|
}
|
|
if (!is.na(tetr)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(ampi)) { # penicillin group
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$fullname %like% "^Enterococcus faecium"
|
|
& tbl[, ampi] == 'R'),
|
|
cols = all_betalactam)
|
|
}
|
|
if (!is.na(ampi)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(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$genus == "Enterococcus"
|
|
& tbl[, norf] == 'R'),
|
|
cols = c(cipr, levo))
|
|
}
|
|
if (info == TRUE) {
|
|
txt_ok()
|
|
}
|
|
# Streptococcus groups A, B, C, G----
|
|
rule <- paste(italic('Streptococcus'), 'groups A, B, C, G')
|
|
if (info == TRUE) {
|
|
warned <- FALSE
|
|
changed_results <- 0
|
|
cat(rule)
|
|
}
|
|
if (!is.na(peni)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(norf)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
|
|
& tbl[, norf] == 'S'),
|
|
cols = c(levo, moxi))
|
|
}
|
|
if (!is.na(eryt)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(tetr)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
|
|
& tbl[, tetr] == 'S'),
|
|
cols = c(doxy, mino))
|
|
}
|
|
if (info == TRUE) {
|
|
txt_ok()
|
|
}
|
|
# Streptococcus pneumoniae ----
|
|
rule <- italic('Streptococcus pneumoniae')
|
|
if (info == TRUE) {
|
|
warned <- FALSE
|
|
changed_results <- 0
|
|
cat(rule)
|
|
}
|
|
if (!is.na(peni)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
|
|
& tbl[, peni] == 'S'),
|
|
cols = c(ampi, amox, amcl, pipe, pita))
|
|
}
|
|
if (!is.na(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$fullname %like% "^Streptococcus pneumoniae"
|
|
& tbl[, ampi] == 'R'),
|
|
cols = c(amox, amcl, pipe, pita))
|
|
}
|
|
if (!is.na(norf)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
|
|
& tbl[, norf] == 'S'),
|
|
cols = c(levo, moxi))
|
|
}
|
|
if (!is.na(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$fullname %like% "^Streptococcus pneumoniae"
|
|
& tbl[, eryt] == 'R'),
|
|
cols = c(azit, clar, roxi))
|
|
}
|
|
if (!is.na(tetr)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(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.na(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.na(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$fullname %like% "^Haemophilus influenzae"
|
|
& tbl[, ampi] == 'R'),
|
|
cols = c(amox, pipe))
|
|
}
|
|
if (!is.na(peni)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
|
|
& tbl[, peni] == 'S'),
|
|
cols = c(ampi, amox, amcl, pipe, pita))
|
|
}
|
|
if (!is.na(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$fullname %like% "^Haemophilus influenzae"
|
|
& tbl[, amcl] == 'R'),
|
|
cols = pita)
|
|
}
|
|
if (!is.na(nali)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
|
|
& tbl[, nali] == 'S'),
|
|
cols = c(cipr, levo, moxi, oflo))
|
|
}
|
|
if (!is.na(tetr)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
|
|
& tbl[, tetr] == 'S'),
|
|
cols = c(doxy, mino))
|
|
}
|
|
if (info == TRUE) {
|
|
txt_ok()
|
|
}
|
|
# Moraxella catarrhalis ----
|
|
rule <- italic('Moraxella catarrhalis')
|
|
if (info == TRUE) {
|
|
warned <- FALSE
|
|
changed_results <- 0
|
|
cat(rule)
|
|
}
|
|
if (!is.na(amcl)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(nali)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
|
|
& tbl[, nali] == 'S'),
|
|
cols = c(cipr, levo, moxi, oflo))
|
|
}
|
|
if (!is.na(eryt)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(tetr)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
|
|
& tbl[, tetr] == 'S'),
|
|
cols = c(doxy, mino))
|
|
}
|
|
if (info == TRUE) {
|
|
txt_ok()
|
|
}
|
|
# Anaerobic Gram positives ----
|
|
rule <- 'Anaerobic Gram positives'
|
|
if (info == TRUE) {
|
|
warned <- FALSE
|
|
changed_results <- 0
|
|
cat(rule)
|
|
}
|
|
if (!is.na(peni)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(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$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas",
|
|
"Fusobacterium", "Bilophila ", "Mobiluncus")
|
|
& tbl[, peni] == 'R'),
|
|
cols = c(ampi, amox, pipe, pita, tica))
|
|
}
|
|
if (info == TRUE) {
|
|
txt_ok()
|
|
}
|
|
# Pasteurella multocida ----
|
|
rule <- italic('Pasteurella multocida')
|
|
if (info == TRUE) {
|
|
warned <- FALSE
|
|
changed_results <- 0
|
|
cat(rule)
|
|
}
|
|
if (!is.na(peni)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(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$fullname %like% "^Campylobacter (jejuni|coli)"
|
|
& tbl[, eryt] == 'R'),
|
|
cols = c(azit, clar))
|
|
}
|
|
if (!is.na(tetr)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(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$fullname %like% "^Aerococcus (sanguinicola|urinae)"
|
|
& tbl[, norf] == 'R'),
|
|
cols = fluoroquinolones)
|
|
}
|
|
if (!is.na(cipr)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(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$fullname %like% "^Kingella kingae"
|
|
& tbl[, peni] == 'R'),
|
|
cols = c(ampi, amox))
|
|
}
|
|
if (!is.na(eryt)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(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$fullname %like% '^Clostridium (ramosum|innocuum)'),
|
|
cols = vanc)
|
|
if (info == TRUE) {
|
|
txt_ok()
|
|
}
|
|
|
|
# Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci ----
|
|
rule <- 'Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci'
|
|
if (info == TRUE) {
|
|
warned <- FALSE
|
|
changed_results <- 0
|
|
cat(rule)
|
|
}
|
|
# rule 8.3
|
|
if (!is.na(peni)) {
|
|
edit_rsi(to = 'S',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(ampi)) {
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$genus == 'Enterococcus'
|
|
& tbl[, ampi] == 'R'),
|
|
cols = c(ureidopenicillins, carbapenems))
|
|
}
|
|
if (!is.na(amox)) {
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(tica) & !is.na(pipe)) {
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$family == 'Enterobacteriaceae'
|
|
& tbl[, tica] == 'R'
|
|
& tbl[, pipe] == 'S'),
|
|
cols = pipe)
|
|
}
|
|
if (info == TRUE) {
|
|
txt_ok()
|
|
}
|
|
|
|
# Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria ----
|
|
rule <- 'Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria'
|
|
if (info == TRUE) {
|
|
warned <- FALSE
|
|
changed_results <- 0
|
|
cat(rule)
|
|
}
|
|
# rule 10.2
|
|
# if (!is.na(ampi)) {
|
|
# you should know first if the are B-lactamase positive, so do not run for now
|
|
# edit_rsi(to = 'R',
|
|
# rule = c(rule_group, rule),
|
|
# rows = which(tbl$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.na(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.na(tobr)) {
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$genus == 'Staphylococcus'
|
|
& tbl[, tobr] == 'R'),
|
|
cols = c(kana, amik))
|
|
}
|
|
# rule 12.3
|
|
if (!is.na(gent)) {
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$genus == 'Staphylococcus'
|
|
& tbl[, gent] == 'R'),
|
|
cols = aminoglycosides)
|
|
}
|
|
# rule 12.8
|
|
if (!is.na(gent) & !is.na(tobr)) {
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$family == 'Enterobacteriaceae'
|
|
& tbl[, gent] == 'I'
|
|
& tbl[, tobr] == 'S'),
|
|
cols = gent)
|
|
}
|
|
# rule 12.9
|
|
if (!is.na(gent) & !is.na(tobr)) {
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(moxi)) {
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$genus == 'Staphylococcus'
|
|
& tbl[, moxi] == 'R'),
|
|
cols = fluoroquinolones)
|
|
}
|
|
# rule 13.4
|
|
if (!is.na(moxi)) {
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$fullname %like% '^Streptococcus pneumoniae'
|
|
& tbl[, moxi] == 'R'),
|
|
cols = fluoroquinolones)
|
|
}
|
|
# rule 13.5
|
|
if (!is.na(cipr)) {
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$family == 'Enterobacteriaceae'
|
|
& tbl[, cipr] == 'R'),
|
|
cols = fluoroquinolones)
|
|
}
|
|
# rule 13.8
|
|
if (!is.na(cipr)) {
|
|
edit_rsi(to = 'R',
|
|
rule = c(rule_group, rule),
|
|
rows = which(tbl$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.na(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.na(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.na(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.na(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.na(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.na(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 (amount_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'),
|
|
amount_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'),
|
|
amount_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(...)
|
|
}
|