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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
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# SOURCE #
# https://gitlab.com/msberends/AMR #
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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 #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
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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}
#' @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. It runs all EUCAST rules, but will not be applied to an output - only an informative \code{data.frame} with changes will be returned as output.
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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_col}} or input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning.
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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 (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
#' \strong{amik}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
#' \strong{amox}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
#' \strong{ampi}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
#' \strong{azit}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
#' \strong{azlo}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
#' \strong{aztr}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
#' \strong{cefa}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
#' \strong{cfep}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
#' \strong{cfot}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
#' \strong{cfox}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
#' \strong{cfra}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
#' \strong{cfta}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
#' \strong{cftr}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
#' \strong{cfur}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
#' \strong{chlo}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
#' \strong{cipr}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
#' \strong{clar}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
#' \strong{clin}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
#' \strong{clox}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
#' \strong{coli}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
#' \strong{czol}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
#' \strong{dapt}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
#' \strong{doxy}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
#' \strong{erta}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
#' \strong{eryt}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
#' \strong{fosf}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
#' \strong{fusi}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
#' \strong{gent}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
#' \strong{imip}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
#' \strong{kana}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
#' \strong{levo}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
#' \strong{linc}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
#' \strong{line}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
#' \strong{mero}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
#' \strong{mezl}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
#' \strong{mino}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
#' \strong{moxi}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
#' \strong{nali}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
#' \strong{neom}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
#' \strong{neti}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
#' \strong{nitr}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
#' \strong{norf}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
#' \strong{novo}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
#' \strong{oflo}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
#' \strong{peni}: (benzyl)penicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
#' \strong{pipe}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
#' \strong{pita}: piperacillin+tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
#' \strong{poly}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
#' \strong{pris}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
#' \strong{qida}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
#' \strong{rifa}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
#' \strong{roxi}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
#' \strong{siso}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
#' \strong{teic}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
#' \strong{tetr}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
#' \strong{tica}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
#' \strong{tige}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
#' \strong{tobr}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
#' \strong{trim}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
#' \strong{trsu}: sulfamethoxazole and trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}),
#' \strong{vanc}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{J01XA01}).
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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 all original and new values of the affected bug-drug combinations.
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#' @source
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#' \itemize{
#' \item{
#' EUCAST Expert Rules. Version 2.0, 2012. \cr
#' Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60. \cr
#' \url{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
#' }
#' \item{
#' EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \cr
#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
#' }
#' \item{
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#' EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \cr
#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx}
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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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#'
#' a <- data.frame(mo = c("Staphylococcus aureus",
#' "Enterococcus faecalis",
#' "Escherichia coli",
#' "Klebsiella pneumoniae",
#' "Pseudomonas aeruginosa"),
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#' vanc = "-", # Vancomycin
#' amox = "-", # Amoxicillin
#' coli = "-", # Colistin
#' cfta = "-", # Ceftazidime
#' cfur = "-", # Cefuroxime
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#' peni = "S", # Benzylpenicillin
#' 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
#' # 1 Staphylococcus aureus - - - - - S S
#' # 2 Enterococcus faecalis - - - - - S S
#' # 3 Escherichia coli - - - - - S S
#' # 4 Klebsiella pneumoniae - - - - - S S
#' # 5 Pseudomonas aeruginosa - - - - - S S
#'
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#'
#' # apply EUCAST rules: 18 results are forced as R or S
#' b <- eucast_rules(a)
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#'
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#' b
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#' # mo vanc amox coli cfta cfur peni cfox
#' # 1 Staphylococcus aureus - S R R S S S
#' # 2 Enterococcus faecalis - - R R R S R
#' # 3 Escherichia coli R - - - - R S
#' # 4 Klebsiella pneumoniae R R - - - R S
#' # 5 Pseudomonas aeruginosa R R - - R R R
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#'
#'
#' # do not apply EUCAST rules, but rather get a a data.frame
#' # with 18 rows, containing all details about the transformations:
#' c <- eucast_rules(a, verbose = TRUE)
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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_col ( ) ,
amik = guess_ab_col ( ) ,
amox = guess_ab_col ( ) ,
ampi = guess_ab_col ( ) ,
azit = guess_ab_col ( ) ,
azlo = guess_ab_col ( ) ,
aztr = guess_ab_col ( ) ,
cefa = guess_ab_col ( ) ,
cfep = guess_ab_col ( ) ,
cfot = guess_ab_col ( ) ,
cfox = guess_ab_col ( ) ,
cfra = guess_ab_col ( ) ,
cfta = guess_ab_col ( ) ,
cftr = guess_ab_col ( ) ,
cfur = guess_ab_col ( ) ,
chlo = guess_ab_col ( ) ,
cipr = guess_ab_col ( ) ,
clar = guess_ab_col ( ) ,
clin = guess_ab_col ( ) ,
clox = guess_ab_col ( ) ,
coli = guess_ab_col ( ) ,
czol = guess_ab_col ( ) ,
dapt = guess_ab_col ( ) ,
doxy = guess_ab_col ( ) ,
erta = guess_ab_col ( ) ,
eryt = guess_ab_col ( ) ,
fosf = guess_ab_col ( ) ,
fusi = guess_ab_col ( ) ,
gent = guess_ab_col ( ) ,
imip = guess_ab_col ( ) ,
kana = guess_ab_col ( ) ,
levo = guess_ab_col ( ) ,
linc = guess_ab_col ( ) ,
line = guess_ab_col ( ) ,
mero = guess_ab_col ( ) ,
mezl = guess_ab_col ( ) ,
mino = guess_ab_col ( ) ,
moxi = guess_ab_col ( ) ,
nali = guess_ab_col ( ) ,
neom = guess_ab_col ( ) ,
neti = guess_ab_col ( ) ,
nitr = guess_ab_col ( ) ,
norf = guess_ab_col ( ) ,
novo = guess_ab_col ( ) ,
oflo = guess_ab_col ( ) ,
oxac = guess_ab_col ( ) ,
peni = guess_ab_col ( ) ,
pipe = guess_ab_col ( ) ,
pita = guess_ab_col ( ) ,
poly = guess_ab_col ( ) ,
pris = guess_ab_col ( ) ,
qida = guess_ab_col ( ) ,
rifa = guess_ab_col ( ) ,
roxi = guess_ab_col ( ) ,
siso = guess_ab_col ( ) ,
teic = guess_ab_col ( ) ,
tetr = guess_ab_col ( ) ,
tica = guess_ab_col ( ) ,
tige = guess_ab_col ( ) ,
tobr = guess_ab_col ( ) ,
trim = guess_ab_col ( ) ,
trsu = guess_ab_col ( ) ,
vanc = guess_ab_col ( ) ) {
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EUCAST_VERSION_BREAKPOINTS <- " 9.0, 2019"
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EUCAST_VERSION_EXPERT_RULES <- " 3.1, 2016"
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if ( ! is.data.frame ( tbl ) ) {
stop ( " `tbl` must be a data frame." , call. = FALSE )
}
# try to find columns based on type
# -- mo
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if ( is.null ( col_mo ) ) {
col_mo <- search_type_in_df ( tbl = tbl , type = " mo" )
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}
if ( is.null ( col_mo ) ) {
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" ) ) ) {
stop ( " Parameter `rules` must be one or more of: 'breakpoints', 'expert', 'other', 'all'." )
}
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if ( is.null ( col_mo ) ) {
stop ( " Parameter `col_mo` must be set" )
}
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warned <- FALSE
changed_results <- 0
txt_error <- function ( ) { cat ( " " , bgRed ( black ( " ERROR " ) ) , " \n" ) }
txt_warning <- function ( ) { if ( warned == FALSE ) { cat ( " " , bgYellow ( black ( " WARNING " ) ) , " \n" ) } ; warned <<- TRUE }
txt_ok <- function ( ) {
if ( warned == FALSE ) {
if ( changed_results > 0 ) {
if ( changed_results == 1 ) {
cat ( blue ( " (1 change)\n" ) )
} else {
cat ( blue ( paste0 ( " (" , changed_results , " changes)\n" ) ) )
}
} else {
cat ( green ( " (no changes)\n" ) )
}
warned <<- FALSE
}
}
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# check columns
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if ( identical ( amcl , as.name ( " guess_ab_col" ) ) ) { amcl <- guess_ab_col ( tbl , " amcl" , verbose = verbose ) }
if ( identical ( amik , as.name ( " guess_ab_col" ) ) ) { amik <- guess_ab_col ( tbl , " amik" , verbose = verbose ) }
if ( identical ( amox , as.name ( " guess_ab_col" ) ) ) { amox <- guess_ab_col ( tbl , " amox" , verbose = verbose ) }
if ( identical ( ampi , as.name ( " guess_ab_col" ) ) ) { ampi <- guess_ab_col ( tbl , " ampi" , verbose = verbose ) }
if ( identical ( azit , as.name ( " guess_ab_col" ) ) ) { azit <- guess_ab_col ( tbl , " azit" , verbose = verbose ) }
if ( identical ( azlo , as.name ( " guess_ab_col" ) ) ) { azlo <- guess_ab_col ( tbl , " azlo" , verbose = verbose ) }
if ( identical ( aztr , as.name ( " guess_ab_col" ) ) ) { aztr <- guess_ab_col ( tbl , " aztr" , verbose = verbose ) }
if ( identical ( cefa , as.name ( " guess_ab_col" ) ) ) { cefa <- guess_ab_col ( tbl , " cefa" , verbose = verbose ) }
if ( identical ( cfep , as.name ( " guess_ab_col" ) ) ) { cfep <- guess_ab_col ( tbl , " cfep" , verbose = verbose ) }
if ( identical ( cfot , as.name ( " guess_ab_col" ) ) ) { cfot <- guess_ab_col ( tbl , " cfot" , verbose = verbose ) }
if ( identical ( cfox , as.name ( " guess_ab_col" ) ) ) { cfox <- guess_ab_col ( tbl , " cfox" , verbose = verbose ) }
if ( identical ( cfra , as.name ( " guess_ab_col" ) ) ) { cfra <- guess_ab_col ( tbl , " cfra" , verbose = verbose ) }
if ( identical ( cfta , as.name ( " guess_ab_col" ) ) ) { cfta <- guess_ab_col ( tbl , " cfta" , verbose = verbose ) }
if ( identical ( cftr , as.name ( " guess_ab_col" ) ) ) { cftr <- guess_ab_col ( tbl , " cftr" , verbose = verbose ) }
if ( identical ( cfur , as.name ( " guess_ab_col" ) ) ) { cfur <- guess_ab_col ( tbl , " cfur" , verbose = verbose ) }
if ( identical ( chlo , as.name ( " guess_ab_col" ) ) ) { chlo <- guess_ab_col ( tbl , " chlo" , verbose = verbose ) }
if ( identical ( cipr , as.name ( " guess_ab_col" ) ) ) { cipr <- guess_ab_col ( tbl , " cipr" , verbose = verbose ) }
if ( identical ( clar , as.name ( " guess_ab_col" ) ) ) { clar <- guess_ab_col ( tbl , " clar" , verbose = verbose ) }
if ( identical ( clin , as.name ( " guess_ab_col" ) ) ) { clin <- guess_ab_col ( tbl , " clin" , verbose = verbose ) }
if ( identical ( clox , as.name ( " guess_ab_col" ) ) ) { clox <- guess_ab_col ( tbl , " clox" , verbose = verbose ) }
if ( identical ( coli , as.name ( " guess_ab_col" ) ) ) { coli <- guess_ab_col ( tbl , " coli" , verbose = verbose ) }
if ( identical ( czol , as.name ( " guess_ab_col" ) ) ) { czol <- guess_ab_col ( tbl , " czol" , verbose = verbose ) }
if ( identical ( dapt , as.name ( " guess_ab_col" ) ) ) { dapt <- guess_ab_col ( tbl , " dapt" , verbose = verbose ) }
if ( identical ( doxy , as.name ( " guess_ab_col" ) ) ) { doxy <- guess_ab_col ( tbl , " doxy" , verbose = verbose ) }
if ( identical ( erta , as.name ( " guess_ab_col" ) ) ) { erta <- guess_ab_col ( tbl , " erta" , verbose = verbose ) }
if ( identical ( eryt , as.name ( " guess_ab_col" ) ) ) { eryt <- guess_ab_col ( tbl , " eryt" , verbose = verbose ) }
if ( identical ( fosf , as.name ( " guess_ab_col" ) ) ) { fosf <- guess_ab_col ( tbl , " fosf" , verbose = verbose ) }
if ( identical ( fusi , as.name ( " guess_ab_col" ) ) ) { fusi <- guess_ab_col ( tbl , " fusi" , verbose = verbose ) }
if ( identical ( gent , as.name ( " guess_ab_col" ) ) ) { gent <- guess_ab_col ( tbl , " gent" , verbose = verbose ) }
if ( identical ( imip , as.name ( " guess_ab_col" ) ) ) { imip <- guess_ab_col ( tbl , " imip" , verbose = verbose ) }
if ( identical ( kana , as.name ( " guess_ab_col" ) ) ) { kana <- guess_ab_col ( tbl , " kana" , verbose = verbose ) }
if ( identical ( levo , as.name ( " guess_ab_col" ) ) ) { levo <- guess_ab_col ( tbl , " levo" , verbose = verbose ) }
if ( identical ( linc , as.name ( " guess_ab_col" ) ) ) { linc <- guess_ab_col ( tbl , " linc" , verbose = verbose ) }
if ( identical ( line , as.name ( " guess_ab_col" ) ) ) { line <- guess_ab_col ( tbl , " line" , verbose = verbose ) }
if ( identical ( mero , as.name ( " guess_ab_col" ) ) ) { mero <- guess_ab_col ( tbl , " mero" , verbose = verbose ) }
if ( identical ( mezl , as.name ( " guess_ab_col" ) ) ) { mezl <- guess_ab_col ( tbl , " mezl" , verbose = verbose ) }
if ( identical ( mino , as.name ( " guess_ab_col" ) ) ) { mino <- guess_ab_col ( tbl , " mino" , verbose = verbose ) }
if ( identical ( moxi , as.name ( " guess_ab_col" ) ) ) { moxi <- guess_ab_col ( tbl , " moxi" , verbose = verbose ) }
if ( identical ( nali , as.name ( " guess_ab_col" ) ) ) { nali <- guess_ab_col ( tbl , " nali" , verbose = verbose ) }
if ( identical ( neom , as.name ( " guess_ab_col" ) ) ) { neom <- guess_ab_col ( tbl , " neom" , verbose = verbose ) }
if ( identical ( neti , as.name ( " guess_ab_col" ) ) ) { neti <- guess_ab_col ( tbl , " neti" , verbose = verbose ) }
if ( identical ( nitr , as.name ( " guess_ab_col" ) ) ) { nitr <- guess_ab_col ( tbl , " nitr" , verbose = verbose ) }
if ( identical ( norf , as.name ( " guess_ab_col" ) ) ) { norf <- guess_ab_col ( tbl , " norf" , verbose = verbose ) }
if ( identical ( novo , as.name ( " guess_ab_col" ) ) ) { novo <- guess_ab_col ( tbl , " novo" , verbose = verbose ) }
if ( identical ( oflo , as.name ( " guess_ab_col" ) ) ) { oflo <- guess_ab_col ( tbl , " oflo" , verbose = verbose ) }
if ( identical ( oxac , as.name ( " guess_ab_col" ) ) ) { oxac <- guess_ab_col ( tbl , " oxac" , verbose = verbose ) }
if ( identical ( peni , as.name ( " guess_ab_col" ) ) ) { peni <- guess_ab_col ( tbl , " peni" , verbose = verbose ) }
if ( identical ( pipe , as.name ( " guess_ab_col" ) ) ) { pipe <- guess_ab_col ( tbl , " pipe" , verbose = verbose ) }
if ( identical ( pita , as.name ( " guess_ab_col" ) ) ) { pita <- guess_ab_col ( tbl , " pita" , verbose = verbose ) }
if ( identical ( poly , as.name ( " guess_ab_col" ) ) ) { poly <- guess_ab_col ( tbl , " poly" , verbose = verbose ) }
if ( identical ( pris , as.name ( " guess_ab_col" ) ) ) { pris <- guess_ab_col ( tbl , " pris" , verbose = verbose ) }
if ( identical ( qida , as.name ( " guess_ab_col" ) ) ) { qida <- guess_ab_col ( tbl , " qida" , verbose = verbose ) }
if ( identical ( rifa , as.name ( " guess_ab_col" ) ) ) { rifa <- guess_ab_col ( tbl , " rifa" , verbose = verbose ) }
if ( identical ( roxi , as.name ( " guess_ab_col" ) ) ) { roxi <- guess_ab_col ( tbl , " roxi" , verbose = verbose ) }
if ( identical ( siso , as.name ( " guess_ab_col" ) ) ) { siso <- guess_ab_col ( tbl , " siso" , verbose = verbose ) }
if ( identical ( teic , as.name ( " guess_ab_col" ) ) ) { teic <- guess_ab_col ( tbl , " teic" , verbose = verbose ) }
if ( identical ( tetr , as.name ( " guess_ab_col" ) ) ) { tetr <- guess_ab_col ( tbl , " tetr" , verbose = verbose ) }
if ( identical ( tica , as.name ( " guess_ab_col" ) ) ) { tica <- guess_ab_col ( tbl , " tica" , verbose = verbose ) }
if ( identical ( tige , as.name ( " guess_ab_col" ) ) ) { tige <- guess_ab_col ( tbl , " tige" , verbose = verbose ) }
if ( identical ( tobr , as.name ( " guess_ab_col" ) ) ) { tobr <- guess_ab_col ( tbl , " tobr" , verbose = verbose ) }
if ( identical ( trim , as.name ( " guess_ab_col" ) ) ) { trim <- guess_ab_col ( tbl , " trim" , verbose = verbose ) }
if ( identical ( trsu , as.name ( " guess_ab_col" ) ) ) { trsu <- guess_ab_col ( tbl , " trsu" , verbose = verbose ) }
if ( identical ( vanc , as.name ( " guess_ab_col" ) ) ) { vanc <- guess_ab_col ( tbl , " vanc" , verbose = verbose ) }
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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 ,
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 ,
roxi , siso , teic , tetr , tica , tige , tobr , trim , trsu , vanc )
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if ( length ( col.list ) < 63 ) {
warning ( ' Some columns do not exist -- THIS MAY STRONGLY INFLUENCE THE OUTCOME.' ,
immediate. = TRUE ,
call. = FALSE )
}
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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 ]
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azlo <- col.list [azlo ]
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aztr <- col.list [aztr ]
cefa <- col.list [cefa ]
cfep <- col.list [cfep ]
cfot <- col.list [cfot ]
cfox <- col.list [cfox ]
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cfra <- col.list [cfra ]
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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 ]
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mezl <- col.list [mezl ]
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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 ]
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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 ]
poly <- col.list [poly ]
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pris <- col.list [pris ]
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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 ]
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number_added_S <- 0
number_added_I <- 0
number_added_R <- 0
number_changed_to_S <- 0
number_changed_to_I <- 0
number_changed_to_R <- 0
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number_affected_rows <- integer ( 0 )
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verbose_info <- data.frame ( row = integer ( 0 ) ,
col = character ( 0 ) ,
mo = character ( 0 ) ,
mo_fullname = character ( 0 ) ,
old = character ( 0 ) ,
new = character ( 0 ) ,
rule_source = character ( 0 ) ,
rule_group = character ( 0 ) ,
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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 ) & ! is.null ( cols ) ] )
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if ( length ( rows ) > 0 & length ( cols ) > 0 ) {
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before_df <- tbl_original
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before <- as.character ( unlist ( as.list ( tbl_original [rows , cols ] ) ) )
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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 )
}
)
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# suppressMessages(
# suppressWarnings(
# tbl[rows, cols] <<- to
# ))
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after <- as.character ( unlist ( as.list ( tbl_original [rows , cols ] ) ) )
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tbl [rows , cols ] <<- tbl_original [rows , cols ]
number_newly_added_S <- sum ( ! before %in% c ( " S" , " I" , " R" ) & after == " S" , na.rm = TRUE )
number_newly_added_I <- sum ( ! before %in% c ( " S" , " I" , " R" ) & after == " I" , na.rm = TRUE )
number_newly_added_R <- sum ( ! before %in% c ( " S" , " I" , " R" ) & after == " R" , na.rm = TRUE )
number_newly_changed_to_S <- sum ( before %in% c ( " I" , " R" ) & after == " S" , na.rm = TRUE )
number_newly_changed_to_I <- sum ( before %in% c ( " S" , " R" ) & after == " I" , na.rm = TRUE )
number_newly_changed_to_R <- sum ( before %in% c ( " S" , " I" ) & after == " R" , na.rm = TRUE )
# totals
number_added_S <<- number_added_S + number_newly_added_S
number_added_I <<- number_added_I + number_newly_added_I
number_added_R <<- number_added_R + number_newly_added_R
number_changed_to_S <<- number_changed_to_S + number_newly_changed_to_S
number_changed_to_I <<- number_changed_to_I + number_newly_changed_to_I
number_changed_to_R <<- number_changed_to_R + number_newly_changed_to_R
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number_affected_rows <<- unique ( c ( number_affected_rows , rows ) )
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# will be reset at start of every rule
changed_results <<- changed_results +
number_newly_added_S +
number_newly_added_I +
number_newly_added_R +
number_newly_changed_to_S +
number_newly_changed_to_I +
number_newly_changed_to_R
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if ( verbose == TRUE ) {
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old <- as.data.frame ( tbl_bak , stringsAsFactors = FALSE ) [rows , ]
new <- as.data.frame ( tbl , stringsAsFactors = FALSE ) [rows , ]
MOs <- as.data.frame ( tbl_original , stringsAsFactors = FALSE ) [rows , col_mo ] [ [1 ] ]
for ( i in 1 : length ( cols ) ) {
verbose_new <- data.frame ( row = rows ,
col = cols [i ] ,
mo = MOs ,
mo_fullname = " " ,
old = as.character ( old [ , cols [i ] ] ) ,
new = as.character ( new [ , cols [i ] ] ) ,
rule_source = strip_style ( rule [1 ] ) ,
rule_group = strip_style ( rule [2 ] ) ,
stringsAsFactors = FALSE )
colnames ( verbose_new ) <- c ( " row" , " col" , " mo" , " mo_fullname" , " old" , " new" , " rule_source" , " rule_group" )
verbose_info <<- rbind ( verbose_info , verbose_new )
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}
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}
}
}
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na.rm <- function ( col ) {
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if ( is.null ( col ) ) {
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" "
} else {
col
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}
}
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# save original table
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tbl_original <- tbl
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tbl_bak <- tbl
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# join to microorganisms data set
tbl <- tbl %>%
mutate_at ( vars ( col_mo ) , as.mo ) %>%
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left_join_microorganisms ( by = col_mo , suffix = c ( " _oldcols" , " " ) ) %>%
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mutate ( gramstain = mo_gramstain ( pull ( ., col_mo ) ) ) %>%
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as.data.frame ( stringsAsFactors = FALSE )
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if ( info == TRUE ) {
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cat ( " \nRules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)\n" )
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}
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# since ampicillin ^= amoxicillin, get the first from the latter (not in original EUCAST table)
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if ( ! is.null ( ampi ) & ! is.null ( amox ) ) {
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if ( verbose == TRUE ) {
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cat ( " \n VERBOSE: transforming" ,
length ( which ( tbl [ , amox ] == " S" & ! tbl [ , ampi ] %in% c ( " S" , " I" , " R" ) ) ) ,
" empty ampicillin fields to 'S' based on amoxicillin. " )
cat ( " \n VERBOSE: transforming" ,
length ( which ( tbl [ , amox ] == " I" & ! tbl [ , ampi ] %in% c ( " S" , " I" , " R" ) ) ) ,
" empty ampicillin fields to 'I' based on amoxicillin. " )
cat ( " \n VERBOSE: transforming" ,
length ( which ( tbl [ , amox ] == " R" & ! tbl [ , ampi ] %in% c ( " S" , " I" , " R" ) ) ) ,
" empty ampicillin fields to 'R' based on amoxicillin. \n" )
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}
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"
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} else if ( is.null ( ampi ) & ! is.null ( amox ) ) {
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# 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
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}
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# 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 )
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if ( any ( c ( " all" , " breakpoints" ) %in% rules ) ) {
# BREAKPOINTS -------------------------------------------------------------
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if ( info == TRUE ) {
cat ( bold ( paste0 ( ' \nEUCAST Clinical Breakpoints (v' , EUCAST_VERSION_BREAKPOINTS , ' )\n' ) ) )
}
rule_group <- " Breakpoints"
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# Enterobacteriales (Order) ----
rule <- ' Enterobacteriales (Order)'
if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
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if ( ! is.null ( ampi ) ) {
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edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ order == ' Enterobacteriales'
& tbl [ , ampi ] == ' S' ) ,
cols = amox )
}
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if ( ! is.null ( ampi ) ) {
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edit_rsi ( to = ' I' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ order == ' Enterobacteriales'
& tbl [ , ampi ] == ' I' ) ,
cols = amox )
}
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if ( ! is.null ( ampi ) ) {
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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 ----
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rule <- italic ( ' Staphylococcus' )
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if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
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if ( ! is.null ( peni ) & ! is.null ( cfox ) ) {
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edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == " Staphylococcus"
& tbl [ , peni ] == ' S'
& tbl [ , cfox ] == ' S' ) ,
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cols = c ( ampi , amox , pipe , tica ) )
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edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == " Staphylococcus"
& tbl [ , peni ] == ' R'
& tbl [ , cfox ] == ' S' ) ,
cols = c ( oxac , clox ) )
}
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if ( ! is.null ( cfox ) ) {
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edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == " Staphylococcus"
& tbl [ , cfox ] == ' R' ) ,
cols = all_betalactam )
}
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if ( ! is.null ( ampi ) ) {
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edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ fullname %like% " ^Staphylococcus saprophyticus"
& tbl [ , ampi ] == ' S' ) ,
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cols = c ( amox , amcl , pipe , pita ) )
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}
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if ( ! is.null ( cfox ) ) {
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# 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 ) ] ) )
}
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if ( ! is.null ( norf ) ) {
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edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == " Staphylococcus"
& tbl [ , norf ] == ' S' ) ,
cols = c ( cipr , levo , moxi , oflo ) )
}
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if ( ! is.null ( eryt ) ) {
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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 ) )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( tetr ) ) {
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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 ----
2018-11-01 20:23:33 +01:00
rule <- italic ( ' Enterococcus' )
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if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
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if ( ! is.null ( ampi ) ) { # penicillin group
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edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ fullname %like% " ^Enterococcus faecium"
2018-11-01 17:06:08 +01:00
& tbl [ , ampi ] == ' R' ) ,
2018-10-18 12:10:10 +02:00
cols = all_betalactam )
}
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if ( ! is.null ( ampi ) ) {
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edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == " Enterococcus"
& tbl [ , ampi ] == ' S' ) ,
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cols = c ( amox , amcl , pipe , pita ) )
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edit_rsi ( to = ' I' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == " Enterococcus"
& tbl [ , ampi ] == ' I' ) ,
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cols = c ( amox , amcl , pipe , pita ) )
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == " Enterococcus"
& tbl [ , ampi ] == ' R' ) ,
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cols = c ( amox , amcl , pipe , pita ) )
2018-10-18 12:10:10 +02:00
}
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if ( ! is.null ( norf ) ) {
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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 ( )
}
2018-11-01 20:23:33 +01:00
# Streptococcus groups A, B, C, G----
rule <- paste ( italic ( ' Streptococcus' ) , ' groups A, B, C, G' )
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if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
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if ( ! is.null ( peni ) ) {
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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 ) )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( norf ) ) {
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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 ) )
}
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if ( ! is.null ( eryt ) ) {
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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 ) )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( tetr ) ) {
2018-10-18 12:10:10 +02:00
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 ----
2018-11-01 20:23:33 +01:00
rule <- italic ( ' Streptococcus pneumoniae' )
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if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
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if ( ! is.null ( peni ) ) {
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ fullname %like% " ^Streptococcus pneumoniae"
& tbl [ , peni ] == ' S' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( ampi , amox , amcl , pipe , pita ) )
2018-10-18 12:10:10 +02:00
}
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if ( ! is.null ( ampi ) ) {
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edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ fullname %like% " ^Streptococcus pneumoniae"
& tbl [ , ampi ] == ' S' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( amox , amcl , pipe , pita ) )
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edit_rsi ( to = ' I' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ fullname %like% " ^Streptococcus pneumoniae"
& tbl [ , ampi ] == ' I' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( amox , amcl , pipe , pita ) )
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ fullname %like% " ^Streptococcus pneumoniae"
& tbl [ , ampi ] == ' R' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( amox , amcl , pipe , pita ) )
2018-10-18 12:10:10 +02:00
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( norf ) ) {
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edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ fullname %like% " ^Streptococcus pneumoniae"
& tbl [ , norf ] == ' S' ) ,
cols = c ( levo , moxi ) )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( eryt ) ) {
2018-10-18 12:10:10 +02:00
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 ) )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( tetr ) ) {
2018-10-18 12:10:10 +02:00
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" )
2019-01-03 23:56:19 +01:00
if ( ! is.null ( peni ) ) {
2018-11-01 17:06:08 +01:00
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 ) )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( ampi ) ) {
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == " Streptococcus" & tbl $ species %in% viridans_group
& tbl [ , ampi ] == ' S' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( amox , amcl , pipe , pita ) )
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' I' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == " Streptococcus" & tbl $ species %in% viridans_group
& tbl [ , ampi ] == ' I' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( amox , amcl , pipe , pita ) )
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == " Streptococcus" & tbl $ species %in% viridans_group
& tbl [ , ampi ] == ' R' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( amox , amcl , pipe , pita ) )
2018-10-18 12:10:10 +02:00
}
if ( info == TRUE ) {
txt_ok ( )
}
# Haemophilus influenzae ----
2018-11-01 20:23:33 +01:00
rule <- italic ( ' Haemophilus influenzae' )
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if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( ampi ) ) {
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ fullname %like% " ^Haemophilus influenzae"
& tbl [ , ampi ] == ' S' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( amox , pipe ) )
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' I' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ fullname %like% " ^Haemophilus influenzae"
& tbl [ , ampi ] == ' I' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( amox , pipe ) )
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ fullname %like% " ^Haemophilus influenzae"
& tbl [ , ampi ] == ' R' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( amox , pipe ) )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( peni ) ) {
2018-11-01 17:06:08 +01:00
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 ) )
2018-10-18 12:10:10 +02:00
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( amcl ) ) {
2018-10-18 12:10:10 +02:00
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 )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( nali ) ) {
2018-10-18 12:10:10 +02:00
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 ) )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( tetr ) ) {
2018-10-18 12:10:10 +02:00
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 ----
2018-11-01 20:23:33 +01:00
rule <- italic ( ' Moraxella catarrhalis' )
2018-10-18 12:10:10 +02:00
if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( amcl ) ) {
2018-10-18 12:10:10 +02:00
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 )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( nali ) ) {
2018-10-18 12:10:10 +02:00
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 ) )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( eryt ) ) {
2018-10-18 12:10:10 +02:00
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 ) )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( tetr ) ) {
2018-10-18 12:10:10 +02:00
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 )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( peni ) ) {
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
2018-11-01 17:06:08 +01:00
rows = which ( tbl $ genus %in% c ( " Clostridium" , " Actinomyces" , " Propionibacterium" ,
" Cutibacterium" , # new name of Propionibacterium
" Bifidobacterium" , " Eggerthella" , " Eubacterium" ,
" Lactobacillus " , " Actinomyces" )
2018-10-18 12:10:10 +02:00
& tbl [ , peni ] == ' S' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( ampi , amox , pipe , pita , tica ) )
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' I' ,
rule = c ( rule_group , rule ) ,
2018-11-01 17:06:08 +01:00
rows = which ( tbl $ genus %in% c ( " Clostridium" , " Actinomyces" , " Propionibacterium" ,
" Cutibacterium" , # new name of Propionibacterium
" Bifidobacterium" , " Eggerthella" , " Eubacterium" ,
" Lactobacillus " , " Actinomyces" )
2018-10-18 12:10:10 +02:00
& tbl [ , peni ] == ' I' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( ampi , amox , pipe , pita , tica ) )
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-11-01 17:06:08 +01:00
rows = which ( tbl $ genus %in% c ( " Clostridium" , " Actinomyces" , " Propionibacterium" ,
" Cutibacterium" , # new name of Propionibacterium
" Bifidobacterium" , " Eggerthella" , " Eubacterium" ,
" Lactobacillus " , " Actinomyces" )
2018-10-18 12:10:10 +02:00
& tbl [ , peni ] == ' R' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( ampi , amox , pipe , pita , tica ) )
2018-10-18 12:10:10 +02:00
}
if ( info == TRUE ) {
txt_ok ( )
}
# Anaerobic Gram negatives ----
rule <- ' Anaerobic Gram negatives'
if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( peni ) ) {
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus %in% c ( " Bacteroides" , " Prevotella" , " Porphyromonas" ,
" Fusobacterium" , " Bilophila " , " Mobiluncus" )
& tbl [ , peni ] == ' S' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( ampi , amox , pipe , pita , tica ) )
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' I' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus %in% c ( " Bacteroides" , " Prevotella" , " Porphyromonas" ,
" Fusobacterium" , " Bilophila " , " Mobiluncus" )
& tbl [ , peni ] == ' I' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( ampi , amox , pipe , pita , tica ) )
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus %in% c ( " Bacteroides" , " Prevotella" , " Porphyromonas" ,
" Fusobacterium" , " Bilophila " , " Mobiluncus" )
& tbl [ , peni ] == ' R' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( ampi , amox , pipe , pita , tica ) )
2018-10-18 12:10:10 +02:00
}
if ( info == TRUE ) {
txt_ok ( )
}
# Pasteurella multocida ----
2018-11-01 20:23:33 +01:00
rule <- italic ( ' Pasteurella multocida' )
2018-10-18 12:10:10 +02:00
if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( peni ) ) {
2018-10-18 12:10:10 +02:00
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 ( )
}
2018-11-01 17:06:08 +01:00
# Campylobacter jejuni and coli ----
2018-11-01 20:23:33 +01:00
rule <- paste ( italic ( ' Campylobacter jejuni' ) , ' and' , italic ( ' C. coli' ) )
2018-10-18 12:10:10 +02:00
if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( eryt ) ) {
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
2018-11-01 17:06:08 +01:00
rows = which ( tbl $ fullname %like% " ^Campylobacter (jejuni|coli)"
2018-10-18 12:10:10 +02:00
& tbl [ , eryt ] == ' S' ) ,
cols = c ( azit , clar ) )
edit_rsi ( to = ' I' ,
rule = c ( rule_group , rule ) ,
2018-11-01 17:06:08 +01:00
rows = which ( tbl $ fullname %like% " ^Campylobacter (jejuni|coli)"
2018-10-18 12:10:10 +02:00
& tbl [ , eryt ] == ' I' ) ,
cols = c ( azit , clar ) )
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-11-01 17:06:08 +01:00
rows = which ( tbl $ fullname %like% " ^Campylobacter (jejuni|coli)"
2018-10-18 12:10:10 +02:00
& tbl [ , eryt ] == ' R' ) ,
cols = c ( azit , clar ) )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( tetr ) ) {
2018-10-18 12:10:10 +02:00
edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
2018-11-01 17:06:08 +01:00
rows = which ( tbl $ fullname %like% " ^Campylobacter (jejuni|coli)"
2018-10-18 12:10:10 +02:00
& tbl [ , tetr ] == ' S' ) ,
cols = doxy )
edit_rsi ( to = ' I' ,
rule = c ( rule_group , rule ) ,
2018-11-01 17:06:08 +01:00
rows = which ( tbl $ fullname %like% " ^Campylobacter (jejuni|coli)"
2018-10-18 12:10:10 +02:00
& tbl [ , tetr ] == ' I' ) ,
cols = doxy )
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-11-01 17:06:08 +01:00
rows = which ( tbl $ fullname %like% " ^Campylobacter (jejuni|coli)"
2018-10-18 12:10:10 +02:00
& tbl [ , tetr ] == ' R' ) ,
cols = doxy )
}
if ( info == TRUE ) {
txt_ok ( )
}
# Aerococcus sanguinicola/urinae ----
2018-11-01 20:23:33 +01:00
rule <- paste ( italic ( ' Aerococcus sanguinicola' ) , ' and' , italic ( ' A. urinae' ) )
2018-10-18 12:10:10 +02:00
if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( norf ) ) {
2018-11-01 17:06:08 +01:00
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 )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( cipr ) ) {
2018-10-18 12:10:10 +02:00
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 ----
2018-11-01 20:23:33 +01:00
rule <- italic ( ' Kingella kingae' )
2018-10-18 12:10:10 +02:00
if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( peni ) ) {
2018-10-18 12:10:10 +02:00
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 ) )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( eryt ) ) {
2018-10-18 12:10:10 +02:00
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 ) )
}
2019-01-03 23:56:19 +01:00
if ( ! is.null ( tetr ) ) {
2018-10-18 12:10:10 +02:00
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 ----
2018-11-01 20:23:33 +01:00
rule <- paste ( ' Table 1: Intrinsic resistance in' , italic ( ' Enterobacteriaceae' ) )
2018-10-18 12:10:10 +02:00
if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
# Intrinsic R for this group
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ family == ' Enterobacteriaceae' ) ,
cols = c ( peni , glycopeptides , fusi , macrolides , linc , streptogramins , rifa , dapt , line ) )
# Citrobacter
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)' ) ,
cols = c ( aminopenicillins , tica ) )
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)' ) ,
cols = c ( aminopenicillins , amcl , czol , cfox ) )
# Enterobacter
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Enterobacter cloacae' ) ,
cols = c ( aminopenicillins , amcl , czol , cfox ) )
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Enterobacter aerogenes' ) ,
cols = c ( aminopenicillins , amcl , czol , cfox ) )
# Escherichia
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Escherichia hermanni' ) ,
cols = c ( aminopenicillins , tica ) )
# Hafnia
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Hafnia alvei' ) ,
cols = c ( aminopenicillins , amcl , czol , cfox ) )
# Klebsiella
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Klebsiella' ) ,
cols = c ( aminopenicillins , tica ) )
# Morganella / Proteus
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Morganella morganii' ) ,
cols = c ( aminopenicillins , amcl , czol , tetracyclines , polymyxins , nitr ) )
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Proteus mirabilis' ) ,
cols = c ( tetracyclines , tige , polymyxins , nitr ) )
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Proteus penneri' ) ,
cols = c ( aminopenicillins , czol , cfur , tetracyclines , tige , polymyxins , nitr ) )
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Proteus vulgaris' ) ,
cols = c ( aminopenicillins , czol , cfur , tetracyclines , tige , polymyxins , nitr ) )
# Providencia
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Providencia rettgeri' ) ,
cols = c ( aminopenicillins , amcl , czol , cfur , tetracyclines , tige , polymyxins , nitr ) )
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Providencia stuartii' ) ,
cols = c ( aminopenicillins , amcl , czol , cfur , tetracyclines , tige , polymyxins , nitr ) )
# Raoultella
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Raoultella' ) ,
cols = c ( aminopenicillins , tica ) )
# Serratia
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Serratia marcescens' ) ,
cols = c ( aminopenicillins , amcl , czol , cfox , cfur , tetracyclines [tetracyclines != na.rm ( mino ) ] , polymyxins , nitr ) )
# Yersinia
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Yersinia enterocolitica' ) ,
cols = c ( aminopenicillins , amcl , tica , czol , cfox ) )
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
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
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
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
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
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
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Achromobacter (xylosoxydans|xylosoxidans)' ) ,
cols = c ( aminopenicillins , czol , cfot , cftr , erta ) )
# Burkholderia
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-11-01 17:06:08 +01:00
# the 'Burkholderia cepacia complex' are all these species: (PMID 16217180)
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis)' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( aminopenicillins , amcl , tica , pipe , pita , czol , cfot , cftr , aztr , erta , cipr , chlo , aminoglycosides , trim , fosf , polymyxins ) )
2018-10-18 12:10:10 +02:00
# Elizabethkingia
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
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' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Ochrobactrum anthropi' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( aminopenicillins , amcl , tica , pipe , pita , czol , cfot , cftr , cfta , cfep , aztr , erta ) )
2018-10-18 12:10:10 +02:00
# Pseudomonas
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Pseudomonas aeruginosa' ) ,
cols = c ( aminopenicillins , amcl , czol , cfot , cftr , erta , chlo , kana , neom , trim , trsu , tetracyclines , tige ) )
# Stenotrophomonas
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Stenotrophomonas maltophilia' ) ,
2018-11-01 17:06:08 +01:00
cols = c ( aminopenicillins , amcl , tica , pipe , pita , czol , cfot , cftr , cfta , aztr , erta , imip , mero , aminoglycosides , trim , fosf , tetr ) )
2018-10-18 12:10:10 +02:00
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' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ genus %in% c ( ' Haemophilus' ,
' Moraxella' ,
' Neisseria' ,
' Campylobacter' ) ) ,
cols = c ( glycopeptides , linc , dapt , line ) )
# Haemophilus
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Haemophilus influenzae' ) ,
cols = c ( fusi , streptogramins ) )
# Moraxella
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Moraxella catarrhalis' ) ,
cols = trim )
# Neisseria
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ genus == ' Neisseria' ) ,
cols = trim )
# Campylobacter
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Campylobacter fetus' ) ,
cols = c ( fusi , streptogramins , trim , nali ) )
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Campylobacter (jejuni|coli)' ) ,
cols = c ( fusi , streptogramins , trim ) )
if ( info == TRUE ) {
txt_ok ( )
}
2018-04-02 16:05:09 +02:00
2018-10-18 12:10:10 +02:00
# 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
2018-02-21 11:52:31 +01:00
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ gramstain == " Gram positive" ) ,
cols = c ( aztr , polymyxins , nali ) )
# Staphylococcus
2018-02-22 21:37:10 +01:00
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Staphylococcus saprophyticus' ) ,
cols = c ( fusi , cfta , fosf , novo ) )
2018-02-21 11:52:31 +01:00
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Staphylococcus (cohnii|xylosus)' ) ,
cols = c ( cfta , novo ) )
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Staphylococcus capitis' ) ,
cols = c ( cfta , fosf ) )
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)' ) ,
cols = cfta )
# Streptococcus
# rule 4.5
2018-10-17 17:32:34 +02:00
edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ genus == ' Streptococcus' ) ,
cols = c ( fusi , aminoglycosides ) )
# Enterococcus
2018-02-21 11:52:31 +01:00
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Enterococcus faecalis' ) ,
cols = c ( fusi , cfta , cephalosporins [cephalosporins != na.rm ( cfta ) ] , aminoglycosides , macrolides , clin , qida , trim , trsu ) )
2018-02-21 11:52:31 +01:00
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Enterococcus (gallinarum|casseliflavus)' ) ,
cols = c ( fusi , cfta , cephalosporins [cephalosporins != na.rm ( cfta ) ] , aminoglycosides , macrolides , clin , qida , vanc , trim , trsu ) )
2018-02-21 11:52:31 +01:00
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Enterococcus faecium' ) ,
cols = c ( fusi , cfta , cephalosporins [cephalosporins != na.rm ( cfta ) ] , aminoglycosides , macrolides , trim , trsu ) )
# Corynebacterium
2018-02-21 11:52:31 +01:00
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ genus == ' Corynebacterium' ) ,
cols = fosf )
# Listeria
2018-02-21 11:52:31 +01:00
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
2018-10-18 12:10:10 +02:00
rows = which ( tbl $ fullname %like% ' ^Listeria monocytogenes' ) ,
cols = c ( cfta , cephalosporins [cephalosporins != na.rm ( cfta ) ] ) )
# other
2018-02-21 11:52:31 +01:00
edit_rsi ( to = ' R' ,
2018-10-17 17:32:34 +02:00
rule = c ( rule_group , rule ) ,
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rows = which ( tbl $ genus %in% c ( ' Leuconostoc' , ' Pediococcus' ) ) ,
cols = glycopeptides )
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edit_rsi ( to = ' R' ,
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rule = c ( rule_group , rule ) ,
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rows = which ( tbl $ genus == ' Lactobacillus' ) ,
cols = glycopeptides )
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edit_rsi ( to = ' R' ,
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rule = c ( rule_group , rule ) ,
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rows = which ( tbl $ fullname %like% ' ^Clostridium (ramosum|innocuum)' ) ,
cols = vanc )
if ( info == TRUE ) {
txt_ok ( )
}
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# 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
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if ( ! is.null ( peni ) ) {
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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
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if ( ! is.null ( ampi ) ) {
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edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == ' Enterococcus'
& tbl [ , ampi ] == ' R' ) ,
cols = c ( ureidopenicillins , carbapenems ) )
}
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if ( ! is.null ( amox ) ) {
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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 ( )
}
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# 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
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if ( ! is.null ( tica ) & ! is.null ( pipe ) ) {
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edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ family == ' Enterobacteriaceae'
& tbl [ , tica ] == ' R'
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& tbl [ , pipe ] == ' S' ) ,
cols = pipe )
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}
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
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# if (!is.null(ampi)) {
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# 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'),
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# cols = c(ampi, amox, amcl, pipe, pita, cfur))
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# }
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
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if ( ! is.null ( eryt ) ) {
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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
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if ( ! is.null ( tobr ) ) {
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edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == ' Staphylococcus'
& tbl [ , tobr ] == ' R' ) ,
cols = c ( kana , amik ) )
}
# rule 12.3
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if ( ! is.null ( gent ) ) {
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edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == ' Staphylococcus'
& tbl [ , gent ] == ' R' ) ,
cols = aminoglycosides )
}
# rule 12.8
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if ( ! is.null ( gent ) & ! is.null ( tobr ) ) {
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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
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if ( ! is.null ( gent ) & ! is.null ( tobr ) ) {
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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 ( )
}
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# 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
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if ( ! is.null ( moxi ) ) {
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edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ genus == ' Staphylococcus'
& tbl [ , moxi ] == ' R' ) ,
cols = fluoroquinolones )
}
# rule 13.4
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if ( ! is.null ( moxi ) ) {
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edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ fullname %like% ' ^Streptococcus pneumoniae'
& tbl [ , moxi ] == ' R' ) ,
cols = fluoroquinolones )
}
# rule 13.5
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if ( ! is.null ( cipr ) ) {
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edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl $ family == ' Enterobacteriaceae'
& tbl [ , cipr ] == ' R' ) ,
cols = fluoroquinolones )
}
# rule 13.8
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if ( ! is.null ( cipr ) ) {
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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 )
}
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if ( ! is.null ( amcl ) ) {
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edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl [ , amcl ] == ' R' ) ,
cols = ampi )
}
if ( info == TRUE ) {
txt_ok ( )
}
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rule <- ' Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R'
if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
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if ( ! is.null ( pita ) ) {
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edit_rsi ( to = ' R' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl [ , pita ] == ' R' ) ,
cols = pipe )
}
if ( info == TRUE ) {
txt_ok ( )
}
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rule <- ' Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R'
if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
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if ( ! is.null ( trsu ) ) {
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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 )
}
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if ( ! is.null ( ampi ) ) {
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edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl [ , ampi ] == ' S' ) ,
cols = amcl )
}
if ( info == TRUE ) {
txt_ok ( )
}
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rule <- ' Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S'
if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
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if ( ! is.null ( pipe ) ) {
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edit_rsi ( to = ' S' ,
rule = c ( rule_group , rule ) ,
rows = which ( tbl [ , pipe ] == ' S' ) ,
cols = pita )
}
if ( info == TRUE ) {
txt_ok ( )
}
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rule <- ' Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S'
if ( info == TRUE ) {
warned <- FALSE
changed_results <- 0
cat ( rule )
}
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if ( ! is.null ( trim ) ) {
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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
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# restore old col_mo values if needed
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# if (!is.null(col_mo_original)) {
# tbl_original[, col_mo] <- col_mo_original
# }
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if ( info == TRUE ) {
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if ( verbose == TRUE ) {
wouldve <- " would have "
} else {
wouldve <- " "
}
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if ( sum ( number_added_S , number_added_I , number_added_R ,
number_changed_to_S , number_changed_to_I , number_changed_to_R ,
na.rm = TRUE ) == 0 ) {
colour <- green # is function
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} else {
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colour <- blue # is function
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}
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decimal.mark <- getOption ( " OutDec" )
big.mark <- ifelse ( decimal.mark != " ," , " ," , " ." )
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formatnr <- function ( x ) {
format ( x , big.mark = big.mark , decimal.mark = decimal.mark )
}
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cat ( bold ( paste ( ' \n=> EUCAST rules' , paste0 ( wouldve , ' affected' ) ,
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number_affected_rows %>% length ( ) %>% formatnr ( ) ,
' out of' , nrow ( tbl_original ) %>% formatnr ( ) ,
' rows\n' ) ) )
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total_added <- number_added_S + number_added_I + number_added_R
total_changed <- number_changed_to_S + number_changed_to_I + number_changed_to_R
cat ( colour ( paste0 ( " -> " , wouldve , " added " ,
bold ( formatnr ( total_added ) , " test results" ) ,
if ( total_added > 0 )
paste0 ( " (" , formatnr ( number_added_S ) , " as S; " ,
formatnr ( number_added_I ) , " as I; " ,
formatnr ( number_added_R ) , " as R)" ) ,
" \n" ) ) )
cat ( colour ( paste0 ( " -> " , wouldve , " changed " ,
bold ( formatnr ( total_changed ) , " test results" ) ,
if ( total_changed > 0 )
paste0 ( " (" , formatnr ( number_changed_to_S ) , " to S; " ,
formatnr ( number_changed_to_I ) , " to I; " ,
formatnr ( number_changed_to_R ) , " to R)" ) ,
" \n" ) ) )
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if ( verbose == FALSE ) {
cat ( paste ( " Use" , bold ( " verbose = TRUE" ) , " to get a data.frame with all specified edits.\n" ) )
}
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}
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if ( verbose == TRUE ) {
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suppressWarnings (
suppressMessages (
verbose_info $ mo_fullname <- mo_fullname ( verbose_info $ mo )
)
)
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verbose_info <- verbose_info %>%
filter ( ! is.na ( new ) & ! identical ( old , new ) ) %>%
arrange ( row )
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return ( verbose_info )
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}
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tbl_original
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}
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#' @rdname eucast_rules
#' @export
EUCAST_rules <- function ( ... ) {
.Deprecated ( " eucast_rules" )
eucast_rules ( ... )
}
#' @rdname eucast_rules
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#' @export
interpretive_reading <- function ( ... ) {
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.Deprecated ( " eucast_rules" )
eucast_rules ( ... )
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}
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