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new antibiotics
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556
R/eucast_rules.R
556
R/eucast_rules.R
@ -27,94 +27,95 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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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 x data with antibiotic columns, like e.g. \code{amox} and \code{amcl}
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#' @param x data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}
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#' @param info print progress
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#' @param rules a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}
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#' @param verbose a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected. 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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#' @param ... column name of an antibiotic, see section Antibiotics
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#' @inheritParams first_isolate
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#' @details
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#' \strong{NOTE:} This function does not translate MIC values to RSI values. It only applies (1) inferred susceptibility and resistance based on results of other antibiotics and (2) intrinsic resistance based on taxonomic properties of a microorganism.
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#' \strong{Note:} This function does not translate MIC values to RSI values. Use \code{\link{as.rsi}} for that. \cr
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#' \strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
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#'
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#' The file used for applying all EUCAST rules can be retrieved with \code{\link{eucast_rules_file}()}. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by this function can be found when running this command: \cr
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#' The file used for applying all EUCAST rules can be retrieved with \code{\link{eucast_rules_file}()}. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by \code{eucast_rules()} can be found by running this command: \cr
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#' \code{AMR::EUCAST_RULES_FILE_LOCATION} (without brackets).
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#'
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#' In the source code it is located under \href{https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv}{\code{./inst/eucast/eucast_rules.tsv}}.
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#' In the source code the file containing all rules is located \href{https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv}{here}.
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#'
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#' \strong{Note:} When ampicillin (J01CA01) is not available but amoxicillin (J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
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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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#' 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{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will 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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#' Available abbrevations of the column containing antibiotics in the form '\strong{antimicrobial ID}: 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}),
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#' \strong{amik}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
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#' \strong{amox}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
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#' \strong{ampi}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
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#' \strong{azit}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
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#' \strong{azlo}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
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#' \strong{aztr}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
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#' \strong{cefa}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
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#' \strong{cfep}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
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#' \strong{cfot}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
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#' \strong{cfox}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
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#' \strong{cfra}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
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#' \strong{cfta}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
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#' \strong{cftr}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
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#' \strong{cfur}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
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#' \strong{chlo}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
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#' \strong{cipr}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
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#' \strong{clar}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
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#' \strong{clin}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
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#' \strong{clox}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
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#' \strong{coli}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
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#' \strong{czol}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
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#' \strong{dapt}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
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#' \strong{doxy}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
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#' \strong{erta}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
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#' \strong{eryt}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
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#' \strong{fosf}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
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#' \strong{fusi}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
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#' \strong{gent}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
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#' \strong{imip}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
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#' \strong{kana}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
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#' \strong{levo}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
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#' \strong{linc}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
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#' \strong{line}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
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#' \strong{mero}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
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#' \strong{mezl}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
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#' \strong{mino}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
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#' \strong{moxi}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
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#' \strong{nali}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
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#' \strong{neom}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
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#' \strong{neti}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
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#' \strong{nitr}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
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#' \strong{norf}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
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#' \strong{novo}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
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#' \strong{oflo}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
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#' \strong{peni}: (benzyl)penicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
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#' \strong{pipe}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
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#' \strong{pita}: piperacillin+tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
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#' \strong{poly}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
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#' \strong{pris}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
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#' \strong{qida}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
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#' \strong{rifa}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
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#' \strong{roxi}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
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#' \strong{siso}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
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#' \strong{teic}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
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#' \strong{tetr}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
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#' \strong{tica}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
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#' \strong{tige}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
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#' \strong{tobr}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
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#' \strong{trim}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
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#' \strong{trsu}: sulfamethoxazole and trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}),
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#' \strong{vanc}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{J01XA01}).
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#' \strong{AMC}: amoxicillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR02}{J01CR02}),
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#' \strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
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#' \strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
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#' \strong{AMP}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
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#' \strong{AZM}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
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#' \strong{AZL}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
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#' \strong{ATM}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
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#' \strong{RID}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
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#' \strong{FEP}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
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#' \strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
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#' \strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
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#' \strong{CED}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
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#' \strong{CAZ}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
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#' \strong{CRO}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
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#' \strong{CXM}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
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#' \strong{CHL}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
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#' \strong{CIP}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
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#' \strong{CLR}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
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#' \strong{CLI}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
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#' \strong{FLC}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
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#' \strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
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#' \strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
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#' \strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
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#' \strong{DOX}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
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#' \strong{ETP}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
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#' \strong{ERY}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
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#' \strong{FOS}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
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#' \strong{FUS}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
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#' \strong{GEN}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
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#' \strong{IPM}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
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#' \strong{KAN}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
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#' \strong{LVX}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
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#' \strong{LIN}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
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#' \strong{LNZ}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
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#' \strong{MEM}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
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#' \strong{MEZ}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
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#' \strong{MNO}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
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#' \strong{MFX}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
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#' \strong{MTR}: metronidazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01XD01}),
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#' \strong{NAL}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
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#' \strong{NEO}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
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#' \strong{NET}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
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#' \strong{NIT}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
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#' \strong{NOR}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
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#' \strong{NOV}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
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#' \strong{OFX}: ofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01MA01}),
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#' \strong{OXA}: oxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA01}{J01CF04}),
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#' \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
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#' \strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
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#' \strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
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#' \strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
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#' \strong{PRI}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
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#' \strong{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
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#' \strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
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#' \strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
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#' \strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
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#' \strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
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#' \strong{TCY}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
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#' \strong{TIC}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
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#' \strong{TGC}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
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#' \strong{TOB}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
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#' \strong{TMP}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
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#' \strong{SXT}: trimethoprim/sulfamethoxazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}),
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#' \strong{VAN}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{J01XA01}).
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#' @keywords interpretive eucast reading resistance
|
||||
#' @rdname eucast_rules
|
||||
#' @export
|
||||
#' @importFrom dplyr %>% select pull mutate_at vars group_by summarise n
|
||||
#' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic strip_style
|
||||
#' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic strip_style white
|
||||
#' @return The input of \code{tbl_}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with all original and new values of the affected bug-drug combinations.
|
||||
#' @source
|
||||
#' \itemize{
|
||||
@ -133,7 +134,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
|
||||
#' }
|
||||
#' }
|
||||
#'
|
||||
#' For editing the reference file (which is available with \code{\link{eucast_rules_file}}), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like amcl. They can be separated by comma: \code{"amcl, fluoroquinolones"}. The mo_property can be any column name from the \code{\link{microorganisms}} data set, or \code{genus_species} or \code{gramstain}. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).
|
||||
#' For editing the reference file (which is available with \code{\link{eucast_rules_file}}), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like AMC. They can be separated by comma: \code{"AMC, fluoroquinolones"}. The mo_property can be any column name from the \code{\link{microorganisms}} data set, or \code{genus_species} or \code{gramstain}. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).
|
||||
#' @inheritSection AMR Read more on our website!
|
||||
#' @examples
|
||||
#' a <- eucast_rules(septic_patients)
|
||||
@ -143,17 +144,17 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
|
||||
#' "Escherichia coli",
|
||||
#' "Klebsiella pneumoniae",
|
||||
#' "Pseudomonas aeruginosa"),
|
||||
#' vanc = "-", # Vancomycin
|
||||
#' amox = "-", # Amoxicillin
|
||||
#' coli = "-", # Colistin
|
||||
#' cfta = "-", # Ceftazidime
|
||||
#' cfur = "-", # Cefuroxime
|
||||
#' peni = "S", # Benzylpenicillin
|
||||
#' cfox = "S", # Cefoxitin
|
||||
#' VAN = "-", # Vancomycin
|
||||
#' AMX = "-", # Amoxicillin
|
||||
#' COL = "-", # Colistin
|
||||
#' CAZ = "-", # Ceftazidime
|
||||
#' CXM = "-", # Cefuroxime
|
||||
#' PEN = "S", # Penicillin G
|
||||
#' FOX = "S", # Cefoxitin
|
||||
#' stringsAsFactors = FALSE)
|
||||
#'
|
||||
#' a
|
||||
#' # mo vanc amox coli cfta cfur peni cfox
|
||||
#' # mo VAN AMX COL CAZ CXM PEN FOX
|
||||
#' # 1 Staphylococcus aureus - - - - - S S
|
||||
#' # 2 Enterococcus faecalis - - - - - S S
|
||||
#' # 3 Escherichia coli - - - - - S S
|
||||
@ -165,7 +166,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
|
||||
#' b <- eucast_rules(a)
|
||||
#'
|
||||
#' b
|
||||
#' # mo vanc amox coli cfta cfur peni cfox
|
||||
#' # mo VAN AMX COL CAZ CXM PEN FOX
|
||||
#' # 1 Staphylococcus aureus - S R R S S S
|
||||
#' # 2 Enterococcus faecalis - - R R R S R
|
||||
#' # 3 Escherichia coli R - - - - R S
|
||||
@ -181,81 +182,12 @@ eucast_rules <- function(x,
|
||||
info = TRUE,
|
||||
rules = c("breakpoints", "expert", "other", "all"),
|
||||
verbose = FALSE,
|
||||
amcl = guess_ab_col(),
|
||||
amik = guess_ab_col(),
|
||||
amox = guess_ab_col(),
|
||||
ampi = guess_ab_col(),
|
||||
azit = guess_ab_col(),
|
||||
azlo = guess_ab_col(),
|
||||
aztr = guess_ab_col(),
|
||||
cefa = guess_ab_col(),
|
||||
cfep = guess_ab_col(),
|
||||
cfot = guess_ab_col(),
|
||||
cfox = guess_ab_col(),
|
||||
cfra = guess_ab_col(),
|
||||
cfta = guess_ab_col(),
|
||||
cftr = guess_ab_col(),
|
||||
cfur = guess_ab_col(),
|
||||
chlo = guess_ab_col(),
|
||||
cipr = guess_ab_col(),
|
||||
clar = guess_ab_col(),
|
||||
clin = guess_ab_col(),
|
||||
clox = guess_ab_col(),
|
||||
coli = guess_ab_col(),
|
||||
czol = guess_ab_col(),
|
||||
dapt = guess_ab_col(),
|
||||
doxy = guess_ab_col(),
|
||||
erta = guess_ab_col(),
|
||||
eryt = guess_ab_col(),
|
||||
fosf = guess_ab_col(),
|
||||
fusi = guess_ab_col(),
|
||||
gent = guess_ab_col(),
|
||||
imip = guess_ab_col(),
|
||||
kana = guess_ab_col(),
|
||||
levo = guess_ab_col(),
|
||||
linc = guess_ab_col(),
|
||||
line = guess_ab_col(),
|
||||
mero = guess_ab_col(),
|
||||
mezl = guess_ab_col(),
|
||||
mino = guess_ab_col(),
|
||||
moxi = guess_ab_col(),
|
||||
nali = guess_ab_col(),
|
||||
neom = guess_ab_col(),
|
||||
neti = guess_ab_col(),
|
||||
nitr = guess_ab_col(),
|
||||
norf = guess_ab_col(),
|
||||
novo = guess_ab_col(),
|
||||
oflo = guess_ab_col(),
|
||||
oxac = guess_ab_col(),
|
||||
peni = guess_ab_col(),
|
||||
pipe = guess_ab_col(),
|
||||
pita = guess_ab_col(),
|
||||
poly = guess_ab_col(),
|
||||
pris = guess_ab_col(),
|
||||
qida = guess_ab_col(),
|
||||
rifa = guess_ab_col(),
|
||||
roxi = guess_ab_col(),
|
||||
siso = guess_ab_col(),
|
||||
teic = guess_ab_col(),
|
||||
tetr = guess_ab_col(),
|
||||
tica = guess_ab_col(),
|
||||
tige = guess_ab_col(),
|
||||
tobr = guess_ab_col(),
|
||||
trim = guess_ab_col(),
|
||||
trsu = guess_ab_col(),
|
||||
vanc = guess_ab_col(),
|
||||
...) {
|
||||
|
||||
|
||||
# support old `tbl` parameter
|
||||
if ("tbl" %in% names(list(...))) {
|
||||
x <- list(...)$tbl
|
||||
}
|
||||
|
||||
tbl_ <- x
|
||||
|
||||
if (!is.data.frame(tbl_)) {
|
||||
stop("`tbl_` must be a data frame.", call. = FALSE)
|
||||
stop("`x` must be a data frame.", call. = FALSE)
|
||||
}
|
||||
|
||||
# try to find columns based on type
|
||||
@ -277,7 +209,7 @@ eucast_rules <- function(x,
|
||||
|
||||
warned <- FALSE
|
||||
|
||||
txt_error <- function() { cat("", bgRed(black(" ERROR ")), "\n") }
|
||||
txt_error <- function() { cat("", bgRed(white(" ERROR ")), "\n") }
|
||||
txt_warning <- function() { if (warned == FALSE) { cat("", bgYellow(black(" WARNING ")), "\n") }; warned <<- TRUE }
|
||||
txt_ok <- function(no_of_changes) {
|
||||
if (warned == FALSE) {
|
||||
@ -294,145 +226,137 @@ eucast_rules <- function(x,
|
||||
}
|
||||
}
|
||||
|
||||
# check columns
|
||||
if (identical(amcl, as.name("guess_ab_col"))) { amcl <- guess_ab_col(tbl_, "amcl", verbose = verbose) }
|
||||
if (identical(amik, as.name("guess_ab_col"))) { amik <- guess_ab_col(tbl_, "amik", verbose = verbose) }
|
||||
if (identical(amox, as.name("guess_ab_col"))) { amox <- guess_ab_col(tbl_, "amox", verbose = verbose) }
|
||||
if (identical(ampi, as.name("guess_ab_col"))) { ampi <- guess_ab_col(tbl_, "ampi", verbose = verbose) }
|
||||
if (identical(azit, as.name("guess_ab_col"))) { azit <- guess_ab_col(tbl_, "azit", verbose = verbose) }
|
||||
if (identical(azlo, as.name("guess_ab_col"))) { azlo <- guess_ab_col(tbl_, "azlo", verbose = verbose) }
|
||||
if (identical(aztr, as.name("guess_ab_col"))) { aztr <- guess_ab_col(tbl_, "aztr", verbose = verbose) }
|
||||
if (identical(cefa, as.name("guess_ab_col"))) { cefa <- guess_ab_col(tbl_, "cefa", verbose = verbose) }
|
||||
if (identical(cfep, as.name("guess_ab_col"))) { cfep <- guess_ab_col(tbl_, "cfep", verbose = verbose) }
|
||||
if (identical(cfot, as.name("guess_ab_col"))) { cfot <- guess_ab_col(tbl_, "cfot", verbose = verbose) }
|
||||
if (identical(cfox, as.name("guess_ab_col"))) { cfox <- guess_ab_col(tbl_, "cfox", verbose = verbose) }
|
||||
if (identical(cfra, as.name("guess_ab_col"))) { cfra <- guess_ab_col(tbl_, "cfra", verbose = verbose) }
|
||||
if (identical(cfta, as.name("guess_ab_col"))) { cfta <- guess_ab_col(tbl_, "cfta", verbose = verbose) }
|
||||
if (identical(cftr, as.name("guess_ab_col"))) { cftr <- guess_ab_col(tbl_, "cftr", verbose = verbose) }
|
||||
if (identical(cfur, as.name("guess_ab_col"))) { cfur <- guess_ab_col(tbl_, "cfur", verbose = verbose) }
|
||||
if (identical(chlo, as.name("guess_ab_col"))) { chlo <- guess_ab_col(tbl_, "chlo", verbose = verbose) }
|
||||
if (identical(cipr, as.name("guess_ab_col"))) { cipr <- guess_ab_col(tbl_, "cipr", verbose = verbose) }
|
||||
if (identical(clar, as.name("guess_ab_col"))) { clar <- guess_ab_col(tbl_, "clar", verbose = verbose) }
|
||||
if (identical(clin, as.name("guess_ab_col"))) { clin <- guess_ab_col(tbl_, "clin", verbose = verbose) }
|
||||
if (identical(clox, as.name("guess_ab_col"))) { clox <- guess_ab_col(tbl_, "clox", verbose = verbose) }
|
||||
if (identical(coli, as.name("guess_ab_col"))) { coli <- guess_ab_col(tbl_, "coli", verbose = verbose) }
|
||||
if (identical(czol, as.name("guess_ab_col"))) { czol <- guess_ab_col(tbl_, "czol", verbose = verbose) }
|
||||
if (identical(dapt, as.name("guess_ab_col"))) { dapt <- guess_ab_col(tbl_, "dapt", verbose = verbose) }
|
||||
if (identical(doxy, as.name("guess_ab_col"))) { doxy <- guess_ab_col(tbl_, "doxy", verbose = verbose) }
|
||||
if (identical(erta, as.name("guess_ab_col"))) { erta <- guess_ab_col(tbl_, "erta", verbose = verbose) }
|
||||
if (identical(eryt, as.name("guess_ab_col"))) { eryt <- guess_ab_col(tbl_, "eryt", verbose = verbose) }
|
||||
if (identical(fosf, as.name("guess_ab_col"))) { fosf <- guess_ab_col(tbl_, "fosf", verbose = verbose) }
|
||||
if (identical(fusi, as.name("guess_ab_col"))) { fusi <- guess_ab_col(tbl_, "fusi", verbose = verbose) }
|
||||
if (identical(gent, as.name("guess_ab_col"))) { gent <- guess_ab_col(tbl_, "gent", verbose = verbose) }
|
||||
if (identical(imip, as.name("guess_ab_col"))) { imip <- guess_ab_col(tbl_, "imip", verbose = verbose) }
|
||||
if (identical(kana, as.name("guess_ab_col"))) { kana <- guess_ab_col(tbl_, "kana", verbose = verbose) }
|
||||
if (identical(levo, as.name("guess_ab_col"))) { levo <- guess_ab_col(tbl_, "levo", verbose = verbose) }
|
||||
if (identical(linc, as.name("guess_ab_col"))) { linc <- guess_ab_col(tbl_, "linc", verbose = verbose) }
|
||||
if (identical(line, as.name("guess_ab_col"))) { line <- guess_ab_col(tbl_, "line", verbose = verbose) }
|
||||
if (identical(mero, as.name("guess_ab_col"))) { mero <- guess_ab_col(tbl_, "mero", verbose = verbose) }
|
||||
if (identical(mezl, as.name("guess_ab_col"))) { mezl <- guess_ab_col(tbl_, "mezl", verbose = verbose) }
|
||||
if (identical(mino, as.name("guess_ab_col"))) { mino <- guess_ab_col(tbl_, "mino", verbose = verbose) }
|
||||
if (identical(moxi, as.name("guess_ab_col"))) { moxi <- guess_ab_col(tbl_, "moxi", verbose = verbose) }
|
||||
if (identical(nali, as.name("guess_ab_col"))) { nali <- guess_ab_col(tbl_, "nali", verbose = verbose) }
|
||||
if (identical(neom, as.name("guess_ab_col"))) { neom <- guess_ab_col(tbl_, "neom", verbose = verbose) }
|
||||
if (identical(neti, as.name("guess_ab_col"))) { neti <- guess_ab_col(tbl_, "neti", verbose = verbose) }
|
||||
if (identical(nitr, as.name("guess_ab_col"))) { nitr <- guess_ab_col(tbl_, "nitr", verbose = verbose) }
|
||||
if (identical(norf, as.name("guess_ab_col"))) { norf <- guess_ab_col(tbl_, "norf", verbose = verbose) }
|
||||
if (identical(novo, as.name("guess_ab_col"))) { novo <- guess_ab_col(tbl_, "novo", verbose = verbose) }
|
||||
if (identical(oflo, as.name("guess_ab_col"))) { oflo <- guess_ab_col(tbl_, "oflo", verbose = verbose) }
|
||||
if (identical(oxac, as.name("guess_ab_col"))) { oxac <- guess_ab_col(tbl_, "oxac", verbose = verbose) }
|
||||
if (identical(peni, as.name("guess_ab_col"))) { peni <- guess_ab_col(tbl_, "peni", verbose = verbose) }
|
||||
if (identical(pipe, as.name("guess_ab_col"))) { pipe <- guess_ab_col(tbl_, "pipe", verbose = verbose) }
|
||||
if (identical(pita, as.name("guess_ab_col"))) { pita <- guess_ab_col(tbl_, "pita", verbose = verbose) }
|
||||
if (identical(poly, as.name("guess_ab_col"))) { poly <- guess_ab_col(tbl_, "poly", verbose = verbose) }
|
||||
if (identical(pris, as.name("guess_ab_col"))) { pris <- guess_ab_col(tbl_, "pris", verbose = verbose) }
|
||||
if (identical(qida, as.name("guess_ab_col"))) { qida <- guess_ab_col(tbl_, "qida", verbose = verbose) }
|
||||
if (identical(rifa, as.name("guess_ab_col"))) { rifa <- guess_ab_col(tbl_, "rifa", verbose = verbose) }
|
||||
if (identical(roxi, as.name("guess_ab_col"))) { roxi <- guess_ab_col(tbl_, "roxi", verbose = verbose) }
|
||||
if (identical(siso, as.name("guess_ab_col"))) { siso <- guess_ab_col(tbl_, "siso", verbose = verbose) }
|
||||
if (identical(teic, as.name("guess_ab_col"))) { teic <- guess_ab_col(tbl_, "teic", verbose = verbose) }
|
||||
if (identical(tetr, as.name("guess_ab_col"))) { tetr <- guess_ab_col(tbl_, "tetr", verbose = verbose) }
|
||||
if (identical(tica, as.name("guess_ab_col"))) { tica <- guess_ab_col(tbl_, "tica", verbose = verbose) }
|
||||
if (identical(tige, as.name("guess_ab_col"))) { tige <- guess_ab_col(tbl_, "tige", verbose = verbose) }
|
||||
if (identical(tobr, as.name("guess_ab_col"))) { tobr <- guess_ab_col(tbl_, "tobr", verbose = verbose) }
|
||||
if (identical(trim, as.name("guess_ab_col"))) { trim <- guess_ab_col(tbl_, "trim", verbose = verbose) }
|
||||
if (identical(trsu, as.name("guess_ab_col"))) { trsu <- guess_ab_col(tbl_, "trsu", verbose = verbose) }
|
||||
if (identical(vanc, as.name("guess_ab_col"))) { vanc <- guess_ab_col(tbl_, "vanc", verbose = verbose) }
|
||||
col.list <- c(amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfra, cfep, cfot,
|
||||
cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli,
|
||||
czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana,
|
||||
levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr,
|
||||
novo, norf, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa,
|
||||
roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc)
|
||||
if (length(col.list) < 63) {
|
||||
warning('Some columns do not exist -- THIS MAY STRONGLY INFLUENCE THE OUTCOME.',
|
||||
immediate. = TRUE,
|
||||
call. = FALSE)
|
||||
}
|
||||
col.list <- check_available_columns(tbl = tbl_, col.list = col.list, info = info)
|
||||
amcl <- col.list[amcl]
|
||||
amik <- col.list[amik]
|
||||
amox <- col.list[amox]
|
||||
ampi <- col.list[ampi]
|
||||
azit <- col.list[azit]
|
||||
azlo <- col.list[azlo]
|
||||
aztr <- col.list[aztr]
|
||||
cefa <- col.list[cefa]
|
||||
cfep <- col.list[cfep]
|
||||
cfot <- col.list[cfot]
|
||||
cfox <- col.list[cfox]
|
||||
cfra <- col.list[cfra]
|
||||
cfta <- col.list[cfta]
|
||||
cftr <- col.list[cftr]
|
||||
cfur <- col.list[cfur]
|
||||
chlo <- col.list[chlo]
|
||||
cipr <- col.list[cipr]
|
||||
clar <- col.list[clar]
|
||||
clin <- col.list[clin]
|
||||
clox <- col.list[clox]
|
||||
coli <- col.list[coli]
|
||||
czol <- col.list[czol]
|
||||
dapt <- col.list[dapt]
|
||||
doxy <- col.list[doxy]
|
||||
erta <- col.list[erta]
|
||||
eryt <- col.list[eryt]
|
||||
fosf <- col.list[fosf]
|
||||
fusi <- col.list[fusi]
|
||||
gent <- col.list[gent]
|
||||
imip <- col.list[imip]
|
||||
kana <- col.list[kana]
|
||||
levo <- col.list[levo]
|
||||
linc <- col.list[linc]
|
||||
line <- col.list[line]
|
||||
mero <- col.list[mero]
|
||||
mezl <- col.list[mezl]
|
||||
mino <- col.list[mino]
|
||||
moxi <- col.list[moxi]
|
||||
nali <- col.list[nali]
|
||||
neom <- col.list[neom]
|
||||
neti <- col.list[neti]
|
||||
nitr <- col.list[nitr]
|
||||
norf <- col.list[norf]
|
||||
novo <- col.list[novo]
|
||||
oflo <- col.list[oflo]
|
||||
oxac <- col.list[oxac]
|
||||
peni <- col.list[peni]
|
||||
pipe <- col.list[pipe]
|
||||
pita <- col.list[pita]
|
||||
poly <- col.list[poly]
|
||||
pris <- col.list[pris]
|
||||
qida <- col.list[qida]
|
||||
rifa <- col.list[rifa]
|
||||
roxi <- col.list[roxi]
|
||||
siso <- col.list[siso]
|
||||
teic <- col.list[teic]
|
||||
tetr <- col.list[tetr]
|
||||
tica <- col.list[tica]
|
||||
tige <- col.list[tige]
|
||||
tobr <- col.list[tobr]
|
||||
trim <- col.list[trim]
|
||||
trsu <- col.list[trsu]
|
||||
vanc <- col.list[vanc]
|
||||
cols_ab <- get_column_abx(tbl = x,
|
||||
soft_dependencies = c("AMC",
|
||||
"AMK",
|
||||
"AMX",
|
||||
"AMP",
|
||||
"AZM",
|
||||
"AZL",
|
||||
"ATM",
|
||||
"RID",
|
||||
"FEP",
|
||||
"CTX",
|
||||
"FOX",
|
||||
"CED",
|
||||
"CAZ",
|
||||
"CRO",
|
||||
"CXM",
|
||||
"CHL",
|
||||
"CIP",
|
||||
"CLR",
|
||||
"CLI",
|
||||
"FLC",
|
||||
"COL",
|
||||
"CZO",
|
||||
"DAP",
|
||||
"DOX",
|
||||
"ETP",
|
||||
"ERY",
|
||||
"FOS",
|
||||
"FUS",
|
||||
"GEN",
|
||||
"IPM",
|
||||
"KAN",
|
||||
"LVX",
|
||||
"LIN",
|
||||
"LNZ",
|
||||
"MEM",
|
||||
"MEZ",
|
||||
"MNO",
|
||||
"MFX",
|
||||
"NAL",
|
||||
"NEO",
|
||||
"NET",
|
||||
"NIT",
|
||||
"NOR",
|
||||
"NOV",
|
||||
"OFX",
|
||||
"OXA",
|
||||
"PEN",
|
||||
"PIP",
|
||||
"TZP",
|
||||
"PLB",
|
||||
"PRI",
|
||||
"QDA",
|
||||
"RIF",
|
||||
"RXT",
|
||||
"SIS",
|
||||
"TEC",
|
||||
"TCY",
|
||||
"TIC",
|
||||
"TGC",
|
||||
"TOB",
|
||||
"TMP",
|
||||
"SXT",
|
||||
"VAN"),
|
||||
hard_dependencies = NULL,
|
||||
verbose = verbose,
|
||||
...)
|
||||
|
||||
AMC <- cols_ab['AMC']
|
||||
AMK <- cols_ab['AMK']
|
||||
AMP <- cols_ab['AMP']
|
||||
AMX <- cols_ab['AMX']
|
||||
ATM <- cols_ab['ATM']
|
||||
AZL <- cols_ab['AZL']
|
||||
AZM <- cols_ab['AZM']
|
||||
CAZ <- cols_ab['CAZ']
|
||||
CED <- cols_ab['CED']
|
||||
CHL <- cols_ab['CHL']
|
||||
CIP <- cols_ab['CIP']
|
||||
CLI <- cols_ab['CLI']
|
||||
CLR <- cols_ab['CLR']
|
||||
COL <- cols_ab['COL']
|
||||
CRO <- cols_ab['CRO']
|
||||
CTX <- cols_ab['CTX']
|
||||
CXM <- cols_ab['CXM']
|
||||
CZO <- cols_ab['CZO']
|
||||
DAP <- cols_ab['DAP']
|
||||
DOX <- cols_ab['DOX']
|
||||
ERY <- cols_ab['ERY']
|
||||
ETP <- cols_ab['ETP']
|
||||
FEP <- cols_ab['FEP']
|
||||
FLC <- cols_ab['FLC']
|
||||
FOS <- cols_ab['FOS']
|
||||
FOX <- cols_ab['FOX']
|
||||
FUS <- cols_ab['FUS']
|
||||
GEN <- cols_ab['GEN']
|
||||
IPM <- cols_ab['IPM']
|
||||
KAN <- cols_ab['KAN']
|
||||
LIN <- cols_ab['LIN']
|
||||
LNZ <- cols_ab['LNZ']
|
||||
LVX <- cols_ab['LVX']
|
||||
MEM <- cols_ab['MEM']
|
||||
MEZ <- cols_ab['MEZ']
|
||||
MFX <- cols_ab['MFX']
|
||||
MNO <- cols_ab['MNO']
|
||||
NAL <- cols_ab['NAL']
|
||||
NEO <- cols_ab['NEO']
|
||||
NET <- cols_ab['NET']
|
||||
NIT <- cols_ab['NIT']
|
||||
NOR <- cols_ab['NOR']
|
||||
NOV <- cols_ab['NOV']
|
||||
OFX <- cols_ab['OFX']
|
||||
OXA <- cols_ab['OXA']
|
||||
PEN <- cols_ab['PEN']
|
||||
PIP <- cols_ab['PIP']
|
||||
PLB <- cols_ab['PLB']
|
||||
PRI <- cols_ab['PRI']
|
||||
QDA <- cols_ab['QDA']
|
||||
RID <- cols_ab['RID']
|
||||
RIF <- cols_ab['RIF']
|
||||
RXT <- cols_ab['RXT']
|
||||
SIS <- cols_ab['SIS']
|
||||
SXT <- cols_ab['SXT']
|
||||
TCY <- cols_ab['TCY']
|
||||
TEC <- cols_ab['TEC']
|
||||
TGC <- cols_ab['TGC']
|
||||
TIC <- cols_ab['TIC']
|
||||
TMP <- cols_ab['TMP']
|
||||
TOB <- cols_ab['TOB']
|
||||
TZP <- cols_ab['TZP']
|
||||
VAN <- cols_ab['VAN']
|
||||
|
||||
ab_missing <- function(ab) {
|
||||
all(ab %in% c(NULL, NA))
|
||||
@ -521,41 +445,41 @@ eucast_rules <- function(x,
|
||||
}
|
||||
|
||||
# since ampicillin ^= amoxicillin, get the first from the latter (not in original EUCAST table)
|
||||
if (!ab_missing(ampi) & !ab_missing(amox)) {
|
||||
if (!ab_missing(AMP) & !ab_missing(AMX)) {
|
||||
if (verbose == TRUE) {
|
||||
cat("\n VERBOSE: transforming",
|
||||
length(which(tbl_[, amox] == "S" & !tbl_[, ampi] %in% c("S", "I", "R"))),
|
||||
length(which(tbl_[, AMX] == "S" & !tbl_[, AMP] %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"))),
|
||||
length(which(tbl_[, AMX] == "I" & !tbl_[, AMP] %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"))),
|
||||
length(which(tbl_[, AMX] == "R" & !tbl_[, AMP] %in% c("S", "I", "R"))),
|
||||
"empty ampicillin fields to 'R' based on amoxicillin. \n")
|
||||
}
|
||||
tbl_[which(tbl_[, amox] == "S" & !tbl_[, ampi] %in% c("S", "I", "R")), ampi] <- "S"
|
||||
tbl_[which(tbl_[, amox] == "I" & !tbl_[, ampi] %in% c("S", "I", "R")), ampi] <- "I"
|
||||
tbl_[which(tbl_[, amox] == "R" & !tbl_[, ampi] %in% c("S", "I", "R")), ampi] <- "R"
|
||||
} else if (ab_missing(ampi) & !ab_missing(amox)) {
|
||||
tbl_[which(tbl_[, AMX] == "S" & !tbl_[, AMP] %in% c("S", "I", "R")), AMP] <- "S"
|
||||
tbl_[which(tbl_[, AMX] == "I" & !tbl_[, AMP] %in% c("S", "I", "R")), AMP] <- "I"
|
||||
tbl_[which(tbl_[, AMX] == "R" & !tbl_[, AMP] %in% c("S", "I", "R")), AMP] <- "R"
|
||||
} else if (ab_missing(AMP) & !ab_missing(AMX)) {
|
||||
# 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
|
||||
message(blue(paste0("NOTE: Using column `", bold(AMX), "` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.")))
|
||||
AMP <- AMX
|
||||
}
|
||||
|
||||
# antibiotic classes
|
||||
aminoglycosides <- c(tobr, gent, kana, neom, neti, siso)
|
||||
tetracyclines <- c(doxy, mino, tetr) # since EUCAST v3.1 tige(cycline) is set apart
|
||||
polymyxins <- c(poly, coli)
|
||||
macrolides <- c(eryt, azit, roxi, clar) # since EUCAST v3.1 clinda is set apart
|
||||
glycopeptides <- c(vanc, teic)
|
||||
streptogramins <- c(qida, pris) # should officially also be quinupristin/dalfopristin
|
||||
cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
|
||||
cephalosporins_without_cfta <- cephalosporins[cephalosporins != ifelse(is.null(cfta), "", cfta)]
|
||||
carbapenems <- c(erta, imip, mero)
|
||||
aminopenicillins <- c(ampi, amox)
|
||||
ureidopenicillins <- c(pipe, pita, azlo, mezl)
|
||||
fluoroquinolones <- c(oflo, cipr, norf, levo, moxi)
|
||||
all_betalactams <- c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, amcl, oxac, clox, peni)
|
||||
aminoglycosides <- c(TOB, GEN, KAN, NEO, NET, SIS)
|
||||
tetracyclines <- c(DOX, MNO, TCY) # since EUCAST v3.1 tigecycline (TGC) is set apart
|
||||
polymyxins <- c(PLB, COL)
|
||||
macrolides <- c(ERY, AZM, RXT, CLR) # since EUCAST v3.1 clinda is set apart
|
||||
glycopeptides <- c(VAN, TEC)
|
||||
streptogramins <- c(QDA, PRI) # should officially also be quinupristin/dalfopristin
|
||||
aminopenicillins <- c(AMP, AMX)
|
||||
cephalosporins <- c(FEP, CTX, FOX, CED, CAZ, CRO, CXM, CZO)
|
||||
cephalosporins_without_CAZ <- cephalosporins[cephalosporins != ifelse(is.null(CAZ), "", CAZ)]
|
||||
carbapenems <- c(ETP, IPM, MEM)
|
||||
ureidopenicillins <- c(PIP, TZP, AZL, MEZ)
|
||||
all_betalactams <- c(aminopenicillins, cephalosporins, carbapenems, ureidopenicillins, AMC, OXA, FLC, PEN)
|
||||
fluoroquinolones <- c(OFX, CIP, NOR, LVX, MFX)
|
||||
|
||||
# Help function to get available antibiotic column names ------------------
|
||||
get_antibiotic_columns <- function(x, df) {
|
||||
@ -578,7 +502,7 @@ eucast_rules <- function(x,
|
||||
rule_group_current <- eucast_rules_df[i, "reference.rule_group"]
|
||||
rule_group_next <- eucast_rules_df[min(nrow(eucast_rules_df), i + 1), "reference.rule_group"]
|
||||
if (is.na(eucast_rules_df[i, 4])) {
|
||||
rule_text <- paste(eucast_rules_df[i, 6], "=", eucast_rules_df[i, 7])
|
||||
rule_text <- paste("always:", eucast_rules_df[i, 6], "=", eucast_rules_df[i, 7])
|
||||
} else {
|
||||
rule_text <- paste("if", eucast_rules_df[i, 4], "=", eucast_rules_df[i, 5],
|
||||
"then", eucast_rules_df[i, 6], "=", eucast_rules_df[i, 7])
|
||||
|
||||
Reference in New Issue
Block a user