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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. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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# global variables
EUCAST_VERSION_BREAKPOINTS <- " 9.0, 2019"
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{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 ... 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. Use \code{\link{as.rsi}} for that. \cr
#' \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 containing all EUCAST rules is located here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
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#'
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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{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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#' The following antibiotics are used for the functions \code{\link{eucast_rules}} and \code{\link{mdro}}. These are shown in the format '\strong{antimicrobial ID}: name (\emph{ATC code})', sorted by name:
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#'
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#' \strong{AMK}: amikacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB06}{J01GB06}),
#' \strong{AMX}: amoxicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA04}{J01CA04}),
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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{AMP}: ampicillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA01}{J01CA01}),
#' \strong{AZM}: azithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA10}{J01FA10}),
#' \strong{AZL}: azlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA09}{J01CA09}),
#' \strong{ATM}: aztreonam (\href{https://www.whocc.no/atc_ddd_index/?code=J01DF01}{J01DF01}),
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#' \strong{CAP}: capreomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB30}{J04AB30}),
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#' \strong{RID}: cefaloridine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB02}{J01DB02}),
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#' \strong{CZO}: cefazolin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB04}{J01DB04}),
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#' \strong{FEP}: cefepime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DE01}{J01DE01}),
#' \strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
#' \strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
#' \strong{CED}: cefradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
#' \strong{CAZ}: ceftazidime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD02}{J01DD02}),
#' \strong{CRO}: ceftriaxone (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD04}{J01DD04}),
#' \strong{CXM}: cefuroxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC02}{J01DC02}),
#' \strong{CHL}: chloramphenicol (\href{https://www.whocc.no/atc_ddd_index/?code=J01BA01}{J01BA01}),
#' \strong{CIP}: ciprofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA02}{J01MA02}),
#' \strong{CLR}: clarithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA09}{J01FA09}),
#' \strong{CLI}: clindamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF01}{J01FF01}),
#' \strong{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
#' \strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
#' \strong{DOX}: doxycycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA02}{J01AA02}),
#' \strong{ETP}: ertapenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH03}{J01DH03}),
#' \strong{ERY}: erythromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA01}{J01FA01}),
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#' \strong{ETH}: ethambutol (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK02}{J04AK02}),
#' \strong{FLC}: flucloxacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CF05}{J01CF05}),
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#' \strong{FOS}: fosfomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX01}{J01XX01}),
#' \strong{FUS}: fusidic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XC01}{J01XC01}),
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#' \strong{GAT}: gatifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA16}{J01MA16}),
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#' \strong{GEN}: gentamicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB03}{J01GB03}),
#' \strong{IPM}: imipenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH51}{J01DH51}),
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#' \strong{INH}: isoniazid (\href{https://www.whocc.no/atc_ddd_index/?code=J04AC01}{J04AC01}),
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#' \strong{KAN}: kanamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB04}{J01GB04}),
#' \strong{LVX}: levofloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA12}{J01MA12}),
#' \strong{LIN}: lincomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FF02}{J01FF02}),
#' \strong{LNZ}: linezolid (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX08}{J01XX08}),
#' \strong{MEM}: meropenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH02}{J01DH02}),
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#' \strong{MTR}: metronidazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01XD01}{J01XD01}),
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#' \strong{MEZ}: mezlocillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA10}{J01CA10}),
#' \strong{MNO}: minocycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA08}{J01AA08}),
#' \strong{MFX}: moxifloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA14}{J01MA14}),
#' \strong{NAL}: nalidixic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01MB02}{J01MB02}),
#' \strong{NEO}: neomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB05}{J01GB05}),
#' \strong{NET}: netilmicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB07}{J01GB07}),
#' \strong{NIT}: nitrofurantoin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XE01}{J01XE01}),
#' \strong{NOR}: norfloxacin (\href{https://www.whocc.no/atc_ddd_index/?code=J01MA06}{J01MA06}),
#' \strong{NOV}: novobiocin (an ATCvet code: \href{https://www.whocc.no/atc_ddd_index/?code=QJ01XX95}{QJ01XX95}),
#' \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=J01CF04}{J01CF04}),
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#' \strong{PEN}: penicillin G (\href{https://www.whocc.no/atc_ddd_index/?code=J01CE01}{J01CE01}),
#' \strong{PIP}: piperacillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA12}{J01CA12}),
#' \strong{TZP}: piperacillin/tazobactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR05}{J01CR05}),
#' \strong{PLB}: polymyxin B (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB02}{J01XB02}),
#' \strong{PRI}: pristinamycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG01}{J01FG01}),
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#' \strong{PZA}: pyrazinamide (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK01}{J04AK01}),
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#' \strong{QDA}: quinupristin/dalfopristin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FG02}{J01FG02}),
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#' \strong{RIB}: rifabutin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB04}{J04AB04}),
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#' \strong{RIF}: rifampicin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
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#' \strong{RIF}: rifampin (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB02}{J04AB02}),
#' \strong{RFP}: rifapentine (\href{https://www.whocc.no/atc_ddd_index/?code=J04AB05}{J04AB05}),
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#' \strong{RXT}: roxithromycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01FA06}{J01FA06}),
#' \strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
#' \strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
#' \strong{TCY}: tetracycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA07}{J01AA07}),
#' \strong{TIC}: ticarcillin (\href{https://www.whocc.no/atc_ddd_index/?code=J01CA13}{J01CA13}),
#' \strong{TGC}: tigecycline (\href{https://www.whocc.no/atc_ddd_index/?code=J01AA12}{J01AA12}),
#' \strong{TOB}: tobramycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB01}{J01GB01}),
#' \strong{TMP}: trimethoprim (\href{https://www.whocc.no/atc_ddd_index/?code=J01EA01}{J01EA01}),
#' \strong{SXT}: trimethoprim/sulfamethoxazole (\href{https://www.whocc.no/atc_ddd_index/?code=J01EE01}{J01EE01}),
#' \strong{VAN}: 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 group_by summarise n
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#' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic strip_style white
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#' @return The input of \code{x}, 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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#' VAN = "-", # Vancomycin
#' AMX = "-", # Amoxicillin
#' COL = "-", # Colistin
#' CAZ = "-", # Ceftazidime
#' CXM = "-", # Cefuroxime
#' PEN = "S", # Penicillin G
#' FOX = "S", # Cefoxitin
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#' stringsAsFactors = FALSE)
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#'
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#' a
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#' # mo VAN AMX COL CAZ CXM PEN FOX
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#' # 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 VAN AMX COL CAZ CXM PEN FOX
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#' # 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 ( x ,
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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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... ) {
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x <- x
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if ( ! is.data.frame ( x ) ) {
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stop ( " `x` must be a data frame." , call. = FALSE )
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}
# try to find columns based on type
# -- mo
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if ( is.null ( col_mo ) ) {
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col_mo <- search_type_in_df ( x = x , 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" ) ) ) {
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stop ( " `rules` must be one or more of: 'breakpoints', 'expert', 'other', 'all'." )
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}
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if ( is.null ( col_mo ) ) {
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stop ( " `col_mo` must be set" )
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}
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warned <- FALSE
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txt_error <- function ( ) { cat ( " " , bgRed ( white ( " ERROR " ) ) , " \n" ) }
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txt_warning <- function ( ) { if ( warned == FALSE ) { cat ( " " , bgYellow ( black ( " WARNING " ) ) , " \n" ) } ; warned <<- TRUE }
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txt_ok <- function ( no_of_changes ) {
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if ( warned == FALSE ) {
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if ( no_of_changes > 0 ) {
if ( no_of_changes == 1 ) {
cat ( blue ( " (1 new change)\n" ) )
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} else {
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cat ( blue ( paste0 ( " (" , no_of_changes , " new changes)\n" ) ) )
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}
} else {
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cat ( green ( " (no new changes)\n" ) )
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}
warned <<- FALSE
}
}
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cols_ab <- get_column_abx ( x = x ,
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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 ,
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verbose = verbose ,
... )
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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' ]
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ab_missing <- function ( ab ) {
all ( ab %in% c ( NULL , NA ) )
}
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verbose_info <- data.frame ( row = integer ( 0 ) ,
col = character ( 0 ) ,
mo_fullname = character ( 0 ) ,
old = character ( 0 ) ,
new = character ( 0 ) ,
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rule = character ( 0 ) ,
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rule_group = character ( 0 ) ,
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rule_name = 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 <- x_original
before <- as.character ( unlist ( as.list ( x_original [rows , cols ] ) ) )
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tryCatch (
# insert into original table
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x_original [rows , cols ] <<- to ,
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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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x [rows , cols ] <<- x_original [rows , cols ]
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after <- as.character ( unlist ( as.list ( x_original [rows , cols ] ) ) )
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# before_df might not be a data.frame, but a tibble of data.table instead
old <- as.data.frame ( before_df , stringsAsFactors = FALSE ) [rows , ]
no_of_changes_this_run <- 0
for ( i in 1 : length ( cols ) ) {
verbose_new <- data.frame ( row = rows ,
col = cols [i ] ,
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mo_fullname = x [rows , " fullname" ] ,
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old = as.character ( old [ , cols [i ] ] ) ,
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new = as.character ( x [rows , cols [i ] ] ) ,
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rule = strip_style ( rule [1 ] ) ,
rule_group = strip_style ( rule [2 ] ) ,
rule_name = strip_style ( rule [3 ] ) ,
stringsAsFactors = FALSE )
colnames ( verbose_new ) <- c ( " row" , " col" , " mo_fullname" , " old" , " new" , " rule" , " rule_group" , " rule_name" )
verbose_new <- verbose_new %>% filter ( old != new | is.na ( old ) )
verbose_info <<- rbind ( verbose_info , verbose_new )
no_of_changes_this_run <- no_of_changes_this_run + nrow ( verbose_new )
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}
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# return number of (new) changes
return ( no_of_changes_this_run )
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}
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# return number of (new) changes: none.
return ( 0 )
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}
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# save original table
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x_original <- x
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# join to microorganisms data set
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suppressWarnings (
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x <- x %>%
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mutate_at ( vars ( col_mo ) , as.mo ) %>%
left_join_microorganisms ( by = col_mo , suffix = c ( " _oldcols" , " " ) ) %>%
mutate ( gramstain = mo_gramstain ( pull ( ., col_mo ) , language = " en" ) ,
genus_species = paste ( genus , species ) ) %>%
as.data.frame ( stringsAsFactors = FALSE )
)
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if ( info == TRUE ) {
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cat ( paste0 (
" \nRules by the " , bold ( " European Committee on Antimicrobial Susceptibility Testing (EUCAST)" ) ,
" \n" , blue ( " http://eucast.org/" ) , " \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 ( ! ab_missing ( AMP ) & ! ab_missing ( AMX ) ) {
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if ( verbose == TRUE ) {
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cat ( " \n VERBOSE: transforming" ,
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length ( which ( x [ , AMX ] == " S" & ! x [ , AMP ] %in% c ( " S" , " I" , " R" ) ) ) ,
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" empty ampicillin fields to 'S' based on amoxicillin. " )
cat ( " \n VERBOSE: transforming" ,
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length ( which ( x [ , AMX ] == " I" & ! x [ , AMP ] %in% c ( " S" , " I" , " R" ) ) ) ,
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" empty ampicillin fields to 'I' based on amoxicillin. " )
cat ( " \n VERBOSE: transforming" ,
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length ( which ( x [ , AMX ] == " R" & ! x [ , AMP ] %in% c ( " S" , " I" , " R" ) ) ) ,
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" empty ampicillin fields to 'R' based on amoxicillin. \n" )
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}
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x [which ( x [ , AMX ] == " S" & ! x [ , AMP ] %in% c ( " S" , " I" , " R" ) ) , AMP ] <- " S"
x [which ( x [ , AMX ] == " I" & ! x [ , AMP ] %in% c ( " S" , " I" , " R" ) ) , AMP ] <- " I"
x [which ( x [ , AMX ] == " R" & ! x [ , AMP ] %in% c ( " S" , " I" , " R" ) ) , AMP ] <- " R"
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} else if ( ab_missing ( AMP ) & ! ab_missing ( AMX ) ) {
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# ampicillin column is missing, but amoxicillin is available
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message ( blue ( paste0 ( " NOTE: Using column `" , bold ( AMX ) , " ` as input for ampicillin (J01CA01) since many EUCAST rules depend on it." ) ) )
AMP <- AMX
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}
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# antibiotic classes
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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 )
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# Help function to get available antibiotic column names ------------------
get_antibiotic_columns <- function ( x , df ) {
x <- trimws ( unlist ( strsplit ( x , " ," , fixed = TRUE ) ) )
y <- character ( 0 )
for ( i in 1 : length ( x ) ) {
y <- c ( y , tryCatch ( get ( x [i ] ) , error = function ( e ) " " ) )
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}
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y [y != " " & y %in% colnames ( df ) ]
}
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eucast_rules_df <- eucast_rules_file # internal data file
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no_of_changes <- 0
for ( i in 1 : nrow ( eucast_rules_df ) ) {
rule_previous <- eucast_rules_df [max ( 1 , i - 1 ) , " reference.rule" ]
rule_current <- eucast_rules_df [i , " reference.rule" ]
rule_next <- eucast_rules_df [min ( nrow ( eucast_rules_df ) , i + 1 ) , " reference.rule" ]
rule_group_previous <- eucast_rules_df [max ( 1 , i - 1 ) , " reference.rule_group" ]
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 ] ) ) {
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rule_text <- paste ( " always:" , eucast_rules_df [i , 6 ] , " =" , eucast_rules_df [i , 7 ] )
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} 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 ] )
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}
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if ( i == 1 ) {
rule_previous <- " "
rule_group_previous <- " "
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}
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if ( i == nrow ( eucast_rules_df ) ) {
rule_next <- " "
rule_group_next <- " "
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}
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# don't apply rules if user doesn't want to apply them
if ( rule_group_current %like% " breakpoint" & ! any ( c ( " all" , " breakpoints" ) %in% rules ) ) {
next
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}
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if ( rule_group_current %like% " expert" & ! any ( c ( " all" , " expert" ) %in% rules ) ) {
next
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}
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if ( rule_group_current %like% " other" & ! any ( c ( " all" , " other" ) %in% rules ) ) {
next
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}
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if ( info == TRUE ) {
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# Print rule (group) ------------------------------------------------------
if ( rule_group_current != rule_group_previous ) {
# is new rule group, one of Breakpoints, Expert Rules and Other
cat ( bold (
case_when (
rule_group_current %like% " breakpoint" ~
paste0 ( " \nEUCAST Clinical Breakpoints (v" , EUCAST_VERSION_BREAKPOINTS , " )\n" ) ,
rule_group_current %like% " expert" ~
paste0 ( " \nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v" , EUCAST_VERSION_EXPERT_RULES , " )\n" ) ,
TRUE ~
" \nOther rules\n"
)
) )
}
# Print rule -------------------------------------------------------------
if ( rule_current != rule_previous ) {
# is new rule within group, print its name
if ( rule_current %in% c ( AMR :: microorganisms $ family ,
AMR :: microorganisms $ fullname ) ) {
cat ( italic ( rule_current ) )
} else {
cat ( rule_current )
}
warned <- FALSE
}
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}
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# Get rule from file ------------------------------------------------------
col_mo_property <- eucast_rules_df [i , 1 ]
like_is_one_of <- eucast_rules_df [i , 2 ]
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# be sure to comprise all coagulase-negative/-positive Staphylococci when they are mentioned
if ( eucast_rules_df [i , 3 ] %like% " coagulase-" ) {
suppressWarnings (
all_staph <- AMR :: microorganisms %>%
filter ( genus == " Staphylococcus" ) %>%
mutate ( CNS_CPS = mo_fullname ( mo , Becker = " all" ) )
)
if ( eucast_rules_df [i , 3 ] %like% " coagulase-" ) {
eucast_rules_df [i , 3 ] <- paste0 ( " ^(" ,
paste0 ( all_staph %>%
filter ( CNS_CPS %like% " coagulase-negative" ) %>%
pull ( fullname ) ,
collapse = " |" ) ,
" )$" )
} else {
eucast_rules_df [i , 3 ] <- paste0 ( " ^(" ,
paste0 ( all_staph %>%
filter ( CNS_CPS %like% " coagulase-positive" ) %>%
pull ( fullname ) ,
collapse = " |" ) ,
" )$" )
}
like_is_one_of <- " like"
}
if ( like_is_one_of == " is" ) {
mo_value <- paste0 ( " ^" , eucast_rules_df [i , 3 ] , " $" )
} else if ( like_is_one_of == " one_of" ) {
# "Clostridium, Actinomyces, ..." -> "^(Clostridium|Actinomyces|...)$"
mo_value <- paste0 ( " ^(" ,
paste ( trimws ( unlist ( strsplit ( eucast_rules_df [i , 3 ] , " ," , fixed = TRUE ) ) ) ,
collapse = " |" ) ,
" )$" )
} else if ( like_is_one_of == " like" ) {
mo_value <- eucast_rules_df [i , 3 ]
} else {
stop ( " invalid like_is_one_of" , call. = FALSE )
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}
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source_antibiotics <- eucast_rules_df [i , 4 ]
source_value <- trimws ( unlist ( strsplit ( eucast_rules_df [i , 5 ] , " ," , fixed = TRUE ) ) )
target_antibiotics <- eucast_rules_df [i , 6 ]
target_value <- eucast_rules_df [i , 7 ]
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if ( is.na ( source_antibiotics ) ) {
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rows <- tryCatch ( which ( x [ , col_mo_property ] %like% mo_value ) ,
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error = function ( e ) integer ( 0 ) )
} else {
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source_antibiotics <- get_antibiotic_columns ( source_antibiotics , x )
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if ( length ( source_value ) == 1 & length ( source_antibiotics ) > 1 ) {
source_value <- rep ( source_value , length ( source_antibiotics ) )
}
if ( length ( source_antibiotics ) == 0 ) {
rows <- integer ( 0 )
} else if ( length ( source_antibiotics ) == 1 ) {
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rows <- tryCatch ( which ( x [ , col_mo_property ] %like% mo_value
& x [ , source_antibiotics [1L ] ] == source_value [1L ] ) ,
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error = function ( e ) integer ( 0 ) )
} else if ( length ( source_antibiotics ) == 2 ) {
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rows <- tryCatch ( which ( x [ , col_mo_property ] %like% mo_value
& x [ , source_antibiotics [1L ] ] == source_value [1L ]
& x [ , source_antibiotics [2L ] ] == source_value [2L ] ) ,
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error = function ( e ) integer ( 0 ) )
} else if ( length ( source_antibiotics ) == 3 ) {
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rows <- tryCatch ( which ( x [ , col_mo_property ] %like% mo_value
& x [ , source_antibiotics [1L ] ] == source_value [1L ]
& x [ , source_antibiotics [2L ] ] == source_value [2L ]
& x [ , source_antibiotics [3L ] ] == source_value [3L ] ) ,
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error = function ( e ) integer ( 0 ) )
} else {
stop ( " only 3 antibiotics supported for source_antibiotics " , call. = FALSE )
}
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}
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cols <- get_antibiotic_columns ( target_antibiotics , x )
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# Apply rule on data ------------------------------------------------------
# this will return the unique number of changes
no_of_changes <- no_of_changes + edit_rsi ( to = target_value ,
rule = c ( rule_text , rule_group_current , rule_current ) ,
rows = rows ,
cols = cols )
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# Print number of new changes ---------------------------------------------
if ( info == TRUE & rule_next != rule_current ) {
# print only on last one of rules in this group
txt_ok ( no_of_changes = no_of_changes )
no_of_changes <- 0
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}
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}
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# Print overview ----------------------------------------------------------
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if ( info == TRUE ) {
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if ( verbose == TRUE ) {
wouldve <- " would have "
} else {
wouldve <- " "
}
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verbose_info <- verbose_info %>%
arrange ( row , rule_group , rule_name , col )
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decimal.mark <- getOption ( " OutDec" )
big.mark <- ifelse ( decimal.mark != " ," , " ," , " ." )
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formatnr <- function ( x ) {
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trimws ( format ( x , big.mark = big.mark , decimal.mark = decimal.mark ) )
}
cat ( paste0 ( " \n" , silver ( strrep ( " -" , options ( ) $ width - 1 ) ) , " \n" ) )
cat ( bold ( paste ( ' EUCAST rules' , paste0 ( wouldve , ' affected' ) ,
formatnr ( n_distinct ( verbose_info $ row ) ) ,
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' out of' , formatnr ( nrow ( x_original ) ) ,
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' rows, making a total of' , formatnr ( nrow ( verbose_info ) ) , ' edits\n' ) ) )
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n_added <- verbose_info %>% filter ( is.na ( old ) ) %>% nrow ( )
n_changed <- verbose_info %>% filter ( ! is.na ( old ) ) %>% nrow ( )
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# print added values ----
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if ( n_added == 0 ) {
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colour <- cat # is function
} else {
colour <- blue # is function
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}
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cat ( colour ( paste0 ( " => " , wouldve , " added " ,
bold ( formatnr ( verbose_info %>%
filter ( is.na ( old ) ) %>%
nrow ( ) ) , " test results" ) ,
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" \n" ) ) )
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if ( n_added > 0 ) {
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verbose_info %>%
filter ( is.na ( old ) ) %>%
# sort it well: S < I < R
mutate ( new = as.rsi ( new ) ) %>%
group_by ( new ) %>%
summarise ( n = n ( ) ) %>%
mutate ( plural = ifelse ( n > 1 , " s" , " " ) ,
txt = paste0 ( formatnr ( n ) , " test result" , plural , " added as " , new ) ) %>%
pull ( txt ) %>%
paste ( " -" , ., collapse = " \n" ) %>%
cat ( )
}
# print changed values ----
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if ( n_changed == 0 ) {
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colour <- cat # is function
} else {
colour <- blue # is function
}
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if ( n_added + n_changed > 0 ) {
cat ( " \n" )
}
cat ( colour ( paste0 ( " => " , wouldve , " changed " ,
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bold ( formatnr ( verbose_info %>%
filter ( ! is.na ( old ) ) %>%
nrow ( ) ) , " test results" ) ,
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" \n" ) ) )
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if ( n_changed > 0 ) {
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verbose_info %>%
filter ( ! is.na ( old ) ) %>%
# sort it well: S < I < R
mutate ( old = as.rsi ( old ) ,
new = as.rsi ( new ) ) %>%
group_by ( old , new ) %>%
summarise ( n = n ( ) ) %>%
mutate ( plural = ifelse ( n > 1 , " s" , " " ) ,
txt = paste0 ( formatnr ( n ) , " test result" , plural , " changed from " , old , " to " , new ) ) %>%
pull ( txt ) %>%
paste ( " -" , ., collapse = " \n" ) %>%
cat ( )
cat ( " \n" )
}
cat ( paste0 ( silver ( strrep ( " -" , options ( ) $ width - 1 ) ) , " \n" ) )
if ( verbose == FALSE & nrow ( verbose_info ) > 0 ) {
cat ( paste ( " \nUse" , bold ( " verbose = TRUE" ) , " to get a data.frame with all specified edits instead.\n" ) )
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}
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}
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# Return data set ---------------------------------------------------------
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if ( verbose == TRUE ) {
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verbose_info
} else {
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x_original
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}
}
