mirror of https://github.com/msberends/AMR.git
864 lines
41 KiB
R
Executable File
864 lines
41 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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# global variables
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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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#' 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 turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.
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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
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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 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 below in the format '\strong{antimicrobial ID}: name (\href{https://www.whocc.no/atc/structure_and_principles/}{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}),
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#' \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}),
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#' \strong{SAM}: ampicillin/sulbactam (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR01}{J01CR01}),
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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{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}),
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#' \strong{CTX}: cefotaxime (\href{https://www.whocc.no/atc_ddd_index/?code=J01DD01}{J01DD01}),
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#' \strong{CTT}: cefotetan (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC05}{J01DC05}),
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#' \strong{FOX}: cefoxitin (\href{https://www.whocc.no/atc_ddd_index/?code=J01DC01}{J01DC01}),
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#' \strong{CPT}: ceftaroline (\href{https://www.whocc.no/atc_ddd_index/?code=J01DI02}{J01DI02}),
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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{CED}: cephradine (\href{https://www.whocc.no/atc_ddd_index/?code=J01DB09}{J01DB09}),
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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{COL}: colistin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XB01}{J01XB01}),
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#' \strong{DAP}: daptomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XX09}{J01XX09}),
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#' \strong{DOR}: doripenem (\href{https://www.whocc.no/atc_ddd_index/?code=J01DH04}{J01DH04}),
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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{ETH}: ethambutol (\href{https://www.whocc.no/atc_ddd_index/?code=J04AK02}{J04AK02}),
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#' \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}),
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#' \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}),
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#' \strong{GEH}: gentamicin-high (no ATC code),
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#' \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}),
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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{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}),
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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{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 (\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=J01CF04}{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{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{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}),
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#' \strong{SIS}: sisomicin (\href{https://www.whocc.no/atc_ddd_index/?code=J01GB08}{J01GB08}),
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#' \strong{STH}: streptomycin-high (no ATC code),
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#' \strong{TEC}: teicoplanin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA02}{J01XA02}),
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#' \strong{TLV}: telavancin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA03}{J01XA03}),
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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{TCC}: ticarcillin/clavulanic acid (\href{https://www.whocc.no/atc_ddd_index/?code=J01CR03}{J01CR03}),
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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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#' @aliases EUCAST
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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 red make_style
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#' @importFrom utils menu
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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{
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#' \item{
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#' EUCAST Expert Rules. Version 2.0, 2012. \cr
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#' Leclercq et al. \strong{EUCAST expert rules in antimicrobial susceptibility testing.} \emph{Clin Microbiol Infect.} 2013;19(2):141-60. \cr
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#' \url{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
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#' }
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#' \item{
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#' EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \cr
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#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
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#' }
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#' \item{
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#' EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \cr
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#' \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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#' }
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' a <- data.frame(mo = c("Staphylococcus aureus",
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#' "Enterococcus faecalis",
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#' "Escherichia coli",
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#' "Klebsiella pneumoniae",
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#' "Pseudomonas aeruginosa"),
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#' VAN = "-", # Vancomycin
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#' AMX = "-", # Amoxicillin
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#' COL = "-", # Colistin
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#' CAZ = "-", # Ceftazidime
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#' CXM = "-", # Cefuroxime
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#' PEN = "S", # Penicillin G
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#' 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
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#' # 2 Enterococcus faecalis - - - - - S S
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#' # 3 Escherichia coli - - - - - S S
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#' # 4 Klebsiella pneumoniae - - - - - S S
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#' # 5 Pseudomonas aeruginosa - - - - - S S
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#'
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#'
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#' # apply EUCAST rules: 18 results are forced as R or S
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#' 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
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#' # 2 Enterococcus faecalis - - R R R S R
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#' # 3 Escherichia coli R - - - - R S
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#' # 4 Klebsiella pneumoniae R R - - - R S
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#' # 5 Pseudomonas aeruginosa R R - - R R R
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#'
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#'
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#' \donttest{
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#' # do not apply EUCAST rules, but rather get a data.frame
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#' # with 18 rows, containing all details about the transformations:
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#' c <- eucast_rules(a, verbose = TRUE)
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#' }
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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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if (verbose == TRUE & interactive()) {
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txt <- paste0("WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way.",
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"\n\nThis may overwrite your existing data if you use e.g.:",
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"\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?")
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if ("rstudioapi" %in% rownames(utils::installed.packages())) {
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q_continue <- rstudioapi::showQuestion("Using verbose = TRUE with eucast_rules()", txt)
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} else {
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q_continue <- menu(choices = c("OK", "Cancel"), graphics = TRUE, title = txt)
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}
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if (q_continue %in% c(FALSE, 2)) {
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message("Cancelled, returning original data")
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return(x)
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}
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}
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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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}
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# try to find columns based on type
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# -- mo
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if (is.null(col_mo)) {
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col_mo <- search_type_in_df(x = x, type = "mo")
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}
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if (is.null(col_mo)) {
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stop("`col_mo` must be set.", call. = FALSE)
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}
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if (!all(rules %in% c("breakpoints", "expert", "other", "all"))) {
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stop("`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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decimal.mark <- getOption("OutDec")
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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))
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}
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grey <- make_style("grey")
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warned <- FALSE
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txt_error <- function() {
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if (info == TRUE) cat("", bgRed(white(" ERROR ")), "\n\n")
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}
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txt_warning <- function() {
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if (warned == FALSE) {
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if (info == TRUE) cat("", bgYellow(black(" WARNING ")))
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}
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warned <<- TRUE
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}
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txt_ok <- function(no_added, no_changed) {
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if (warned == FALSE) {
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if (no_added + no_changed == 0) {
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cat(pillar::style_subtle(" (no changes)\n"))
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} else {
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# opening
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cat(grey(" ("))
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# additions
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if (no_added > 0) {
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if (no_added == 1) {
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cat(green("1 value added"))
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} else {
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cat(green(formatnr(no_added), "values added"))
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}
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}
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# separator
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if (no_added > 0 & no_changed > 0) {
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cat(grey(", "))
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}
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# changes
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if (no_changed > 0) {
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if (no_changed == 1) {
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cat(blue("1 value changed"))
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} else {
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cat(blue(formatnr(no_changed), "values changed"))
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}
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}
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# closing
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cat(grey(")\n"))
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}
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warned <<- FALSE
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}
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}
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cols_ab <- get_column_abx(x = x,
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soft_dependencies = c("AMC",
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"AMK",
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"AMX",
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"AMP",
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"AZM",
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"AZL",
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"ATM",
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"RID",
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"FEP",
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"CTX",
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"FOX",
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"CED",
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"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))
|
|
}
|
|
|
|
verbose_info <- data.frame(row = integer(0),
|
|
col = character(0),
|
|
mo_fullname = character(0),
|
|
old = as.rsi(character(0)),
|
|
new = as.rsi(character(0)),
|
|
rule = character(0),
|
|
rule_group = character(0),
|
|
rule_name = character(0),
|
|
stringsAsFactors = FALSE)
|
|
|
|
# helper function for editing the table
|
|
edit_rsi <- function(to, rule, rows, cols) {
|
|
cols <- unique(cols[!is.na(cols) & !is.null(cols)])
|
|
if (length(rows) > 0 & length(cols) > 0) {
|
|
before_df <- x_original
|
|
|
|
tryCatch(
|
|
# insert into original table
|
|
x_original[rows, cols] <<- to,
|
|
warning = function(w) {
|
|
if (w$message %like% "invalid factor level") {
|
|
x_original <<- x_original %>% mutate_at(vars(cols), ~factor(x = as.character(.), levels = c(to, levels(.))))
|
|
x <<- x %>% mutate_at(vars(cols), ~factor(x = as.character(.), levels = c(to, levels(.))))
|
|
x_original[rows, cols] <<- to
|
|
warning('Value "', to, '" added to the factor levels of column(s) `', paste(cols, collapse = "`, `"), "` because this value was not an existing factor level.\nA better way is to use as.rsi() on beforehand on antimicrobial columns to guarantee the right structure.", call. = FALSE)
|
|
txt_warning()
|
|
warned <<- FALSE
|
|
} else {
|
|
warning(w$message, call. = FALSE)
|
|
txt_warning()
|
|
cat("\n") # txt_warning() does not append a "\n" on itself
|
|
}
|
|
},
|
|
error = function(e) {
|
|
txt_error()
|
|
stop(paste0("In row(s) ", paste(rows[1:min(length(rows), 10)], collapse = ","),
|
|
ifelse(length(rows) > 10, "...", ""),
|
|
" while writing value '", to,
|
|
"' to column(s) `", paste(cols, collapse = "`, `"),
|
|
"`:\n", e$message),
|
|
call. = FALSE)
|
|
}
|
|
)
|
|
|
|
tryCatch(
|
|
x[rows, cols] <<- x_original[rows, cols],
|
|
error = function(e) {
|
|
stop(paste0("In row(s) ", paste(rows[1:min(length(rows), 10)], collapse = ","),
|
|
"... while writing value '", to,
|
|
"' to column(s) `", paste(cols, collapse = "`, `"),
|
|
"`:\n", e$message), call. = FALSE)
|
|
}
|
|
)
|
|
|
|
# before_df might not be a data.frame, but a tibble or data.table instead
|
|
old <- as.data.frame(before_df, stringsAsFactors = FALSE)[rows, ]
|
|
track_changes <- list(added = 0,
|
|
changed = 0)
|
|
for (i in seq_len(length(cols))) {
|
|
verbose_new <- data.frame(row = rows,
|
|
col = cols[i],
|
|
mo_fullname = x[rows, "fullname"],
|
|
old = as.rsi(as.character(old[, cols[i]]), warn = FALSE),
|
|
new = as.rsi(as.character(x[rows, cols[i]])),
|
|
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))
|
|
# save changes to data set 'verbose_info'
|
|
verbose_info <<- rbind(verbose_info, verbose_new)
|
|
# count adds and changes
|
|
track_changes$added <- track_changes$added + verbose_new %>% filter(is.na(old)) %>% nrow()
|
|
track_changes$changed <- track_changes$changed + verbose_new %>% filter(!is.na(old)) %>% nrow()
|
|
}
|
|
# after the applied changes: return list with counts of added and changed
|
|
return(track_changes)
|
|
}
|
|
# no changes were applied: return number of (new) changes: none.
|
|
return(list(added = 0,
|
|
changed = 0))
|
|
}
|
|
|
|
# save original table
|
|
x_original <- x
|
|
|
|
# join to microorganisms data set
|
|
suppressWarnings(
|
|
x <- x %>%
|
|
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)
|
|
)
|
|
|
|
if (info == TRUE) {
|
|
cat(paste0(
|
|
"\nRules by the ", bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"),
|
|
"\n", blue("http://eucast.org/"), "\n"))
|
|
}
|
|
|
|
# since ampicillin ^= amoxicillin, get the first from the latter (not in original EUCAST table)
|
|
if (!ab_missing(AMP) & !ab_missing(AMX)) {
|
|
if (verbose == TRUE) {
|
|
cat("\n VERBOSE: transforming",
|
|
length(which(x[, AMX] == "S" & !x[, AMP] %in% c("S", "I", "R"))),
|
|
"empty ampicillin fields to 'S' based on amoxicillin. ")
|
|
cat("\n VERBOSE: transforming",
|
|
length(which(x[, AMX] == "I" & !x[, AMP] %in% c("S", "I", "R"))),
|
|
"empty ampicillin fields to 'I' based on amoxicillin. ")
|
|
cat("\n VERBOSE: transforming",
|
|
length(which(x[, AMX] == "R" & !x[, AMP] %in% c("S", "I", "R"))),
|
|
"empty ampicillin fields to 'R' based on amoxicillin. \n")
|
|
}
|
|
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"
|
|
} else if (ab_missing(AMP) & !ab_missing(AMX)) {
|
|
# ampicillin column is missing, but amoxicillin is available
|
|
message(blue(paste0("NOTE: Using column `", bold(AMX), "` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.")))
|
|
AMP <- AMX
|
|
}
|
|
|
|
# nolint start
|
|
# antibiotic classes
|
|
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)
|
|
# nolint end
|
|
|
|
# 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 seq_len(length(x))) {
|
|
if (is.function(get(x[i]))) {
|
|
stop("Column ", x[i], " is also a function. Please create an issue on github.com/msberends/AMR/issues.")
|
|
}
|
|
y <- c(y, tryCatch(get(x[i]), error = function(e) ""))
|
|
}
|
|
y[y != "" & y %in% colnames(df)]
|
|
}
|
|
get_antibiotic_names <- function(x) {
|
|
x %>%
|
|
strsplit(",") %>%
|
|
unlist() %>%
|
|
trimws() %>%
|
|
sapply(function(x) if (x %in% AMR::antibiotics$ab) ab_name(x, language = NULL, tolower = TRUE) else x) %>%
|
|
sort() %>%
|
|
paste(collapse = ", ")
|
|
}
|
|
format_antibiotic_names <- function(ab_names, ab_results) {
|
|
ab_names <- trimws(unlist(strsplit(ab_names, ",")))
|
|
ab_results <- trimws(unlist(strsplit(ab_results, ",")))
|
|
if (length(ab_results) == 1) {
|
|
if (length(ab_names) == 1) {
|
|
# like FOX S
|
|
x <- paste(ab_names, "is")
|
|
} else if (length(ab_names) == 2) {
|
|
# like PEN,FOX S
|
|
x <- paste(paste0(ab_names, collapse = " and "), "are both")
|
|
} else {
|
|
# like PEN,FOX,GEN S (although dependency on > 2 ABx does not exist at the moment)
|
|
x <- paste(paste0(ab_names, collapse = " and "), "are all")
|
|
}
|
|
return(paste0(x, " '", ab_results, "'"))
|
|
} else {
|
|
if (length(ab_names) == 2) {
|
|
# like PEN,FOX S,R
|
|
paste0(ab_names[1], " is '", ab_results[1], "' and ",
|
|
ab_names[2], " is '", ab_results[2], "'")
|
|
} else {
|
|
# like PEN,FOX,GEN S,R,R (although dependency on > 2 ABx does not exist at the moment)
|
|
paste0(ab_names[1], " is '", ab_results[1], "' and ",
|
|
ab_names[2], " is '", ab_results[2], "' and ",
|
|
ab_names[3], " is '", ab_results[3], "'")
|
|
}
|
|
}
|
|
}
|
|
|
|
eucast_rules_df <- eucast_rules_file # internal data file
|
|
no_added <- 0
|
|
no_changed <- 0
|
|
for (i in seq_len(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"]
|
|
if (is.na(eucast_rules_df[i, 4])) {
|
|
rule_text <- paste0("always report as '", eucast_rules_df[i, 7], "': ", get_antibiotic_names(eucast_rules_df[i, 6]))
|
|
} else {
|
|
rule_text <- paste0("report as '", eucast_rules_df[i, 7], "' when ",
|
|
format_antibiotic_names(ab_names = get_antibiotic_names(eucast_rules_df[i, 4]),
|
|
ab_results = eucast_rules_df[i, 5]), ": ",
|
|
get_antibiotic_names(eucast_rules_df[i, 6]))
|
|
}
|
|
if (i == 1) {
|
|
rule_previous <- ""
|
|
rule_group_previous <- ""
|
|
}
|
|
if (i == nrow(eucast_rules_df)) {
|
|
rule_next <- ""
|
|
}
|
|
|
|
# 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
|
|
}
|
|
if (rule_group_current %like% "expert" & !any(c("all", "expert") %in% rules)) {
|
|
next
|
|
}
|
|
if (rule_group_current %like% "other" & !any(c("all", "other") %in% rules)) {
|
|
next
|
|
}
|
|
|
|
|
|
if (info == TRUE) {
|
|
# 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$fullname)) {
|
|
cat(italic(rule_current))
|
|
} else {
|
|
cat(rule_current)
|
|
}
|
|
warned <- FALSE
|
|
}
|
|
}
|
|
|
|
# Get rule from file ------------------------------------------------------
|
|
col_mo_property <- eucast_rules_df[i, 1]
|
|
like_is_one_of <- eucast_rules_df[i, 2]
|
|
|
|
# be sure to comprise all coagulase-negative/-positive Staphylococci when they are mentioned
|
|
if (eucast_rules_df[i, 3] %like% "coagulase-") {
|
|
suppressWarnings(
|
|
all_staph <- AMR::microorganisms %>%
|
|
filter(genus == "Staphylococcus") %>%
|
|
mutate(CNS_CPS = mo_name(mo, Becker = "all"))
|
|
)
|
|
if (eucast_rules_df[i, 3] %like% "coagulase-") {
|
|
eucast_rules_df[i, 3] <- paste0("^(",
|
|
paste0(all_staph %>%
|
|
filter(CNS_CPS %like% "coagulase-negative") %>%
|
|
pull(fullname),
|
|
collapse = "|"),
|
|
")$")
|
|
} 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") {
|
|
# so 'Clostridium, Actinomyces, ...' will turn into '^(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)
|
|
}
|
|
|
|
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]
|
|
|
|
if (is.na(source_antibiotics)) {
|
|
rows <- tryCatch(which(x[, col_mo_property] %like% mo_value),
|
|
error = function(e) integer(0))
|
|
} else {
|
|
source_antibiotics <- get_antibiotic_columns(source_antibiotics, x)
|
|
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) {
|
|
rows <- tryCatch(which(x[, col_mo_property] %like% mo_value
|
|
& x[, source_antibiotics[1L]] == source_value[1L]),
|
|
error = function(e) integer(0))
|
|
} else if (length(source_antibiotics) == 2) {
|
|
rows <- tryCatch(which(x[, col_mo_property] %like% mo_value
|
|
& x[, source_antibiotics[1L]] == source_value[1L]
|
|
& x[, source_antibiotics[2L]] == source_value[2L]),
|
|
error = function(e) integer(0))
|
|
} else if (length(source_antibiotics) == 3) {
|
|
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]),
|
|
error = function(e) integer(0))
|
|
} else {
|
|
stop("only 3 antibiotics supported for source_antibiotics ", call. = FALSE)
|
|
}
|
|
}
|
|
|
|
cols <- get_antibiotic_columns(target_antibiotics, x)
|
|
|
|
# Apply rule on data ------------------------------------------------------
|
|
# this will return the unique number of changes
|
|
run_changes <- edit_rsi(to = target_value,
|
|
rule = c(rule_text, rule_group_current, rule_current),
|
|
rows = rows,
|
|
cols = cols)
|
|
no_added <- no_added + run_changes$added
|
|
no_changed <- no_changed + run_changes$changed
|
|
|
|
# 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_added = no_added, no_changed = no_changed)
|
|
# and reset counters
|
|
no_added <- 0
|
|
no_changed <- 0
|
|
}
|
|
}
|
|
|
|
# Print overview ----------------------------------------------------------
|
|
if (info == TRUE) {
|
|
if (verbose == TRUE) {
|
|
wouldve <- "would have "
|
|
} else {
|
|
wouldve <- ""
|
|
}
|
|
|
|
verbose_info <- verbose_info %>%
|
|
arrange(row, rule_group, rule_name, col)
|
|
|
|
cat(paste0("\n", grey(strrep("-", options()$width - 1)), "\n"))
|
|
cat(bold(paste("EUCAST rules", paste0(wouldve, "affected"),
|
|
formatnr(n_distinct(verbose_info$row)),
|
|
"out of", formatnr(nrow(x_original)),
|
|
"rows, making a total of", formatnr(nrow(verbose_info)), "edits\n")))
|
|
|
|
n_added <- verbose_info %>% filter(is.na(old)) %>% nrow()
|
|
n_changed <- verbose_info %>% filter(!is.na(old)) %>% nrow()
|
|
|
|
# print added values ----
|
|
if (n_added == 0) {
|
|
colour <- cat # is function
|
|
} else {
|
|
colour <- green # is function
|
|
}
|
|
cat(colour(paste0("=> ", wouldve, "added ",
|
|
bold(formatnr(verbose_info %>%
|
|
filter(is.na(old)) %>%
|
|
nrow()), "test results"),
|
|
"\n")))
|
|
if (n_added > 0) {
|
|
verbose_info %>%
|
|
filter(is.na(old)) %>%
|
|
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 ----
|
|
if (n_changed == 0) {
|
|
colour <- cat # is function
|
|
} else {
|
|
colour <- blue # is function
|
|
}
|
|
if (n_added + n_changed > 0) {
|
|
cat("\n")
|
|
}
|
|
cat(colour(paste0("=> ", wouldve, "changed ",
|
|
bold(formatnr(verbose_info %>%
|
|
filter(!is.na(old)) %>%
|
|
nrow()), "test results"),
|
|
"\n")))
|
|
if (n_changed > 0) {
|
|
verbose_info %>%
|
|
filter(!is.na(old)) %>%
|
|
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(grey(strrep("-", options()$width - 1)), "\n"))
|
|
|
|
if (verbose == FALSE & nrow(verbose_info) > 0) {
|
|
cat(paste("\nUse", bold("eucast_rules(..., verbose = TRUE)"), "(on your original data) to get a data.frame with all specified edits instead.\n\n"))
|
|
} else if (verbose == TRUE) {
|
|
cat(paste0("\nUsed 'Verbose mode' (", bold("verbose = TRUE"), "), which returns a data.frame with all specified edits.\nUse ", bold("verbose = FALSE"), " to apply the rules on your data.\n\n"))
|
|
}
|
|
}
|
|
|
|
# Return data set ---------------------------------------------------------
|
|
if (verbose == TRUE) {
|
|
verbose_info
|
|
} else {
|
|
x_original
|
|
}
|
|
}
|