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(v0.8.0.9036) complete documentation rewrite
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227
R/eucast_rules.R
227
R/eucast_rules.R
@ -26,141 +26,131 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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#' EUCAST rules
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#'
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#' @description
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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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#' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <http://eucast.org>), see *Source*. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
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#'
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#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules are applied at default, see Details.
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#' @param x data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}
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#' @param x data with antibiotic columns, like e.g. `AMX` and `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 rules a character vector that specifies which rules should be applied - one or more of `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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#' @param ... column name of an antibiotic, please see section *Antibiotics* below
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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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#' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] for that. \cr
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#' **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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#' Before further processing, some non-EUCAST rules are applied to improve the efficacy of the EUCAST rules. These non-EUCAST rules, that are applied to all isolates, are:
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#' \itemize{
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#' \item{Inherit amoxicillin (AMX) from ampicillin (AMP), where amoxicillin (AMX) is unavailable;}
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#' \item{Inherit ampicillin (AMP) from amoxicillin (AMX), where ampicillin (AMP) is unavailable;}
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#' \item{Set amoxicillin (AMX) = R where amoxicillin/clavulanic acid (AMC) = R;}
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#' \item{Set piperacillin (PIP) = R where piperacillin/tazobactam (TZP) = R;}
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#' \item{Set trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R;}
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#' \item{Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;}
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#' \item{Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;}
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#' \item{Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.}
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#' }
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#' To \emph{not} use these rules, please use \code{eucast_rules(..., rules = c("breakpoints", "expert"))}.
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#' - Inherit amoxicillin (AMX) from ampicillin (AMP), where amoxicillin (AMX) is unavailable;
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#' - Inherit ampicillin (AMP) from amoxicillin (AMX), where ampicillin (AMP) is unavailable;
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#' - Set amoxicillin (AMX) = R where amoxicillin/clavulanic acid (AMC) = R;
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#' - Set piperacillin (PIP) = R where piperacillin/tazobactam (TZP) = R;
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#' - Set trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R;
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#' - Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;
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#' - Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;
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#' - Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.
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#' To *not* use these rules, please use `eucast_rules(..., rules = c("breakpoints", "expert"))`.
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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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#' The file containing all EUCAST rules is located here: <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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#' To define antibiotics column names, leave as it is to determine it automatically with [guess_ab_col()] or input a text (case-insensitive), or use `NULL` to skip a column (e.g. `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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#' The following antibiotics are used for the functions [eucast_rules()] and [mdro()]. These are shown below in the format '**antimicrobial ID**: name ([ATC code](https://www.whocc.no/atc/structure_and_principles/))', 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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#' **AMK**: amikacin ([J01GB06](https://www.whocc.no/atc_ddd_index/?code=J01GB06)),
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#' **AMX**: amoxicillin ([J01CA04](https://www.whocc.no/atc_ddd_index/?code=J01CA04)),
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#' **AMC**: amoxicillin/clavulanic acid ([J01CR02](https://www.whocc.no/atc_ddd_index/?code=J01CR02)),
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#' **AMP**: ampicillin ([J01CA01](https://www.whocc.no/atc_ddd_index/?code=J01CA01)),
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#' **SAM**: ampicillin/sulbactam ([J01CR01](https://www.whocc.no/atc_ddd_index/?code=J01CR01)),
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#' **AZM**: azithromycin ([J01FA10](https://www.whocc.no/atc_ddd_index/?code=J01FA10)),
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#' **AZL**: azlocillin ([J01CA09](https://www.whocc.no/atc_ddd_index/?code=J01CA09)),
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#' **ATM**: aztreonam ([J01DF01](https://www.whocc.no/atc_ddd_index/?code=J01DF01)),
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#' **CAP**: capreomycin ([J04AB30](https://www.whocc.no/atc_ddd_index/?code=J04AB30)),
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#' **RID**: cefaloridine ([J01DB02](https://www.whocc.no/atc_ddd_index/?code=J01DB02)),
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#' **CZO**: cefazolin ([J01DB04](https://www.whocc.no/atc_ddd_index/?code=J01DB04)),
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#' **FEP**: cefepime ([J01DE01](https://www.whocc.no/atc_ddd_index/?code=J01DE01)),
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#' **CTX**: cefotaxime ([J01DD01](https://www.whocc.no/atc_ddd_index/?code=J01DD01)),
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#' **CTT**: cefotetan ([J01DC05](https://www.whocc.no/atc_ddd_index/?code=J01DC05)),
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#' **FOX**: cefoxitin ([J01DC01](https://www.whocc.no/atc_ddd_index/?code=J01DC01)),
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#' **CPT**: ceftaroline ([J01DI02](https://www.whocc.no/atc_ddd_index/?code=J01DI02)),
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#' **CAZ**: ceftazidime ([J01DD02](https://www.whocc.no/atc_ddd_index/?code=J01DD02)),
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#' **CRO**: ceftriaxone ([J01DD04](https://www.whocc.no/atc_ddd_index/?code=J01DD04)),
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#' **CXM**: cefuroxime ([J01DC02](https://www.whocc.no/atc_ddd_index/?code=J01DC02)),
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#' **CED**: cephradine ([J01DB09](https://www.whocc.no/atc_ddd_index/?code=J01DB09)),
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#' **CHL**: chloramphenicol ([J01BA01](https://www.whocc.no/atc_ddd_index/?code=J01BA01)),
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#' **CIP**: ciprofloxacin ([J01MA02](https://www.whocc.no/atc_ddd_index/?code=J01MA02)),
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#' **CLR**: clarithromycin ([J01FA09](https://www.whocc.no/atc_ddd_index/?code=J01FA09)),
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#' **CLI**: clindamycin ([J01FF01](https://www.whocc.no/atc_ddd_index/?code=J01FF01)),
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#' **COL**: colistin ([J01XB01](https://www.whocc.no/atc_ddd_index/?code=J01XB01)),
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#' **DAP**: daptomycin ([J01XX09](https://www.whocc.no/atc_ddd_index/?code=J01XX09)),
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#' **DOR**: doripenem ([J01DH04](https://www.whocc.no/atc_ddd_index/?code=J01DH04)),
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#' **DOX**: doxycycline ([J01AA02](https://www.whocc.no/atc_ddd_index/?code=J01AA02)),
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#' **ETP**: ertapenem ([J01DH03](https://www.whocc.no/atc_ddd_index/?code=J01DH03)),
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#' **ERY**: erythromycin ([J01FA01](https://www.whocc.no/atc_ddd_index/?code=J01FA01)),
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#' **ETH**: ethambutol ([J04AK02](https://www.whocc.no/atc_ddd_index/?code=J04AK02)),
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#' **FLC**: flucloxacillin ([J01CF05](https://www.whocc.no/atc_ddd_index/?code=J01CF05)),
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#' **FOS**: fosfomycin ([J01XX01](https://www.whocc.no/atc_ddd_index/?code=J01XX01)),
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#' **FUS**: fusidic acid ([J01XC01](https://www.whocc.no/atc_ddd_index/?code=J01XC01)),
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#' **GAT**: gatifloxacin ([J01MA16](https://www.whocc.no/atc_ddd_index/?code=J01MA16)),
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#' **GEN**: gentamicin ([J01GB03](https://www.whocc.no/atc_ddd_index/?code=J01GB03)),
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#' **GEH**: gentamicin-high (no ATC code),
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#' **IPM**: imipenem ([J01DH51](https://www.whocc.no/atc_ddd_index/?code=J01DH51)),
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#' **INH**: isoniazid ([J04AC01](https://www.whocc.no/atc_ddd_index/?code=J04AC01)),
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#' **KAN**: kanamycin ([J01GB04](https://www.whocc.no/atc_ddd_index/?code=J01GB04)),
|
||||
#' **LVX**: levofloxacin ([J01MA12](https://www.whocc.no/atc_ddd_index/?code=J01MA12)),
|
||||
#' **LIN**: lincomycin ([J01FF02](https://www.whocc.no/atc_ddd_index/?code=J01FF02)),
|
||||
#' **LNZ**: linezolid ([J01XX08](https://www.whocc.no/atc_ddd_index/?code=J01XX08)),
|
||||
#' **MEM**: meropenem ([J01DH02](https://www.whocc.no/atc_ddd_index/?code=J01DH02)),
|
||||
#' **MTR**: metronidazole ([J01XD01](https://www.whocc.no/atc_ddd_index/?code=J01XD01)),
|
||||
#' **MEZ**: mezlocillin ([J01CA10](https://www.whocc.no/atc_ddd_index/?code=J01CA10)),
|
||||
#' **MNO**: minocycline ([J01AA08](https://www.whocc.no/atc_ddd_index/?code=J01AA08)),
|
||||
#' **MFX**: moxifloxacin ([J01MA14](https://www.whocc.no/atc_ddd_index/?code=J01MA14)),
|
||||
#' **NAL**: nalidixic acid ([J01MB02](https://www.whocc.no/atc_ddd_index/?code=J01MB02)),
|
||||
#' **NEO**: neomycin ([J01GB05](https://www.whocc.no/atc_ddd_index/?code=J01GB05)),
|
||||
#' **NET**: netilmicin ([J01GB07](https://www.whocc.no/atc_ddd_index/?code=J01GB07)),
|
||||
#' **NIT**: nitrofurantoin ([J01XE01](https://www.whocc.no/atc_ddd_index/?code=J01XE01)),
|
||||
#' **NOR**: norfloxacin ([J01MA06](https://www.whocc.no/atc_ddd_index/?code=J01MA06)),
|
||||
#' **NOV**: novobiocin ([QJ01XX95](https://www.whocc.no/atc_ddd_index/?code=QJ01XX95)),
|
||||
#' **OFX**: ofloxacin ([J01MA01](https://www.whocc.no/atc_ddd_index/?code=J01MA01)),
|
||||
#' **OXA**: oxacillin ([J01CF04](https://www.whocc.no/atc_ddd_index/?code=J01CF04)),
|
||||
#' **PEN**: penicillin G ([J01CE01](https://www.whocc.no/atc_ddd_index/?code=J01CE01)),
|
||||
#' **PIP**: piperacillin ([J01CA12](https://www.whocc.no/atc_ddd_index/?code=J01CA12)),
|
||||
#' **TZP**: piperacillin/tazobactam ([J01CR05](https://www.whocc.no/atc_ddd_index/?code=J01CR05)),
|
||||
#' **PLB**: polymyxin B ([J01XB02](https://www.whocc.no/atc_ddd_index/?code=J01XB02)),
|
||||
#' **PRI**: pristinamycin ([J01FG01](https://www.whocc.no/atc_ddd_index/?code=J01FG01)),
|
||||
#' **PZA**: pyrazinamide ([J04AK01](https://www.whocc.no/atc_ddd_index/?code=J04AK01)),
|
||||
#' **QDA**: quinupristin/dalfopristin ([J01FG02](https://www.whocc.no/atc_ddd_index/?code=J01FG02)),
|
||||
#' **RIB**: rifabutin ([J04AB04](https://www.whocc.no/atc_ddd_index/?code=J04AB04)),
|
||||
#' **RIF**: rifampicin ([J04AB02](https://www.whocc.no/atc_ddd_index/?code=J04AB02)),
|
||||
#' **RFP**: rifapentine ([J04AB05](https://www.whocc.no/atc_ddd_index/?code=J04AB05)),
|
||||
#' **RXT**: roxithromycin ([J01FA06](https://www.whocc.no/atc_ddd_index/?code=J01FA06)),
|
||||
#' **SIS**: sisomicin ([J01GB08](https://www.whocc.no/atc_ddd_index/?code=J01GB08)),
|
||||
#' **STH**: streptomycin-high (no ATC code),
|
||||
#' **TEC**: teicoplanin ([J01XA02](https://www.whocc.no/atc_ddd_index/?code=J01XA02)),
|
||||
#' **TLV**: telavancin ([J01XA03](https://www.whocc.no/atc_ddd_index/?code=J01XA03)),
|
||||
#' **TCY**: tetracycline ([J01AA07](https://www.whocc.no/atc_ddd_index/?code=J01AA07)),
|
||||
#' **TIC**: ticarcillin ([J01CA13](https://www.whocc.no/atc_ddd_index/?code=J01CA13)),
|
||||
#' **TCC**: ticarcillin/clavulanic acid ([J01CR03](https://www.whocc.no/atc_ddd_index/?code=J01CR03)),
|
||||
#' **TGC**: tigecycline ([J01AA12](https://www.whocc.no/atc_ddd_index/?code=J01AA12)),
|
||||
#' **TOB**: tobramycin ([J01GB01](https://www.whocc.no/atc_ddd_index/?code=J01GB01)),
|
||||
#' **TMP**: trimethoprim ([J01EA01](https://www.whocc.no/atc_ddd_index/?code=J01EA01)),
|
||||
#' **SXT**: trimethoprim/sulfamethoxazole ([J01EE01](https://www.whocc.no/atc_ddd_index/?code=J01EE01)),
|
||||
#' **VAN**: vancomycin ([J01XA01](https://www.whocc.no/atc_ddd_index/?code=J01XA01)).
|
||||
#' @aliases EUCAST
|
||||
#' @rdname eucast_rules
|
||||
#' @export
|
||||
#' @importFrom dplyr %>% select pull mutate_at vars group_by summarise n
|
||||
#' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic strip_style white red make_style
|
||||
#' @importFrom utils menu
|
||||
#' @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.
|
||||
#' @return The input of `x`, possibly with edited values of antibiotics. Or, if `verbose = TRUE`, a [`data.frame`] with all original and new values of the affected bug-drug combinations.
|
||||
#' @source
|
||||
#' \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{
|
||||
#' 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}
|
||||
#' }
|
||||
#' }
|
||||
#' - EUCAST Expert Rules. Version 2.0, 2012. \cr
|
||||
#' Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility testing.** *Clin Microbiol Infect.* 2013;19(2):141-60. \cr
|
||||
#' <https://doi.org/10.1111/j.1469-0691.2011.03703.x>
|
||||
#' - EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. \cr
|
||||
#' <http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf>
|
||||
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. \cr
|
||||
#' <http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx>
|
||||
#' @inheritSection AMR Read more on our website!
|
||||
#' @examples
|
||||
#' \donttest{
|
||||
@ -548,7 +538,7 @@ eucast_rules <- function(x,
|
||||
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)]
|
||||
cephalosporins_except_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)
|
||||
@ -568,13 +558,16 @@ eucast_rules <- function(x,
|
||||
y[y != "" & y %in% colnames(df)]
|
||||
}
|
||||
get_antibiotic_names <- function(x) {
|
||||
x %>%
|
||||
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 = ", ")
|
||||
x <- gsub("_", " ", x, fixed = TRUE)
|
||||
x <- gsub("except CAZ", paste("except", ab_name("CAZ", language = NULL, tolower = TRUE)), x, fixed = TRUE)
|
||||
x
|
||||
}
|
||||
format_antibiotic_names <- function(ab_names, ab_results) {
|
||||
ab_names <- trimws(unlist(strsplit(ab_names, ",")))
|
||||
|
||||
Reference in New Issue
Block a user