AMR/man/interpretive_rules.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/interpretive_rules.R
\name{interpretive_rules}
\alias{interpretive_rules}
\alias{EUCAST}
\alias{eucast_rules}
\alias{clsi_rules}
\alias{eucast_dosage}
\title{Apply Interpretive Rules}
\usage{
interpretive_rules(
  x,
  col_mo = NULL,
  info = interactive(),
  rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
    "expected_phenotypes")),
  guideline = getOption("AMR_guideline", "EUCAST"),
  verbose = FALSE,
  version_breakpoints = 16,
  version_expected_phenotypes = 1.2,
  version_expertrules = 3.3,
  ampc_cephalosporin_resistance = NA,
  only_sir_columns = any(is.sir(x)),
  custom_rules = NULL,
  overwrite = FALSE,
  add_if_missing = TRUE,
  ...
)

eucast_rules(
  x,
  col_mo = NULL,
  info = interactive(),
  rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
    "expected_phenotypes")),
  ...
)

clsi_rules(
  x,
  col_mo = NULL,
  info = interactive(),
  rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
    "expected_phenotypes")),
  ...
)

eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
}
\arguments{
\item{x}{A data set with antimicrobials columns, such as \code{amox}, \code{AMX} and \code{AMC}.}

\item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}

\item{info}{A \link{logical} to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.}

\item{rules}{A \link{character} vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expected_phenotypes"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expected_phenotypes")}. The default value can be set to another value using the package option \code{\link[=AMR-options]{AMR_interpretive_rules}}: \code{options(AMR_interpretive_rules = "all")}. If using \code{"custom"}, be sure to fill in argument \code{custom_rules} too. Custom rules can be created with \code{\link[=custom_interpretive_rules]{custom_interpretive_rules()}}.}

\item{guideline}{A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}.}

\item{verbose}{A \link{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. Using Verbose mode takes a lot more time.}

\item{version_breakpoints}{The version number to use for the EUCAST Clinical Breakpoints guideline. Can be \code{"16.0"}, \code{"15.0"}, \code{"14.0"}, \code{"13.1"}, \code{"12.0"}, \code{"11.0"}, or \code{"10.0"}.}

\item{version_expected_phenotypes}{The version number to use for the EUCAST Expected Phenotypes. Can be \code{"1.2"}.}

\item{version_expertrules}{The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be \code{"3.3"}.}

\item{ampc_cephalosporin_resistance}{(only applies when \code{rules} contains \code{"expert"} or \code{"all"}) a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these versions of '\emph{EUCAST Expert Rules on Enterobacterales}' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of \code{NA} (the default) for this argument will remove results for these three drugs, while e.g. a value of \code{"R"} will make the results for these drugs resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, and \emph{Klebsiella aerogenes}.}

\item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.}

\item{custom_rules}{Custom rules to apply, created with \code{\link[=custom_interpretive_rules]{custom_interpretive_rules()}}.}

\item{overwrite}{A \link{logical} indicating whether to overwrite existing SIR values (default: \code{FALSE}). When \code{FALSE}, only non-SIR values are modified (i.e., any value that is not already S, I or R). To ensure compliance with EUCAST guidelines, \strong{this should remain} \code{FALSE}, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant".}

\item{add_if_missing}{A \link{logical} indicating whether rules should also be applied to missing (\code{NA}) values (default: \code{TRUE}). When \code{FALSE}, rules are only applied to cells that already contain an SIR value; cells with \code{NA} are left untouched. This is particularly useful when using \code{overwrite = TRUE} with custom rules and you want to update reported results without imputing values for untested drugs.}

\item{...}{Column names of antimicrobials. To automatically detect antimicrobial column names, do not provide any named arguments; \code{\link[=guess_ab_col]{guess_ab_col()}} will then be used for detection. To manually specify a column, provide its name (case-insensitive) as an argument, e.g. \code{AMX = "amoxicillin"}. To skip a specific antimicrobial, set it to \code{NULL}, e.g. \code{TIC = NULL} to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.}

\item{ab}{Any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}.}

\item{administration}{Route of administration, either \code{""}, \code{"im"}, \code{"iv"}, \code{"oral"}, or NA.}
}
\value{
The input of \code{x}, possibly with edited values of antimicrobials. Or, if \code{verbose = TRUE}, a \link{data.frame} with all original and new values of the affected bug-drug combinations.
}
\description{
Apply rules from clinical breakpoints notes and expected resistant phenotypes as defined by e.g. the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{https://www.eucast.org}), see \emph{Source}. Use \code{\link[=eucast_dosage]{eucast_dosage()}} to get a \link{data.frame} with advised dosages of a certain bug-drug combination, which is based on the \link{dosage} data set.

To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive rules are applied, some AMR-specific rules can be applied at default, see \emph{Details}.
}
\details{
\strong{Note:} This function does not translate MIC or disk values to SIR values. Use \code{\link[=as.sir]{as.sir()}} 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. \cr

The file containing all interpretive rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv}.  \strong{Note:} Old taxonomic names are replaced with the current taxonomy where applicable. For example, \emph{Ochrobactrum anthropi} was renamed to \emph{Brucella anthropi} in 2020; older interpretive rules may not yet contain this new taxonomic name. The \code{AMR} package contains the full microbial taxonomy updated until 5th of October, 2026, see \link{microorganisms}.
\subsection{Custom Rules}{

Custom rules can be created using \code{\link[=custom_interpretive_rules]{custom_interpretive_rules()}}, e.g.:

\if{html}{\out{<div class="sourceCode r">}}\preformatted{x <- custom_interpretive_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
                               AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")

interpretive_rules(example_isolates, rules = "custom", custom_rules = x)
}\if{html}{\out{</div>}}
}

\subsection{'Other' Rules}{

Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:
\enumerate{
\item A drug \strong{with} enzyme inhibitor will be set to S if the same drug \strong{without} enzyme inhibitor is S
\item A drug \strong{without} enzyme inhibitor will be set to R if the same drug \strong{with} enzyme inhibitor is R
}

Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.

Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include \code{"other"} to the \code{rules} argument, or use \code{interpretive_rules(..., rules = "all")}. You can also set the package option \code{\link[=AMR-options]{AMR_interpretive_rules}}, i.e. run \code{options(AMR_interpretive_rules = "all")}.
}
}
\section{Download Our Reference Data}{

All reference data sets in the AMR package - including information on microorganisms, antimicrobials, and clinical breakpoints - are freely available for download in multiple formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata.

For maximum compatibility, we also provide machine-readable, tab-separated plain text files suitable for use in any software, including laboratory information systems.

Visit \href{https://amr-for-r.org/articles/datasets.html}{our website for direct download links}, or explore the actual files in \href{https://github.com/msberends/AMR/tree/main/data-raw/datasets}{our GitHub repository}.
}

\examples{
\donttest{
a <- data.frame(
  mo = c(
    "Staphylococcus aureus",
    "Enterococcus faecalis",
    "Escherichia coli",
    "Klebsiella pneumoniae",
    "Pseudomonas aeruginosa"
  ),
  VAN = "-", # Vancomycin
  AMX = "-", # Amoxicillin
  COL = "-", # Colistin
  CAZ = "-", # Ceftazidime
  CXM = "-", # Cefuroxime
  PEN = "S", # Benzylpenicillin
  FOX = "S", # Cefoxitin
  stringsAsFactors = FALSE
)

head(a)


# apply EUCAST rules: some results wil be changed
b <- eucast_rules(a, overwrite = TRUE)

head(b)


# do not apply EUCAST rules, but rather get a data.frame
# containing all details about the transformations:
c <- eucast_rules(a, overwrite = TRUE, verbose = TRUE)
head(c)
}

# Dosage guidelines:

eucast_dosage(c("tobra", "genta", "cipro"), "iv")

eucast_dosage(c("tobra", "genta", "cipro"), "iv", version_breakpoints = 10)
}
\references{
\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; \doi{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
\item EUCAST Expected Phenotypes. \href{https://www.eucast.org/bacteria/important-additional-information/expected-phenotypes/}{(link)}
\item EUCAST Breakpoint tables for interpretation of MICs and zone diameters. \href{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/}{(link)}
}
}