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dr. M.S. (Matthijs) Berends
2026-05-01 18:24:12 +02:00
parent 7c945b8081
commit b6d80f9578
18 changed files with 85 additions and 74 deletions
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man/interpretive_rules.Rd
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@@ -46,7 +46,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
\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_eucast_rules]{custom_eucast_rules()}}.}
\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}}.}
@@ -62,7 +62,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
\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_eucast_rules]{custom_eucast_rules()}}.}
\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".}
@@ -86,15 +86,15 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
\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 EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/eucast_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; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The \code{AMR} package contains the full microbial taxonomy updated until June 24th, 2024, see \link{microorganisms}.
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; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The \code{AMR} package contains the full microbial taxonomy updated until June 24th, 2024, see \link{microorganisms}.
\subsection{Custom Rules}{
Custom rules can be created using \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}, e.g.:
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_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
\if{html}{\out{<div class="sourceCode r">}}\preformatted{x <- custom_interpretive_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
eucast_rules(example_isolates, rules = "custom", custom_rules = x)
interpretive_rules(example_isolates, rules = "custom", custom_rules = x)
}\if{html}{\out{</div>}}
}
@@ -108,7 +108,7 @@ Before further processing, two non-EUCAST rules about drug combinations can be a
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{eucast_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")}.
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}{