mirror of https://github.com/msberends/AMR.git
44 lines
2.2 KiB
Plaintext
44 lines
2.2 KiB
Plaintext
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/custom_eucast_rules.R
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\name{custom_eucast_rules}
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\alias{custom_eucast_rules}
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\title{Create Custom EUCAST Rules}
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\usage{
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custom_eucast_rules(...)
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}
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\arguments{
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\item{...}{rules in formula notation, see \emph{Examples}}
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}
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\description{
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Create Custom EUCAST Rules
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}
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\details{
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This documentation page will be updated shortly. \strong{This function is experimental.}
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}
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\section{How it works}{
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..
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It is also possible to define antibiotic groups instead of single antibiotics. The following groups are allowed (case-insensitive): \code{aminoglycosides}, \code{aminopenicillins}, \code{betalactams}, \code{carbapenems}, \code{cephalosporins}, \code{cephalosporins_1st}, \code{cephalosporins_2nd}, \code{cephalosporins_3rd}, \code{cephalosporins_except_caz}, \code{fluoroquinolones}, \code{glycopeptides}, \code{glycopeptides_except_lipo}, \code{lincosamides}, \code{lipoglycopeptides}, \code{macrolides}, \code{oxazolidinones}, \code{penicillins}, \code{polymyxins}, \code{streptogramins}, \code{tetracyclines}, \code{tetracyclines_except_tgc} and \code{ureidopenicillins}.
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}
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\section{Experimental Lifecycle}{
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\if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this \code{AMR} package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
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}
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\examples{
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x <- custom_eucast_rules(AMC == "R" & genus == "Klebsiella" ~ aminopenicillins == "R",
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AMC == "I" & genus == "Klebsiella" ~ aminopenicillins == "I")
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eucast_rules(example_isolates,
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rules = "custom",
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custom_rules = x,
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info = FALSE)
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# combine rule sets
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x2 <- c(x,
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custom_eucast_rules(TZP == "R" ~ carbapenems == "R"))
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x2
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}
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