AMR/man/key_antibiotics.Rd

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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/first_isolates.R
\name{key_antibiotics}
\alias{key_antibiotics}
\title{Key antibiotics based on bacteria ID}
\usage{
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key_antibiotics(tbl, col_bactcode = "bactid", info = TRUE, amcl = "amcl",
amox = "amox", cfot = "cfot", cfta = "cfta", cftr = "cftr",
cfur = "cfur", cipr = "cipr", clar = "clar", clin = "clin",
clox = "clox", doxy = "doxy", gent = "gent", line = "line",
mero = "mero", peni = "peni", pita = "pita", rifa = "rifa",
teic = "teic", trsu = "trsu", vanc = "vanc")
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}
\arguments{
\item{tbl}{table with antibiotics coloms, like \code{amox} and \code{amcl}.}
\item{col_bactcode}{column of bacteria IDs in \code{tbl}; these should occur in \code{bactlist$bactid}, see \code{\link{bactlist}}}
\item{info}{print warnings}
\item{amcl, amox, cfot, cfta, cftr, cfur, cipr, clar, clin, clox, doxy, gent, line, mero, peni, pita, rifa, teic, trsu, vanc}{column names of antibiotics, case-insensitive}
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}
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\value{
Character of length 1.
}
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\description{
Key antibiotics based on bacteria ID
}
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\examples{
\donttest{
#' # set key antibiotics to a new variable
tbl$keyab <- key_antibiotics(tbl)
}
}
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\seealso{
\code{\link{mo_property}} \code{\link{antibiotics}}
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}