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AMR/man/key_antibiotics.Rd
dr. M.S. (Matthijs) Berends 53464ff1c8
- For functions first_isolate, EUCAST_rules the antibiotic column names are case-insensitive
- Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore)
- Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
- Renamed dataset `bactlist` to `microorganisms`
2018-03-23 14:46:02 +01:00

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R

% 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{
key_antibiotics(tbl, col_bactid = "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")
}
\arguments{
\item{tbl}{table with antibiotics coloms, like \code{amox} and \code{amcl}.}
\item{col_bactid}{column of bacteria IDs in \code{tbl}; these should occur in \code{microorganisms$bactid}, see \code{\link{microorganisms}}}
\item{info}{print warnings}
\item{amcl, amox, cfot, cfta, cftr, cfur, cipr, clar, clin, clox, doxy, gent, line, mero, peni, pita, rifa, teic, trsu, vanc}{column names of antibiotics, case-insensitive}
}
\value{
Character of length 1.
}
\description{
Key antibiotics based on bacteria ID
}
\examples{
\donttest{
#' # set key antibiotics to a new variable
tbl$keyab <- key_antibiotics(tbl)
}
}
\seealso{
\code{\link{mo_property}} \code{\link{antibiotics}}
}