mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 22:06:11 +01:00
32 lines
1.1 KiB
R
32 lines
1.1 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/atc.R
|
|
\name{guess_bactid}
|
|
\alias{guess_bactid}
|
|
\title{Find bacteria ID based on genus/species}
|
|
\usage{
|
|
guess_bactid(x)
|
|
}
|
|
\arguments{
|
|
\item{x}{character vector to determine \code{bactid}}
|
|
}
|
|
\value{
|
|
Character (vector).
|
|
}
|
|
\description{
|
|
Use this function to determine a valid ID based on a genus (and species). This input could be a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), or just a genus. You could also use a \code{\link{paste}} of a genus and species column to use the full name as input: \code{x = paste(df$genus, df$species)}, where \code{df} is your dataframe.
|
|
}
|
|
\examples{
|
|
# These examples all return "STAAUR", the ID of S. aureus:
|
|
guess_bactid("stau")
|
|
guess_bactid("STAU")
|
|
guess_bactid("staaur")
|
|
guess_bactid("S. aureus")
|
|
guess_bactid("S aureus")
|
|
guess_bactid("Staphylococcus aureus")
|
|
guess_bactid("MRSA") # Methicillin-resistant S. aureus
|
|
guess_bactid("VISA") # Vancomycin Intermediate S. aureus
|
|
}
|
|
\seealso{
|
|
\code{\link{microorganisms}} for the dataframe that is being used to determine ID's.
|
|
}
|