AMR/man/as.bactid.Rd

93 lines
4.2 KiB
R
Raw Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/bactid.R
\name{as.bactid}
\alias{as.bactid}
\alias{guess_bactid}
\alias{is.bactid}
\title{Transform to bacteria ID}
\source{
[1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870926. \cr
\url{https://dx.doi.org/10.1128/CMR.00109-13} \cr
[2] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 57195. \cr
\url{https://dx.doi.org/10.1084/jem.57.4.571}
}
\usage{
as.bactid(x, Becker = FALSE, Lancefield = FALSE)
guess_bactid(x, Becker = FALSE, Lancefield = FALSE)
is.bactid(x)
}
\arguments{
\item{x}{a character vector or a dataframe with one or two columns}
\item{Becker}{a logical to indicate whether \emph{Staphylococci} should be categorised into Coagulase Negative \emph{Staphylococci} ("CoNS") and Coagulase Positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} [1]. This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".}
\item{Lancefield}{a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [2]. These \emph{Streptococci} will be categorised in their first group, i.e. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L. Groups D and E will be ignored, since they are \emph{Enterococci}.}
}
\value{
Character (vector) with class \code{"bactid"}. Unknown values will return \code{NA}.
}
\description{
Use this function to determine a valid ID based on a genus (and species). This input can be a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), or just a genus. You could also \code{\link{select}} a genus and species column, zie Examples.
}
\details{
\code{guess_bactid} is an alias of \code{as.bactid}.
Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. These are:
\itemize{
\item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
\item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae}}
\item{Something like \code{"p aer"} will return the ID of \emph{Pseudomonas aeruginosa} and not \emph{Pasteurella aerogenes}}
\item{Something like \code{"stau"} or \code{"staaur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
}
Moreover, this function also supports ID's based on only Gram stain, when the species is not known. \cr
For example, \code{"Gram negative rods"} and \code{"GNR"} will both return the ID of a Gram negative rod: \code{GNR}.
}
\examples{
# These examples all return "STAAUR", the ID of S. aureus:
as.bactid("stau")
as.bactid("STAU")
as.bactid("staaur")
as.bactid("S. aureus")
as.bactid("S aureus")
as.bactid("Staphylococcus aureus")
as.bactid("MRSA") # Methicillin Resistant S. aureus
as.bactid("VISA") # Vancomycin Intermediate S. aureus
as.bactid("VRSA") # Vancomycin Resistant S. aureus
guess_bactid("S. epidermidis") # will remain species: STAEPI
guess_bactid("S. epidermidis", Becker = TRUE) # will not remain species: STACNS
guess_bactid("S. pyogenes") # will remain species: STCAGA
guess_bactid("S. pyogenes", Lancefield = TRUE) # will not remain species: STCGRA
\dontrun{
df$bactid <- as.bactid(df$microorganism_name)
# the select function of tidyverse is also supported:
library(dplyr)
df$bactid <- df \%>\%
select(microorganism_name) \%>\%
guess_bactid()
# and can even contain 2 columns, which is convenient for genus/species combinations:
df$bactid <- df \%>\%
select(genus, species) \%>\%
guess_bactid()
# same result:
df <- df \%>\%
mutate(bactid = guess_bactid(paste(genus, species)))
}
}
\seealso{
\code{\link{microorganisms}} for the dataframe that is being used to determine ID's.
}
\keyword{Becker}
\keyword{Lancefield}
\keyword{bactid}
\keyword{becker}
\keyword{guess}
\keyword{lancefield}