% Generated by roxygen2: do not edit by hand % Please edit documentation in R/bactid.R \name{as.bactid} \alias{as.bactid} \alias{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): 870–926. \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): 571–95. \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}. Use the \code{\link{mo_property}} functions to get properties based on the returned bactid, see Examples. 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 is an alias of as.bactid and works the same 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 # Use mo_* functions to get a specific property based on a bactid Ecoli <- as.bactid("E. coli") # returns `ESCCOL` mo_genus(Ecoli) # returns "Escherichia" mo_gramstain(Ecoli) # returns "Negative rods" \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}