mirror of https://github.com/msberends/AMR.git
70 lines
2.5 KiB
R
70 lines
2.5 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/bactid.R
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\name{as.bactid}
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\alias{as.bactid}
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\alias{guess_bactid}
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\alias{is.bactid}
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\title{Transform to bacteria ID}
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\usage{
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as.bactid(x)
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guess_bactid(x)
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is.bactid(x)
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}
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\arguments{
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\item{x}{a character vector or a dataframe with one or two columns}
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}
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\value{
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Character (vector) with class \code{"bactid"}. Unknown values will return \code{NA}.
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}
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\description{
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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.
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}
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\details{
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Some exceptions have been built in to get more logical results, based on prevalence of human pathogens. For example:
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\itemize{
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\item{\code{"E. coli"} will return the ID of \emph{Escherichia coli} and not \emph{Entamoeba coli}, although the latter would alphabetically come first}
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\item{\code{"H. influenzae"} will return the ID of \emph{Haemophilus influenzae} and not \emph{Haematobacter influenzae}}
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\item{Something like \code{"p aer"} will return the ID of \emph{Pseudomonas aeruginosa} and not \emph{Pasteurella aerogenes}}
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\item{Something like \code{"stau"} or \code{"staaur"} will return the ID of \emph{Staphylococcus aureus} and not \emph{Staphylococcus auricularis}}
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}
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Moreover, this function also supports ID's based on only Gram stain, when the species is not known. \cr
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For example, \code{"Gram negative rods"} and \code{"GNR"} will both return the ID of a Gram negative rod: \code{GNR}.
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}
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\examples{
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# These examples all return "STAAUR", the ID of S. aureus:
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as.bactid("stau")
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as.bactid("STAU")
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as.bactid("staaur")
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as.bactid("S. aureus")
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as.bactid("S aureus")
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as.bactid("Staphylococcus aureus")
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as.bactid("MRSA") # Methicillin Resistant S. aureus
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as.bactid("VISA") # Vancomycin Intermediate S. aureus
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as.bactid("VRSA") # Vancomycin Resistant S. aureus
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\dontrun{
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df$bactid <- as.bactid(df$microorganism_name)
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# the select function of tidyverse is also supported:
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library(dplyr)
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df$bactid <- df \%>\%
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select(microorganism_name) \%>\%
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as.bactid()
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# and can even contain 2 columns, which is convenient for genus/species combinations:
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df$bactid <- df \%>\%
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select(genus, species) \%>\%
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as.bactid()
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# same result:
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df <- df \%>\%
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mutate(bactid = paste(genus, species) \%>\%
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as.bactid())
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}
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}
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\seealso{
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\code{\link{microorganisms}} for the dataframe that is being used to determine ID's.
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}
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