mirror of https://github.com/msberends/AMR.git
32 lines
1.1 KiB
R
32 lines
1.1 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/first_isolates.R
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\name{guess_bactid}
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\alias{guess_bactid}
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\title{Find bacteria ID based on genus/species}
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\usage{
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guess_bactid(x)
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}
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\arguments{
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\item{x}{character vector to determine \code{bactid}}
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}
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\value{
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Character (vector).
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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 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.
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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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guess_bactid("stau")
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guess_bactid("STAU")
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guess_bactid("staaur")
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guess_bactid("S. aureus")
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guess_bactid("S aureus")
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guess_bactid("Staphylococcus aureus")
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guess_bactid("MRSA") # Methicillin-resistant S. aureus
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guess_bactid("VISA") # Vancomycin Intermediate S. aureus
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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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