mirror of https://github.com/msberends/AMR.git
44 lines
1.5 KiB
R
Executable File
44 lines
1.5 KiB
R
Executable File
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/guess_bactid.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 or a dataframe with one or two columns}
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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 \code{\link{select}} a genus and species column, zie Examples.
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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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\dontrun{
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df$bactid <- guess_bactid(df$microorganism_name)
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# the select function of tidyverse is also supported:
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df$bactid <- df \%>\% select(microorganism_name) \%>\% guess_bactid()
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# and can even contain 2 columns, which is convenient for genus/species combinations:
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df$bactid <- df \%>\% select(genus, species) \%>\% guess_bactid()
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# same result:
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df <- df \%>\% mutate(bactid = paste(genus, species) \%>\% guess_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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