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dr. M.S. (Matthijs) Berends
2022-12-28 15:04:59 +01:00
parent ba3b237bdf
commit 61c0bdb7af
5 changed files with 9 additions and 6 deletions
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man/add_custom_microorganisms.Rd
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@ -13,7 +13,7 @@ clear_custom_microorganisms()
\item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing columns "genus" and "species"}
}
\description{
With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom antimicrobial drug codes to the \code{AMR} package.
With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom microorganisms to the \code{AMR} package, such the non-taxonomic outcome of laboratory analysis.
}
\details{
This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see \emph{Examples}.
@ -67,8 +67,10 @@ add_custom_microorganisms(
# E. asburiae/cloacae is now a new microorganism:
mo_name("Enterobacter asburiae/cloacae")
# its code:
as.mo("Enterobacter asburiae/cloacae")
# all internal algorithms will work as well:
mo_name("Ent asburia cloacae")