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allow column name for ab in as.sir()

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dr. M.S. (Matthijs) Berends
2024-05-20 21:29:13 +02:00
parent fc269e667d
commit d214f74e25
10 changed files with 139 additions and 106 deletions
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6
man/as.sir.Rd
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@ -98,9 +98,9 @@ sir_interpretation_history(clean = FALSE)
\item{S, I, R, N, SDD}{a case-indepdendent \link[base:regex]{regular expression} to translate input to this result. This regular expression will be run \emph{after} all non-letters are removed from the input.}
\item{mo}{any (vector of) text that can be coerced to valid microorganism codes with \code{\link[=as.mo]{as.mo()}}, can be left empty to determine it automatically}
\item{mo}{a vector (or column name) with \link{character}s that can be coerced to valid microorganism codes with \code{\link[=as.mo]{as.mo()}}, can be left empty to determine it automatically}
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
\item{ab}{a vector (or column name) with \link{character}s that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
\item{guideline}{defaults to EUCAST 2023 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2011-2023) and CLSI (2011-2023), see \emph{Details}.}
@ -284,7 +284,7 @@ if (require("dplyr")) {
df \%>\% mutate(across(AMP:TOB, as.sir))
df \%>\%
mutate_at(vars(AMP:TOB), as.sir, mo = .$microorganism)
mutate_at(vars(AMP:TOB), as.sir, mo = "microorganism")
# to include information about urinary tract infections (UTI)
data.frame(