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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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4
man/key_antimicrobials.Rd
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@ -21,7 +21,7 @@ antimicrobials_equal(y, z, type = c("points", "keyantimicrobials"),
ignore_I = TRUE, points_threshold = 2, ...)
}
\arguments{
\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank to determine automatically}
\item{x}{a \link{data.frame} with antimicrobials columns, like \code{AMX} or \code{amox}. Can be left blank to determine automatically.}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
@ -112,7 +112,7 @@ antimicrobials_equal(strainA, strainB, type = "keyantimicrobials", ignore_I = FA
\donttest{
if (require("dplyr")) {
# set key antibiotics to a new variable
# set key antimicrobials to a new variable
my_patients <- example_isolates \%>\%
mutate(keyab = key_antimicrobials(antifungal = NULL)) \%>\% # no need to define `x`
mutate(