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use dplyr where available, new antibiogram() for WISCA, fixed Salmonella Typhi/Paratyphi

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dr. M.S. (Matthijs) Berends
2023-02-06 11:57:22 +01:00
parent 4b133d4c96
commit 9e99e66f01
69 changed files with 1670 additions and 650 deletions
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8
man/bug_drug_combinations.Rd
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@ -16,14 +16,14 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
add_ab_group = TRUE,
remove_intrinsic_resistant = FALSE,
decimal.mark = getOption("OutDec"),
big.mark = ifelse(decimal.mark == ",", ".", ","),
big.mark = ifelse(decimal.mark == ",", " ", ","),
...
)
}
\arguments{
\item{x}{a data set with antibiotic columns, such as \code{amox}, \code{AMX} and \code{AMC}}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{FUN}{the function to call on the \code{mo} column to transform the microorganism codes, defaults to \code{\link[=mo_shortname]{mo_shortname()}}}
@ -59,6 +59,10 @@ The function \code{\link[=format]{format()}} calculates the resistance per bug-d
}
\examples{
\donttest{
#' # example_isolates is a data set available in the AMR package.
# run ?example_isolates for more info.
example_isolates
x <- bug_drug_combinations(example_isolates)
head(x)
format(x, translate_ab = "name (atc)")