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(v3.0.1.9031) fix MDRO for non-RStudio terminal

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dr. M.S. (Matthijs) Berends
2026-03-08 11:30:18 +01:00
parent e2102c081a
commit b6f8584994
6 changed files with 80 additions and 59 deletions
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7
man/mdro.Rd
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@@ -18,7 +18,8 @@
mdro(x = NULL, guideline = "CMI 2012", col_mo = NULL, esbl = NA,
carbapenemase = NA, mecA = NA, mecC = NA, vanA = NA, vanB = NA,
info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE,
verbose = FALSE, only_sir_columns = any(is.sir(x)), ...)
verbose = FALSE, only_sir_columns = any(is.sir(x)),
infer_from_combinations = TRUE, ...)
brmo(x = NULL, only_sir_columns = any(is.sir(x)), ...)
@@ -35,7 +36,7 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
\arguments{
\item{x}{A \link{data.frame} with antimicrobials columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}
\item{guideline}{A specific guideline to follow, see sections \emph{Supported international / national guidelines} and \emph{Using Custom Guidelines} below. When left empty, the publication by Magiorakos \emph{et al.} (see below) will be followed.}
\item{guideline}{A specific guideline to follow, see sections \emph{Supported International / National Guidelines} and \emph{Using Custom Guidelines} below. When left empty, the publication by Magiorakos \emph{et al.} (see below) will be followed.}
\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()}}.}
@@ -61,6 +62,8 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
\item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.}
\item{infer_from_combinations}{A \link{logical} to indicate whether resistance for a missing base beta-lactam drug should be inferred from an available drug+inhibitor combination (e.g., piperacillin from piperacillin/tazobactam). The clinical basis is that resistance in a combination always implies resistance in the base drug, since the enzyme inhibitor provides no benefit when the organism is truly resistant. Only resistance is inferred; susceptibility in a combination does \strong{not} imply susceptibility in the base drug (the inhibitor may be responsible). Defaults to \code{TRUE}.}
\item{...}{Column names of antimicrobials. To automatically detect antimicrobial column names, do not provide any named arguments; \code{\link[=guess_ab_col]{guess_ab_col()}} will then be used for detection. To manually specify a column, provide its name (case-insensitive) as an argument, e.g. \code{AMX = "amoxicillin"}. To skip a specific antimicrobial, set it to \code{NULL}, e.g. \code{TIC = NULL} to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.}
}
\value{