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(v2.1.1.9276) mdro() fix

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dr. M.S. (Matthijs) Berends
2025-05-15 10:39:48 +02:00
parent 48a59ee31a
commit 4b171745de
14 changed files with 64 additions and 94 deletions
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2
man/antimicrobial_selectors.Rd
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@ -131,7 +131,7 @@ not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL,
version_expected_phenotypes = 1.2, ...)
}
\arguments{
\item{only_sir_columns}{A \link{logical} to indicate whether only columns of class \code{sir} must be selected (default is \code{FALSE}), see \code{\link[=as.sir]{as.sir()}}.}
\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}.}
\item{only_treatable}{A \link{logical} to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE}).}

10
man/eucast_rules.Rd
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File diff suppressed because one or more lines are too long

2
man/guess_ab_col.Rd
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@ -14,7 +14,7 @@ guess_ab_col(x = NULL, search_string = NULL, verbose = FALSE,
\item{verbose}{A \link{logical} to indicate whether additional info should be printed.}
\item{only_sir_columns}{A \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \code{sir} (see \code{\link[=as.sir]{as.sir()}}) on beforehand (default is \code{FALSE}).}
\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}.}
}
\value{
A column name of \code{x}, or \code{NULL} when no result is found.

6
man/key_antimicrobials.Rd
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@ -13,9 +13,9 @@ key_antimicrobials(x = NULL, col_mo = NULL, universal = c("ampicillin",
"ceftazidime", "meropenem"), gram_positive = c("vancomycin", "teicoplanin",
"tetracycline", "erythromycin", "oxacillin", "rifampin"),
antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole",
"nystatin", "voriconazole"), only_sir_columns = FALSE, ...)
"nystatin", "voriconazole"), only_sir_columns = any(is.sir(x)), ...)
all_antimicrobials(x = NULL, only_sir_columns = FALSE, ...)
all_antimicrobials(x = NULL, only_sir_columns = any(is.sir(x)), ...)
antimicrobials_equal(y, z, type = c("points", "keyantimicrobials"),
ignore_I = TRUE, points_threshold = 2, ...)
@ -33,7 +33,7 @@ antimicrobials_equal(y, z, type = c("points", "keyantimicrobials"),
\item{antifungal}{Names of antifungal drugs for \strong{fungi}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antifungal drugs.}
\item{only_sir_columns}{A \link{logical} to indicate whether only columns must be included that were transformed to class \code{sir} (see \code{\link[=as.sir]{as.sir()}}) on beforehand (default is \code{FALSE}).}
\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{...}{Ignored, only in place to allow future extensions.}

21
man/mdro.Rd
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