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(v2.1.1.9121) support tidymodels

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dr. M.S. (Matthijs) Berends
2024-12-19 20:17:15 +01:00
parent 8249cfda46
commit 15fc72fc66
16 changed files with 638 additions and 89 deletions
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31
man/mdro.Rd
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@ -23,6 +23,12 @@ mdro(
x = NULL,
guideline = "CMI2012",
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,
@ -35,13 +41,18 @@ custom_mdro_guideline(..., as_factor = TRUE)
brmo(x = NULL, only_sir_columns = FALSE, ...)
mrgn(x = NULL, only_sir_columns = FALSE, ...)
mrgn(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...)
mdr_tb(x = NULL, only_sir_columns = FALSE, ...)
mdr_tb(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...)
mdr_cmi2012(x = NULL, only_sir_columns = FALSE, ...)
mdr_cmi2012(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...)
eucast_exceptional_phenotypes(x = NULL, only_sir_columns = FALSE, ...)
eucast_exceptional_phenotypes(
x = NULL,
only_sir_columns = FALSE,
verbose = FALSE,
...
)
}
\arguments{
\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}
@ -50,6 +61,18 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = FALSE, ...)
\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()}}.}
\item{esbl}{\link{logical} values, or a column name containing logical values, indicating the presence of an ESBL gene (or production of its proteins)}
\item{carbapenemase}{\link{logical} values, or a column name containing logical values, indicating the presence of a carbapenemase gene (or production of its proteins)}
\item{mecA}{\link{logical} values, or a column name containing logical values, indicating the presence of a \emph{mecA} gene (or production of its proteins)}
\item{mecC}{\link{logical} values, or a column name containing logical values, indicating the presence of a \emph{mecC} gene (or production of its proteins)}
\item{vanA}{\link{logical} values, or a column name containing logical values, indicating the presence of a \emph{vanA} gene (or production of its proteins)}
\item{vanB}{\link{logical} values, or a column name containing logical values, indicating the presence of a \emph{vanB} gene (or production of its proteins)}
\item{info}{a \link{logical} to indicate whether progress should be printed to the console - the default is only print while in interactive sessions}
\item{pct_required_classes}{minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for \emph{S. aureus}. Setting this \code{pct_required_classes} argument to \code{0.5} (default) means that for every \emph{S. aureus} isolate at least 8 different classes must be available. Any lower number of available classes will return \code{NA} for that isolate.}