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(v1.5.0.9016) only_rsi_columns update, documentation

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dr. M.S. (Matthijs) Berends
2021-02-08 14:18:42 +01:00
parent 8fda473e49
commit 4a84894f79
88 changed files with 654 additions and 375 deletions
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21
man/mdro.Rd
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@ -20,33 +20,28 @@ See the supported guidelines above for the list of publications used for this fu
}
\usage{
mdro(
x,
x = NULL,
guideline = "CMI2012",
col_mo = NULL,
info = interactive(),
pct_required_classes = 0.5,
combine_SI = TRUE,
verbose = FALSE,
only_rsi_columns = any(is.rsi(x)),
only_rsi_columns = FALSE,
...
)
custom_mdro_guideline(..., as_factor = TRUE)
brmo(x, guideline = "BRMO", only_rsi_columns = any(is.rsi(x)), ...)
brmo(x = NULL, only_rsi_columns = FALSE, ...)
mrgn(x, guideline = "MRGN", only_rsi_columns = any(is.rsi(x)), ...)
mrgn(x = NULL, only_rsi_columns = FALSE, ...)
mdr_tb(x, guideline = "TB", only_rsi_columns = any(is.rsi(x)), ...)
mdr_tb(x = NULL, only_rsi_columns = FALSE, ...)
mdr_cmi2012(x, guideline = "CMI2012", only_rsi_columns = any(is.rsi(x)), ...)
mdr_cmi2012(x = NULL, only_rsi_columns = FALSE, ...)
eucast_exceptional_phenotypes(
x,
guideline = "EUCAST",
only_rsi_columns = any(is.rsi(x)),
...
)
eucast_exceptional_phenotypes(x = NULL, only_rsi_columns = FALSE, ...)
}
\arguments{
\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}
@ -63,7 +58,7 @@ eucast_exceptional_phenotypes(
\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand. Defaults to \code{TRUE} if any column of \code{x} is of class \verb{<rsi>}.}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand (defaults to \code{FALSE})}
\item{...}{in case of \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}}: a set of rules, see section \emph{Using Custom Guidelines} below. Otherwise: column name of an antibiotic, see section \emph{Antibiotics} below.}