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(v3.0.1.9059) Fix WISCA in vignette

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dr. M.S. (Matthijs) Berends
2026-06-23 14:38:59 +02:00
parent 3f9f931777
commit 9898b5df4b
41 changed files with 1310 additions and 757 deletions
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34
man/mdro.Rd
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@@ -15,11 +15,24 @@
\alias{eucast_exceptional_phenotypes}
\title{Determine Multidrug-Resistant Organisms (MDRO)}
\usage{
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)),
infer_from_combinations = TRUE, ...)
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)),
infer_from_combinations = TRUE,
...
)
brmo(x = NULL, only_sir_columns = any(is.sir(x)), ...)
@@ -27,11 +40,14 @@ mrgn(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)
mdr_tb(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)
mdr_cmi2012(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE,
...)
mdr_cmi2012(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)
eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
verbose = FALSE, ...)
eucast_exceptional_phenotypes(
x = NULL,
only_sir_columns = any(is.sir(x)),
verbose = FALSE,
...
)
}
\arguments{
\item{x}{A \link{data.frame} with antimicrobials columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}