P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-05-14 05:10:46 +02:00
Code Releases Activity

prepare for documentation

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-05-03 11:50:05 +02:00
parent 9707450b89
commit a5e8beff69
12 changed files with 93 additions and 67 deletions
Download Patch File Download Diff File Expand all files Collapse all files

22
man/mdro.Rd
View File

@@ -67,16 +67,18 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
\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{
- If `verbose` is set to `TRUE`:\cr
A [data.frame] containing columns `row_number`, `microorganism`, `MDRO`, `reason`, `all_nonsusceptible_columns`, `guideline`
- CMI 2012 paper - function [mdr_cmi2012()] or [mdro()]:\cr
Ordered [factor] with levels `Negative` < `Multi-drug-resistant (MDR)` < `Extensively drug-resistant (XDR)` < `Pandrug-resistant (PDR)`
- TB guideline - function [mdr_tb()] or [`mdro(..., guideline = "TB")`][mdro()]:\cr
Ordered [factor] with levels `Negative` < `Mono-resistant` < `Poly-resistant` < `Multi-drug-resistant` < `Extensively drug-resistant`
- German guideline - function [mrgn()] or [`mdro(..., guideline = "MRGN")`][mdro()]:\cr
Ordered [factor] with levels `Negative` < `3MRGN` < `4MRGN`
- Everything else, except for custom guidelines:\cr
Ordered [factor] with levels `Negative` < `Positive, unconfirmed` < `Positive`. The value `"Positive, unconfirmed"` means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. genotypic) tests
\itemize{
\item If \code{verbose} is set to \code{TRUE}:\cr
A \link{data.frame} containing columns \code{row_number}, \code{microorganism}, \code{MDRO}, \code{reason}, \code{all_nonsusceptible_columns}, \code{guideline}
\item CMI 2012 paper - function \code{\link[=mdr_cmi2012]{mdr_cmi2012()}} or \code{\link[=mdro]{mdro()}}:\cr
Ordered \link{factor} with levels \code{Negative} < \code{Multi-drug-resistant (MDR)} < \verb{Extensively drug-resistant (XDR)} < \code{Pandrug-resistant (PDR)}
\item TB guideline - function \code{\link[=mdr_tb]{mdr_tb()}} or \code{\link[=mdro]{mdro(..., guideline = "TB")}}:\cr
Ordered \link{factor} with levels \code{Negative} < \code{Mono-resistant} < \code{Poly-resistant} < \code{Multi-drug-resistant} < \verb{Extensively drug-resistant}
\item German guideline - function \code{\link[=mrgn]{mrgn()}} or \code{\link[=mdro]{mdro(..., guideline = "MRGN")}}:\cr
Ordered \link{factor} with levels \code{Negative} < \verb{3MRGN} < \verb{4MRGN}
\item Everything else, except for custom guidelines:\cr
Ordered \link{factor} with levels \code{Negative} < \verb{Positive, unconfirmed} < \code{Positive}. The value \code{"Positive, unconfirmed"} means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. genotypic) tests
}
}
\description{
Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines.