mirror of https://github.com/msberends/AMR.git
94 lines
3.3 KiB
R
94 lines
3.3 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/filter_ab_class.R
|
|
\name{filter_ab_class}
|
|
\alias{filter_ab_class}
|
|
\alias{filter_aminoglycosides}
|
|
\alias{filter_carbapenems}
|
|
\alias{filter_cephalosporins}
|
|
\alias{filter_1st_cephalosporins}
|
|
\alias{filter_2nd_cephalosporins}
|
|
\alias{filter_3rd_cephalosporins}
|
|
\alias{filter_4th_cephalosporins}
|
|
\alias{filter_5th_cephalosporins}
|
|
\alias{filter_fluoroquinolones}
|
|
\alias{filter_glycopeptides}
|
|
\alias{filter_macrolides}
|
|
\alias{filter_tetracyclines}
|
|
\title{Filter isolates on result in antibiotic class}
|
|
\usage{
|
|
filter_ab_class(x, ab_class, result = NULL, scope = "any", ...)
|
|
|
|
filter_aminoglycosides(x, result = NULL, scope = "any", ...)
|
|
|
|
filter_carbapenems(x, result = NULL, scope = "any", ...)
|
|
|
|
filter_cephalosporins(x, result = NULL, scope = "any", ...)
|
|
|
|
filter_1st_cephalosporins(x, result = NULL, scope = "any", ...)
|
|
|
|
filter_2nd_cephalosporins(x, result = NULL, scope = "any", ...)
|
|
|
|
filter_3rd_cephalosporins(x, result = NULL, scope = "any", ...)
|
|
|
|
filter_4th_cephalosporins(x, result = NULL, scope = "any", ...)
|
|
|
|
filter_5th_cephalosporins(x, result = NULL, scope = "any", ...)
|
|
|
|
filter_fluoroquinolones(x, result = NULL, scope = "any", ...)
|
|
|
|
filter_glycopeptides(x, result = NULL, scope = "any", ...)
|
|
|
|
filter_macrolides(x, result = NULL, scope = "any", ...)
|
|
|
|
filter_tetracyclines(x, result = NULL, scope = "any", ...)
|
|
}
|
|
\arguments{
|
|
\item{x}{a data set}
|
|
|
|
\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}, as can be found in \code{AMR::antibiotics$group}}
|
|
|
|
\item{result}{an antibiotic result: S, I or R (or a combination of more of them)}
|
|
|
|
\item{scope}{the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}}
|
|
|
|
\item{...}{parameters passed on to \code{\link[dplyr]{filter_at}}}
|
|
}
|
|
\description{
|
|
Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.
|
|
}
|
|
\details{
|
|
The \code{group} column in \code{\link{antibiotics}} data set will be searched for \code{ab_class} (case-insensitive). If no results are found, the \code{atc_group1} and \code{atc_group2} columns will be searched. Next, \code{x} will be checked for column names with a value in any abbreviations, codes or official names found in the \code{antibiotics} data set.
|
|
}
|
|
\examples{
|
|
library(dplyr)
|
|
|
|
# filter on isolates that have any result for any aminoglycoside
|
|
example_isolates \%>\% filter_aminoglycosides()
|
|
|
|
# this is essentially the same as (but without determination of column names):
|
|
example_isolates \%>\%
|
|
filter_at(.vars = vars(c("GEN", "TOB", "AMK", "KAN")),
|
|
.vars_predicate = any_vars(. \%in\% c("S", "I", "R")))
|
|
|
|
|
|
# filter on isolates that show resistance to ANY aminoglycoside
|
|
example_isolates \%>\% filter_aminoglycosides("R")
|
|
|
|
# filter on isolates that show resistance to ALL aminoglycosides
|
|
example_isolates \%>\% filter_aminoglycosides("R", "all")
|
|
|
|
# filter on isolates that show resistance to
|
|
# any aminoglycoside and any fluoroquinolone
|
|
example_isolates \%>\%
|
|
filter_aminoglycosides("R") \%>\%
|
|
filter_fluoroquinolones("R")
|
|
|
|
# filter on isolates that show resistance to
|
|
# all aminoglycosides and all fluoroquinolones
|
|
example_isolates \%>\%
|
|
filter_aminoglycosides("R", "all") \%>\%
|
|
filter_fluoroquinolones("R", "all")
|
|
}
|
|
\keyword{fillter_class}
|
|
\keyword{filter}
|