mirror of https://github.com/msberends/AMR.git
106 lines
4.2 KiB
R
106 lines
4.2 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_penicillins}
|
|
\alias{filter_tetracyclines}
|
|
\title{Filter isolates on result in antimicrobial 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_penicillins(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{\link[=antibiotics]{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{filter_at} from the \code{dplyr} package}
|
|
}
|
|
\description{
|
|
Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.
|
|
}
|
|
\details{
|
|
The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched for the input given in \code{ab_class} (case-insensitive). Next, \code{x} will be checked for column names with a value in any abbreviation, code or official name found in the \link{antibiotics} data set.
|
|
}
|
|
\section{Stable lifecycle}{
|
|
|
|
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
|
|
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
|
|
|
|
If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
|
|
}
|
|
|
|
\examples{
|
|
\dontrun{
|
|
library(dplyr)
|
|
|
|
# filter on isolates that have any result for any aminoglycoside
|
|
example_isolates \%>\% filter_ab_class("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", "any")
|
|
|
|
# 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")
|
|
}
|
|
}
|