mirror of https://github.com/msberends/AMR.git
92 lines
3.3 KiB
R
92 lines
3.3 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/filter_ab_class.R
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\name{filter_ab_class}
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\alias{filter_ab_class}
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\alias{filter_aminoglycosides}
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\alias{filter_carbapenems}
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\alias{filter_cephalosporins}
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\alias{filter_1st_cephalosporins}
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\alias{filter_2nd_cephalosporins}
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\alias{filter_3rd_cephalosporins}
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\alias{filter_4th_cephalosporins}
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\alias{filter_5th_cephalosporins}
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\alias{filter_fluoroquinolones}
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\alias{filter_glycopeptides}
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\alias{filter_macrolides}
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\alias{filter_tetracyclines}
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\title{Filter isolates on result in antibiotic class}
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\usage{
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filter_ab_class(x, ab_class, result = NULL, scope = "any", ...)
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filter_aminoglycosides(x, result = NULL, scope = "any", ...)
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filter_carbapenems(x, result = NULL, scope = "any", ...)
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filter_cephalosporins(x, result = NULL, scope = "any", ...)
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filter_1st_cephalosporins(x, result = NULL, scope = "any", ...)
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filter_2nd_cephalosporins(x, result = NULL, scope = "any", ...)
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filter_3rd_cephalosporins(x, result = NULL, scope = "any", ...)
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filter_4th_cephalosporins(x, result = NULL, scope = "any", ...)
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filter_5th_cephalosporins(x, result = NULL, scope = "any", ...)
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filter_fluoroquinolones(x, result = NULL, scope = "any", ...)
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filter_glycopeptides(x, result = NULL, scope = "any", ...)
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filter_macrolides(x, result = NULL, scope = "any", ...)
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filter_tetracyclines(x, result = NULL, scope = "any", ...)
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}
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\arguments{
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\item{x}{a data set}
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\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}, as can be found in \code{AMR::antibiotics$group}}
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\item{result}{an antibiotic result: S, I or R (or a combination of more of them)}
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\item{scope}{the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}}
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\item{...}{parameters passed on to \code{filter_at} from the \code{dplyr} package}
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}
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\description{
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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.
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}
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\details{
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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.
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}
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\examples{
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library(dplyr)
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# filter on isolates that have any result for any aminoglycoside
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example_isolates \%>\% filter_aminoglycosides()
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# this is essentially the same as (but without determination of column names):
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example_isolates \%>\%
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filter_at(.vars = vars(c("GEN", "TOB", "AMK", "KAN")),
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.vars_predicate = any_vars(. \%in\% c("S", "I", "R")))
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# filter on isolates that show resistance to ANY aminoglycoside
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example_isolates \%>\% filter_aminoglycosides("R")
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# filter on isolates that show resistance to ALL aminoglycosides
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example_isolates \%>\% filter_aminoglycosides("R", "all")
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# filter on isolates that show resistance to
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# any aminoglycoside and any fluoroquinolone
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example_isolates \%>\%
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filter_aminoglycosides("R") \%>\%
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filter_fluoroquinolones("R")
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# filter on isolates that show resistance to
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# all aminoglycosides and all fluoroquinolones
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example_isolates \%>\%
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filter_aminoglycosides("R", "all") \%>\%
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filter_fluoroquinolones("R", "all")
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}
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