mirror of https://github.com/msberends/AMR.git
91 lines
3.4 KiB
R
91 lines
3.4 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_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(tbl, ab_class, result = NULL, scope = "any", ...)
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filter_aminoglycosides(tbl, result = NULL, scope = "any", ...)
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filter_carbapenems(tbl, result = NULL, scope = "any", ...)
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filter_cephalosporins(tbl, result = NULL, scope = "any", ...)
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filter_1st_cephalosporins(tbl, result = NULL, scope = "any", ...)
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filter_2nd_cephalosporins(tbl, result = NULL, scope = "any", ...)
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filter_3rd_cephalosporins(tbl, result = NULL, scope = "any", ...)
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filter_4th_cephalosporins(tbl, result = NULL, scope = "any", ...)
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filter_fluoroquinolones(tbl, result = NULL, scope = "any", ...)
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filter_glycopeptides(tbl, result = NULL, scope = "any", ...)
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filter_macrolides(tbl, result = NULL, scope = "any", ...)
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filter_tetracyclines(tbl, result = NULL, scope = "any", ...)
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}
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\arguments{
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\item{tbl}{a data set}
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\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. More specifically, this should be a text that can be found in a 4th level ATC group (chemical subgroup) or a 5th level ATC group (chemical substance), please see \href{https://www.whocc.no/atc/structure_and_principles/}{this explanation on the WHOCC website}.}
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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{\link[dplyr]{filter_at}}}
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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{\link{antibiotics}} data set will be searched for \code{ab_class} in the columns \code{atc_group1} and \code{atc_group2} (case-insensitive). Next, \code{tbl} 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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septic_patients \%>\% filter_aminoglycosides()
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# this is essentially the same as:
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septic_patients \%>\%
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filter_at(.vars = vars(c("gent", "tobr", "amik", "kana")),
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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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septic_patients \%>\% filter_aminoglycosides("R")
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# filter on isolates that show resistance to ALL aminoglycosides
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septic_patients \%>\% 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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septic_patients \%>\%
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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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septic_patients \%>\%
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filter_aminoglycosides("R", "all") \%>\%
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filter_fluoroquinolones("R", "all")
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}
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\keyword{fillter_class}
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\keyword{filter}
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