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con WHONET, filter ab class

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dr. M.S. (Matthijs) Berends
2019-03-05 22:47:42 +01:00
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% 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_fluoroquinolones}
\alias{filter_glycopeptides}
\alias{filter_macrolides}
\alias{filter_tetracyclines}
\title{Filter on antibiotic class}
\usage{
filter_ab_class(tbl, ab_class, result = NULL, scope = "any", ...)
filter_aminoglycosides(tbl, result = NULL, scope = "any", ...)
filter_carbapenems(tbl, result = NULL, scope = "any", ...)
filter_cephalosporins(tbl, result = NULL, scope = "any", ...)
filter_1st_cephalosporins(tbl, result = NULL, scope = "any", ...)
filter_2nd_cephalosporins(tbl, result = NULL, scope = "any", ...)
filter_3rd_cephalosporins(tbl, result = NULL, scope = "any", ...)
filter_4th_cephalosporins(tbl, result = NULL, scope = "any", ...)
filter_fluoroquinolones(tbl, result = NULL, scope = "any", ...)
filter_glycopeptides(tbl, result = NULL, scope = "any", ...)
filter_macrolides(tbl, result = NULL, scope = "any", ...)
filter_tetracyclines(tbl, result = NULL, scope = "any", ...)
}
\arguments{
\item{tbl}{a data set}
\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}}
\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 on specific antibiotic variables based on their class (ATC groups).
}
\details{
The \code{\code{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.
}
\examples{
library(dplyr)
# filter on isolates that have any result for any aminoglycoside
septic_patients \%>\% filter_aminoglycosides()
# this is essentially the same as:
septic_patients \%>\%
filter_at(.vars = vars(c("gent", "tobr", "amik", "kana")),
.vars_predicate = any_vars(. \%in\% c("S", "I", "R")))
# filter on isolates that show resistance to ANY aminoglycoside
septic_patients \%>\% filter_aminoglycosides("R")
# filter on isolates that show resistance to ALL aminoglycosides
septic_patients \%>\% filter_aminoglycosides("R", "all")
# filter on isolates that show resistance to
# any aminoglycoside and any fluoroquinolone
septic_patients \%>\%
filter_aminoglycosides("R", "any") \%>\%
filter_fluoroquinolones("R", "any")
}