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(v1.2.0.9001) filter_ab_class() update
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@ -13,6 +13,7 @@
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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_penicillins}
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\alias{filter_tetracyclines}
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\title{Filter isolates on result in antimicrobial class}
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\usage{
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@ -40,6 +41,8 @@ filter_glycopeptides(x, result = NULL, scope = "any", ...)
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filter_macrolides(x, result = NULL, scope = "any", ...)
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filter_penicillins(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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@ -54,10 +57,10 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
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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 antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.
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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.
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}
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\details{
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The \code{group} column in \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 \link{antibiotics} data set.
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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.
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}
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\section{Stable lifecycle}{
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@ -72,6 +75,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp
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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_ab_class("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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@ -81,7 +85,7 @@ example_isolates \%>\%
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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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example_isolates \%>\% filter_aminoglycosides("R", "any")
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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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