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(v1.2.0.9001) filter_ab_class() update

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dr. M.S. (Matthijs) Berends
2020-06-03 11:48:00 +02:00
parent 02d07b9fb3
commit 5dc4c96b7d
18 changed files with 159 additions and 77 deletions
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10
man/filter_ab_class.Rd
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@ -13,6 +13,7 @@
\alias{filter_fluoroquinolones}
\alias{filter_glycopeptides}
\alias{filter_macrolides}
\alias{filter_penicillins}
\alias{filter_tetracyclines}
\title{Filter isolates on result in antimicrobial class}
\usage{
@ -40,6 +41,8 @@ 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{
@ -54,10 +57,10 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
\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.
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 \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.
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}{
@ -72,6 +75,7 @@ If the unlying code needs breaking changes, they will occur gradually. For examp
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):
@ -81,7 +85,7 @@ example_isolates \%>\%
# filter on isolates that show resistance to ANY aminoglycoside
example_isolates \%>\% filter_aminoglycosides("R")
example_isolates \%>\% filter_aminoglycosides("R", "any")
# filter on isolates that show resistance to ALL aminoglycosides
example_isolates \%>\% filter_aminoglycosides("R", "all")