(v1.2.0.9007) Tidyverse selections

man/antibiotic_class_selectors.Rd

@@ -0,0 +1,75 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ab_class_selectors.R
+\name{antibiotic_class_selectors}
+\alias{antibiotic_class_selectors}
+\alias{aminoglycosides}
+\alias{carbapenems}
+\alias{cephalosporins}
+\alias{cephalosporins_1st}
+\alias{cephalosporins_2nd}
+\alias{cephalosporins_3rd}
+\alias{cephalosporins_4th}
+\alias{cephalosporins_5th}
+\alias{fluoroquinolones}
+\alias{glycopeptides}
+\alias{macrolides}
+\alias{penicillins}
+\alias{tetracyclines}
+\title{Antibiotic class selectors}
+\usage{
+aminoglycosides()
+
+carbapenems()
+
+cephalosporins()
+
+cephalosporins_1st()
+
+cephalosporins_2nd()
+
+cephalosporins_3rd()
+
+cephalosporins_4th()
+
+cephalosporins_5th()
+
+fluoroquinolones()
+
+glycopeptides()
+
+macrolides()
+
+penicillins()
+
+tetracyclines()
+}
+\description{
+Use these selection helpers inside any function that allows \href{https://tidyselect.r-lib.org/reference/language.html}{Tidyverse selections}, like \code{dplyr::select()} or \code{tidyr::pivot_longer()}. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
+}
+\details{
+All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a selector like e.g. \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
+
+These functions only work if the \code{tidyselect} package is installed, that comes with the \code{dplyr} package. An error will be thrown if \code{tidyselect} package is not installed, or if the functions are used outside a function that allows Tidyverse selections like \code{select()} or \code{pivot_longer()}.
+}
+\examples{
+if (require("dplyr")) {
+
+  # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
+  example_isolates \%>\% 
+    select(carbapenems())
+    
+    
+  # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
+  example_isolates \%>\% 
+    select(mo, aminoglycosides())
+    
+    
+  data.frame(irrelevant = "value",
+             J01CA01 = "S") \%>\%   # ATC code of ampicillin
+    select(penicillins())         # so the 'J01CA01' column is selected
+    
+}
+}
+\seealso{
+\code{\link[=filter_ab_class]{filter_ab_class()}} for the \code{filter()} equivalent.
+}

man/filter_ab_class.Rd

@@ -48,7 +48,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
 \arguments{
 \item{x}{a data set}
 
-\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}, as can be found in \code{\link[=antibiotics]{antibiotics$group}}}
+\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
 
 \item{result}{an antibiotic result: S, I or R (or a combination of more of them)}
 
@@ -60,7 +60,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
 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 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.
+All columns of \code{x} will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a filter function like e.g. \code{\link[=filter_aminoglycosides]{filter_aminoglycosides()}} will include column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
 }
 \section{Stable lifecycle}{
 
@@ -103,3 +103,6 @@ example_isolates \%>\%
   filter_fluoroquinolones("R", "all")
 }
 }
+\seealso{
+\code{\link[=antibiotic_class_selectors]{antibiotic_class_selectors()}} for the \code{select()} equivalent.
+}