P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-13 03:12:11 +02:00
Code Releases Activity

(v2.1.1.9116) selectors as separate functions

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-12-13 09:44:54 +01:00
parent e231352617
commit 175a6777f3
16 changed files with 113 additions and 67 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
man/antibiotic_class_selectors.Rd
View File

@ -124,7 +124,7 @@ not_intrinsic_resistant(
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".}
}
\value{
(internally) a \link{character} vector of column names, with additional class \code{"ab_selector"}
When used inside selecting or filtering, this returns a \link{character} vector of column names, with additional class \code{"ab_selector"}. When used individually, this returns an \link[=as.ab]{'ab' vector} with all possible antimicrobial that the function would be able to select or filter.
}
\description{
These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group (according to the \link{antibiotics} data set), without the need to define the columns or antibiotic abbreviations.
@ -189,9 +189,15 @@ All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR
example_isolates
# you can use the selectors separately to retrieve all possible antimicrobials:
carbapenems()
# Though they are primarily intended to use for selections and filters.
# Examples sections below are split into 'dplyr', 'base R', and 'data.table':
\donttest{
\dontrun{
# dplyr -------------------------------------------------------------------
library(dplyr, warn.conflicts = FALSE)
@ -277,7 +283,7 @@ y <- example_isolates \%>\% filter(carbapenems() == "R")
z <- example_isolates \%>\% filter(if_all(carbapenems(), ~ .x == "R"))
identical(x, y) && identical(y, z)
}
# base R ------------------------------------------------------------------
# select columns 'IPM' (imipenem) and 'MEM' (meropenem)