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(v2.1.1.9217) allow + in amr selectors

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dr. M.S. (Matthijs) Berends
2025-03-18 16:35:22 +01:00
parent 8d8444c607
commit 4dc4398ad1
23 changed files with 543 additions and 440 deletions
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11
R/amr_selectors.R
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@@ -29,7 +29,7 @@
#' Antimicrobial Selectors
#'
#' @description These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations.
#' @description These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations. They can be used in base \R, tidyverse, tidymodels, and `data.table`.
#'
#' In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up using:
#'
@@ -949,6 +949,15 @@ any.amr_selector_any_all <- function(..., na.rm = FALSE) {
class = c("amr_selector", "character")
)
}
#' @method + amr_selector
#' @export
#' @noRd
`+.amr_selector` <- function(e1, e2) {
# this is useful for `antibiogram()`: antibiogram(example_isolates, carbapenems() + c("", "GEN", "TOB"))
structure(as.character(outer(e1, e2, paste, sep = " + ")),
class = c("amr_selector", "character")
)
}
is_any <- function(el1) {
syscalls <- paste0(trimws2(deparse(sys.calls())), collapse = " ")