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mirror of https://github.com/msberends/AMR.git synced 2025-09-06 04:09:39 +02:00

(v1.6.0.9013) website update

This commit is contained in:
2021-04-29 17:16:30 +02:00
parent 5e06b20d43
commit a9fd4aa49f
41 changed files with 931 additions and 842 deletions

View File

@@ -35,7 +35,7 @@
#' @param gram_positive names of antibiotic agents for **Gram-negatives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents.
#' @param antifungal names of antifungal agents for **fungi**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents.
#' @param only_rsi_columns a logical to indicate whether only columns must be included that were transformed to class `<rsi>` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
#' @param ... ignored, allows for future extensions
#' @param ... ignored, only in place to allow future extensions
#' @details
#' The [key_antimicrobials()] and [all_antimicrobials()] functions are context-aware. This means that then the `x` argument can be left blank, see *Examples*.
#'
@@ -264,14 +264,12 @@ generate_antimcrobials_string <- function(df) {
}
#' @rdname key_antimicrobials
#' @param info unused - previously used to indicate whether a progress bar should print
#' @export
antimicrobials_equal <- function(y,
z,
type = c("points", "keyantimicrobials"),
ignore_I = TRUE,
points_threshold = 2,
info = FALSE,
...) {
meet_criteria(y, allow_class = "character")
meet_criteria(z, allow_class = "character")
@@ -279,7 +277,6 @@ antimicrobials_equal <- function(y,
meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("points", "keyantimicrobials"))
meet_criteria(ignore_I, allow_class = "logical", has_length = 1)
meet_criteria(points_threshold, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(info, allow_class = "logical", has_length = 1)
stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")
key2rsi <- function(val) {