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(v1.6.0.9000) custom EUCAST rules

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dr. M.S. (Matthijs) Berends
2021-04-07 08:37:42 +02:00
parent 551f99dc8f
commit 7a3139f7cc
49 changed files with 1363 additions and 594 deletions
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25
R/like.R
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@ -23,14 +23,14 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Pattern Matching with Keyboard Shortcut
#' Vectorised Pattern Matching with Keyboard Shortcut
#'
#' Convenient wrapper around [grepl()] to match a pattern: `x %like% pattern`. It always returns a [`logical`] vector and is always case-insensitive (use `x %like_case% pattern` for case-sensitive matching). Also, `pattern` can be as long as `x` to compare items of each index in both vectors, or they both can have the same length to iterate over all cases.
#' @inheritSection lifecycle Stable Lifecycle
#' @param x a character vector where matches are sought, or an object which can be coerced by [as.character()] to a character vector.
#' @param pattern a character string containing a regular expression (or [character] string for `fixed = TRUE`) to be matched in the given character vector. Coerced by [as.character()] to a character string if possible. If a [character] vector of length 2 or more is supplied, the first element is used with a warning.
#' @param ignore.case if `FALSE`, the pattern matching is *case sensitive* and if `TRUE`, case is ignored during matching.
#' @return A [`logical`] vector
#' @return A [logical] vector
#' @name like
#' @rdname like
#' @export
@ -39,10 +39,10 @@
#' * Is case-insensitive (use `%like_case%` for case-sensitive matching)
#' * Supports multiple patterns
#' * Checks if `pattern` is a regular expression and sets `fixed = TRUE` if not, to greatly improve speed
#' * Always uses compatibility with Perl
#' * Always uses compatibility with Perl unless `fixed = TRUE`, to greatly improve speed
#'
#' Using RStudio? The text `%like%` can also be directly inserted in your code from the Addins menu and can have its own Keyboard Shortcut like `Ctrl+Shift+L` or `Cmd+Shift+L` (see `Tools` > `Modify Keyboard Shortcuts...`).
#' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/master/R/like.R)
#' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R)
#' @seealso [grepl()]
#' @inheritSection AMR Read more on Our Website!
#' @examples
@ -68,7 +68,7 @@
#' \donttest{
#' if (require("dplyr")) {
#' example_isolates %>%
#' filter(mo_name(mo) %like% "^ent")
#' filter(mo_name() %like% "^ent")
#' }
#' }
like <- function(x, pattern, ignore.case = TRUE) {
@ -98,14 +98,17 @@ like <- function(x, pattern, ignore.case = TRUE) {
if (length(x) == 1) {
x <- rep(x, length(pattern))
} else if (length(pattern) != length(x)) {
stop_("arguments `x` and `pattern` must be of same length, or either one must be 1")
stop_("arguments `x` and `pattern` must be of same length, or either one must be 1 ",
"(`x` has length ", length(x), " and `pattern` has length ", length(pattern), ")")
}
unlist(
Map(f = grepl,
pattern,
x,
MoreArgs = list(ignore.case = FALSE, fixed = fixed, perl = !fixed)),
use.names = FALSE)
mapply(FUN = grepl,
x = x,
pattern = pattern,
MoreArgs = list(ignore.case = FALSE, fixed = fixed, perl = !fixed),
SIMPLIFY = FALSE,
USE.NAMES = FALSE)
)
}
}