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130 lines
5.7 KiB
R
Executable File
130 lines
5.7 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Vectorised Pattern Matching with Keyboard Shortcut
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#'
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#' 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.
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#' @inheritSection lifecycle Stable Lifecycle
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#' @param x a character vector where matches are sought, or an object which can be coerced by [as.character()] to a character vector.
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#' @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.
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#' @param ignore.case if `FALSE`, the pattern matching is *case sensitive* and if `TRUE`, case is ignored during matching.
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#' @return A [logical] vector
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#' @name like
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#' @rdname like
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#' @export
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#' @details
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#' The `%like%` function:
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#' * Is case-insensitive (use `%like_case%` for case-sensitive matching)
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#' * Supports multiple patterns
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#' * Checks if `pattern` is a regular expression and sets `fixed = TRUE` if not, to greatly improve speed
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#' * Always uses compatibility with Perl unless `fixed = TRUE`, to greatly improve speed
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#'
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#' 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...`).
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#' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/ec1259af1bf13fc0c96a1d3f9e84d55d8106a9a4/R/like.R)
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#' @seealso [grepl()]
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#' @inheritSection AMR Read more on Our Website!
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#' @examples
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#' # simple test
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#' a <- "This is a test"
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#' b <- "TEST"
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#' a %like% b
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#' #> TRUE
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#' b %like% a
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#' #> FALSE
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#'
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#' # also supports multiple patterns
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#' a <- c("Test case", "Something different", "Yet another thing")
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#' b <- c( "case", "diff", "yet")
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#' a %like% b
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#' #> TRUE TRUE TRUE
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#' a[1] %like% b
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#' #> TRUE FALSE FALSE
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#' a %like% b[1]
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#' #> TRUE FALSE FALSE
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#'
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#' # get isolates whose name start with 'Ent' or 'ent'
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#' \donttest{
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#' if (require("dplyr")) {
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#' example_isolates %>%
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#' filter(mo_name() %like% "^ent")
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#' }
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#' }
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like <- function(x, pattern, ignore.case = TRUE) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(pattern, allow_NA = FALSE)
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meet_criteria(ignore.case, allow_class = "logical", has_length = 1)
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if (all(is.na(x))) {
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return(rep(FALSE, length(x)))
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}
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# set to fixed if no regex found
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fixed <- !any(is_possibly_regex(pattern))
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if (ignore.case == TRUE) {
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# set here, otherwise if fixed = TRUE, this warning will be thrown: argument `ignore.case = TRUE` will be ignored
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x <- tolower(x)
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pattern <- tolower(pattern)
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}
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if (is.factor(x)) {
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x <- as.character(x)
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}
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if (length(pattern) == 1) {
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grepl(pattern, x, ignore.case = FALSE, fixed = fixed, perl = !fixed)
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} else {
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if (length(x) == 1) {
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x <- rep(x, length(pattern))
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} else if (length(pattern) != length(x)) {
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stop_("arguments `x` and `pattern` must be of same length, or either one must be 1 ",
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"(`x` has length ", length(x), " and `pattern` has length ", length(pattern), ")")
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}
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unlist(
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mapply(FUN = grepl,
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x = x,
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pattern = pattern,
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MoreArgs = list(ignore.case = FALSE, fixed = fixed, perl = !fixed),
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SIMPLIFY = FALSE,
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USE.NAMES = FALSE)
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)
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}
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}
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#' @rdname like
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#' @export
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"%like%" <- function(x, pattern) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(pattern, allow_NA = FALSE)
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like(x, pattern, ignore.case = TRUE)
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}
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#' @rdname like
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#' @export
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"%like_case%" <- function(x, pattern) {
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meet_criteria(x, allow_NA = TRUE)
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meet_criteria(pattern, allow_NA = FALSE)
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like(x, pattern, ignore.case = FALSE)
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}
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