mirror of https://github.com/msberends/AMR.git
172 lines
7.4 KiB
R
Executable File
172 lines
7.4 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) 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) 2018-2020 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 analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Pattern Matching
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#'
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#' Convenient wrapper around [grep()] 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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#' * Tries again with `perl = TRUE` if regex fails
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#'
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#' Using RStudio? This function can also be inserted 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/master/R/like.R)
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#' @seealso [grep()]
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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, length must be equal to x
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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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#'
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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(mo) %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_class = "character")
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meet_criteria(ignore.case, allow_class = "logical", has_length = 1)
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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 (length(pattern) > 1 & length(x) == 1) {
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x <- rep(x, length(pattern))
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}
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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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if (length(pattern) > 1) {
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res <- vector(length = length(pattern))
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if (length(x) != length(pattern)) {
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if (length(x) == 1) {
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x <- rep(x, length(pattern))
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}
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# return TRUE for every 'x' that matches any 'pattern', FALSE otherwise
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for (i in seq_len(length(res))) {
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if (is.factor(x[i])) {
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res[i] <- as.integer(x[i]) %in% grep(pattern[i], levels(x[i]), ignore.case = FALSE, fixed = fixed)
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} else {
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res[i] <- grepl(pattern[i], x[i], ignore.case = FALSE, fixed = fixed)
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}
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}
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res <- sapply(pattern, function(pttrn) grepl(pttrn, x, ignore.case = FALSE, fixed = fixed))
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res2 <- as.logical(rowSums(res))
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# get only first item of every hit in pattern
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res2[duplicated(res)] <- FALSE
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res2[rowSums(res) == 0] <- NA
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return(res2)
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} else {
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# x and pattern are of same length, so items with each other
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for (i in seq_len(length(res))) {
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if (is.factor(x[i])) {
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res[i] <- as.integer(x[i]) %in% grep(pattern[i], levels(x[i]), ignore.case = FALSE, fixed = fixed)
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} else {
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res[i] <- grepl(pattern[i], x[i], ignore.case = FALSE, fixed = fixed)
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}
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}
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return(res)
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}
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}
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# the regular way how grepl works; just one pattern against one or more x
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if (is.factor(x)) {
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as.integer(x) %in% grep(pattern, levels(x), ignore.case = FALSE, fixed = fixed)
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} else {
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tryCatch(grepl(pattern, x, ignore.case = FALSE, fixed = fixed),
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error = function(e) {
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if (grepl("invalid reg(ular )?exp", e$message, ignore.case = TRUE)) {
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# try with perl = TRUE:
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return(grepl(pattern = pattern,
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x = x,
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ignore.case = FALSE,
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fixed = fixed,
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perl = TRUE))
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} else {
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# stop otherwise
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stop(e$message)
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}
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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_class = "character")
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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_class = "character")
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like(x, pattern, ignore.case = FALSE)
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}
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# don't export his one, it's just for convenience in eucast_rules()
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# match all Klebsiella and Raoultella, but not K. aerogenes: fullname %like_perl% "^(Klebsiella(?! aerogenes)|Raoultella)"
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"%like_perl%" <- function(x, pattern) {
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meet_criteria(x)
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meet_criteria(pattern, allow_class = "character")
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grepl(x = tolower(x),
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pattern = tolower(pattern),
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perl = TRUE,
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fixed = FALSE,
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ignore.case = TRUE)
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}
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