mirror of https://github.com/msberends/AMR.git
109 lines
5.4 KiB
R
Executable File
109 lines
5.4 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.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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# #
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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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# #
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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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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' Pattern Matching
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#'
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#' Convenient wrapper around [base::grep()] to match a pattern: `a %like% b`. It always returns a [`logical`] vector and is always case-insensitive (use `a %like_case% b` for case-sensitive matching). Also, `pattern` (*b*) can be as long as `x` (*a*) 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 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), but made it case insensitive at default and let it support multiple patterns. Also, if the regex fails the first time, it tries again with `perl = TRUE`.
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#' @seealso [base::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 frequencies of bacteria whose name start with 'Ent' or 'ent'
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#' library(dplyr)
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#' example_isolates %>%
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#' filter(mo_genus(mo) %like% '^ent') %>%
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#' freq(mo_fullname(mo))
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like <- function(x, pattern, ignore.case = TRUE) {
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if (length(pattern) > 1) {
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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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res <- sapply(pattern, function(pttrn) base::grepl(pttrn, x, ignore.case = ignore.case))
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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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res <- vector(length = length(pattern))
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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% base::grep(pattern[i], levels(x[i]), ignore.case = ignore.case)
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} else {
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res[i] <- base::grepl(pattern[i], x[i], ignore.case = ignore.case)
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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% base::grep(pattern, levels(x), ignore.case = ignore.case)
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} else {
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tryCatch(base::grepl(pattern, x, ignore.case = ignore.case),
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error = function(e) ifelse(grepl("Invalid regexp", e$message),
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# try with perl = TRUE:
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return(base::grepl(pattern = pattern, x = x,
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ignore.case = ignore.case, perl = TRUE)),
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# stop otherwise
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stop(e$message)))
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}
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}
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#' @rdname like
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#' @export
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"%like%" <- function(x, pattern) {
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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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like(x, pattern, ignore.case = FALSE)
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}
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