mirror of https://github.com/msberends/AMR.git
90 lines
4.2 KiB
R
Executable File
90 lines
4.2 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# #
|
|
# This R package was created for academic research and was publicly #
|
|
# released in the hope that it will be useful, but it comes WITHOUT #
|
|
# ANY WARRANTY OR LIABILITY. #
|
|
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
#' Pattern Matching
|
|
#'
|
|
#' Convenient wrapper around \code{\link[base]{grep}} to match a pattern: \code{a \%like\% b}. It always returns a \code{logical} vector and is always case-insensitive. Also, \code{pattern} (\code{b}) can be as long as \code{x} (\code{a}) to compare items of each index in both vectors.
|
|
#' @inheritParams base::grepl
|
|
#' @return A \code{logical} vector
|
|
#' @name like
|
|
#' @rdname like
|
|
#' @export
|
|
#' @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...).
|
|
#' @source Idea from the \href{https://github.com/Rdatatable/data.table/blob/master/R/like.R}{\code{like} function from the \code{data.table} package}, 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 \code{perl = TRUE}.
|
|
#' @seealso \code{\link[base]{grep}}
|
|
#' @inheritSection AMR Read more on our website!
|
|
#' @examples
|
|
#' # simple test
|
|
#' a <- "This is a test"
|
|
#' b <- "TEST"
|
|
#' a %like% b
|
|
#' #> TRUE
|
|
#' b %like% a
|
|
#' #> FALSE
|
|
#'
|
|
#' # also supports multiple patterns, length must be equal to x
|
|
#' a <- c("Test case", "Something different", "Yet another thing")
|
|
#' b <- c("case", "diff", "yet")
|
|
#' a %like% b
|
|
#' #> TRUE TRUE TRUE
|
|
#'
|
|
#' # get frequencies of bacteria whose name start with 'Ent' or 'ent'
|
|
#' library(dplyr)
|
|
#' library(clean)
|
|
#' example_isolates %>%
|
|
#' left_join_microorganisms() %>%
|
|
#' filter(genus %like% '^ent') %>%
|
|
#' freq(genus, species)
|
|
like <- function(x, pattern) {
|
|
if (length(pattern) > 1) {
|
|
if (length(x) != length(pattern)) {
|
|
pattern <- pattern[1]
|
|
warning('only the first element of argument `pattern` used for `%like%`', call. = TRUE)
|
|
} else {
|
|
# x and pattern are of same length, so items with each other
|
|
res <- vector(length = length(pattern))
|
|
for (i in 1:length(res)) {
|
|
if (is.factor(x[i])) {
|
|
res[i] <- as.integer(x[i]) %in% base::grep(pattern[i], levels(x[i]), ignore.case = TRUE)
|
|
} else {
|
|
res[i] <- base::grepl(pattern[i], x[i], ignore.case = TRUE)
|
|
}
|
|
}
|
|
return(res)
|
|
}
|
|
}
|
|
|
|
# the regular way how grepl works; just one pattern against one or more x
|
|
if (is.factor(x)) {
|
|
as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = TRUE)
|
|
} else {
|
|
tryCatch(base::grepl(pattern, x, ignore.case = TRUE),
|
|
error = function(e) ifelse(test = grepl("Invalid regexp", e$message),
|
|
# try with perl = TRUE:
|
|
yes = return(base::grepl(pattern, x, ignore.case = TRUE, perl = TRUE)),
|
|
no = stop(e$message)))
|
|
}
|
|
}
|
|
|
|
#' @rdname like
|
|
#' @export
|
|
"%like%" <- like
|