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(v1.1.0.9004) lose dependencies

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dr. M.S. (Matthijs) Berends
2020-05-16 13:05:47 +02:00
parent 9fce546901
commit 7f3da74b17
111 changed files with 3211 additions and 2345 deletions
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37
R/like.R
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@ -30,10 +30,15 @@
#' @name like
#' @rdname like
#' @export
#' @details When running a regular expression fails, these functions try again with `base::grepl(..., perl = TRUE)`.
#' @details
#' The `%like%` function:
#' * 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
#' * Tries again with `perl = TRUE` if regex fails
#'
#' 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 [`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`.
#' @source Idea from the [`like` function from the `data.table` package](https://github.com/Rdatatable/data.table/blob/master/R/like.R)
#' @seealso [base::grep()]
#' @inheritSection AMR Read more on our website!
#' @examples
@ -51,19 +56,27 @@
#' a %like% b
#' #> TRUE TRUE TRUE
#'
#' # get frequencies of bacteria whose name start with 'Ent' or 'ent'
#' # get isolates whose name start with 'Ent' or 'ent'
#' library(dplyr)
#' example_isolates %>%
#' filter(mo_name(mo) %like% "^ent") %>%
#' freq(mo_genus(mo))
#' filter(mo_name(mo) %like% "^ent") %>%
#' freq(mo)
like <- function(x, pattern, ignore.case = TRUE) {
# set to fixed if no regex found
fixed <- all(!grepl("[$.^*?+}{|)(]", pattern))
if (ignore.case == TRUE) {
# set here, otherwise if fixed = TRUE, this warning will be thrown: argument 'ignore.case = TRUE' will be ignored
x <- tolower(x)
pattern <- tolower(pattern)
}
if (length(pattern) > 1) {
if (length(x) != length(pattern)) {
if (length(x) == 1) {
x <- rep(x, length(pattern))
}
# return TRUE for every 'x' that matches any 'pattern', FALSE otherwise
res <- sapply(pattern, function(pttrn) base::grepl(pttrn, x, ignore.case = ignore.case))
res <- sapply(pattern, function(pttrn) base::grepl(pttrn, x, ignore.case = FALSE, fixed = fixed))
res2 <- as.logical(rowSums(res))
# get only first item of every hit in pattern
res2[duplicated(res)] <- FALSE
@ -74,9 +87,9 @@ like <- function(x, pattern, ignore.case = TRUE) {
res <- vector(length = length(pattern))
for (i in seq_len(length(res))) {
if (is.factor(x[i])) {
res[i] <- as.integer(x[i]) %in% base::grep(pattern[i], levels(x[i]), ignore.case = ignore.case)
res[i] <- as.integer(x[i]) %in% base::grep(pattern[i], levels(x[i]), ignore.case = FALSE, fixed = fixed)
} else {
res[i] <- base::grepl(pattern[i], x[i], ignore.case = ignore.case)
res[i] <- base::grepl(pattern[i], x[i], ignore.case = FALSE, fixed = fixed)
}
}
return(res)
@ -85,13 +98,15 @@ like <- function(x, pattern, ignore.case = TRUE) {
# the regular way how grepl works; just one pattern against one or more x
if (is.factor(x)) {
as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = ignore.case)
as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = FALSE, fixed = fixed)
} else {
tryCatch(base::grepl(pattern, x, ignore.case = ignore.case),
tryCatch(base::grepl(pattern, x, ignore.case = FALSE, fixed = fixed),
error = function(e) ifelse(grepl("Invalid regexp", e$message),
# try with perl = TRUE:
return(base::grepl(pattern = pattern, x = x,
ignore.case = ignore.case, perl = TRUE)),
ignore.case = FALSE,
fixed = fixed,
perl = TRUE)),
# stop otherwise
stop(e$message)))
}