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(v1.0.1.9006) added generic CLSI rules
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10
R/like.R
10
R/like.R
@ -21,7 +21,7 @@
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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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#' 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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@ -30,7 +30,9 @@
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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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#' @details When running a regular expression fails, these functions try again with `base::grepl(..., perl = TRUE)`.
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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), 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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@ -52,7 +54,7 @@
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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_name(mo) %like% '^ent') %>%
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#' filter(mo_name(mo) %like% "^ent") %>%
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#' freq(mo_genus(mo))
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like <- function(x, pattern, ignore.case = TRUE) {
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if (length(pattern) > 1) {
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@ -89,7 +91,7 @@ like <- function(x, pattern, ignore.case = TRUE) {
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error = function(e) ifelse(grepl("Invalid regexp", e$message),
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# try with perl = TRUE:
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return(base::grepl(pattern = pattern, x = x,
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ignore.case = ignore.case, perl = TRUE)),
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ignore.case = ignore.case, perl = TRUE)),
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# stop otherwise
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stop(e$message)))
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}
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