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(v1.0.1.9006) added generic CLSI rules

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dr. M.S. (Matthijs) Berends
2020-04-14 14:12:31 +02:00
parent d1cb7d3b6f
commit 7a6f819232
23 changed files with 4318 additions and 496 deletions
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10
R/like.R
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@ -21,7 +21,7 @@
#' Pattern Matching
#'
#' 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.
#' 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.
#' @inheritSection lifecycle Stable lifecycle
#' @param x a character vector where matches are sought, or an object which can be coerced by [as.character()] to a character vector.
#' @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.
@ -30,7 +30,9 @@
#' @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...`).
#' @details When running a regular expression fails, these functions try again with `base::grepl(..., perl = TRUE)`.
#'
#' 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`.
#' @seealso [base::grep()]
#' @inheritSection AMR Read more on our website!
@ -52,7 +54,7 @@
#' # get frequencies of bacteria whose name start with 'Ent' or 'ent'
#' library(dplyr)
#' example_isolates %>%
#' filter(mo_name(mo) %like% '^ent') %>%
#' filter(mo_name(mo) %like% "^ent") %>%
#' freq(mo_genus(mo))
like <- function(x, pattern, ignore.case = TRUE) {
if (length(pattern) > 1) {
@ -89,7 +91,7 @@ like <- function(x, pattern, ignore.case = TRUE) {
error = function(e) ifelse(grepl("Invalid regexp", e$message),
# try with perl = TRUE:
return(base::grepl(pattern = pattern, x = x,
ignore.case = ignore.case, perl = TRUE)),
ignore.case = ignore.case, perl = TRUE)),
# stop otherwise
stop(e$message)))
}