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(v1.6.0.9007) documentation custom eucast rules, progress bar as.mo

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dr. M.S. (Matthijs) Berends
2021-04-20 10:46:17 +02:00
parent de66eccf43
commit c6289c3fc3
44 changed files with 338 additions and 128 deletions
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5
R/ab_from_text.R
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@ -32,6 +32,7 @@
#' @param collapse character to pass on to `paste(, collapse = ...)` to only return one character per element of `text`, see *Examples*
#' @param translate_ab if `type = "drug"`: a column name of the [antibiotics] data set to translate the antibiotic abbreviations to, using [ab_property()]. Defaults to `FALSE`. Using `TRUE` is equal to using "name".
#' @param thorough_search logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to `TRUE` will take considerably more time than when using `FALSE`. At default, it will turn `TRUE` when all input elements contain a maximum of three words.
#' @param info logical to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
#' @param ... arguments passed on to [as.ab()]
#' @details This function is also internally used by [as.ab()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the [as.ab()] function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems.
#'
@ -92,6 +93,7 @@ ab_from_text <- function(text,
collapse = NULL,
translate_ab = FALSE,
thorough_search = NULL,
info = interactive(),
...) {
if (missing(type)) {
type <- type[1L]
@ -102,12 +104,13 @@ ab_from_text <- function(text,
meet_criteria(collapse, has_length = 1, allow_NULL = TRUE)
meet_criteria(translate_ab, allow_NULL = FALSE) # get_translate_ab() will be more informative about what's allowed
meet_criteria(thorough_search, allow_class = "logical", has_length = 1, allow_NULL = TRUE)
meet_criteria(info, allow_class = "logical", has_length = 1)
type <- tolower(trimws(type))
text <- tolower(as.character(text))
text_split_all <- strsplit(text, "[ ;.,:\\|]")
progress <- progress_ticker(n = length(text_split_all), n_min = 5)
progress <- progress_ticker(n = length(text_split_all), n_min = 5, print = info)
on.exit(close(progress))
if (type %like% "(drug|ab|anti)") {