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(v2.1.1.9232) is.mic() iteration, documentation cleanup

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dr. M.S. (Matthijs) Berends
2025-03-31 10:51:31 +02:00
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R/ab_from_text.R
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@ -30,13 +30,13 @@
#' Retrieve Antimicrobial Drug Names and Doses from Clinical Text
#'
#' Use this function on e.g. clinical texts from health care records. It returns a [list] with all antimicrobial drugs, doses and forms of administration found in the texts.
#' @param text text to analyse
#' @param type type of property to search for, either `"drug"`, `"dose"` or `"administration"`, see *Examples*
#' @param collapse a [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 [antimicrobials] data set to translate the antibiotic abbreviations to, using [ab_property()]. The default is `FALSE`. Using `TRUE` is equal to using "name".
#' @param thorough_search a [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 a [logical] to indicate whether a progress bar should be printed - the default is `TRUE` only in interactive mode
#' @param ... arguments passed on to [as.ab()]
#' @param text Text to analyse
#' @param type Type of property to search for, either `"drug"`, `"dose"` or `"administration"`, see *Examples*
#' @param collapse A [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 [antimicrobials] data set to translate the antibiotic abbreviations to, using [ab_property()]. The default is `FALSE`. Using `TRUE` is equal to using "name".
#' @param thorough_search A [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 A [logical] to indicate whether a progress bar should be printed - the default is `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 drugs. This may fail on some systems.
#'
#' ### Argument `type`