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(v1.6.0.9021) join functions update

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dr. M.S. (Matthijs) Berends
2021-05-12 18:15:03 +02:00
parent 3319fbae58
commit 29dbfa2f49
119 changed files with 973 additions and 1040 deletions
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R/ab_from_text.R
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@ -29,17 +29,17 @@
#' @inheritSection lifecycle Stable Lifecycle
#' @param text text to analyse
#' @param type type of property to search for, either `"drug"`, `"dose"` or `"administration"`, see *Examples*
#' @param collapse character to pass on to `paste(, collapse = ...)` to only return one character per element of `text`, 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 [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 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, 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.
#'
#' ## Argument `type`
#' At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses [as.ab()] internally, it will correct for misspelling.
#'
#' With `type = "dose"` (or similar, like "dosing", "doses"), all text elements will be searched for numeric values that are higher than 100 and do not resemble years. The output will be numeric. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see *Examples*.
#' With `type = "dose"` (or similar, like "dosing", "doses"), all text elements will be searched for [numeric] values that are higher than 100 and do not resemble years. The output will be [numeric]. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see *Examples*.
#'
#' With `type = "administration"` (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see *Examples*.
#'