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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Retrieve antimicrobial drugs from text
#'
#' Use this function on e.g. clinical texts from health care records. It returns a vector of antimicrobial drugs found in the texts.
#' @param text text to analyse
#' @param collapse character to pass on to `paste(..., collapse = ...)` to only return one character per element of `text`, see Examples
#' @param translate_ab a column name of the [antibiotics] data set to translate the antibiotic abbreviations to, using [ab_property()]. Defaults to "name", which is equal to using `TRUE`. Use a value `FALSE`, `NULL` or `NA` to prevent translation of the `<ab>` code.
#' @param ... parameters passed on to [as.ab()]
#' @details To use this for creating a new variable in a data set (e.g. with `mutate()`), it could be convenient to paste the outcome together with the `collapse` parameter so every value in your new variable will be a character of length 1:\cr
#' `df %>% mutate(abx = ab_from_text(clinical_text, collapse = "|"))`
#'
#' This function is also internally used by [as.ab()], although it then only returns the first hit.
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#' @export
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#' @examples
#' # mind the bad spelling of amoxicillin in this line,
#' # straight from a true health care record:
#' ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds")
#'
#' ab_from_text("administered amoxi/clav and cipro")
#' ab_from_text("administered amoxi/clav and cipro", collapse = ", ")
#'
#' # if you want to know which antibiotic groups were administered, check it:
#' abx <- ab_from_text("administered amoxi/clav and cipro")
#' ab_group(abx)
ab_from_text <- function ( text , collapse = NULL , translate_ab = " name" , ... ) {
text <- tolower ( text )
abbr <- unlist ( antibiotics $ abbreviations )
abbr <- abbr [nchar ( abbr ) >= 4 ]
names <- substr ( antibiotics $ name , 1 , 5 )
synonyms <- unlist ( antibiotics $ synonyms )
synonyms <- synonyms [nchar ( synonyms ) >= 4 ]
to_regex <- function ( x ) {
paste0 ( " ^(" ,
paste0 ( unique ( gsub ( " [^a-z0-9]" , " .*" , sort ( tolower ( x ) ) ) ) , collapse = " |" ) ,
" ).*" )
}
text_split <- unlist ( strsplit ( text , " [ ;.,:/\\|-]" ) )
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result <- suppressWarnings (
as.ab ( unique ( c ( text_split [grep ( to_regex ( abbr ) , text_split ) ] ,
text_split [grep ( to_regex ( names ) , text_split ) ] ,
# regular expression must not be too long, so split synonyms in two:
text_split [grep ( to_regex ( synonyms [c ( 1 : 0.5 * length ( synonyms ) ) ] ) , text_split ) ] ,
text_split [grep ( to_regex ( synonyms [c ( 0.5 * length ( synonyms ) : length ( synonyms ) ) ] ) , text_split ) ] ) ) ,
... ) )
result <- result [ ! is.na ( result ) ]
if ( length ( result ) == 0 ) {
result <- as.ab ( NA )
}
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translate_ab <- get_translate_ab ( translate_ab )
if ( ! isFALSE ( translate_ab ) ) {
result <- ab_property ( result , property = translate_ab )
}
if ( ! is.null ( collapse ) ) {
result <- paste0 ( result , collapse = collapse )
}
result
}