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