R/string_counts.R

In medExtractR: Extraction of Medication Information from Clinical Text

#' Counts Strings in Text
#'
#' This function counts occurrences of text within one or more phrases.
#'
#' @param strings character vector; value(s) to find
#' @param search_data character vector; phrase(s) where values may exist
#' @param ignore.case logical; indicates if spelling case matters, defaulting to \sQuote{TRUE}
#'
#' @return list with two elements; \sQuote{cntByTotal} contains total occurrences
#' and \sQuote{cntByData} contains occurrences for each element in \sQuote{search_data}
#'
#' @examples
#' note1 <- "I am the very model of a modern major general
#' I've information vegetable, animal, and mineral
#' I know the kings of England, and I quote the fights historical
#' From marathon to Waterloo in order categorical;
#' I'm very well acquainted, too, with matters mathematical,
#' I understand equations both the simple and quadratical
#' About binomial theorem I'm teeming with a lot o' news,
#' With many cheerful facts about the square of the hypotenuse"
#' note2 <- "The quick brown fox jumps over the lazy dog"
#' string_counts(c('I','the','couth'), c(note1, note2))
#' @export

string_counts <- function(strings, search_data, ignore.case = TRUE) {
  allsrch <- do.call(rbind, lapply(strings, stringPlace, search_data, stringPlaceExact, ignore.case = ignore.case))
  total.cnt <- as.data.frame(table(allsrch[,'value']), stringsAsFactors = FALSE)
  names(total.cnt) <- c('value','Freq')

  keys <- do.call(paste, c(allsrch, sep = '|'))
  tk <- table(keys)
  allsrch[,'Freq'] <- unname(tk[match(keys, names(tk))])
  allsrch <- allsrch[!duplicated(keys),]
  file.cnt <- allsrch[order(allsrch[,'place']),]

  total.cnt <- total.cnt[order(total.cnt[,'Freq'], decreasing = TRUE),]
  rownames(total.cnt) <- NULL
  rownames(file.cnt) <- NULL
  list(cntByTotal = total.cnt, cntByData = file.cnt)
}