R/separate_refs.R

In tidypmc: Parse Full Text XML Documents from PubMed Central

#' Separate references cited into multiple rows
#'
#' Separates references cited in brackets or parentheses into multiple rows and
#' splits the comma-delimited numeric strings and expands ranges like 7-9 into
#' new rows
#'
#' @param txt a table
#' @param column column name, default "text"
#'
#' @return a tibble
#'
#' @author Chris Stubben
#'
#' @examples
#' x <- data.frame(row = 1, text = "some important studies [7-9,15]")
#' separate_refs(x)
#' @export

separate_refs <- function(txt, column = "text") {
  pattern <- "(\\(|\\[)[0-9, -]+(\\]|\\))"
  x <- separate_text(txt, pattern, column)
  if (is.null(x)) {
    x1 <- NULL
  } else {
    # remove any parentheses, spaces and brackets
    y <- gsub("[)( ]|\\]|\\[", "", x$match)
    ## split commas
    y <- strsplit(y, ",")
    ## split ranges
    z <- lapply(y, strsplit, "-")
    ## apply seq if length is 2
    y <- lapply(z, function(x) unlist(
        lapply(x, function(x1)
          if (length(x1) == 2) seq(x1[1], x1[2]) else as.numeric(x1))
      ))
    n <- vapply(y, length, integer(1))
    x1 <- dplyr::bind_cols(id = unlist(y), x[ rep(seq_len(nrow(x)), n), ])
  }
  x1
}