Extract IEEE citation numbers from a PDF

extract citation numbers.R

# Extract all citation numbers such as [1] from a PDF's text
# It also includes cases for multiples [1, 3] and ranges [1-5]
# It tries to exclude confidence intervals by skipping 
#
# written by Steve Haroz with help from ChatGPT
# MIT license

library(tidyverse)
library(pdftools)

filename = "path/to/file.pdf"

# get text
text = pdftools::pdf_text(filename)
text = paste(text, collapse = "\n")

# Extract the citation numbers using regular expressions
citation_strings <- str_extract_all(text, "\\[(\\d+(?:, \\d+)*)(?:\\-\\d+)?\\]", simplify = TRUE)

# convert a bracket string to numbers
extract_citation_numbers <- function(citation_string) {
  # Initialize an empty vector to store the citation numbers
  citation_numbers <- c()
  
  # Drop the brackets
  citation_string = str_sub(citation_string, 2, -2)
  
  # Detect confidence interval (a decimal point or percent sign)
  if (str_detect(citation_string, "[\\.%]"))
    return(NA)
  
  # Split the text into separate entries
  entries <- str_split(citation_string, ", ", simplify = TRUE)
  
  # Loop through each entry
  for (entry in entries) {
    # Check if the entry is a range of numbers
    if (str_detect(entry, "\\d+\\s*[-–]\\s*\\d+")) {
      # Extract the start and end of the range
      start <- as.integer(str_extract(entry, "^\\d+"))
      end <- as.integer(str_extract(entry, "\\d+$"))
      
      # Add the numbers in the range to the vector
      citation_numbers <- c(citation_numbers, start:end)
    } else {
      # Extract the number
      number <- as.integer(str_extract(entry, "\\d+"))
      
      # Add the number to the vector
      citation_numbers <- c(citation_numbers, number)
    }
  }
  
  # Return the citation numbers
  return(citation_numbers)
}

# Test the function
extract_citation_numbers("[1, 3 - 5, 8]")
# Output: 1 3 4 5 8
extract_citation_numbers("[0.2 - 7.4]")
# Output: NA

citation_numbers = sapply(citation_strings, extract_citation_numbers, simplify = TRUE) %>% 
  unlist(use.names = FALSE)

citation_numbers = tibble(citation_number = citation_numbers) %>% 
  filter(!is.na(citation_number)) %>% 
  count(citation_number) %>% 
  arrange(citation_number)

print(citation_numbers, n=999)

# a citation should appear at least twice (the citation and the reference)
citation_numbers %>% 
  filter(n < 2)