R/scan_file.R

In nealhaddaway/bibfix: Repair and enrich bibliographic data

#' Scan RIS file for damage
#' @param refs A RIS file with biblographic records
#' @export
#' @examples
#' \dontrun{
#' library(openalexR)
#' refs <- synthesisr::read_refs(file.choose())
#' report <- scan_file(refs)
#' }
scan_file <- function(refs) {
  # Convert all 'NA's to NAs
  refs[refs == "NA"] <- NA

  # Ensure required columns exist
  required_cols <- c(
    "source_type", "author", "year", "title", "journal",
    "volume", "issue", "start_page", "end_page",
    "abstract", "doi", "publisher"
  )
  for (col in required_cols) {
    if (is.null(refs[[col]])) refs[[col]] <- NA
  }

  # Subset relevant columns
  refs <- refs[required_cols]

  # Total records
  n_total <- nrow(refs)

  # Count missing fields
  n_author <- sum(!is.na(refs$author))
  n_year <- sum(!is.na(refs$year))
  n_title <- sum(!is.na(refs$title))
  n_journal <- sum(!is.na(refs$journal))
  n_volume <- sum(!is.na(refs$volume))
  n_issue <- sum(!is.na(refs$issue))
  n_start_page <- sum(!is.na(refs$start_page))
  n_end_page <- sum(!is.na(refs$end_page))
  n_doi <- sum(!is.na(refs$doi))
  n_abstract <- sum(!is.na(refs$abstract))

  # Count complete records
  refs$missing_data <- apply(refs, 1, function(row) {
    paste0(names(refs)[is.na(row)], collapse = "; ")
  })
  n_complete <- sum(refs$missing_data == "")

  # Count findable records (without DOI but with title)
  n_findable_titles <- sum(is.na(refs$doi) & !is.na(refs$title))

  # Search for "retracted"
  # Testing with local - needs to change

  #  retracted<-read.csv("https://api.labs.crossref.org/data/retractionwatch?name@email.org")

  url <- "https://raw.githubusercontent.com/nealhaddaway/bibfix/refs/heads/master/data/retraction_watch.csv"
  #read csv from url
Retracted<-read.csv(url)

  refs <- refs |>
    mutate(isRetracted = dplyr::if_else(doi %in% Retracted$OriginalPaperDOI, 1, 0))

  n_retracted <- sum(refs$isRetracted)

  # Return results
  output <- list(
    refs = refs,
    n_complete = n_complete,
    n_author = n_author,
    n_year = n_year,
    n_title = n_title,
    n_journal = n_journal,
    n_volume = n_volume,
    n_issue = n_issue,
    n_start_page = n_start_page,
    n_end_page = n_end_page,
    n_doi = n_doi,
    n_abstract = n_abstract,
    n_findable_titles = n_findable_titles,
    n_retracted = n_retracted,
    n_total = n_total
  )

  return(output)
}