R/read-lens.R

In bibnets: Importing, Constructing, and Exporting Bibliometric Networks

#' Read Lens.org CSV export
#'
#' Parses a CSV file exported from Lens.org into a standardized bibliometric
#' data frame.
#'
#' @param file Path to a Lens.org CSV export file.
#' @param encoding Character. File encoding. Default `"UTF-8"`.
#'
#' @return A data frame in the standard bibnets format: `id`, `title`,
#'   `year`, `journal`, `doi`, `cited_by_count`, `abstract`, `type`,
#'   plus list-columns `authors`, `references`, and `keywords`.
#'
#' @export
#' @examples
#' f <- system.file("extdata", "lens_sample.csv", package = "bibnets")
#' data <- read_lens(f)
#' head(data[, c("id", "title", "year", "journal")])
read_lens <- function(file, encoding = "UTF-8") {
  check_file(file)

  raw <- utils::read.csv(file, stringsAsFactors = FALSE, fileEncoding = encoding,
                          check.names = FALSE)

  n <- nrow(raw)

  get_col <- function(names_vec, default = NA_character_) {
    for (nm in names_vec) {
      if (nm %in% names(raw)) return(raw[[nm]])
    }
    if (length(default) == n) default else rep(default, length.out = n)
  }

  id <- get_col(c("Lens ID", "ID"), paste0("LENS", seq_len(n)))

  result <- data.frame(
    id = id,
    title = get_col(c("Title")),
    year = as.integer(get_col(c("Publication Year", "Year of Publication"),
                               NA_integer_)),
    journal = get_col(c("Source Title", "Journal")),
    doi = get_col(c("DOI")),
    cited_by_count = as.integer(get_col(
      c("Citing Works Count", "Cited By Count", "Times Cited"), 0L
    )),
    abstract = get_col(c("Abstract")),
    type = get_col(c("Publication Type", "Document Type")),
    stringsAsFactors = FALSE
  )

  result$authors <- split_field(
    get_col(c("Authors", "Author/s")), sep = ";"
  )
  result$authors <- lapply(result$authors, standardize_authors)

  result$references <- split_field(
    get_col(c("References", "Cited Works")), sep = ";"
  )
  result$references <- lapply(result$references, standardize_refs)

  result$keywords <- split_field(
    get_col(c("Keywords", "MeSH Terms", "Fields of Study")), sep = ";"
  )
  result$keywords <- lapply(result$keywords, trimws)

  result
}