R/mergeDbSources.R

In massimoaria/bibliometrix: Comprehensive Science Mapping Analysis

utils::globalVariables(c("num"))
#' Merge bibliographic data frames from supported bibliogtraphic DBs
#'
#' Merge bibliographic data frames from different databases (WoS,SCOPUS, Lens, Openalex, etc-) into a single one.
#'
#' bibliographic data frames are obtained by the converting function \code{\link{convert2df}}.
#' The function merges data frames identifying common tag fields and duplicated records.
#'
#' @param ... are the bibliographic data frames to merge.
#' @param remove.duplicated is logical. If TRUE duplicated documents will be deleted from the bibliographic collection.
#' @param verbose is logical.  If TRUE, information on duplicate documents is printed on the screen.
#' @return the value returned from \code{mergeDbSources} is a bibliographic data frame.
#'
#'
#' @examples
#'
#' data(isiCollection, package = "bibliometrixData")
#'
#' data(scopusCollection, package = "bibliometrixData")
#'
#' M <- mergeDbSources(isiCollection, scopusCollection, remove.duplicated = TRUE)
#'
#' dim(M)
#'
#' @seealso \code{\link{convert2df}} to import and convert an ISI or SCOPUS Export file in a bibliographic data frame.
#' @seealso \code{\link{biblioAnalysis}} function for bibliometric analysis.
#' @seealso \code{\link{summary}} to obtain a summary of the results.
#' @seealso \code{\link{plot}} to draw some useful plots of the results.
#'
#' @export


mergeDbSources <- function(..., remove.duplicated = TRUE, verbose = TRUE) {
  index <- NULL

  mc <- match.call(expand.dots = TRUE)

  if (length(mc) > 3) {
    M <- dplyr::bind_rows(list(...))
  } else {
    M <- dplyr::bind_rows(...)
  }
  # create KW_Merged field 
  M <- M %>% mergeKeywords(force=TRUE)

  dbLabels <- data.frame(
    DB = toupper(c("isi", "scopus", "openalex", "lens", "dimensions", "pubmed", "cochrane")),
    num = c(1, 2, 3, 4, 5, 6, 7)
  )
  # order by db
  M <- M %>%
    left_join(dbLabels, by = "DB") %>%
    arrange(num) %>%
    select(-num) %>%
    rename("CR_raw" = "CR") %>%
    mutate(CR = "NA")


  if (isTRUE(remove.duplicated)) {
    # remove by DOI
    if ("DI" %in% names(M)) {
      M$DI[M$DI == ""] <- NA
      index <- which(duplicated(M$DI) & !is.na(M$DI))
      if (length(index) > 0) M <- M[-index, ]
    }

    # remove by title
    if ("TI" %in% names(M)) {
      TI <- gsub("[^[:alnum:] ]", "", M$TI)
      TI <- gsub("(?<=[\\s])\\s*|^\\s+|\\s+$", "", TI, perl = TRUE)
      d <- duplicated(paste(TI, " ", M$PY))
      if (isTRUE(verbose)) cat("\n", sum(d) + length(index), "duplicated documents have been removed\n")
      M <- M[!d, ]
    }
  }

  if (length(unique(M$DB)) > 1) {
    M$DB_Original <- M$DB
    M$DB <- "ISI"

    ## author data cleaning
    if ("AU" %in% names(M)) {
      M$AU <- gsub(",", " ", M$AU)
      AUlist <- strsplit(M$AU, ";")
      AU <- lapply(AUlist, function(l) {
        l <- trim(l)
        name <- strsplit(l, " ")
        lastname <- unlist(lapply(name, function(ln) {
          ln[1]
        }))
        firstname <- lapply(name, function(ln) {
          f <- paste(substr(ln[-1], 1, 1), collapse = " ")
        })
        AU <- paste(lastname, unlist(firstname), sep = " ", collapse = ";")
        return(AU)
      })
      M$AU <- unlist(AU)
    }
  }

  M <- metaTagExtraction(M, "SR")
  row.names(M) <- M$SR

  class(M) <- c("bibliometrixDB", "data.frame")
  return(M)
}