R/bib2df.R

In bibliometrix: Comprehensive Science Mapping Analysis

utils::globalVariables(c("Paper","Tag","content","cont"))

bib2df<-function(D, dbsource = "isi"){
  
  #D <- D[nchar(D)>1]  
  
  # remove empty rows and strange characters
  res <- try(D <- D[nchar(D)>1], silent = T)
  if(inherits(res, "try-error")){
    D <- removeStrangeChar(D)
    #next
  }else{
    D <- res
    rm(res)
  }
  
  D <- gsub("\\{\\[\\}","[",D)
  D <- gsub("\\{\\]\\}","]",D)
  Papers <- which(substr(D,1,1)=="@")  # # first row of each document
  if (Papers[1]>1){
    D <- D[-(1:(Papers[1]-1))]
    Papers <- Papers-(Papers[1]-1)
  }
  
  if (dbsource == "isi") D <- gsub(" = \\{","={",D)
  
  D <- gsub("\\\t","",gsub(" = \\{","=\\{",D)) # to work also with new scopus bib format
  
  D[Papers] <- paste("Paper={",D[Papers],sep="")

  ind <- regexpr("=\\{",D) # sep among tags and contents
  ind[Papers] <- 6
  
  nP=length(Papers)  # number of documents
  
  for (i in 1:length(D)){
    if (ind[i]==-1){
      D[i] <- trimES(paste(substr(D[i-1],1,ind[i-1]+1),D[i],collapse=" "))
      ind[i] <- ind[i-1]}
  }
  
  rowPapers <- diff(c(Papers, length(D)+1))
  
  numPapers <- rep(1:nP,rowPapers)
  
  DATA <- data.frame(Tag = substr(D,1,ind+1), content = substr(D,ind+2,nchar(D)), Paper=numPapers)
  DATA$content <- gsub("\\}|\\},|\\{","",DATA$content)
  #DATA$content <- gsub("\\{","",DATA$content)
  df <- DATA %>% group_by(Paper, Tag) %>%
    summarise(cont=paste(content, collapse="---",sep="")) %>%
    arrange(Tag, Paper) %>%
    pivot_wider(names_from =Tag,values_from = cont) %>%
    ungroup()
  
  df <- as.data.frame(df)
  
  rm(DATA)
  bibtag <- NULL
  data("bibtag",envir=environment())
  bibtag=as.data.frame(bibtag)
  
  Tag <- tolower(names(df))
  switch(dbsource,
         scopus = {
           bibtag <- bibtag[(bibtag[,"SCOPUS"] %in% Tag),]
           for (i in 1:nrow(bibtag)){
             Tag[Tag == bibtag$SCOPUS[i]] <- bibtag$TAG[i]
           }
         },
         isi = {
           bibtag <- bibtag[(bibtag[,"ISI"] %in% Tag),]
           for (i in 1:nrow(bibtag)){
             Tag[Tag == bibtag$ISI[i]] <- bibtag$TAG[i]
           }
         },
         generic={
           bibtag <- bibtag[(bibtag[,"GENERIC"] %in% Tag),]
           for (i in 1:nrow(bibtag)){
             Tag[Tag == bibtag$GENERIC[i]] <- bibtag$TAG[i]
           }
         })
  
  
  
  names(df) <- gsub("=\\{","",Tag)
  
  ### replace "---" with ";"
  tagsComma <- c("AU","DE","ID","C1","CR")
  nolab <- setdiff(tagsComma,names(df))
  if (length(nolab)>0){
    cat("\nWarning:\nIn your file, some mandatory metadata are missing. Bibliometrix functions may not work properly!\n
Please, take a look at the vignettes:
- 'Data Importing and Converting' (https://www.bibliometrix.org/vignettes/Data-Importing-and-Converting.html)
- 'A brief introduction to bibliometrix' (https://www.bibliometrix.org/vignettes/Introduction_to_bibliometrix.html)\n\n")
    cat("\nMissing fields: ",nolab,"\n")
    }
  
  tagsComma <- tagsComma[(!(tagsComma %in% nolab))]
  df1 <- data.frame(lapply(df[tagsComma],function(x){
    gsub("---",";",x)
  }))
  
  df1$AU <- gsub(" and;| and ",";",df1$AU)
  
  ### replace "---" with " "
  otherTags <- setdiff(names(df),tagsComma)
  df2 <- data.frame(lapply(df[otherTags],function(x){
    trimES(gsub("---"," ",x))
  }),stringsAsFactors = FALSE)
  df <- cbind(df1,df2)
  rm(df1,df2)
  
  # Funding info
  ind <- which(regexpr("funding_text",names(df))>-1)
  if (!("FX" %in% Tag) & length(ind)>0){
    df$FX <- apply((as.data.frame(df[,ind], stringsAsFactors = FALSE)),1,
                   function(x) paste(x,collapse=" "))
    df <- df[,-ind]
  }
  
  df <- postprocessing(df, dbsource)
  
  df <- df[!names(df) %in% c("Paper", "paper")]

  return(df)
}

### DATA FRAME postprocessing
postprocessing <-function(DATA,dbsource){
  
  # Authors' names cleaning (surname and initials)
  #remove ; and 2 or more spaces
  DATA$AU <- gsub("\\s+", " ", DATA$AU)
  DATA$AF <- gsub("\\.|,","",DATA$AU)
  
  listAU <- strsplit(DATA$AU, ";")
  
  AU <- lapply(listAU,function(l){
    
    lastname <- trim(gsub(",.*","",l))
    firstname <- strsplit(trim(gsub(".*,","",l))," ")
    firstname <- gsub("[^:A-Z:]","",firstname)
    AU <- paste(lastname,unlist(firstname),sep=" ",collapse=";")
    return(AU)
  })
  
  
  DATA$AU <- unlist(AU)
  
  # TC post-processing
  if ("TC" %in% names(DATA)){
    DATA$TC <- as.numeric(sub("\\D*(\\d+).*", "\\1", DATA$TC))
  }
  # CR post-processing
  if ("CR" %in% names(DATA)){
    # reomve dots after DOIs
    DATA$CR <- gsub("\\.;", ";", DATA$CR)
    DATA$CR <- substr(DATA$CR,1,(nchar(DATA$CR)-1))
  }
  # Year
  if ("PY" %in% names(DATA)){
    DATA$PY <- as.numeric(sub("\\D*(\\d+).*", "\\1", DATA$PY))
  }
  
  if ("UT" %in% names(DATA)){
    DATA$UT <- gsub(":","",DATA$UT,fixed=TRUE)
  }
  
  if (!("RP" %in% names(DATA)) & ("C1" %in% names(DATA))){
    DATA$RP <- unlist(lapply(strsplit(DATA$C1,"\\."),function (l) l[1]))
  }
  
  # keywords post-processing (missing ";" in some rows)
  if ("ID" %in% names(DATA)){
    DATA$ID <- gsub("   |,",";",DATA$ID)
    #DATA$ID <- gsub(",",";",DATA$ID)
  }
  
  if ("DE" %in% names(DATA)){
    DATA$DE <- gsub("   |,",";",DATA$DE)
    #DATA$DE <- gsub(",",";",DATA$DE)
  }
  #row.names(DATA)=DATA$UT
  
  ### merge Sources and Proceedings
  if (("SO" %in% names(DATA)) & ("BO" %in% names(DATA))){
    ind <- which(is.na(DATA$SO))
    DATA$SO[ind] <- DATA$BO[ind]
  }
  
  if ("PN" %in% names(DATA)){
    DATA$PN <- as.numeric(gsub("[^0-9]", "", DATA$PN))
  }
  
  if (dbsource!="generic"){
    DATA$DB=dbsource
  } else {DATA$DB="SCOPUS"}
  
  
  # Toupper
  DI <- DATA$DI
  URL <- DATA$url
  DATA <- data.frame(lapply(DATA,toupper),stringsAsFactors = FALSE)
  if ("JI" %in% names(DATA)){
    DATA$J9 <- gsub("\\.","",DATA$JI)
  }else{
    DATA$J9 <- DATA$JI <- sapply(DATA$SO, AbbrevTitle, USE.NAMES = FALSE)
  }
  DATA$DI <- DI
  DATA$url <- URL
  return(DATA)
}