R/pubmed2df.R

In bibliometrix: Comprehensive Science Mapping Analysis

utils::globalVariables(c("Paper", "Tag", "content", "cont"))
pubmed2df <- function(D) {
  D <- D[nchar(D) > 0] # remove empty rows

  for (i in 1:length(D)) {
    if (substr(D[i], 1, 4) == "    ") substr(D[i], 1, 4) <- substr(D[i - 1], 1, 4)
  }

  Papers <- which(regexpr("PMID-", D) == 1) # first row of each document
  nP <- length(Papers) # number of docuemnts

  rowPapers <- diff(c(Papers, length(D) + 1))

  numPapers <- rep(1:nP, rowPapers)

  DATA <- data.frame(Tag = substr(D, 1, 4), content = substr(D, 7, nchar(D)), Paper = numPapers)
  DATA$Tag <- gsub(" ", "", DATA$Tag)
  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)

  # rename field tags
  error <- 0
  old_labs <- c("AD", "AUID", "FAU", "IS", "IP", "SO", "JT", "TA", "MH", "PG", "PT", "VI", "DP")
  new_labs <- c("C1", "OI", "AF", "SN", "IS", "SO2", "SO", "J9", "DE", "PP", "DT", "VL", "PY")
  lab <- names(df)
  for (j in 1:length(old_labs)) {
    i <- which(lab %in% old_labs[j])
    if (length(i) > 0) {
      lab[i] <- new_labs[j]
    } else {
      error <- 1
    }
  }
  names(df) <- lab
  if (error == 1) {
    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")
  }

  # extract DOIs
  df$DI <- trimws(unlist(lapply(strsplit(df$LID, "\\["), "[", 1)))
  df$PY <- as.numeric(substr(df$PY, 1, 4))


  ### replace "---" with ";"
  tagsComma <- c("AU", "AF", "DE", "AID", "OT", "PHST", "DT")
  nolab <- setdiff(tagsComma, names(df))
  tagsComma <- tagsComma[(!(tagsComma %in% nolab))]

  df1 <- data.frame(lapply(df[tagsComma], function(x) {
    gsub("---", ";", x)
  }))

  ### replace "---" with " "
  otherTags <- setdiff(names(df), tagsComma)
  df2 <- data.frame(lapply(df[otherTags], function(x) {
    trimES(gsub("---", " ", x))
  }))
  df <- cbind(df1, df2)
  rm(df1, df2)

  df$DB <- "PUBMED"

  # remove * char from keywords
  df$DE <- df$ID <- gsub("\\*", "", df$DE)
  AB <- df$AB
  TI <- df$TI
  DE <- df$DE
  df <- data.frame(lapply(df, toupper))
  df$AB_raw <- AB
  df$TI_raw <- TI
  df$DE_raw <- DE
  # add sep ; to affiliations
  df$C1 <- gsub("\\.", ".;", df$C1)
  df$RP <- NA
  df <- df[names(df) != "Paper"]

  return(df)
}