R/table_articles_mod.R

In joelmlevin/uglypaRse: uglypaRse: tools for dealing with missing delimiters

table.articles.mod <-
  function(pubmed_data, included_authors = "all", max_chars = 500, autofill = TRUE, dest_file = NULL) {
    if (!included_authors %in% c("all", "first", "last"))
      stop("Method is not supported!")
    #
    message("Processing PubMed data ", appendLF = FALSE)
    paper.data <- articles_to_list(pubmed_data)
    papers.authors.list <- lapply(1:length(paper.data), (function(i){
      if (length(paper.data)>50) {
        rep.dot <- as.integer(seq(1, length(paper.data), length.out = 50))
        if (i %in% rep.dot)
          message(".", appendLF = FALSE)
      } else {
        message(".", appendLF = FALSE) 
      }
      #
      art <- paper.data[[i]]
      out <-  tryCatch(article_to_df(pubmedArticle = art, autofill = autofill, max_chars = max_chars), error = function(e) {NULL})
      if (is.null(out)){
        out <- data.frame(pmid=NA, doi=NA, title=NA, abstract=NA, 
                          year=NA, month=NA, day=NA, jabbrv=NA, 
                          journal=NA, lastname=NA, firstname=NA, 
                          address=NA, email=NA)
      }
      if (included_authors == "first"){
        out <- out[1, ] 
      } else if (included_authors == "last") {
        out <- out[nrow(out), ]
      } else {
        # do nothing
      }
      out   
    }))
    message(" done!")
    papers.authors.df <- dplyr::bind_rows(papers.authors.list) #this line modified
    keep.rw <- apply(papers.authors.df, 1, (function(rw) {sum(is.na(rw)) < length(rw)}))
    papers.authors.df <- papers.authors.df[keep.rw,]
    #
    if(!is.null(dest_file)){
      if(class(dest_file) == "character" & length(dest_file) == 1){
        tryCatch(utils::write.table(papers.authors.df, dest_file), error = function(e){NULL})
      }
    }
    return(papers.authors.df)
  }