Pubmed_Citation_Generator.R

library(officer)
library(dplyr)
library(stringr)
citation.font = "Garamond"
citation.font.size = 12


doc_add_reference <-
  function(doc,
           paper_info,
           bold_Authors,
           citation.font = "Garamond",
           citation.font.size = 12,
           citation.link.color = "blue") {
    standard_text <-
      fp_text(font.family = citation.font, font.size = citation.font.size)
    standard_text_bold <-
      fp_text(font.family = citation.font,
              font.size = citation.font.size,
              bold = TRUE)
    standard_hyperlink <-
      fp_text(font.family = citation.font,
              font.size = citation.font.size,
              color = "blue")
    
    Title <- paper_info$Title
    Citation <- paper_info$Citation
    PMID <- paper_info$PMID
    PMCID <- paper_info$PMCID
    Authors <- paper_info$Authors
    NIHMSID <- paper_info$NIHMS.ID
    Authors <- str_split(Authors, ",", simplify = TRUE)
    
    fpar_authors <- c()
    
    paper_reference_pubmed <- lapply(seq(1:length(Authors)),
                                     function(i) {
                                       Author_i <- str_trim(Authors[i])
                                       
                                       
                                       if (Author_i %in% bold_Authors) {
                                         Author_i_style <- standard_text_bold
                                       } else{
                                         Author_i_style <- standard_text
                                       }
                                       if (i != length(Authors)) {
                                         Author_i <- paste0(Author_i, ", ")
                                       } else{
                                         Author_i <- paste0(Author_i, " ")
                                       }
                                       ftext_Author_i <-
                                         ftext(Author_i, prop = Author_i_style)
                                       ftext_Author_i
                                     })
    
    
    end_index = length(paper_reference_pubmed) + 1
    paper_reference_pubmed[[end_index]] <-
      hyperlink_ftext(
        href = paste0("https://pubmed.ncbi.nlm.nih.gov/", PMID),
        text = paste0(Title, ". "),
        prop = standard_hyperlink
      )
    end_index <- end_index + 1
    paper_reference_pubmed[[end_index]] <-
      ftext(Citation, prop = standard_text)
    end_index <- end_index + 1
    if (!is.na(PMID)) {
      paper_reference_pubmed[[end_index]] <-
        ftext(paste0("; PubMed PMID: ", PMID), prop = standard_text)
      end_index <- end_index + 1
    }
    if (!is.na(PMCID)) {
      paper_reference_pubmed[[end_index]] <-
        ftext(paste0("; PubMed Central PMCID: ", PMCID), prop = standard_text)
      end_index <- end_index + 1
    }
    if (!is.na(NIHMSID)) {
      paper_reference_pubmed[[end_index]] <-
        ftext(paste0("; NIHMSID: ", NIHMSID), prop = standard_text)
      end_index <- end_index + 1
    }
    
    fp <- do.call(fpar,
                  paper_reference_pubmed)
    
    
    doc <- body_add_fpar(doc, fp)
    #doc <-  body_add_par(doc, " ")
    doc
  }

get_citation_doc <-
  function(csv_pubmed_loc,
           save_references_name,
           bold_Authors,
           seperate_in_year = FALSE,
           citation.font = "Garamond",
           citation.font.size = 12,
           citation.link.color = "blue") {
    csv_pubmed <- read.csv(csv_pubmed_loc)
    csv_pubmed[csv_pubmed == ""] <- NA
    Authors_order <- c()
    for (i in seq(1:nrow(csv_pubmed))) {
      paper_info <- csv_pubmed[i,]
      Authors <- paper_info$Authors
      Authors <- str_split(Authors, ",", simplify = TRUE)
      Author_first <- str_trim(Authors[1])
      Author_last <- str_trim(Authors[length(Authors)])
      Author_order <- 3
      if (Author_first %in% bold_Authors) {
        Author_order <- 1
      }
      if (Author_last %in% bold_Authors) {
        Author_order <- 2
      }
      Authors_order <- c(Authors_order, Author_order)
    }
    csv_pubmed$Authors_order <- Authors_order
    
    csv_pubmed <-
      csv_pubmed %>% arrange(-Publication.Year, Authors_order, First.Author)
    
    if (seperate_in_year) {
      for (year in unique(csv_pubmed$Publication.Year)) {
        csv_pubmed_year <- csv_pubmed[csv_pubmed$Publication.Year == year,]
        doc = read_docx()
        for (i in seq(1:nrow(csv_pubmed_year))) {
          paper_info <- csv_pubmed_year[i,]
          doc <-
            doc_add_reference(
              doc,
              paper_info,
              bold_Authors,
              citation.font,
              citation.font.size,
              citation.link.color
            )
        }
        print(doc, target = paste0(save_references_name,"_",year, ".docx"))
      }
    } else{
      doc = read_docx()
      for (i in seq(1:nrow(csv_pubmed))) {
        paper_info <- csv_pubmed[i,]
        doc <-
          doc_add_reference(
            doc,
            paper_info,
            bold_Authors,
            citation.font,
            citation.font.size,
            citation.link.color
          )
      }
      print(doc, target = paste0(save_references_name, ".docx", ))
    }
  }