R/rmarkdown_functions.R

In JConigrave/papertools: Useful Tools For Writing Papers in Rmarkdown

file.opened <- function(path) {
  suppressWarnings("try-error" %in% class(try({
    x = file(path,
             open = "w")
    close.connection(x)
  }, silent = T)))
}

globalVariables(c("Author","Title","Extra","Notes","Type","Year"))

#'clean_docx
#'
#'Removes random tags and a mark
#'@param docx_path a character vector
#'@param landscape a bool. If true, document will become landscape
#'@importFrom dplyr %>%
#'@importFrom officer read_docx body_replace_all_text
#'@importFrom utils capture.output

clean_docx = function(docx_path, landscape = F){
x = officer::read_docx(docx_path)
x = x %>%
  officer::body_replace_all_text("\\(#tab:destroythistag\\)","") %>%
  officer::body_replace_all_text("\\`","")

if(landscape){
  x = officer::body_end_section_landscape(x)
}
  print(x, target = docx_path) %>%
  capture.output()
}

#'to_docx
#'
#'Sends a data.frame to a word doc.
#'@param table a dataframe or list of data.frames
#'@param path a string. Where you want to save the file.
#'@param title string. If provided, allows tables to be named
#'@param note a string. Allows for notes
#'@param landscape a bool. If true, outputs a landscape word doc
#'@param save_over a bool. If true, to_docx will save over files with same path
#'@param ... additional arguements passed to apa_table
#'@importFrom papaja apa_table
#'@export to_docx


to_docx = function(table,
                   path,
                   title = NULL,
                   note = NULL,
                   landscape = F,
                   save_over = T,
                   ...) {
  if (tools::file_ext(path) != "docx") {
    #if path isn't to .docx, it is now.
    path <- paste0(path, ".docx")
  }

  if (!save_over) {
    path = prevent_duplicates(path)
  }

  file_name = basename(path)

  dir_name = dirname(path)
  file_path = paste0(dir_name, "/", file_name)
  if (dir_name == ".") {
    dir_name = getwd()
  }

  if (file.opened(file_path)) {
    stop("Target file is currently open, cannot write.")
  }

  if (!"list" %in% class(table)) {
    table = list(table)
  }

  if (!is.null(title)) {
    if (length(title) != length(table)) {
      stop(
        "'title' is not the same length as 'table'. If titles are provided, they must be provided for each object."
      )
    }
  }

  rmarkdownpath = system.file("rmd", "docx_table.Rmd", package = "papertools")

  rmarkdown::render(
    rmarkdownpath,
    output_file = file_name,
    output_dir = dir_name,
    quiet = T
  )
  clean_docx(paste0(dir_name, "/", file_name), landscape = landscape)
  message(paste0("saved to: '", dir_name, "/", file_name, "'"))
}

#'zotero_notes
#'
#'Sends a data.frame to a word doc.
#'@param csv an exported csv from zotero. Study type stored in the extra field
#'@param path a string. must end in .html
#'@param title a string. Defaults to "Zotero notes"
#'@param date a string. Defaults to current date
#'@importFrom magrittr %>%
#'@importFrom dplyr select mutate arrange desc
#'@importFrom utils read.csv
#'@export zotero_notes
#csv = "C:/Users/jcon4884/Dropbox (Sydney Uni)/2_Grog Survey App - 1087192/10_reporting_publicity/papers/paper_5 - patterns of drinking meta analysis_James/7_paper/Literature review/Exported Items.csv"
zotero_notes = function(csv, path, title = "Zotero notes", date = format(Sys.time(), '%d %B, %Y')){
  x = read.csv(csv)
  x$Author = gsub(",.*",", et al.",x$Author)
  x$Notes = as.character(x$Notes)
  x$Notes[is.na(x$Notes)] = "   "

  file_name = basename(path)
  dir_name = dirname(path)
  file_path = paste0(dir_name, "/", file_name)
  if (dir_name == ".") {
    dir_name = getwd()
  }

  if (file.opened(file_path)) {
    stop("Target file is currently open, cannot write.")
  }

  rmarkdownpath = system.file("rmd", "zotero_notes.Rmd", package = "papertools")
x$Title = as.character(x$Title)
x$Publication.Title = as.character(x$Publication.Title)
  final_table = x %>%
    dplyr::select(
      Author,
      Year = "Publication.Year",
      Title,
      Journal = "Publication.Title",
      Type = Extra,
      Notes
    ) %>%
    dplyr::mutate(Type = tolower(Type)) %>%
    dplyr::arrange(desc(Year), Author)

  rmarkdown::render(rmarkdownpath,
                    output_file = file_name,
                    output_dir = dir_name,
                    quiet = T)
  message(paste0("saved to: '", dir_name, "/", file_name, "'"))


}

replace_papaja_docx_template = function(){
  papertools_apa6 = system.file("rmd", "apa6_man.docx", package = "papertools")
  papaja_apa6 = system.file("rmarkdown/templates/apa6/resources", "apa6_man.docx", package = "papaja")
  if(papaja_apa6 == ""){
    stop("The files could not be located. Is papaja installed?")
  }

  unlink(papaja_apa6)
  file.copy(papertools_apa6, papaja_apa6)
  return(message("file assasinated."))
}


#'prevent_duplicates
#'
#'Stops users accidentally overriding important files
#'@param path character string to path

prevent_duplicates = function(path){
  folder = dirname(path)
  filename = basename(path) %>%
    tools::file_path_sans_ext() #isolate file name (remove full path)
  ext = tools::file_ext(path)

  while(paste(filename,ext,sep = ".") %in% list.files(folder)){ #while the folder contains a file with the same name
    if(!grepl("\\(\\d\\)",filename)){ #if there's not brackets with a name inside
      filename = paste0(filename,"(1)") #add brackets with the number 1 in side
    }else{
      pod = stringr::str_extract(filename, "\\(\\d\\)") #otherwise grab the brackets
      num = as.numeric(gsub("\\D","", pod))+1 #get the number out and add 1 to it
      filename = gsub("\\(\\d\\)","",filename) #remove the old brackets with numbers in it
      filename = paste0(filename,"(",num,")") #add the new brackets with higher number in it
    }
  }
  return(paste0(folder,"/",filename,".",ext)) #return the filename with the folder address pasted to it.
}