R/create_custom_ddict.R

In omair-a-khan/ddictR: Create a Data Dictionary for any Data Set

create_custom_ddict <- function(data = merged.df, 
                                file_name = paste0("vmap_data_dictionary_m", format(Sys.time(),'%Y%m%d')), 
                                save_directory = "~/dev/ddictR", 
                                overwrite = TRUE, 
                                report_title = "VMAP Data Dictionary", 
                                data_download_date = NULL, 
                                data_merge_date = NULL
) {
  
  ### set up file names and paths ###
  
  rmd_file_name = paste0(file_name, ".Rmd")
  pdf_file_name = paste0(file_name, ".pdf")
  
  rmd_file_path <- file.path(save_directory, rmd_file_name)
  pdf_file_path <- file.path(save_directory, pdf_file_name)
  
  # delete existing files, if requested
  if (overwrite & file.exists(rmd_file_path)) {
    file.remove(rmd_file_path)
  }
  
  if (overwrite & file.exists(pdf_file_path)) {
    file.remove(pdf_file_path)
  }
  
  # open file connection
  file_connection <<- file(rmd_file_path, "w")
  
  ### YAML header ###
  
  if (!is.null(data_download_date) & !is.null(data_merge_date)) {
    subtitle <- paste0("Data Download Date: ", data_download_date, " | Data Merge Date: ", data_merge_date)
  } else {
    subtitle <- NULL
  }
  
  write_out("---")
  # write_out(paste("title:", report_title))
  # if (!is.null(subtitle)) write_out(paste0('subtitle: \"', subtitle, '\"'))
  # write_out(paste("date:", format(Sys.time(),'%B %d, %Y %H:%M')))
  # write_out("subparagraph: yes")
  write_out("output:")
  write_out("  pdf_document:")
  write_out("    includes:")
  write_out("      in_header: header.sty")
  write_out("      before_body: title.sty")
  # write_out("    toc: true") # disabled because table of contents is called in title.sty
  # write_out("    toc_depth: 1") # disabled because table of contents is called in title.sty; counter is manually specified
  write_out("    df_print: kable")
  # write_out("    latex_engine: xelatex")
  write_out("---")
  
  ### Hidden Setup Chunk ###
  
  chunk_wrapper(
    x = paste0('library(Hmisc) \nlibrary(dplyr) \nlibrary(ggplot2) \nlibrary(kableExtra)'),
    quiet = TRUE
  )
  
  chunk_wrapper(
    x = paste0('label_epoch <- function(string) { lapply(string, function(x) paste0("Epoch ", x)) }'),
    quiet = TRUE
  )
  
  ### Entries ###
  
  write_out("\\newpage")
  
  
  for (var_groups.i in 1:length(variables.list)) {
    
    write_out(paste0("# ", variables.list[[var_groups.i]][["title"]], " \n"))
    
    for (variable.i in variables.list[[var_groups.i]][["variables"]]) {
      create_individual_entry(data = data, variable = variable.i)
    }
  }
  
  write_out("# IDs of Participants Missing All Data by Epoch \n")
  create_missing_summary()
  
  write_out("\\newpage")
  write_out("# Session Info \n")
  
  # chunk_wrapper(paste0('devtools::session_info()$platform'))
  # write_out(utils::toLatex(sessionInfo()))
  chunk_wrapper(
    paste0('tibble::enframe(sapply(devtools::session_info()$platform, unname)) %>% kable(format = \"latex\", booktabs = TRUE) %>% kable_styling(position = \"center\")')
  )
  
  # force flush and close connection
  flush(file_connection)
  close(file_connection)
  
  ### Knit Document ###
  rmarkdown::render(rmd_file_path, 'all', pdf_file_name)
}