R/Render.R

In adapr: Implementation of an Accountable Data Analysis Process

#' Renders and Rmarkdown file
#' @param Rmd.file Filename of .Rmd file within the R Markdown directory (source_info$markdown.dir)
#' @param description of rendered file
#' @param ... extra arguments for rmarkdown::render
#' @return Rendered output file information
#' @details Not for direct use. Uses rmarkdown library to access objects in the R script. Will track dependencies for objects used within Rmd file.
#' @export
#' @examples 
#'\dontrun{
#' source_info <- create_source_file_dir("adaprHome","read_data.R")
#' renderRmd("read_data.Rmd")
#'} 
renderRmd <- function(Rmd.file,description="Rmarkdown",...){
  
  #equire(rmarkdown)
  
  if(!exists("source_info")){
    
    source_info <- list()
    
    stop("Render (adapr) error: source_info not found")
    
  }
  
  
  mdfile <- createFileInfo(source_info$markdown.dir,Rmd.file,description)
  
  Read.cap(mdfile,I,source_info)#,envir=parent.frame())
  
  shiftmdfile <- file.path(source_info$results.dir,Rmd.file)
  
  file.copy(mdfile$fullname,shiftmdfile,overwrite=TRUE)
  
  outputfile <- rmarkdown::render(shiftmdfile,...)
  
  file.remove(shiftmdfile)
    
  outfile <- createFileInfo(source_info$results.dir,basename(outputfile),paste("rendered Rmarkdown of",description))
    
  Write.cap(NULL,outfile,I,source_info)#,envir=parent.frame())
  
  file.remove(shiftmdfile)
  
  return(outfile)
  
}