R/rmd2rscript.R

In mkapur/kaputils: Utilities for Stock Assessment Simulation and Data Analysis

#' Convert RMD to R SCRIPT. Will save a file same location with noncode blocks commented out.
#'  adapted from http://rstudio-pubs-static.s3.amazonaws.com/12734_0a38887f19a34d92b7311a2c9cb15022.html
#'   @export
rmd2rscript <- function(infile){
  # read the file
  flIn <- readLines(infile)
  # identify the start of code blocks
  cdStrt <- which(grepl(flIn, pattern = "```{r*", perl = TRUE))
  # identify the end of code blocks
  cdEnd <- sapply(cdStrt, function(x){
    preidx <- which(grepl(flIn[-(1:x)], pattern = "```", perl = TRUE))[1]
    return(preidx + x)
  })
  # define an expansion function
  # strip code block indacators
  flIn[c(cdStrt, cdEnd)] <- ""
  expFun <- function(strt, End){
    strt <- strt+1
    End <- End-1
    return(strt:End)
  }
  idx <- unlist(mapply(FUN = expFun, strt = cdStrt, End = cdEnd,
                       SIMPLIFY = FALSE))
  # add comments to all lines except code blocks
  comIdx <- 1:length(flIn)
  comIdx <- comIdx[-idx]
  for(i in comIdx){
    flIn[i] <- paste("#' ", flIn[i], sep = "")
  }
  # create an output file
  nm <- strsplit(infile, split = "\\.")[[1]][1]
  flOut <- file(paste(nm, "[rmd2r].R", sep = ""), "w")
  for(i in 1:length(flIn)){
    cat(flIn[i], "\n", file = flOut, sep = "\t")
  }
  close(flOut)
}