#Run script with $Rscript createDoc.R input.Rmd output.html

require(knitr) # required for knitting from rmd to md
require(markdown) # required for md to html

args <- commandArgs(TRUE)

if(length(args) != 2)
    stop("Please provide 2 arguments corresponding to input and output file!")

inputFile <- args[[1]] # .Rmd file
outputFile <- args[[2]] # .html file

# Create and fill temp .md file from existing .Rmd file
tempMdFile <- tempfile("tempREADME", fileext = "md")
knitr::knit(inputFile, tempMdFile) 

# Generate HTML from temporary .md file
markdown::markdownToHTML(tempMdFile, outputFile)