Improvement: detect the file type and set markup option accordingly

[dewittpe]

The default is to generate LaTeX. It would be nice if the .Rmd files or if the target is .html/.docx the default would automatically be markdown.

[dewittpe]

An example of why this is needed is #84

[dewittpe]

Some code that might help with this:

FILE <- (function() {
  attr(body(sys.function()), "srcfile")
})()$filename

From https://stat.ethz.ch/pipermail/r-devel/2008-April/048914.html