Re-factor Rcpp code

[kylebaron]

1. Moves the sourceCpp call outside of the outer loop (it should be called only once), and prior to the start of the timer (so that the timing results don't include compilation time)
2. The compiled code is re-factored so that there is just a single call to the Rcpp stuff to do the calculations (prevents repeated switching back and forth between R and Rcpp)
3. I maintained the original flow of the code as much as possible and retained the original Rcpp files for comparison

Thanks for considering the pull request.

Kyle