Further clean up

Additional cleaning up required:

 * The figure-generating chunks were renamed prior to submission but the figures were not rendered or committed
 * Deleted the now obsolete versions of the figures
 * Updated `Makefile` to include an `make R` option to `purl()` the `.Rmd` into an `.R` script.
 * Included `Neotoma_paper.R`, the `purl()`ed version of the `.Rmd`

I think we are now pretty much clean; except for deleting `.Rproj` the main repo is clean and we can decide if we want to retain the `misc/` folder later.