Cleaning up the directory based on issue #7 from @karthik.  Also includes some changes to the mapping to try to fix issue #4, resolved the issue with changes to the neotoma package, but also changed mapping.
Resolved conflicts caused by my forgetting to pull before I edit.

Merge branch 'master' of https://github.com/SimonGoring/neotoma_paper

Conflicts:
	Neotoma_paper.Rmd