made a few changes to Neotoma_paper.Rmd, see html escaped comments

hey @SimonGoring - made just a few changes, and a few comments. See html escaped comments. There are a bunch of white space changes that i didn't notice until after I made changes. Sorry about that. If you look at the diff with `?w=1` appended at the end (https://github.com/SimonGoring/neotoma_paper/pull/6/files?w=1) you can see changes without the purely whitespace changes. In the future I'll make sure to not introduce white space changes. 

All examples seemed to work fine, except that `ggmap` thing I already reported in the `neotoma` repo