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 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