Hello,
This is how to replicate my analysis on my data using RStudio.
It should be as simple as changing the filepaths at the tops of R Markdown chunks in RStudio to this folder's filepath, and then executing whichever chunks you want. This will generate the maps and plots that I used to understand patterns within my survey and growth data. Not all of the outputs were used in the paper.
If you have any trouble, you can email me at lhk@berkeley.edu.
Also, I suspect my identifications were incorrect, at least at the species level. A great follow-up would be to survey these mats using real 16S RNA sequencing for identification. If you pursue that, I wish you luck, and I hope you enjoy your commute as much as I did.
Yours truly, Lucas Kampman