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 [email protected].
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