prep_TEDDY_for_VOE.Rmd is an R RMD file. That is the place to start. It is the master file that uses many of the scripts in this directory.
From there you can go to run_humann_on_TEDDY.Rmd. After that you can follow TEDDY_logistic.Rmd, TEDDY_logistic_humann.Rmd.
Lastly go to analyze_TEDDY_models.Rmd. This will reproduce all figures in the manuscript. You can also go directly here if you just want to reproduce the figures using the data on figshare at https://figshare.com/authors/Samuel_Zimmerman/10885572