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. Stop before reaching section "#extract output into nice table format" We will come back to that later.
From there you can go to run_humann_on_TEDDY.Rmd. After that you can follow TEDDY_logistic.Rmd, TEDDY_logistic_humann.Rmd.
Now go back to prep_TEDDY_for_VOE.Rmd and run #extract output into nice table format section of the Rmd file.
Lastly go to analyze_TEDDY_models.Rmd