/2023_Blake_TrEAT-PREVENT-TD

Data, code, and analyses for Blake, Schwartz, Paruthiyil et al. (2023). mBio. PMID: 38085102.

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TrEAT-PREVENT-TD

Code and data used to generate figures and datatables associated with the TrEAT / PREVENT TD manuscript:

Blake K.S., Schwartz D.J., Paruthiyil S., Wang B., Ning J., Isidean S.D., Burns D.S., Whiteson H., Lalani T., Fraser J.A., Connor P., Troth T., Porter C.K., Tribble D.R., Riddle M.S., Gutiérrez R.L., Simons M.P., Dantas G. Gut microbiome and antibiotic resistance effects during travelers’ diarrhea treatment and prevention. mBio. 2023 Dec 12:e0279023. doi: 10.1128/mbio.02790-23. PMID: 38085102.

How to run:

  1. Open TrEAT-PREVENT-TD.Rproj. This will open the RStudio window and set this as the working directory.
  2. Open and run all of _common.R. This will load packages, data files, source functions, output directory structure, etc.
  3. Open a .Rmd file and begin.