Each R Markdown file generates the data and corresponding figure (or table) specified in the file name. For example. Figure1A.Rmd generates the data presented in Figure1A of the paper.
Note that in order to reproduce the data and figures in the paper (https://figshare.com/s/10bd487952892b5c939a), it would be necessary to have the Beth Israel Deaconeness Medical Center (BIDMC) dataset, which cannot be made public.