The user can go through the pdf src_guide.pdf although currently if the user would like to run the code locally, we advise to run the code from the Rmd file, as for the sake of clarity, not all the code chunks are being shown.
All the code is in R. Main dependencies and input files are discussed in the pdf. We provide links to all the packages and input files.
This repo also contains the pre-computed input files necessary to replicate the results in the vignette.