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egfR0

Current plan

We are using the slow/ slowtarget/ pair both for faster compilation, and for sharing non-sensitive files that people can use to replicate the downstream part of our work. It would be fun to make a separate share/ directory.

to get up and running...

re: make

To run code in this repo using the Makefile, use shellpipes remotes::install_github("dushoff/shellpipes") https://dushoff.github.io/shellpipes/

To pull and push (on git) idiomatically, simply run in terminal make sync.

other R packages

I think I installed epiGrowthFit manually/outside the make file, but don't recall -MER 20240130

Documents and documentation

  • TODO.md contains some long-term desiderata from JD
  • notes.md contains meeting notes from meetings primarily between JD, KH, and ML
  • README.md (this document) is where MR is writing user notes as he gets to know the project...
  • Makefile describes workflows.
  • Not in this repo, but to understand the make workflows, it may help to see the shellpipes package documentation: https://dushoff.github.io/shellpipes/. for more, https://github.com/mac-theobio/useMakestuff
  • makestuff/README.md has lots of make documentation