update README

[ernestguevarra]

As per discussion/feedback from Noam, update README:

• structure to sequence sections as follows:

  • [x] targets overview;
  • [x] renv overview;
  • [x] GitHub Actions overview;
  • [x] Steps on how to use the template repo

• [x] For the steps on how to use the template repo, use steps done to create ecohealthalliance/nipah-bangladesh-automation (see https://github.com/ecohealthalliance/nipah-bangladesh-automation/issues/1) and the learnings from that to develop the guidance for this.

[noamross]

• Reorganize to open with buletted "quickstart" section: Make new repo, clone, rename .Rproj, rename other things, activate git-crypt and add keys, add relevant env vars, write functions, targets, and Rmd reports
• Don't make the other sections too long

[collinschwantes]

Could provide links to the Handbook chapters for renv and targets

[collinschwantes]

should include language about citing paper vs data

[noamross]

Somewhere between README, comments in _targets.R, and handbook links we should include a short version of targets best practices:

• One function per file in R/
• Non-function R scripts in another directory like scripts/
• Use the same names for targets and function arguments for those targets unless a function
• Nouns for targets, verbs for functions
• Use common suffixes for target types: _file for files, _raw for read-in but unprocessed data
• Use fnmate and tflow RStudio Add-Ins to make this easy, create shortcuts for these add-ins, link to Miles McBain's NYR talk

Also, note containerTemplateUtils has functions available for common EHA tasks for this type of repo/workflow.