README.md

woRkflow

How we do collaborative reproducible data analysis and reporting. Mostly (but not only) using R. Inspired by @AlexaLFH.

This repo does three things:

• it is a collection of R how-to resources including some notes on:
  • how to use git branches
  • how to use drake to massively speed up and manage your workflow
  • how to access the University Iridis HPC
  • how to use R/RStudio on the University SVE (remote desktop) service
  • where to keep your data
• it is a template repo that illustrates how we work and which you can copy;
• it is an R package. This means:
  • package functions are kept in /R
  • help files auto-created by roxygen are in /man
  • if you clone it you can build it using 'install and restart' from the RStudio Build menu and use the functions viz: woRkflow::functionName() (not that it has many)

Using drake:

• make_XX.R contains a call to drake::r_make(source = "_drake_XX.R")
• _drake_XX.R contains the drake plan and the functions & package loading. This is not quite what the drake book recommends but it works for us
• Rmd scripts called by the drake plan to report results are kept in /Rmd
• outputs are kept in /docs (reports, plots etc)
• if you can, run Rscript ./make_cleanFeeders.R in a terminal not at the RStudio console <- this stops RStudio from locking up

We'd love your contributions - feel free to:

• fork & go
• make a new branch in your fork
• make some improvements
• send us a pull request (just code, no data please, keep your data elsewhere!)

As a number of people have pointed out fork & go only works if you have an account on git.soton.ac.uk. If you don't, you can import the repo to (for example) your github.com account and go from there. And presumably on gitlab.com too...