Following on from my previous post about my data workflow, I outline my basic writing workflow here. As mentioned in the previous post, I use Scapple as a tool to organise my thoughts, brainstorm, and plan my work, including basic outline for my write-up (background on the figure above).1
I start my initial drafts, particularly methods and results sections within RStudio, as it is where I do my data analysis and visualisation and it is simply easier to write about methods and results while they are being worked on.
I have been using GitHub to collaborate/share data analysis (and a bit of writeup) with my co-authors/collaborators for the last year or so. As most journals now require (or at the very least recommend) submitting original data used in the analysis, alongside the relevant scripts/codes, during the manuscript submission process, I thought it was easiest simply to submit the persistent link to the GitHub repository containing all the data and the scripts/codes used in the analysis and visualisation as part of the manuscript submission.