Working setup
I often experiment with different workflows and adapt them to my needs and likings. I have written papers in Word, Latex, google docs, and Markdown, while I have produced and tweaked figures with R, Gimp, Inkscape, the yEd diagram editor, etc. I will quickly summarize what, for me, is the best workflow for a complete project.
1 - Setting up a code/data project
Set up a github repository for the code and, if it applies, for the raw data.