Simple

• Code: / (single top level script)
• Project File: /
• README: / (description of what you’re doing and how to run w/top level script)
• Data: /data (sub dirs if useful)
• Results: /results (sub dirs if useful)

/README
/myproject.Rproj
/mydatascript.R
/myanalysisscript.R
/data/datafile1.txt
/data/datafile2.txt
/results/graph1.png
/results/graph2.png
/paper/mypaper.Rmd
/paper/mypaper.pdf

Advanced

• Project file & README: /
• Docs: /doc
• Paper: /paper or /doc/paper
• Code: /src
• Data: /data
• Results: /results