Simple

• Main/Root directory (./)
  • Code file (.R)
    • single top level script
    • linked data manipulation and analysis scripts
  • Project File (.Rproj)
  • README
    • description of what you’re doing and how to run w/top level script
    • .txt or .md
  • Data (./data/)
    • Sub directories may be useful
  • Results (./results/)
    • Sub directories may be useful

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

Advanced

• Code directory (./code/ or ./src/)
• Documentation file (./docs/)
• Manuscript files (./paper/ or ./doc/paper/)