Project Structure

Fonti Kar & Emi Tanaka

Australian National University

2025-07-14

Motivating example

When we enter a new kitchen where do you go to find:

• cutlery?
• drinking glasses?
• rubbish bin?

Motivating example

When we enter a new project where do you go to find:

• code?
• data?
• supporting information?

Motivating example

When we enter a new project where do you go to find:

• code?
• data?
• supporting information?

A well thought-out project directory should feel intuitive and effortless! ✨

The alternative…💔

• Very slow to get started
• Sharing data via emails
• Dropbox/Cloud conflicted copies

A consistent format and understanding will make life easier 💗

No need to start from scratch 👩‍🍳

https://github.com/anu-aagi/template-project

template-project/                 # Root of the project folder (rename)
│
├── README.qmd                    # Edit this one
|── README.md                     # Automatically generated from .qmd
│
├── data/                         # Raw and derived data
|
├── code/                         # Scripts  to run analysis
|
├── outputs/                      # Outputs (code generated)
│
├── misc/                         # Misc documents
|
├── .git/                         # Git tracking folder
├── .gitignore                    # Files/folders to be ignored by git
|── .Rproj                        # RStudio project file

README: The landing page

https://github.com/anu-aagi/template-project

template-project/                
│
├── README.qmd                    # Edit this one
|── README.md                     # Automatically generated from .qmd
│

Data

https://github.com/anu-aagi/template-project

template-project/                 
│
├── data/                         # Raw and derived data
|   ├── README.md                 # When and how data was received
│   ├── data-raw/                 # Read-only files
│   ├── data-input/               # Extracted and coerced from raw data
│   └── data-valid/               # Edit and imputed from input data

Code

https://github.com/anu-aagi/template-project

template-project/                 
│
├── code/                         # Scripts  to run analysis
|   |__ 00_utils.R                # Custom functions 
|   |__ 01_data-prep.R            # Prepare input and valid data
|   |__ 02_purpose.R
|   |__ 03_purpose.R

Regeneratable outputs

https://github.com/anu-aagi/template-project

• Generated by content in code/

template-project/                 
│
├── outputs/                      # Outputs 
│   ├── stats/                    # Analysed results (R objects, .csv, etc.)
│   ├── figures/                   # Figures (.png, .pdf, etc.) 
│   ├── paper/                    # Paper format (delete if not applicable)
│   └── report/                   # Report format (delete if not applicable)

Everything else

https://github.com/anu-aagi/template-project

template-project/                 
│
├── misc/                         # Misc documents
│   ├── unsorted/                 # Unsorted files
│   ├── images/                   # Images (not created by code)
│   ├── notes/                    # Read-only files
│   └── meetings/                 # Edit and imputed from input data

Key takeaways

• Project structure gives you and your team an unspoken understanding
  • Keeps your workspace organised
• This gives makes your work intuitive and efficient
• A solid project structure sets the foundation for more reproducible workflows