GitHub without fear

(or an Appropriate Amount of Fear!)

Open workflows for ecology and wildlife research

Topics:

  • Repositories
  • Commits
  • Push/pull
  • README files
  • Version control basics

Learning Goals

By the end of this session you should be able to:

  • Understand what Git and GitHub are
  • Create and clone repositories
  • Make commits confidently
  • Push and pull changes

What Problem Does Git Solve?

A familiar workflow problem

analysis_final.R
analysis_final_v2.R
analysis_final_v2_REAL.R
analysis_final_USE_THIS_ONE.R

Common issues

  • Files overwritten
  • Unsure what changed
  • Difficult collaboration
  • No backup history
  • Impossible to undo mistakes safely

Git is not GitHub

Git

  • Version control system
  • Tracks changes to files
  • Works locally on your computer

GitHub

  • Online hosting platform for Git repositories
  • Collaboration and sharing
  • Backup and project management

Version control

Git keeps a history of changes:

  • What changed
  • When it changed
  • Who changed it
  • Why it changed

Benefits

  • Undo mistakes
  • Track project history
  • Collaborate safely
  • Experiment without fear

Why GitHub Matters in Ecology

Ecology is collaborative

Examples:

  • Multi-author papers
  • Monitoring projects
  • Shared codebases
  • Long-term projects
  • Student supervision
  • Evidence synthesis workflows

What Is a Repository?

Repository = project folder + history

A repository contains:

  • Code
  • Data (although it shouldn’t)
  • Documentation
  • Figures
  • Workflow history

Think of it as:

A project folder with memory.

Commits

Commits are snapshots

A commit records:

  • What changed
  • When it changed
  • A short explanation

Good commit messages

Add cleaning script for camera trap data
Fix species names in processed dataset

Bad commit messages

stuff
asdfgh

A Helpful Mental Model

Edit files
    ↓
Review changes
    ↓
Commit changes
    ↓
Push to GitHub

Push and Pull

Push

Send your local commits to GitHub.

Pull

Download changes from GitHub.

Typical workflow

Pull
Work
Commit
Push

GitHub is useful for:

  • Backup
  • Project sharing
  • Collaboration (even with youself)
  • Public documentation
  • Teaching
  • Open science portfolios

Common Fear #1

“What if I break everything?”

Good news:

Git is designed to:

  • Track changes
  • Recover mistakes
  • Restore earlier versions

Mistakes are normal.

Even experienced users regularly:

  • Commit the wrong file
  • Merge incorrectly
  • Forget to pull

Common Fear #2

“I don’t understand branches”

That is okay.

Branches come later…

You do not need to master Git immediately.

Common Fear #3

“The terminal is scary”

Yes it is! You can do a lot using:

  • RStudio Git pane
  • GitHub Desktop
  • VS Code interfaces

Understanding concepts matters more than memorising commands.

Common Mistakes

Common “beginner” mistakes

  • Forgetting to commit
  • Committing large files
  • Editing directly on GitHub accidentally
  • Conflicts after forgetting to pull
  • Uploading sensitive data

Guided practice

You will:

  1. Create a GitHub repository
  2. Connect it to RStudio
  3. Add your reproducible project
  4. Commit changes
  5. Push to GitHub
  6. Edit README
  7. Pull updates

Create a GitHub repository

On GitHub:

  1. Click “New repository”
  2. Choose a repository name
  3. Add a README
  4. Set visibility
  5. Create repository

Suggested name:

wildlife-reproducibility-workshop

“Clone” repository into RStudio

In RStudio:

File → New Project → Version Control → Git

Paste repository URL.

Result

You now have:

  • Local repository
  • Git tracking enabled
  • GitHub connection established

Add project files

Copy into the repository:

  • data_raw/
  • scripts/
  • outputs/
  • README.md

Observe Git pane

RStudio now shows changed files.

Make your first commit

In Git pane:

  1. Tick changed files
  2. Click “Commit”
  3. Write message

Example:

Add initial project structure and scripts

Push to GitHub

Click:

Push

Refresh GitHub page

Your project is now online.

Edit the README

Add:

  • Project description
  • Your name
  • Workshop details
  • Folder explanation

Commit and push changes.

Important habits

  • Always pull before starting work.

  • Commit often

Be careful with:

  • Sensitive species locations
  • Confidential data
  • Personal information
  • Large raw files
  • Passwords/API keys