Appendix B — Command Reference

Quick reference for essential commands.

B.1 Conda

B.1.1 Environment Management

# Create environment
conda create -n ENV_NAME python=3.11

# Create with packages
conda create -n ENV_NAME python=3.11 pandas numpy

# Activate
conda activate ENV_NAME

# Deactivate
conda deactivate

# List environments
conda env list

# Remove environment
conda env remove -n ENV_NAME

# Export environment
conda env export > environment.yml

# Create from file
conda env create -f environment.yml

# Update from file
conda env update -f environment.yml

B.1.2 Package Management

# Install package
conda install PACKAGE

# Install specific version
conda install PACKAGE=1.2.3

# Update package
conda update PACKAGE

# Update all
conda update --all

# List installed
conda list

# Search for package
conda search PACKAGE

B.2 renv (R)

# Initialize renv
renv::init()

# Install package
install.packages("package")
renv::install("package")

# Snapshot (save state)
renv::snapshot()

# Restore (load state)
renv::restore()

# Check status
renv::status()

# Update packages
renv::update()
renv::update("package")

# Deactivate renv
renv::deactivate()

B.3 Git

B.3.1 Setup

# Initialize repo
git init

# Clone repo
git clone URL

# Configure identity
git config --global user.name "Name"
git config --global user.email "email@example.com"

# Add remote
git remote add origin URL

B.3.2 Daily Workflow

# Check status
git status

# View changes
git diff
git diff --staged

# Stage files
git add FILE
git add .

# Commit
git commit -m "message"

# Push
git push

# Pull
git pull

B.3.3 Branches

# List branches
git branch

# Create and switch
git checkout -b BRANCH

# Switch branch
git checkout BRANCH

# Merge branch
git merge BRANCH

# Delete branch
git branch -d BRANCH

B.3.4 History

# View log
git log
git log --oneline
git log --oneline -n 10

# View specific commit
git show COMMIT_HASH

# View file history
git log -p FILE

B.3.5 Undoing

# Unstage file
git reset HEAD FILE

# Discard changes to file
git checkout -- FILE

# Undo last commit (keep changes)
git reset --soft HEAD~1

# Amend last commit
git commit --amend

B.4 GitHub CLI (gh)

# Authenticate
gh auth login

# Create repo
gh repo create NAME --private

# Clone repo
gh repo clone OWNER/REPO

# Create PR
gh pr create --title "Title" --body "Description"

# View PR
gh pr view NUMBER

# List issues
gh issue list

# Create issue
gh issue create --title "Title" --body "Description"

B.5 Quarto

# Create project
quarto create project book NAME

# Render document
quarto render FILE.qmd

# Render project
quarto render

# Preview (live reload)
quarto preview

# Publish to GitHub Pages
quarto publish gh-pages

B.6 File Operations (Bash)

# Create directory
mkdir DIRNAME
mkdir -p path/to/nested/dir

# List files
ls
ls -la

# Change directory
cd DIRNAME
cd ..
cd ~

# Copy file
cp SOURCE DEST

# Move/rename
mv SOURCE DEST

# Remove file
rm FILE

# Remove directory
rm -r DIRNAME

# View file
cat FILE
less FILE
head FILE
tail FILE

B.7 Python Quick Reference

# Virtual environment (alternative to conda)
python -m venv .venv
source .venv/bin/activate  # macOS/Linux
.venv\Scripts\activate     # Windows

# Install from requirements
pip install -r requirements.txt

# Save requirements
pip freeze > requirements.txt

# Run script
python script.py

# Run module
python -m module_name

# Interactive Python
python
ipython

B.8 R Quick Reference

# Run script from command line
Rscript script.R

# Install package
install.packages("package")

# Load package
library(package)

# Get help
?function
help(function)

# Set working directory
setwd("path")

# Get working directory
getwd()

# List objects
ls()

# Remove object
rm(object)

# Clear environment
rm(list = ls())