Tools

Unless otherwise noted, software below is open source and free. On macOS, most can be installed with Homebrew.

Statistical Programming

• R
• RStudio (open source IDE)
• Shiny (web application framework)
• Tidyverse (useful packages)
• RSwitch (macOS menubar utility)

Books on R

Programming

• Advanced R [previous edition / (unofficial) exercise solutions]
• R Packages
• Happy Git and GitHub for the useR
• Efficient R programming
• Mastering Software Development in R
• Hands-On Programming with R

Data science

• R for Data Science
• R Programming for Data Science
• Statistical Inference via Data Science: A ModernDive into R and the Tidyverse
• Text Mining with R: A Tidy Approach

RMarkdown

• R Markdown: The Definitive Guide
• R Markdown Cookbook
• bookdown: Authoring Books and Technical Documents with R Markdown

Visualization

• Data Visualization: A practical introduction
• R Graphics Cookbook
• ggplot2: Elegant Graphics for Data Analysis
• Mastering Shiny
• Interactive web-based data visualization with R, plotly, and shiny

Other resources for learning

• Quick-R
• Cookbook for R
• IDRE UCLA
• Survey analysis in R

Creating documents

• Quarto (publishing system)
• The LaTeX Project (professional typesetting) & macTeX (distribution for macOS)
• The Not So Short Introduction to LaTeX2ε (PDF)
• formatting information: A beginner’s introduction to typesetting with LaTeX
• Pandoc (powerful document converter)
• Bookends (customizable reference manager for macOS, not open source or free)
• Zotero (reference manager)
• biblatex (state-of-the-art citations in LaTeX & Quarto)

Notes & Markdown

• Joplin (excellent markdown notes)
• Agenda (great, notes linked to dates, not open source or free)
• The Plain Person’s Guide to Plain Text Social Science
• CommonMark (Markdown specification)
• MultiMarkdown (Markdown specification)
• Pandoc’s Markdown (Markdown specification)
• RMarkdown (Markdown specification with R computations)

Editors & Versioning

• Sublime Text (awesome IDE, not open source or free) [official documentation]
• Zettlr (IDE for writing)
• Modern CSV (excellent CSV editor, not open source or free for some features)
• git [Pro Git book] & GitHub (version control collaboration with yourself and others)

PDF

• Skim (PDF reader and annotator)
• Textricator (PDF text extraction)
• Tabula (PDF table extraction)
• Camelot (PDF table extraction) / Excalibur (web interface)

Databases

• SQLite (lightweight, serverless SQL database engine)
• Litestream (continuous SQLite replication)
• NocoDB (no code cloud database platform)
• Neon (Serverless Postgres, subscription)
• Railway (easy development cloud infrastructure, subscription)

Web

• Firefox (browser)
• W3Schools (web technologies reference)
• Jekyll (static site generator)
• Hugo (static site generator)
• Bootstrap (front-end web framework)
• Cyberduck (cloud storage browser, i.e. FTP etc)
• Colorpicker

macOS

• Homebrew (package manager)
• Objective-See (security tools)
• Mac Backup Guru (bootable backups, not open source or free)
• OnyX (multifunction utility)
• CheatSheet (help with keyboard shortcuts)
• Scheduler
• f.lux (adjust screen colour according to time of day)
• Rectangle (window management)
• Clocker (timezone tool)
• Kap (screen recordings)

Security

• pwSafe (password manager, not free)
• Cryptomator (file encryption)
• OnionShare (secure and anonymous sharing)