Part I: Tools

This part of the textbook provides an overview of the different tools we will be using: terminals and consoles, R, python, quarto, markdown, pandoc, and git. It can be a bit confusing at first, especially if you’re not familiar with how your computer works, where files are stored, and different ways to tell your computer what to do.

1  Computer Basics gives you some important background material about how a computer functions.

2  Setting Up Your Computer tells you exactly what software you need to install for the rest of this textbook.

4  Scripts and Notebooks and Terminals discusses the different ways we can talk to R and python, and the pros and cons of each.

5  Version Control with Git discusses how to use git (setup is covered in 2  Setting Up Your Computer) and how to solve common git problems.

6  Reproducibility and Professional Communication discusses some solutions for dynamic document creation and literate programming (storing code, writeup, and documentation in the same file) using knitr, quarto, rmarkdown, and more.