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Introduction to R, RStudio, and Quarto

Zhaoxia Yu

R

What Is R?

  • A programming language and software environment for statistical computing and data analysis.
  • Created by statisticians Ross Ihaka and Robert Gentleman at the University of Auckland in the early 1990s.
  • Runs on Windows, macOS, and Linux.
  • Widely used in academia, industry, government, and research around the world.
  • Supports data analysis, visualization, machine learning, and reproducible research through thousands of contributed packages.

How Does R Look Like?

Why R?

  • Designed for statistics. Created by statisticians for statistical computing and education.
  • Excellent graphics. Create publication-quality figures with packages such as ggplot2.
  • Large scientific community.
    • How many packages?
    • 20,000+ packages on CRAN
  • Open source. Free to use, free to share, and free to modify.
  • Reproducible research. Analysis, figures, and reports can be generated from a single source.

Evolution of Statistical Computing

R Ecosystem

R is much more than a programming language.

  • R: The programming language
  • CRAN: Repository of 20,000+ contributed packages
  • RStudio: An integrated development environment (IDE) for R
  • RMarkdown / Quarto: publishing systems for reports, slides, websites, and books
  • Git & GitHub: Version control and collaboration (optional but highly recommended)

Today we’ll use: R + RStudio + Quarto

Getting Started with R

To use R effectively, we need three pieces of software:

  1. R: the programming language. The engine.

  2. RStudio (recommended). The dashboard.

    • Where we write and run R code.

  3. Quarto (optional but highly recommended). The publishing system.

    • Where we create reproducible reports and presentations.

Today’s workflow: R → RStudio → Quarto

Installing the Software

Installation order: R → RStudio → Quarto

  1. R
    • The programming language.
    • Everything else depends on it. If R is not installed, RStudio will not work.
  2. RStudio
    • Detects and uses your R installation
  3. Quarto (optional)
    • Works with R and RStudio to create reports, slides, and websites

RStudio

What Is RStudio?

  • RStudio is an integrated development environment (IDE) for R.

  • Easy to use: write, run, and debug R code in one place.

  • Organized workspace: editor, console, environment, plots, files, and help.

  • Productivity tools: syntax highlighting, code completion, project management, and package management.

  • Works seamlessly with Quarto to create reports, presentations, and websites.

How Does RStudio Look Like?

Why RStudio?

  • An integrated development environment (IDE) for writing, running, and debugging R code.

  • User-friendly interface with separate panes for the script editor, console, environment, plots, and files.

  • Improves productivity by providing syntax highlighting, code completion, project management, and package management.

  • Works seamlessly with R and Quarto to create reproducible reports, presentations, and websites.

  • Free, open source, and running on Windows, macOS, and Linux.

RStudio Ecosystem

RStudio is more than an editor. It integrates with many tools

  • Git & GitHub
  • Quarto
  • Python
  • SQL
  • Jupyter Notebooks

Today we’ll focus on Quarto, which allows us to combine text, code, figures, and results into a single document.

From Code to Communication

Writing code is only part of data science. We also need to communicate our work. Quarto allows us to combine

  • text
  • R code
  • tables
  • figures

into one reproducible document.

Next, let’s learn Quarto.

Quarto

What Is Quarto?

  • Quarto is an open-source scientific and technical publishing system.

  • It combines text, code, figures, and results in a single document.

  • It works with multiple programming languages, including R, Python, and Julia.

  • Quarto is a standalone application that can be used with or without R.

  • We will use Quarto together with R and RStudio.

Why Quarto?

  • Reproducible research: analysis and results are generated from the same source file.

  • Easy to update: changing the data automatically updates tables and figures.

  • Professional output: produce reports, presentations, websites, and books.

  • Works seamlessly with RStudio.

What Can Quarto Create?

Quarto can generate

  • PDF reports
  • HTML reports
  • Reveal.js presentations
  • Websites
  • Books

These lecture slides were created with Quarto!

Anatomy of a Quarto Document

RStudio + Quarto

RStudio makes Quarto easy to use.

  • Edit a .qmd file.
  • Write text using Markdown.
  • Add R code.
  • Click Render to produce the final document.

Summary

Today we introduced three essential tools:

  • R computes.
  • RStudio helps us write and organize code.
  • Quarto communicates results.

Together they form a modern workflow for data science.

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