3 Installing Core Tools

Before you can begin your journey in data science and statistical analysis, you need to set up your computing environment with the essential tools. This chapter guides you through installing R, RStudio, LaTeX, and command-line tools on Mac, Windows, and Linux systems.

3.1 Overview of Required Software

The core tools you will need throughout this course include:

Tool	Purpose
R	Statistical computing and graphics
RStudio	Integrated development environment (IDE) for R
LaTeX	Document preparation system for typesetting
Quarto	Scientific publishing system (included with RStudio)
Command-line tools	Unix shell access for file management and scripting

3.2 Installing R

R is the foundation of our statistical computing environment. It must be installed before RStudio.

Mac

Visit the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/
Click “Download R for macOS”
Download the latest .pkg file appropriate for your Mac:
- For Apple Silicon Macs (M1/M2/M3): Download the arm64 version
- For Intel Macs: Download the x86_64 version
Open the downloaded file and follow the installation prompts
R will be installed in your Applications folder

Checking Your Mac’s Processor

Click the Apple menu () → “About This Mac”. If you see “Apple M1” or similar, you have an Apple Silicon Mac. If you see “Intel”, you have an Intel Mac.

Windows

Visit CRAN: https://cran.r-project.org/
Click “Download R for Windows”
Click “base”
Click the download link for the latest version
Run the downloaded .exe installer
Accept the default options during installation
R will be added to your Start menu

Linux (Ubuntu/Debian)

Open a terminal and run:

# Update package index
sudo apt update

# Install R
sudo apt install r-base r-base-dev

# Verify installation
R --version

For other Linux distributions, consult the CRAN documentation for specific instructions.

3.3 Installing RStudio

RStudio provides an integrated development environment that makes working with R much more convenient. It includes a code editor, console, file browser, and many other tools.

All Platforms

Visit the RStudio download page: https://posit.co/download/rstudio-desktop/
The website should automatically detect your operating system
Click the download button for your platform
Run the installer:
- Mac: Open the .dmg file and drag RStudio to your Applications folder
- Windows: Run the .exe installer and follow the prompts
- Linux: Install the .deb or .rpm package using your package manager

Verifying the Installation

Open RStudio (not R directly)
In the Console pane, type R.version and press Enter
You should see version information displayed

# Check R version
R.version.string

# Check that common packages can load
library(stats)

3.4 Installing LaTeX

LaTeX is used for creating beautifully typeset documents, particularly those containing mathematical equations. You have two main options: a full LaTeX distribution or the lightweight TinyTeX.

Option 1: TinyTeX (Recommended)

TinyTeX is a minimal LaTeX distribution that works well with R and Quarto. It automatically installs missing packages as needed.

In RStudio, open the Console and run:

# Install tinytex package
install.packages("tinytex")

# Install TinyTeX distribution
tinytex::install_tinytex()

This process may take several minutes. Once complete, restart RStudio.

Option 2: Full LaTeX Distribution

If you prefer a complete LaTeX installation:

Mac:

Download MacTeX from https://www.tug.org/mactex/
Run the installer (this is a large download, approximately 4 GB)
Restart your computer after installation

Windows:

Download MiKTeX from https://miktex.org/download
Run the installer
During installation, choose “Yes” for automatic package installation
Restart your computer

Linux:

# Ubuntu/Debian
sudo apt install texlive-full

# Or for a smaller installation
sudo apt install texlive texlive-latex-extra texlive-fonts-recommended

Verifying LaTeX Installation

In RStudio, run:

# Check if LaTeX is available
tinytex::is_tinytex()

# Or check the LaTeX path
Sys.which("pdflatex")

3.5 Installing Command-Line Tools

Mac

macOS has a Unix foundation, so command-line tools are partially available by default. However, you should install the full Xcode Command Line Tools:

Open Terminal (Applications → Utilities → Terminal)
Type the following command and press Enter:

xcode-select --install

A dialog will appear asking to install the tools—click “Install”
Wait for the installation to complete (may take 5-10 minutes)

Alternatively, if you plan to develop software, you can install the full Xcode from the Mac App Store.

Windows

Windows does not natively include Unix command-line tools, but you have several options:

Option 1: Windows Subsystem for Linux (WSL) - Recommended

WSL allows you to run a full Linux environment within Windows:

Open PowerShell as Administrator (right-click Start → Windows Terminal (Admin))
Run:

wsl --install

Restart your computer when prompted
After restart, Ubuntu will install automatically
Create a username and password when prompted
You now have access to a full Linux terminal

Option 2: Git Bash

A lighter alternative that provides basic Unix commands:

Download Git for Windows: https://git-scm.com/download/win
Run the installer
Select “Use Git from the Windows Command Prompt” during installation
Git Bash will be available from your Start menu

Linux

Linux distributions come with a full suite of command-line tools by default. Open your terminal application to access them.

3.6 Installing Additional R Packages

Once R and RStudio are installed, you should install the tidyverse collection of packages:

# Install tidyverse (may take several minutes)
install.packages("tidyverse")

# Install additional useful packages
install.packages(c("knitr", "rmarkdown", "quarto", "devtools"))

# For this course, also install
install.packages(c("pwr", "car", "lme4", "gapminder"))

Package Installation

Package installation only needs to be done once. After installation, you load packages in each R session using library().

3.7 Installing Quarto

Quarto is a scientific and technical publishing system that works with R, Python, and other languages. Recent versions of RStudio include Quarto, but you can also install it separately.

All Platforms

Visit https://quarto.org/docs/get-started/
Download the installer for your operating system
Run the installer

Verifying Quarto Installation

In RStudio’s Terminal pane:

quarto --version

Or create a new Quarto document in RStudio (File → New File → Quarto Document) and verify it renders correctly.

3.8 Troubleshooting Common Issues

R and RStudio

Problem	Solution
RStudio cannot find R	Reinstall R, then reinstall RStudio
Package installation fails	Check your internet connection; try `install.packages("name", dependencies = TRUE)`
“Package not available” error	Update R to the latest version

LaTeX

Problem	Solution
PDF compilation fails	Run `tinytex::tlmgr_update()` to update packages
Missing `.sty` file	Run `tinytex::tlmgr_install("package-name")`
TinyTeX installation hangs	Check firewall settings; try installing behind a different network

Command Line

Problem	Solution
“Command not found” errors	Verify the tool is installed; check your PATH environment variable
WSL installation fails	Enable virtualization in BIOS; run Windows Update
Permission denied	Use `sudo` on Mac/Linux; run as Administrator on Windows

3.9 Keeping Software Updated

Regularly update your tools to get bug fixes and new features:

R and RStudio: - Check for RStudio updates: Help → Check for Updates - Update R by downloading the latest version from CRAN

R Packages:

# Update all installed packages
update.packages(ask = FALSE)

TinyTeX:

tinytex::tlmgr_update()

Command-line tools:

# Mac (with Homebrew)
brew update && brew upgrade

# Ubuntu/Debian Linux
sudo apt update && sudo apt upgrade

# Windows (WSL)
sudo apt update && sudo apt upgrade

3.10 Summary

You now have a complete scientific computing environment:

R provides the statistical computing foundation
RStudio offers a powerful integrated development environment
LaTeX/TinyTeX enables professional document typesetting
Command-line tools provide essential utilities for file management and scripting
Quarto supports reproducible scientific publishing

With these tools installed, you are ready to begin learning data science and statistical analysis. In the following chapters, we will explore each of these tools in depth.

3.11 Practice Exercises

Exercise I.1: Verify Your Installation

Open RStudio and run sessionInfo() to see your R configuration
Install the tidyverse package if you have not already
Create a new Quarto document and render it to PDF
Open a terminal and run pwd (Mac/Linux) or cd (Windows) to verify command-line access

Exercise I.2: Explore RStudio

Familiarize yourself with the four main panes in RStudio
Try the keyboard shortcut Ctrl+Enter (Windows/Linux) or Cmd+Enter (Mac) to run code
Create and save an R script (.R file)
Access the built-in help by typing ?mean in the console

# Installing Core Tools {#sec-installing-tools} ```{r} #| echo: false #| message: false library(tidyverse) theme_set(theme_minimal()) ``` Before you can begin your journey in data science and statistical analysis, you need to set up your computing environment with the essential tools. This chapter guides you through installing R, RStudio, LaTeX, and command-line tools on Mac, Windows, and Linux systems. ## Overview of Required Software The core tools you will need throughout this course include: | Tool | Purpose | |:-----|:--------| | **R** | Statistical computing and graphics | | **RStudio** | Integrated development environment (IDE) for R | | **LaTeX** | Document preparation system for typesetting | | **Quarto** | Scientific publishing system (included with RStudio) | | **Command-line tools** | Unix shell access for file management and scripting | ## Installing R R is the foundation of our statistical computing environment. It must be installed before RStudio. ### Mac 1. Visit the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/ 2. Click "Download R for macOS" 3. Download the latest `.pkg` file appropriate for your Mac: - For Apple Silicon Macs (M1/M2/M3): Download the arm64 version - For Intel Macs: Download the x86_64 version 4. Open the downloaded file and follow the installation prompts 5. R will be installed in your Applications folder ::: {.callout-tip} ## Checking Your Mac's Processor Click the Apple menu () → "About This Mac". If you see "Apple M1" or similar, you have an Apple Silicon Mac. If you see "Intel", you have an Intel Mac. ::: ### Windows 1. Visit CRAN: https://cran.r-project.org/ 2. Click "Download R for Windows" 3. Click "base" 4. Click the download link for the latest version 5. Run the downloaded `.exe` installer 6. Accept the default options during installation 7. R will be added to your Start menu ### Linux (Ubuntu/Debian) Open a terminal and run: ```bash # Update package index sudo apt update # Install R sudo apt install r-base r-base-dev # Verify installation R --version ``` For other Linux distributions, consult the CRAN documentation for specific instructions. ## Installing RStudio RStudio provides an integrated development environment that makes working with R much more convenient. It includes a code editor, console, file browser, and many other tools. ### All Platforms 1. Visit the RStudio download page: https://posit.co/download/rstudio-desktop/ 2. The website should automatically detect your operating system 3. Click the download button for your platform 4. Run the installer: - **Mac**: Open the `.dmg` file and drag RStudio to your Applications folder - **Windows**: Run the `.exe` installer and follow the prompts - **Linux**: Install the `.deb` or `.rpm` package using your package manager ### Verifying the Installation 1. Open RStudio (not R directly) 2. In the Console pane, type `R.version` and press Enter 3. You should see version information displayed ```r # Check R version R.version.string # Check that common packages can load library(stats) ``` ## Installing LaTeX LaTeX is used for creating beautifully typeset documents, particularly those containing mathematical equations. You have two main options: a full LaTeX distribution or the lightweight TinyTeX. ### Option 1: TinyTeX (Recommended) TinyTeX is a minimal LaTeX distribution that works well with R and Quarto. It automatically installs missing packages as needed. In RStudio, open the Console and run: ```r # Install tinytex package install.packages("tinytex") # Install TinyTeX distribution tinytex::install_tinytex() ``` This process may take several minutes. Once complete, restart RStudio. ### Option 2: Full LaTeX Distribution If you prefer a complete LaTeX installation: **Mac:** 1. Download MacTeX from https://www.tug.org/mactex/ 2. Run the installer (this is a large download, approximately 4 GB) 3. Restart your computer after installation **Windows:** 1. Download MiKTeX from https://miktex.org/download 2. Run the installer 3. During installation, choose "Yes" for automatic package installation 4. Restart your computer **Linux:** ```bash # Ubuntu/Debian sudo apt install texlive-full # Or for a smaller installation sudo apt install texlive texlive-latex-extra texlive-fonts-recommended ``` ### Verifying LaTeX Installation In RStudio, run: ```r # Check if LaTeX is available tinytex::is_tinytex() # Or check the LaTeX path Sys.which("pdflatex") ``` ## Installing Command-Line Tools ### Mac macOS has a Unix foundation, so command-line tools are partially available by default. However, you should install the full Xcode Command Line Tools: 1. Open Terminal (Applications → Utilities → Terminal) 2. Type the following command and press Enter: ```bash xcode-select --install ``` 3. A dialog will appear asking to install the tools—click "Install" 4. Wait for the installation to complete (may take 5-10 minutes) Alternatively, if you plan to develop software, you can install the full Xcode from the Mac App Store. ### Windows Windows does not natively include Unix command-line tools, but you have several options: **Option 1: Windows Subsystem for Linux (WSL) - Recommended** WSL allows you to run a full Linux environment within Windows: 1. Open PowerShell as Administrator (right-click Start → Windows Terminal (Admin)) 2. Run: ```powershell wsl --install ``` 3. Restart your computer when prompted 4. After restart, Ubuntu will install automatically 5. Create a username and password when prompted 6. You now have access to a full Linux terminal **Option 2: Git Bash** A lighter alternative that provides basic Unix commands: 1. Download Git for Windows: https://git-scm.com/download/win 2. Run the installer 3. Select "Use Git from the Windows Command Prompt" during installation 4. Git Bash will be available from your Start menu ### Linux Linux distributions come with a full suite of command-line tools by default. Open your terminal application to access them. ## Installing Additional R Packages Once R and RStudio are installed, you should install the tidyverse collection of packages: ```r # Install tidyverse (may take several minutes) install.packages("tidyverse") # Install additional useful packages install.packages(c("knitr", "rmarkdown", "quarto", "devtools")) # For this course, also install install.packages(c("pwr", "car", "lme4", "gapminder")) ``` ::: {.callout-note} ## Package Installation Package installation only needs to be done once. After installation, you load packages in each R session using `library()`. ::: ## Installing Quarto Quarto is a scientific and technical publishing system that works with R, Python, and other languages. Recent versions of RStudio include Quarto, but you can also install it separately. ### All Platforms 1. Visit https://quarto.org/docs/get-started/ 2. Download the installer for your operating system 3. Run the installer ### Verifying Quarto Installation In RStudio's Terminal pane: ```bash quarto --version ``` Or create a new Quarto document in RStudio (File → New File → Quarto Document) and verify it renders correctly. ## Troubleshooting Common Issues ### R and RStudio | Problem | Solution | |:--------|:---------| | RStudio cannot find R | Reinstall R, then reinstall RStudio | | Package installation fails | Check your internet connection; try `install.packages("name", dependencies = TRUE)` | | "Package not available" error | Update R to the latest version | ### LaTeX | Problem | Solution | |:--------|:---------| | PDF compilation fails | Run `tinytex::tlmgr_update()` to update packages | | Missing `.sty` file | Run `tinytex::tlmgr_install("package-name")` | | TinyTeX installation hangs | Check firewall settings; try installing behind a different network | ### Command Line | Problem | Solution | |:--------|:---------| | "Command not found" errors | Verify the tool is installed; check your PATH environment variable | | WSL installation fails | Enable virtualization in BIOS; run Windows Update | | Permission denied | Use `sudo` on Mac/Linux; run as Administrator on Windows | ## Keeping Software Updated Regularly update your tools to get bug fixes and new features: **R and RStudio:** - Check for RStudio updates: Help → Check for Updates - Update R by downloading the latest version from CRAN **R Packages:** ```r # Update all installed packages update.packages(ask = FALSE) ``` **TinyTeX:** ```r tinytex::tlmgr_update() ``` **Command-line tools:** ```bash # Mac (with Homebrew) brew update && brew upgrade # Ubuntu/Debian Linux sudo apt update && sudo apt upgrade # Windows (WSL) sudo apt update && sudo apt upgrade ``` ## Summary You now have a complete scientific computing environment: - **R** provides the statistical computing foundation - **RStudio** offers a powerful integrated development environment - **LaTeX/TinyTeX** enables professional document typesetting - **Command-line tools** provide essential utilities for file management and scripting - **Quarto** supports reproducible scientific publishing With these tools installed, you are ready to begin learning data science and statistical analysis. In the following chapters, we will explore each of these tools in depth. ## Practice Exercises ::: {.callout-note} ### Exercise I.1: Verify Your Installation 1. Open RStudio and run `sessionInfo()` to see your R configuration 2. Install the tidyverse package if you have not already 3. Create a new Quarto document and render it to PDF 4. Open a terminal and run `pwd` (Mac/Linux) or `cd` (Windows) to verify command-line access ::: ::: {.callout-note} ### Exercise I.2: Explore RStudio 1. Familiarize yourself with the four main panes in RStudio 2. Try the keyboard shortcut `Ctrl+Enter` (Windows/Linux) or `Cmd+Enter` (Mac) to run code 3. Create and save an R script (.R file) 4. Access the built-in help by typing `?mean` in the console :::