1  Introduction

1.1 What is Shell/Terminal?

Shell is a text based application for viewing, handling & manipulating files. It takes in commands and passes them on to the operating system. It is also known as

  • CLI (Command Line Interface)
  • Bash (Bourne Again Shell)
  • Terminal

It is sufficient to know a handful of commands to get started with the shell.

1.2 Choose your setup

Pick the first tier that fits you. All tiers run every command in this book, except where noted.

  • Tier 0 (recommended, zero setup): Posit Cloud project — one-click RStudio in your browser with Linux bash and all book files ready. Nothing to install.
  • Tier 1 (Windows without admin rights): Git Bash inside RStudio — install Git for Windows, then open Git Bash via Tools -> Terminal -> New Terminal in RStudio. Runs everything except sudo chapter (sudo apt-get needs Linux) and the free command in the System Info chapter. For those two chapters, switch to the Tier 0 Posit Cloud project.
  • Tier 2 (Windows with admin rights): WSL2 + Windows Terminal — full Ubuntu Linux on your machine (see below). Runs everything, including sudo and free.
  • macOS: use the built-in Terminal (Zsh since Catalina). Every command in this book works identically in Zsh; see the BSD note below.
  • Linux: use your native Bash terminal.

Do not run book commands in Windows PowerShell. PowerShell aliases ls to Get-ChildItem and curl/wget to Invoke-WebRequest, which reject standard Unix syntax. Always use Git Bash, WSL2, or Posit Cloud on Windows.

Note (macOS: Zsh default and BSD differences). macOS uses Zsh by default (since Catalina, 2019) and ships BSD coreutils instead of GNU coreutils. Book commands work the same, except: head -n -5 (negative counts), sed -i, and the output format of cal and date -d differ from Linux. When a result looks slightly different on your Mac, it is still correct.

1.3 Launch Terminal

Although we recommend the Posit Cloud project so that everyone uses the same environment, you should still know how to launch a terminal on your own machine.

1.3.1 mac

Applications -> Utility -> Terminal

Figure 1.1: Terminal on macOS

1.3.2 Windows

1.3.2.1 Option 1 — Git Bash (no admin rights needed)

Install Git for Windows and launch Git Bash. Inside RStudio, select Tools -> Terminal -> New Terminal; if Git Bash is your configured terminal you can run every Tier 1 chapter right there.

1.3.2.2 Option 2 — WSL2 with Windows Terminal (full Ubuntu Linux)

  1. Open PowerShell as Administrator and run wsl --install -d Ubuntu.
  2. Reboot when prompted, then launch Ubuntu and create your Linux user.
  3. Install Windows Terminal and open an Ubuntu tab.

You can learn more about the Windows Subsystem for Linux here.

1.3.3 Linux

  • Applications -> Accessories -> Terminal
  • Applications -> System -> Terminal
Figure 1.2: Terminal on Linux

1.3.4 RStudio Terminal

RStudio introduced the terminal with version 1.1.383. The terminal tab is next to the console tab. If it is not visible, use any of the below methods to launch it

  • Shift + Alt + T
  • Tools -> Terminal -> New Terminal

Note, the terminal depends on the underlying operating system. To learn more about the RStudio terminal, see the terminal pane documentation in RStudio (Tools -> Terminal). In this book, we will use the RStudio terminal on Posit Cloud to ensure that all users have access to Linux bash. You can try all the commands used in this book on your local system as well except in case of Windows users.

Figure 1.3: RStudio terminal

1.4 Prompt

As soon as you launch the terminal, you will see the hostname, machine name and the prompt. In case of mac & Linux users, the prompt is $. For Windows users, it is >.

OS Prompt
macOS $
Linux $
Windows >
Figure 1.4: Anatomy of the shell prompt

1.5 Get Started

To begin with, let us learn to display

  • basic information about the user
  • the current date & time
  • the calendar
  • and clear the screen.
Command Description
whoami Who is the user?
date Get date, time and timezone
cal Display calendar
clear Clear the screen

whoami prints the effective user id i.e. the name of the user who runs the command. Use it to verify the user as which you are logged into the system.

whoami
runner

date will display or change the value of the system’s time and date information.

date
Mon Oct  5 19:10:18 UTC 2026

cal will display a formatted calendar and clear will clear all text on the screen and display a new prompt. You can clear the screen by pressing Ctrl + L as well.

cal
    October 2026      
Su Mo Tu We Th Fr Sa  
             1  2  3  
 4  5  6  7  8  9 10  
11 12 13 14 15 16 17  
18 19 20 21 22 23 24  
25 26 27 28 29 30 31

In R, we can get the user information from Sys.info() or whoami() from the whoami package. The current date & time are returned by Sys.date() & Sys.time(). To clear the R console, we use Ctrl + L.

Command R
whoami Sys.info() / whoami::whoami()
date Sys.date() / Sys.time()
cal
clear Ctrl + L

1.6 Help/Documentation

Before we proceed further, let us learn to view the documentation/manual pages of the commands.

Command Description
man Display manual pages for a command
whatis Single line description of a command

man is used to view the system’s reference manual. Git Bash ships no manpages, so if man is unavailable in your terminal, append --help to any command instead (works everywhere) and consult tldr.sh for practical examples.

man ls
ls --help | head -n 12
Usage: ls [OPTION]... [FILE]...
List information about the FILEs (the current directory by default).
Sort entries alphabetically if none of -cftuvSUX nor --sort is specified.

Mandatory arguments to long options are mandatory for short options too.
  -a, --all                  do not ignore entries starting with .
  -A, --almost-all           do not list implied . and ..
      --author               with -l, print the author of each file
  -b, --escape               print C-style escapes for nongraphic characters
      --block-size=SIZE      with -l, scale sizes by SIZE when printing them;
                             e.g., '--block-size=M'; see SIZE format below

whatis displays short manual page descriptions (each manual page has a short description available within it). Like man, it needs the system manual database, so it is shown but not executed here.

whatis ls

You will find tldr.sh very useful while exploring new commands and there is a related R package, tldrrr as well.

# devtools::install_github("kirillseva/tldrrr")
tldrrr::tldr("pwd")

1.7 Exercises

  1. Run whoami, then date, then cal one after another in your terminal. For each command, write down in one sentence what was displayed. Then run clear (or press Ctrl + L) and confirm you get a fresh empty prompt.
  2. Run ls --help | head -n 12. Identify one option flag mentioned there and write down what the help text says it does. Then try man ls — note whether it opens a manual page or reports no manual on your system (Git Bash ships no manpages; --help is the fallback).
  3. Visit tldr.sh in a browser (or run tldr ls if installed) and find one practical example for ls you had not seen in this chapter.

Worked solutions in solutions/introduction.md (attempt first).