Creating your personal website using Quarto

Published

August 5, 2022

Modified

June 11, 2024


This document was originally developed as teaching material for the Bren School of Environmental Science & Management’s Master of Environmental Data Science (MEDS) program. Beginning Fall 2024, these materials will be taught as a part of a 2-unit course offered at Bren. You can find these, along with other related materials, linked on the course website.

What is Quarto?

Quarto is a publishing system built on Pandoc that allows users to create dynamic content using R, Python, Julia, and ObservableJS (with plans to add more languages too!).

R users have long loved RMarkdown for combining prose, code, and outputs into single “knitted” documents. Quarto extends all of RMarkdown’s best features (plus many more!) to additional languages.

If you’re already an avid RMarkdown user, great news! RMarkdown (.rmd) and Quarto Markdown (.qmd) files look super similar:

  • document-level metadata and configurations are included in the document’s YAML (denoted by the --- gates at the top of the document)
  • code is written inside executable code chunks
  • prose is written in the body of the document

There are some slight differences to be aware of:

  • some YAML option names differ between the two document types (e.g. output in .rmd vs. format in .qmd)
  • chunk-level execution options are are written within with code block braces (e.g. ```{r echo=FALSE}) in .rmd files, and written below code block braces following hash pipes, |# (e.g. |# echo: false) in .qmd files
  • booleans are capitalized in YAML and chunk-level metadata in .rmd files (e.g. FALSE) and lowercase in .qmd files (e.g. false)
  • you Knit .rmd files and Render .qmd files to convert your work to your desired output type (e.g. .html)

They also look pretty similar when knitted/rendered. Below is a side-by-side comparison of a knitted .rmd file and a rendered .qmd file (both as .html files):

A schematic representing the multi-language input (e.g. Python, R, Observable, Julia) and multi-format output (e.g. PDF, html, Word documents, and more) versatility of Quarto.

Palette Art by Allison Horst. Be sure to check out the rest of Allison’s seriously cute Quarto penguin art in the #rstudioconf2022 keynote talk, Hello Quarto, by Julie Lowndes & Mine Çetinkaya-Rundel!

You can explore Quarto’s documentation to learn more about creating documents, websites, blogs, books, slides, dashboards, etc.

Do I need to use Quarto to build my website?

Nope! There are a number of R-based tools that make building websites and blogs fun and easy, including the still-widely-used {blogdown} and {distill} packages.

Alternatively, you can skip R altogether and build really beautiful sites using HTML templates (check out this tutorial by NCEAS’ Science Communication and Policy Officer, Alex Phillips) or a variety of static site generators (e.g. Hugo, Jekyll).

That said, Quarto has the data science community abuzz – it’s versatile, user-friendly, and looks pretty great out-of-the-box (while still being customizable), and there’s an ever-growing number of excellent resources (see Mickaël Canouil’s awesome-quarto as a starting point) to help you on your own Quarto journey.

Create the scaffolding for your website

Before getting started…

To follow along, you’ll need:

  • R & RStudio installed
  • Quarto installed – Quarto is now included with RStudio v2022.07.1+ i.e. no need for a separate download/install if you have the latest version of RStudio
  • A GitHub account
  • Git installed / configured

Please refer to the MEDS Installation Guide for detailed setup instructions (follow steps 1-7).

This document reviews two ways to get started with using Quarto to build your website.

  1. R Project Using the RStudio IDE
  2. Terminal Through the command line

The order of operations is slightly different depending on which approach you decide to take, but the concepts remain the same.

Why use RStudio to set up your Quarto website?

  • It’s super easy to do with the click of just a few buttons! Remember, the commands we type out in our Terminal window underlie the buttons we click on in the RStudio IDE – RStudio simply provides a user-friendly interface for executing those commands.

Steps:

  1. Create a new R project with some necessary website files. Start by opening up RStudio and clicking on the A blue cube symbol with 'R' in the center is on the left. To the right are the words 'Project: (None)' in white, with a downward facing arrow, signifying a drop down menu button in the top right corner. Select New Project…

Choose New Directory, then Quarto Website.

Throughout this document, we’ll use the words directory and folder interchangeably.

And finally, fill out the Directory name: field (this is the name of your R project, and eventually, your remote (i.e. GitHub) repo name – Important: see note below re: naming!), and choose where to save your directory to using the Browse button. Click Create Project.

Name your project YourGitHubUsername.github.io if you plan to deploy using GitHub pages

Because we’ll be using GitHub pages to publish / host our websites, it’s recommended that you name your project YourGitHubUsername.github.io (you’re allowed one user website with the github.io suffix) – for example, the project / GitHub repository, which contains the code for my personal website, is named samanthacsik.github.io. Otherwise, name it something reasonable (this will become the slug for your site if publishing with GitHub pages, so choose carefully). I’m calling my project mysite just for tutorial purposes only – you should definitely give yours a more practical / creative name.

Organizing R projects / git repositories

There are lots of differing opinions on how to keep your R projects / git repositories organized on your computer. I personally save all of mine to a folder called git in my computer’s (Mac) home directory (e.g. Users/samanthacsik/git/) so everything is in one place.

  • You should now see a folder called mysite (or whatever you named your Quarto project) with a series of files (_quarto.yml, about.qmd, index.qmd, styles.css) that provide the scaffolding for your website in the Files tab (in the bottom right panel in RStudio, if you haven’t altered the pane layout).

When you create a new Quarto website, a handful of files are generated by default:

  1. index.qmd renders your website’s landing page. Whatever you add to this file will be the first content visitors see when they visit your site. Update the content of index.qmd (or any other website page) using markdown and / or HTML (you can mix and match both on the same page), add and execute code chunks and embed outputs, etc. Importantly, do not change the name of index.qmd – this is the default / expected name given to website landing / home pages. If you change the name of this file, you risk breaking your (eventual) deployment.

  2. about.qmd is a regular ’ole website page. You’re able to change both the name of this file (e.g. change about.qmd to my-new-name.qmd) and / or the title of the file by updating its YAML – by default, the YAML only includes a title:

about.qmd
---
title: "About"
---
  • YAML is a human-readable data serialization language, which is commonly used for creating configuration files. Quarto recognizes lots of different YAML options for controlling the appearance and behavior of your individual website pages. YAML is always written at the top of a .qmd file and is denoted by a pair of “gates”, ---.
  1. _quarto.yml is your website configuration file. Any document rendered within your project directory will automatically inherit the metadata defined in this project-level configuration file (though you can control metadata on a page-by-page basis by making edits to an individual page’s YAML, which will override any options specified in _quarto.yml). Importantly, this is where you define your website’s structure (e.g. your navbar, sidebar, footer, etc.). By default, your file should look similar to this:
_quarto.yml
project: 
  type: website

website:
  title: "OHI-methods-EXAMPLE"
  navbar:
    left:
      - href: index.qmd
        text: Home
      - about.qmd

format:
  html:
    theme: cosmo
    css: styles.css
    toc: true
  1. styles.css is a stylesheet, where you can write CSS rules to alter the appearance of your website. We’ll actually create and use a different type of stylesheet (called a “sassy css file”, .scss) in a bit.

  2. .gitignore is a place where we can specify any files that we don’t want Git to track (i.e. that we want Git to ignore). This is not a “Quarto thing,” but rather a valuable file that lives inside git directories. One common use is to add any large data files that you don’t want to accidentally push to GitHub (GitHub isn’t designed to handle LARGE files).

  3. The _site/ directory is where all of your rendered HTML (and other important) files live. When you render your site, Quarto takes all of your .qmd files and converts them to .html files, and saves them to this folder (which is important because web browsers don’t know how to read .qmd files, but do know how to read .html files). We’re actually going to change the name of this folder once we configure our website for deployment, but _site is the default name that Quarto uses (we can leave as-is, for now). You don’t want to physically edit or move any files inside this directory (if you want to make a change to your website, update the .qmd or _quarto.yml file, then re-render).

  1. Preview your very basic, but functional website by typing the following command in the Terminal:
Terminal
quarto preview
  • Your site preview should open up in your browser. Quit your preview by clicking the Stop button in the top right corner of your Terminal.

quarto preview makes it easy to quickly view iterative changes

Running quarto preview launches a preview of your website in a browser window. So long as you leave the preview running, it will update each time you make and save changes to website files (which makes iterating on your work really easy!).

  1. Install the {usethis} package, if necessary. At this point you’ve created a directory (folder) with the website scaffolding files, but it’s not yet being tracked by git, nor is it connected to a remote repository on GitHub. We can use the {usethis} package to help us set this up. First, install the {usethis} package if you don’t already have it. Do so by running the following in your console:
Console
install.packages("usethis")

We’re using the {usethis} workflow here because (1) it’s super easy, and (2) because it’s worth knowing that the {usethis} package exists if you haven’t explore it already! Read more about the tooling this package offers on the usethis documentation.

  1. Initialize your R Project folder as a git repository using usethis::use_git(): In the Console, run usethis::use_git() to create a local git repository. Choose yes when asked if it’s okay to commit any uncommitted files. If asked to restart R, choose yes. Once complete, you should see the Git tab appear in your top left pane in RStudio.

When we initialize our R project, mysite/ (or YourGitHubUsername.github.io/), as a git repository using usethis::use_git(), a hidden .git/ folder is created within that project folder. This hidden .git/ folder is the git repository. As you use git commands (or RStudio’s GUI buttons) to capture versions or “snapshots” of your work, those versions (and their associated metadata) get stored within the .git/ folder. This allows you to access and / or recover any previous versions of your work. If you delete .git/, you delete your project’s history. Here is an example website repository, represented visually:

  1. Create an upstream remote repository (i.e. GitHub repo) using usethis::use_github(). Running usethis::use_github() in the Console will open up your web browser to your new remote repository on GitHub – it should already have the same name as your local git repo / R project.

Git is a version control software designed to manage the versioning and tracking of source code files and project history. It operates locally on your computer, allowing you to create repositories and track changes. It works directly with files on your computer, and is primarily used through a command line interface (e.g. Terminal, Git Bash). Some GUIs (Graphical User Interfaces), like RStudio, provide user-friendly buttons to execute git commands as well.

GitHub is a cloud-based hosting service that allows you to manage Git repositories – as Jenny Bryan describes in her book Happy Git and GitHub for the useR, hosting services like GitHub “provide a home for your Git-based projects on the internet.” GitHub provides us with the tools for storing, managing, and collaborating on git repositories. It also offers additional features on top of Git, like issue tracking, project management tools, code review, pull requests, and more.

The illustration below depicts how we use Git and GitHub together to version control our work locally (e.g. on our computer(s)), and send versions to and receive updates from a remote (i.e. GitHub) repository.

A basic git workflow represented as two islands, one with "local repo" and "working directory", and another with "remote repo." Bunnies move file boxes from the working directory to the staging area, then with Commit move them to the local repo. Bunnies in rowboats move changes from the local repo to the remote repo (labeled "PUSH") and from the remote repo to the working directory (labeled "PULL").

Illustration by Allison Horst

After running usethis::use_github() your browser window should open up to your new GitHub repository and look similar to the browser above.
  1. Check the name of your default branch (the only branch you should have at the moment) – that is, the branch that all changes eventually get merged back into (if you’re building a website, this branch is typically the one you’ll want to deploy). There are multiple ways to check this – here are two easy options:

    1. Open RStudio’s Terminal window (next to the Console) and run either git branch (this prints all local branches and highlights the one that you’re currently on) or git status (the first printed line should say On branch <branch_name>).

    2. Click on the Git tab in the top right pane of RStudio. Next to the A white diamond with two purple squares, one directly above and one directly to the right, connected to the diamond by a line. symbol, you should see a dropdown menu that displays the name of your current branch.

  2. If your current branch is named master, update the name to main. (If your branch is named main, you’re good to go! You can skip this step continue to the next section on publishing your site with GitHub Pages. In the console, run usethis::git_default_branch_rename(from = "master", to = "main") to update your default branch name. Confirm that it updated (a) locally by running git status again in your Terminal – the first printed line should now read, On branch main, and (b) on your remote by refreshing your GitHub repo (in your web browser) – you should see the updated default branch name at the top of your repo.

The above instructions follow the “create local R project (and initialize as a git repo) first > create upstream remote repo (on GitHub) second workflow. However, if you already have a remote GitHub repository that you want to use for your website, clone the GitHub repo, then run the following command in the command line:

Command Line
quarto create-project --type website

This adds the the default files (_quarto.yml, .gitignore, index.qmd, about.qmd, styles.css) for getting started on your website.

You may also use this approach if you already have an existing local directory of documents or R project that you’d like to use as the directory for your website. First, navigate to that directory / open that R project, then run the above command in the command line.

Why use the command line to set up your Quarto website?

  • You’ll start to get more comfortable working in a command line interface (CLI)
  • You’re able to interact with Quarto via the command line regardless of which language (R, Python, Julia, ObservableJS) or IDE (Integrated Development Environment) you might find yourself working with

Steps:

  1. Open up your command line interface (often Terminal on Macs or Git Bash on Windows)

  2. Navigate to the location on your computer where you’d like your project to live. Determine where you are in your file system using pwd (print working directory). Use cd (change directory) to navigate your file system to wherever you’d like your project to live.

Organizing R projects / git repositories

There are lots of differing opinions on how to keep your R projects / git repositories organized on your computer. I personally save all of mine to a folder called git in my computer’s (Mac) home directory (e.g. Users/samanthacsik/git/) so everything is in one place.

  1. Create the scaffolding (i.e. folder structure & necessary files) for your website by running the following in the command line (substitute mysite with whatever name you want to give your repo):
Command Line
quarto create-project mysite --type website 

Throughout this document, we’ll use the words directory and folder interchangeably.

Name your project YourGitHubUsername.github.io if you plan to deploy using GitHub pages

Because we’ll be using GitHub pages to publish / host our websites, it’s recommended that you name your project YourGitHubUsername.github.io (you’re allowed one user website with the github.io suffix) – for example, the project / GitHub repository, which contains the code for my personal website, is named samanthacsik.github.io. Otherwise, name it something reasonable (this will become the slug for your site if publishing with GitHub pages, so choose carefully). I’m calling my project mysite just for tutorial purposes only – you should definitely give yours a more practical / creative name.

Use pwd to see your current working directory. Use cd to change directories.

Create a new quarto project using the quarto create-project your_project_name --type website commands.
  • If you cd into your new mysite directory, and use the ls command to list out all the contents of that directory, you should see a series of files (_quarto.yml, about.qmd, index.qmd, styles.css) that provide the scaffolding for your website. For example:
Command Line
# print current working directory
(base) Samanthas-MacBook-Air:git samanthacsik$ pwd 
/Users/samanthacsik/git

# move into `mysite` directory
(base) Samanthas-MacBook-Air:git samanthacsik$ cd mysite/ 
(base) Samanthas-MacBook-Air:mysite samanthacsik$ 

# list out all files in the `mysite` directory
(base) Samanthas-MacBook-Air:mysite samanthacsik$ ls
_quarto.yml _site       about.qmd   index.qmd   styles.css
  • Alternatively, you can use Finder (Mac) or Windows Explorer (Windows) to view your new directory and files.

When you create a new Quarto website, a handful of files are generated by default:

  1. index.qmd renders your website’s landing page. Whatever you add to this file will be the first content visitors see when they visit your site. Update the content of index.qmd (or any other website page) using markdown and / or HTML (you can mix and match both on the same page), add and execute code chunks and embed outputs, etc. Importantly, do not change the name of index.qmd – this is the default / expected name given to website landing / home pages. If you change the name of this file, you risk breaking your (eventual) deployment.

  2. about.qmd is a regular ’ole website page. You’re able to change both the name of this file (e.g. change about.qmd to my-new-name.qmd) and / or the title of the file by updating its YAML – by default, the YAML only includes a title:

about.qmd
---
title: "About"
---
  • YAML is a human-readable data serialization language, which is commonly used for creating configuration files. Quarto recognizes lots of different YAML options for controlling the appearance and behavior of your individual website pages. YAML is always written at the top of a .qmd file and is denoted by a pair of “gates”, ---.
  1. _quarto.yml is your website configuration file. Any document rendered within your project directory will automatically inherit the metadata defined in this project-level configuration file (though you can control metadata on a page-by-page basis by making edits to an individual page’s YAML, which will override any options specified in _quarto.yml). Importantly, this is where you define your website’s structure (e.g. your navbar, sidebar, footer, etc.). By default, your file should look similar to this:
_quarto.yml
project: 
  type: website

website:
  title: "OHI-methods-EXAMPLE"
  navbar:
    left:
      - href: index.qmd
        text: Home
      - about.qmd

format:
  html:
    theme: cosmo
    css: styles.css
    toc: true
  1. styles.css is a stylesheet, where you can write CSS rules to alter the appearance of your website. We’ll actually create and use a different type of stylesheet (called a “sassy css file”, .scss) in a bit.

  2. .gitignore is a place where we can specify any files that we don’t want Git to track (i.e. that we want Git to ignore). This is not a “Quarto thing,” but rather a valuable file that lives inside git directories. One common use is to add any large data files that you don’t want to accidentally push to GitHub (GitHub isn’t designed to handle LARGE files).

  3. The _site/ directory is where all of your rendered HTML (and other important) files live. When you render your site, Quarto takes all of your .qmd files and converts them to .html files, and saves them to this folder (which is important because web browsers don’t know how to read .qmd files, but do know how to read .html files). We’re actually going to change the name of this folder once we configure our website for deployment, but _site is the default name that Quarto uses (we can leave as-is, for now). You don’t want to physically edit or move any files inside this directory (if you want to make a change to your website, update the .qmd or _quarto.yml file, then re-render).

  1. Preview your very basic, but functional website straight from the command line by typing (you’ll need to navigate to your project directory (e.g mysite/)):
Command Line
quarto preview
  • Your site preview should open up in your browser. Quit your preview by pressing control + C.

quarto preview makes it easy to quickly view iterative changes

Running quarto preview launches a preview of your website in a browser window. So long as you leave the preview running, it will update each time you make and save changes to website files (which makes iterating on your work really easy!).

You can also preview your website from different locations using file paths. You’ll need to supply the path to your website directory when previewing from a different location. For example, if my Quarto website directory is at Users/samanthacsik/git/mysite, but I am one directory above in Users/samanthacsik/git, I can run quarto preview mysite. Alternatively I could provide the full path quarto preview User/samanthacsik/git/mysite or relative path quarto preview ~/git/mysite, no matter which directory I’m currently in.

  1. Initialize your project as a git repository. At this point you’ve created a directory (folder) containing some important website scaffolding files, but they’re not yet being tracked by Git. First be sure to cd into your website folder. Then, initialize this folder as a git repository using the git init command in the terminal window.
Command Line
git init

When we initialize our R project, mysite/ (or YourGitHubUsername.github.io/), as a git repository using git init, a hidden .git/ folder is created within that project folder. This hidden .git/ folder is the git repository. As you use git commands (or RStudio’s GUI buttons) to capture versions or “snapshots” of your work, those versions (and their associated metadata) get stored within the .git/ folder. This allows you to access and / or recover any previous versions of your work. If you delete .git/, you delete your project’s history. Here is an example website repository, represented visually:

  1. Check the name of your default branch – that is, the branch that all changes eventually get merged back into (if you’re building a website, this branch is typically the one you’ll want to deploy). Run git status in the command line to identify the name of your default branch (this should be the only branch you have at the moment). Running git status will return something that looks like this, where the first line tells you which branch you’re currently on:
Command Line
(base) Samanthas-MacBook-Air:mysite samanthacsik$ git status
On branch master

No commits yet

Untracked files:
  (use "git add <file>..." to include in what will be committed)
    .quarto/
    _quarto.yml
    _site/
    about.qmd
    index.qmd
    styles.css

nothing added to commit but untracked files present (use "git add" to track)

I use this command often when working on the command line to double check that I’m actually where I think I am, and to see tracked files and untracked or changed files. It’s a good habit to run git status after switching branches or before / after adding files to commit.

  1. If your default branch is named master, update the name to main. If your default branch (you should only have one branch so far, the default branch) is already named main, you can head straight to step 8. Otherwise, choose your workflow below based on your Git version (check your version by running git --version in the command line):

You can update the default branch to main by running the following line in the command line:

Command Line
git config --global init.defaultBranch main

This sets the default branch name to main for any new repositories you create moving forward (it does not rename branches in existing projects).

You can double check that this worked by typing out the git status command again. The first printed line should now read, On branch main.

Rename the default branch as main by running the following line in the command line:

Command Line
git branch -m master main

The -m attribute is used to rename the branch without affecting the branch’s history.

This sets the default branch name to main ONLY for this repository (so you’ll need to do this with any new local git repositories that you create.

You can double check that this worked by typing out the git status command again. The first printed line should now read, On branch main.

The racist “master” terminology for git branches motivates us to update our default branch to “main” instead.

There is a push across platforms and software to update this historical default branch name from master to main. GitHub has already done so – creating a remote repository first results in a default branch named main. Depending on your version of Git and / or your configuration settings, however, you may need to set update the name manually when creating a local git repository first (as we’re doing here).

  1. Stage / add all of your website’s scaffolding files (analogous to checking the boxes next to your files in RStudio’s Git tab)
Command Line
# this adds all untracked or changed files at once
git add . 

# alternatively, you can add files individually
git add <file_name>
Tip

Use the git status command again to see if your files have been successfully added before committing them – any untracked or changed files that were once printed in red should now appear in green.

…and commit them (analogous to pressing the “Commit” button in RStudio and typing your commit message into the dialog box that appears):

Command Line
git commit -m "initial commit"
  1. Create an empty remote repository on GitHub. At this point, we’ve created a local git repository that contains the basic files needed to build our Quarto website. Now, we need to create a “remote” repository (i.e. a version of your project that is hosted on the internet) on GitHub. There are multiple ways to do this, but we’ll cover the workflow that makes most intuitive sense to me. Login to GitHub, create a new repository, and give it the same name as your local git repository / R Project (e.g. username.github.io).
Do not initialize your remote repository (on GitHub) with a README.md, license, or .gitignore file!

Doing so now can lead to merge conflicts. We can add them after our local and remote repositories have been connected.

Git is a version control software designed to manage the versioning and tracking of source code files and project history. It operates locally on your computer, allowing you to create repositories and track changes. It works directly with files on your computer, and is primarily used through a command line interface (e.g. Terminal, Git Bash). Some GUIs (Graphical User Interfaces), like RStudio, provide user-friendly buttons to execute git commands as well.

GitHub is a cloud-based hosting service that allows you to manage Git repositories – as Jenny Bryan describes in her book Happy Git and GitHub for the useR, hosting services like GitHub “provide a home for your Git-based projects on the internet.” GitHub provides us with the tools for storing, managing, and collaborating on git repositories. It also offers additional features on top of Git, like issue tracking, project management tools, code review, pull requests, and more.

The illustration below depicts how we use Git and GitHub together to version control our work locally (e.g. on our computer(s)), and send versions to and receive updates from a remote (i.e. GitHub) repository.

A basic git workflow represented as two islands, one with "local repo" and "working directory", and another with "remote repo." Bunnies move file boxes from the working directory to the staging area, then with Commit move them to the local repo. Bunnies in rowboats move changes from the local repo to the remote repo (labeled "PUSH") and from the remote repo to the working directory (labeled "PULL").

Illustration by Allison Horst

  1. Connect your remote (GitHub) repository to your local git repository. Your empty GitHub repo conveniently includes instructions for doing so. Copy the code under “push an existing repository from the command line” to your clipboard, paste into the command line, and run.

Command Line
git remote add origin https://github.com/YourGitHubUsername/yourRepoName.git
git branch -M main
git push -u origin main

It does three things:

  • Adds the GitHub repository as the remote repository (i.e. connects your local repo to the remote repo)
  • Renames the default branch to main (if you didn’t complete step 7, this will take care of it for you!)
  • Pushes the main branch to the remote GitHub repository

You should see something similar to this print out, if successful!

Command Line
(base) Samanthas-Air:mysite samanthacsik$ git remote add origin https://github.com/samanthacsik/mysite.git
(base) Samanthas-Air:mysite samanthacsik$ git branch -M main
(base) Samanthas-Air:mysite samanthacsik$ git push -u origin main
Enumerating objects: 42, done.
Counting objects: 100% (42/42), done.
Delta compression using up to 8 threads
Compressing objects: 100% (35/35), done.
Writing objects: 100% (42/42), 311.78 KiB | 15.59 MiB/s, done.
Total 42 (delta 2), reused 0 (delta 0), pack-reused 0
remote: Resolving deltas: 100% (2/2), done.
To https://github.com/samanthacsik/mysite.git
 * [new branch]      main -> main
Branch 'main' set up to track remote branch 'main' from 'origin'.
(base) Samanthas-Air:mysite samanthacsik$ 
  1. Refresh your GitHub repository (in your web browser) to see that your updates have been successfully pushed!

  1. (Optional) Add .gitignore, LICENSE, README.md files, which we chose not to initialize our remote repository with. The touch command can be used to create any file type that we want (just make sure you’re in the desired location – typically, you want to create these in your project’s root directory). For example:
Command Line
touch .gitignore

The above instructions follow the “create local R project (and initialize as a git repo) first > create upstream remote repo (on GitHub) second workflow. However, if you already have a remote GitHub repository that you want to use for your website, clone the GitHub repo, then run the following command in the command line:

Command Line
quarto create-project --type website

This adds the the default files (_quarto.yml, .gitignore, index.qmd, about.qmd, styles.css) for getting started on your website.

You may also use this approach if you already have an existing local directory of documents or R project that you’d like to use as the directory for your website. First, navigate to that directory / open that R project, then run the above command in the command line.

Build & publish your site with GitHub Pages

There are a lots of options to publish your website. We’ll use the GitHub Pages option, which allows you to publish a website from any GitHub repository. To do so, there are a few configuration steps:

  1. Create a file named .nojekyll in your repository’s root directory (e.g. mysite/), which is required to disable some processing of HTML files that GitHub does by default. There are two ways you can do this:

    1. From your Terminal (you can use the RStudio Terminal or a separate command line interface – just make sure you’re in the correct directory) using the following command:
    touch .nojekyll
    1. From RStudio’s File pane by clicking New Blank File > Text File, then typing in .nojekyll.

The touch command can be used to create a new, empty file from the command line. Similarly, RStudio’s Text File button allows you to define and create any file type. Since there’s no default button in RStudio for creating a .nojekyll file, you’ll want to use one of these two approaches.

.nojekyll is a hidden file which won’t visibly appear in your directory. You should see it show up as a file to track with git (either under the Git tab in RStudio, or when you run git status in the command line). You can also view hidden files in Finder (Mac) using the keyboard shortcut Command + Shift + ., or follow these instructions for Windows 10, 8.1, and 7.

  1. Set the output-dir in your _quarto.yml file to docs (it’s easiest to open and edit this from RStudio):
_quarto.yml
project:
  type: website
  output-dir: docs
  
# ~ additional metadata excluded for brevity ~

The output-dir is the directory (i.e. folder) where your rendered .html (and other important) files will automatically be saved to when you “Build” your website (see the next step!) – that is, when you convert all your .qmd files to the .html files that your web browser can interpret / display.

You can delete _site/ if it exists and if you’re publishing with GitHub Pages

If you previewed or built your site before setting output-dir to docs in _quarto.yml, you’ll notice a _site/ directory inside your repository – this is the default output directory name. Because GitHub Pages will expect a docs/ folder to deploy from, you can delete _site/ altogether (and push your deletion, if you’ve already committed / pushed _site/ to GitHub).

  1. Render your website. Click on the Build tab (top left pane in RStudio if you have the default layout), then Render Website (alternatively, you can run quarto render in the Terminal). You should see your minimal, albeit functional, soon-to-be website appear in the Viewer tab. You can click on the A browser window overlaid by an arrow pointing up and angled to the right. button to open your file in your web browser. Note: your website is currently being hosted by your local machine, not at a searchable URL. We’ll get there soon though!

Always “Render Website” before pushing changes that you want to deploy!

Clicking Render Website in the Build tab (or running quarto render in the Terminal) is a necessary pre-deployment (and redeployment) step – it converts all .qmd files to .html and ensures that all website components are stitched together correctly. If you do not render your website before pushing your files, your changes will not deploy.

Note: Previewing your website is different than rendering your website. Previewing alone does not formally prepare all of your website files for deployment.

  1. Send all of your website files from your local git repository to your remote GitHub repository:

    1. Stage your files by checking all the boxes in the Git tab (this is analogous to the git add . command used in the Terminal for staging all files)
    2. Commit your files by clicking the Commit button, adding a commit message, and clicking “Commit” (analogous to git commit -m "my commit message")
    3. Push your files to the remote repository (on GitHub) by clicking the “Push” button with the green upward facing arrow (analogous to git push).
  2. Configure GitHub pages to serve content from the “docs” directory by clicking on the Settings tab in the top menu bar, then the Pages tab from the left-hand menu bar. Make sure that Branch is set to main and that the selected folder is set to /docs. Click Save. Once deployed (this may take a few minutes), your website’s URL will appear inside a box at the top of the page (you may have to try refreshing a few times).

Your website’s URL will appear at the top of the page once you’ve configured GitHub pages to host your Quarto site

A hosted Quarto website! Now time to customize and add content.
Check out the Actions tab on GitHub to view deployment status

See deployment status, time of each deployment, and how long it took to deploy each run. You can also find failed deployments here (yes, it does happen on occasion) and take action on fixing them.

Where you should start changing stuff

Right now, our website is built using Quarto’s default styling. Let’s learn about where things live and how to start customizing some stuff.

Don’t mess with stuff in /docs

When you Render your site (by clicking Build > Render Website), Quarto takes all your .qmd files, converts them to .html files (along with some other important stuff), and saves everything to your /docs folder. Your site now deploys from this folder, so you really don’t want to mess with anything in here directly.

Add content to your landing page (index.qmd)

Do not change the name of index.qmd

This is the default / expected name given to website landing / home pages. If you change the name of this file, you risk breaking your deployment.

index.html (which is built from index.qmd) is the page people will arrive at when navigating to your website – give this landing / home page a makeover by trying out some of the following:

  • Update the YAML title in your index.qmd file. Here, I changed mine from "mysite" to my name, "Samantha Csik"

  • Delete the sample text and begin adding your own content – a great place to start is a short blurb introducing yourself!

My Quarto website home page, which now includes my name and some content, but isn’t super visually pleasing…

Arrange your landing page (index.qmd) using a pre-build template

When the about option is added to a document’s YAML, a special template will be used to layout the content of that page. Choose from one of Quarto’s five built-in templates, each with a slightly different layout style. Some YAML options to play around with:

  • template: choose from Quarto’s built-in template options

  • image (note that this is a document-level option i.e. is not a sub-item of about): supply it the file path to your photo

  • image-width & image-shape: adjust your image’s size and shape (round, rounded, rectangle)

  • links: add buttons with links to your social media pages

index.qmd
---
title: "Samantha Csik"
1image: media/headshot.jpg
2toc: false
about: 
3  template: trestles
4  image-shape: round
  image-width: 20em
5  links:
    - text: LinkedIn
      href: https://www.linkedin.com/in/samanthacsik/
    - text: GitHub
      href: https://github.com/samanthacsik
    - text: Email
      href: mailto:scsik@ucsb.edu
---
        
# page content excluded for brevity ~
1
add a photo by supplying a relative file path & image name (here, headshot.jpg lives in a folder called media/)
2
remove “On this page” menu by setting toc: false
3
use a pre-built template (here, trestles) to update the layout of your landing page (or any page!)
4
set image shape (round, rounded, rectangle) & size
5
add button links to your favorite social media pages (e.g. LinkedIn, GitHub, and even your email – Note the mailto:: ahead of your email address, mailto::youremail.com)

Fun Tip: Install the Font Awesome Extension for Quarto to add free Font Awesome Font Awesome icons to your site! Be sure to check out the icon option when adding linked buttons to your About Page.

My Quarto website after updating my landing page with the built-in trestles template, adding an image, and linked buttons. (Note: using three dashes, ---, creates a page divider, as seen between sections in the screenshot above.) Overall, a big improvement! However, our text is a bit squished in the center of the page – we’ll fix then in the next step.

Quarto’s built-in About Page templates are great for a couple reasons, primarily:

  1. they provide a quick and easy way to create visually-pleasing web pages (particularly website landing pages)
  2. they take care of a lot of the finicky “under-the-hood” styling (e.g. creating “responsive” page elements i.e. automatically rearranging content to fit changing viewport sizes) that would otherwise require a fair bit of CSS knowledge

As you get more comfortable with the Quarto framework and CSS for styling webpages (we’ll learn more about this in a later workshop!), you may decide to build a completely custom webpage layout. The following Quarto websites leverage custom layouts to arrange contents on individual webpages:

I briefly touch on using Bootstrap CSS Grid to build these responsive custom webpage layouts in this blog post. Check out the Quarto documentation to learn more.

Modify website appearance in _quarto.yml

The _quarto.yml file is a configuration file – any document rendered within the project directory will automatically inherit the metadata defined within this file. Some easy updates that make a big difference:

_quarto.yml
project:
  type: website
  output-dir: docs

website:
  navbar:
1    title: "Samantha Csik"
    left:
      - href: index.qmd
        text: Home
      - about.qmd

format:
  html:
    theme: cosmo
    css: styles.css
2    toc: true
3    page-layout: full
1
Give your website a better title (e.g. your name)! This is the text that appears in the top left corner of your website (by default, it appears as your repo name) – when clicked, a user will be brought back to the landing page. Note: I removed my site-level title option and added it instead as a navbar title. Functionally, they appear the same way, but organizationally I think this makes more intuitive sense – if I wanted to add a logo instead of a title, I’d similarly need to place that option beneath navbar.
2
Note that the default toc: true here (in _quarto.yml) renders a navigation menu on all web pages by default (but we can update options on a page-by-page basis e.g. we set toc: false in our index.qmd YAML)
3
Set your page-layout to full so that your page content takes up more of the page width

My website with a new title (see top left corner) and with page-layout set to full, so that content doesn’t appear as squished in the middle of the page.

Add additional pages to your website

In the default Quarto website skeleton, there are two items in the navbar that appear as “Home” and “About” (Note: don’t confuse the special-formatted “About Page” we created in index.qmd with the navbar page currently titled “About”). Those navbar tabs link to two .html files (index.html and about.html) and are automatically rendered when when you Build to /docs. Adding a new page to your website requires two steps:

  1. Create a new .qmd file (from RStudio’s File pane, click Blank File > Quarto Document and save it to your project’s root directory) and add any necessary YAML options, along with any content that you want to appear on that page. Here, I’m creating a new page titled “All of my favorite resources!” and saved it to my root directory as resources.qmd.
resources.qmd
---
title: "All my favorite resources!"
---
  1. Update _quarto.yml by adding your new .qmd to the list of navbar pages. My website’s _quarto.yml file now looks like this:
_quarto.yml
project:
  type: website
  output-dir: docs

website:
  title: "Samantha Csik"
  navbar:
   background: primary
   left:
     - href: index.qmd
       text: Home
     - about.qmd
1     - resources.qmd

format:
  html:
    theme: cosmo
    css: styles.css

editor: visual
1
A newly-added navbar page. Note: The page name, as it appears in the navbar of your website, will be the same as whatever is listed in the title field of that file’s YAML. For example, I have set title: "All my favorite resources!" in the YAML of resources.qmd – this is how it will appear in my website’s navbar. If you’d like to set the navbar name as something other than the page’s title, use the href and text options together (e.g. see how index.qmd is rendered as Home in my website’s navbar).

A newly added navbar page, titled “All of my favorite resources!”

A newly added navbar page, with an alternate navbar title (set using the href and text options together in _quarto.yml)

Change the theme

Update the appearance of your site by choosing from one of the 25 predefined Bootswatch themes. By default, Quarto sites are built using the cosmo theme. Supply just one theme name to the theme option in your _quarto.qmd file:

_quarto.yml
# ~ additional metadata excluded for brevity ~

# supplying just one theme ("minty")
format:
  html:
    theme: minty
    css: styles.css

With theme, ‘minty’, a prebuilt Bootswatch theme

or supply both a dark and a light theme for users to toggle between:

_quarto.yml
# ~ additional metadata excluded for brevity ~

# supplying a light ("minty") and dark ("slate") theme to toggle between
format:
  html:
    theme: 
      light: minty
      dark: solar
    css: styles.css

With light/dark theme options applied; here, the dark theme, which is set to the prebuilt Bootswatch theme theme, slate, is toggled on.
One last reminder to “Render Website” before pushing changes that you want to deploy!

If you’ve made and pushed changes to your website, but you’re not seeing your website actually update, you may have forgotten to Render Website! Try doing so, then commit / push your files again.

Looking forward

You should now have a basic version of your website up and running 🎉 During Fall quarter, we’ll learn how to:

a. customize the appearance of our site using Sass & CSS

b. add a blog and blog posts to our websites

c. continue developing your online “brand”

In the meantime, explore some current student & alumni websites (Note: MEDS class of 2022 used the {distill} package to build their websites) for inspiration, or dig into the Quarto Website documentation if you’re hoping to get started now on further customization.

Additional resources to get you stoked about Quarto

  • Awesome Quarto (GitHub repository of curated Quarto resources), by Mickaël Canouil | GitHub repo

  • Reproducible Authoring with Quarto, by Mine Çetinkaya-Rundel | slides | recording

  • Hello Quarto! A Chat with NASA Openscapes, Co-Hosted with R-Ladies Santa Barbara | blog post | recording

  • rstudio::conf 2022 keynote, Hello Quarto, by Julie Lowndes and Mine Çetinkaya-Rundel | recording

Acknowledgements

Lots of wonderful content and tips included here were borrowed / adapted from Allison Horst’s workshop, Getting started with distill sites – check it out if you’re looking to go the {distill} route! Many thanks to Jim Gardner, who provided super helpful feedback on the flexibility of Quarto’s command line tools. And of course, much gratitude for all those who’ve shared these materials with colleagues, online, etc. – it’s been amazing to receive so many shout outs as folks share their fresh new Quarto sites Face Smile Beam.

Contribute

I’ve learned a lot about Quarto since it was released in 2022, and I continue to discover new things on the regular! If you have suggestions on how to correct, improve, or expand on these instructions, please feel free to file an issue on GitHub GitHub. Alternatively, you may fork this repository, make any suggested changes, and submit a pull request – if you’d like to go this route, I ask that you first open an issue to discuss your ideas with me Face Smile.