Skip to Tutorial Content

## Information

###

## Introduction

###

This tutorial covers material from Chapter 28 Quarto and Chapter 29 Quarto formats in R for Data Science (2e) by Hadley Wickham, Mine Çetinkaya-Rundel, and Garrett Grolemund, although much of the information from Chapter 28 has already appeared in the “RStudio and Github Introduction” tutorial in this package. You will learn the process of creating and organizing the Quarto websites using the Quarto CLI (command line interface) and commands like `quarto create project`, `quarto render`, `quarto preview` and `quarto publish`.

## Creating files

###

Let’s make a Quarto website.

### Exercise 1

Run `quarto --version` from the Terminal. CP/CR.

###

My answer:

    Davids-MBP:r4ds.tutorials dkane$ quarto --version
    bash: quarto: command not found

If it works for you — i.e., if this command returns a Quarto version number — then don’t worry.

This failure is somewhat surprising since RStudio comes bundled with a version of Quarto, but that version is tucked away in a hard-to-use location, usually (on a Mac) something like:

    /Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto

You can see the location on your machine by running `quarto::quarto_path()` at the R Console. Instead of installing a second version of Quarto — and having to deal with all the weird problems which can arise from that — we might just add this location to our PATH. But that can be tricky, so we just install another version of Quarto which will appear on the PATH by default.

### Exercise 2

If `quarto --version` failed in the previous Exercise, install Quarto CLI on your computer. Then, run `quarto --version` again from the Terminal. CP/CR. (You may need to restart RStudio after installing Quarto.)

###

My answer:

    Davids-MBP:r4ds.tutorials dkane$ quarto --version
    1.4.554
    Davids-MBP:r4ds.tutorials dkane$

As long as the version is at least 1.4, you are OK. Again, having Quarto installed in two separate locations is a bit hacky, especially if they are different versions. But this seems a better approach then messing with your PATH.

### Exercise 3

Create a public Github repo (called “first-website”). Make sure to click the “Add a README file” check box. Copy/paste the URL for its Github location.

###

Your answer should look something like:

    https://github.com/davidkane9/first-website

Always start a new data science project with a new Github repo.

### Exercise 4

Connect the `first-website` Github repo to an R project on your computer. Name the R project `first-website` also. Keeping the names of repos/projects aligned makes organization simpler.

You will need to “Terminate Jobs” this tutorial. And you will be placed into the new project after RStudio restarts, as usual. Just restart the tutorial after this happens.

From the Terminal, run `ls`. CP/CR.

###

Your answer should look something like this:

    Davids-MBP:first-website dkane$ ls
    README.md               first-website.Rproj
    Davids-MBP:first-website dkane$

The default README has an “md” suffix to indicate that it is a Markdown document.

### Exercise 5

In the Terminal, run `quarto create project website .`. Don’t forget the `.` at the end of the command. This indicates that the new files should be placed in the current working directory.

Depending on your computer setup, this command will generate require you to answer some questions. Do so as best you can.

If you are asked for a “Title,” use `A New Website`.

If given a choice, choose “rstudio” rather than “vscode.”

This command will usually result in a restart of your RStudio instance. Or it might create a second R instance, also located in the `first-website` directory. If so, close one of the instances. It does not matter which.

CP/CR.

###

Your answer should look like this:

    Davids-MacBook-Pro-2:first-website dkane$ quarto create project website .
    ? Title (website) › A New Website
    Creating project at /Users/dkane/Desktop/projects/first-website:
      - Created _quarto.yml
      - Created .gitignore
      - Created index.qmd
      - Created about.qmd
      - Created styles.css
    Davids-MacBook-Pro-2:first-website dkane$

Quarto is telling you what it did: creating 5 new files and placing them in the current directory. Recall that, on the command line, a `.` refers to the current directory.

### Exercise 6

In the Console, run `list.files()`. CP/CR.

###

Your answer should look like:

    > list.files()
    [1] "_quarto.yml"         "about.qmd"           "first-website.Rproj" "index.qmd"
    [5] "README.md"           "styles.css"

The basic set of files necessary for making a Quarto website has been added to the current directory. Note how we can work with the current directory either from the Terminal, with commands like `ls`, or from the Console, with commands like `list.files()`. It is important for you to be comfortable with both approaches, so we intermix them in this tutorial.

### Exercise 7

In the Console, run `list.files(all.files = TRUE)`. CP/CR.

###

Your answer should look something like:

    > list.files(all.files = TRUE)
     [1] "_quarto.yml"         "."                   ".."                  ".git"
     [5] ".gitignore"          ".Rhistory"           ".Rproj.user"         "about.qmd"
     [9] "first-website.Rproj" "index.qmd"           "README.md"           "styles.css"
    >

###

You would get the same set of files if, in the Terminal, you ran `ls -a`. The `-a` ensures that all the files are listed, included the “hidden” ones which begin with a dot. Recall that `..` means the directory one level above the current one.

###

In general, we do not touch/manipulate “dot” directories, meaning directories whose names begin with a period. Such directories are meant to be used by the operating system and other programs. For example, the program Git uses the `.git` directory to store information about changes in all the files in the project.

## Examining files

###

Now that we have created the necessary files, it is useful to examine them one-by-one. The goal is to provide you with a good introductory lesson about how websites are put together.

### Exercise 1

In the Console, run:

    show_file("_quarto.yml")

CP/CR.

Did you get an error when you ran this? Something about ‘could not find function “show_file”’? This is because you need to `library(tutorial.helpers)` to have direct acccess to `show_file()`, which is a function in the tutorial.helpers package. Of course, you could use the double colon notation — `tutorial.helpers::show_file("_quarto.yml")` — as we did in previous tutorials. But, at this stage in your R education, we want you to become more comfortable with packages, and knowing yourself when they need to be loaded.

###

YAML files are how Quarto projects tell the world what they are. You can tell that `_quarto.yml` is a YAML file by both its `yml` file name suffix and by its content. The initial lines specify that this is a website.

    project:
      type: website

But other values for `type` are possible.

### Exercise 2

In the Console, run:

    show_file("_quarto.yml", start = 4, end = 10)

CP/CR.

###

These lines provide meta-information about the website and its organization.

    website:
      title: "A New Website"
      navbar:
        left:
          - href: index.qmd
            text: Home
          - about.qmd

Indents and other whitespace matter in the interpretation of a YAML file.

### Exercise 3

In the Source pane, open the `_quarto.yml` file. If the `title` field is not correct, often because it just contains a `.`, replace `title: "."` with `title: "A New Website"`. Save the file.

In the Console, run:

    show_file("_quarto.yml", start = 4, end = 10)

CP/CR.

###

The indentation before `title` should match that for`navbar` below it.

### Exercise 4

In the Console, run:

    show_file("_quarto.yml", start = 12, end = 16)

CP/CR.

###

These lines provide formatting information about the pages of the website.

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

The `css` line tells Quarto to use the `styles.css` file, located in the same directory, for the “style” of the pages.

### Exercise 5

In the Console, run:

    show_file("index.qmd")

CP/CR.

###

The answer should look like:

    > show_file("index.qmd")
    ---
    title: "A New Website"
    ---

    This is a Quarto website.

    To learn more about Quarto websites visit <https://quarto.org/docs/websites>.
    >

Whenever a web browser goes to a directory on the internet, it looks for an `index.html` file. If found, that file is displayed. So, the `index.qmd` file, which we will soon render as `index.html`, is important.

###

Note that the `title` (`"A New Website"`) in `_quarto.yml` has no necessary connection to the `title` (`"A New Website"`) in `index.qmd`. The former is the title for the entire website. The latter is the title for just the (yet-to-be-created) `index.html` page. They are set to the same values by default when we use `quarto create project website .` and answer the question about the title.

If you do not answer the question or if you are using an old version of Quarto which does not ask the question, then the title will be `.` in both locations.

### Exercise 6

In the Console, run:

    show_file(".gitignore")

CP/CR.

###

Your answer should look like this:

    > show_file(".gitignore")
    .Rproj.user
    .Rhistory
    .RData
    .Ruserdata

    /.quarto/
    >

Note that `.gitignore` contains a new line: `/.quarto/`. This was added when we ran `quarto create project`. The leading `/` escapes the `.`. In other words, we need the leading `/` if we want to ignore the files in a dotted directory.

In fact, the `.quarto` directory does not yet exist. But the `quarto create project` command wanted to ensure that, once it does, Git would ignore it and its contents.

### Exercise 7

We don’t want to put all the files on Github. So, let’s make two changes to the `.gitignore` file:

- Add `*Rproj` to exclude the `first-website.Rproj` file.
- Add an empty last line.

Save the file.

In the Console, run:

    show_file(".gitignore")

CP/CR.

###

Good data scientists believe in transparency and reproducibility. We want people — include “future” us — to be able to reproduce our work. By default, almost every file belongs on Github. But settings for R projects are both not necessary for replication and often specific to each individual.

### Exercise 8

Commit and push all the files in the project. Run `git log` in the Terminal. CP/CR.

###

The output from the `git log` command is too complex for us to fully parse. If you want to learn more about how to work with Git/Github and R, check out Happy Git with R, a very useful resource.

## Rendering and previewing

###

We now have the infrastructure for our website. We want to create (or “render”) the webpages themselves and then “preview” them to see what they will look like when we place them on the web.

### Exercise 1

From the Terminal, run `quarto render`. CP/CR.

###

Your answer should look something like:

    Davids-MBP:first-website dkane$ quarto render
    [1/2] index.qmd
    [2/2] about.qmd

    Output created: _site/index.html

    Davids-MBP:first-website dkane$

Quarto reports to us what it has done, working on our two QMD files and creating a new directory, `_site`, in which it has placed an `index.html` file.

###

If you look at the `_site` directory in the Files tab, you will see lots of new files, including `about.hmtl`. Quarto just tells you about the home page for the site, which is `index.html` by default, since that is the file that browsers like Google Chrome always look for.

### Exercise 2

From the Console, run `list.files("_site")`. CP/CR.

###

Your answer will probably look something like:

    > list.files("_site")
    [1] "about.html"  "index.html"  "search.json" "site_libs"   "styles.css"
    >

The `about.html` and `index.html` files are simply the rendered `about.qmd` and `index.qmd` input files. They are placed into the `_site` directory because the convention, when constructing websites and other large projects, is to separate out the outputs from the inputs.

###

The webpages which make up a website are often placed in a directory named either `_site` or `docs`, depending on the setup of your web hosting service.

We won’t discuss the `search.json` and `styles.css` files. The `site_libs` directory includes many files beyond the scope of this tutorial. The basic idea is that the entire `_site` directory is a functioning website, ready to be deployed.

### Exercise 3

Add `/_site` to the `.gitignore`. Don’t forget that the last line of a `.gitignore` should always be blank. Save the file.

In the Console, run:

    show_file(".gitignore")

CP/CR.

###

This command is convenient because the `_site` directory contains of lot of weird files that change often enough to annoy. We don’t create any of them directly, so we don’t really need to back them up. Moreover, they will still get published directly to the web from our computer.

###

The initial backslash in `/_site` allows Git to interpret `_site` correctly. The `/` escapes the `_`, allowing it to be treated as a literal, rather than special, character. See the “Regular expressions” tutorial in this package for more information. `_site` is a directory, so we could end the expression with a backslash, but Git, like most programs interpret `_site` and `_site/` to refer to the same thing, which they do.

### Exercise 4

From the Terminal, run `quarto preview`. CP/CR.

###

Your answer should look something like this:

    Davids-MBP:first-website dkane$ quarto preview
    Preparing to preview
    [1/1] index.qmd

    Watching files for changes
    Browse at http://localhost:7412/
    GET: /

The `quarto preview` command does two things. First, it renders the QMD files, just like `quarto render` does. Second, it sets up a viewer — probably your default web browser but possibly the “Viewer” tab in the Output pane — so that you can see what the website looks like. Click around and check it out!

The message at the end indicates that Quarto is now “watching” your files to see if you make any changes. If you do, it will automatically update the website.

### Exercise 5

Look at your website in the browser. (You might need to enter the URL by hand. It is `http://localhost:7412/` in my case, but yours will be different.) Click on the “About” link.

Now, go to the Terminal. Copy-and-paste everything from the previous invocation of `quarto preview`.

###

Your answer should look like this:

    Davids-MBP:first-website dkane$ quarto preview
    Preparing to preview

    Watching files for changes
    Browse at http://localhost:7193/
    GET: /
    GET: /about.html

Quarto is hanging out, still running in the background, monitoring your website. So, when you clicked the “About” link, it went to “GET” the `about.html` page to show to you.

### Exercise 6

Look again at your website in the browser. Click on the “Home” link and then copy/paste the entire screen.

###

Your answer should look something like:

    A New Website

    Home
    About
    A New Website
    This is a Quarto website.

    To learn more about Quarto websites visit https://quarto.org/docs/websites.

The title of the entire project (“A New Website”), taken from the `_quarto.yml` file, appears in the upper left hand corner. The title of the main home page (“A New Website”), taken from the `index.qmd` file, appears at the top of the Home page, which, by default, is always the `index.html` file.

(Depending on your browser and other settings, the copy/paste might also capture the “Home” and “About” links. No worry either way.)

### Exercise 7

Copy/paste the URL for your previewed website.

###

Your answer should be something like:

    http://localhost:7193/

The website is being “hosted” on your computer. That is what the word “localhost” refers to. It is not available on the web.

### Exercise 8

The advantage of using `quarto preview` is that the website is automatically updated whenever you edit and save the underlying QMD file. Try it by changing the `about.qmd` file, replacing “About this site” with your name. Save the file.

At the Terminal, you should see a new message. Copy and paste it here.

###

Your answer should look something like this:

    pandoc
      to: html
      output-file: about.html
      standalone: true
      title-prefix: A New Website
      section-divs: true
      html-math-method: mathjax
      wrap: none
      default-image-extension: png
      css:
        - styles.css
      toc: true

    metadata
      document-css: false
      link-citations: true
      date-format: long
      lang: en
      theme: cosmo
      title: About

    GET: /about.html

Quarto has noticed that you changed/saved the `about.qmd` file. It rendered the new version, creating a new `about.html` which it has now gotten and is displaying.

### Exercise 9

Copy/paste the About page from the Viewer pane or your browser. (We will just say “browser” going forward, but we mean wherever your website appears.)

###

Your answer should look like this, except with your name instead of mine!

    A New Website

    Home
    About
    About
    David Kane

If you want to stop `quarto preview` you can cancel the command by hitting the red stop sign which is located in the upper right of the Terminal tab. (If the red stop sign is not visible, you can also stop `quarto preview` by typing `Ctrl + c`.)

## Publishing

###

To make your website publicly visible, you need to “publish” it to the web. The Quarto documentation provides a thorough discussion. We will be using GitHub Pages.

### Exercise 1

Go to your `first-website` Github repository.

Click on the “Settings” option on the right side of the top menu.

Click on the “Pages” option on the lefthand side menu.

Copy/paste the resulting URL.

###

Your answer should look like:

    https://github.com/davidkane9/first-website/settings/pages

This page shows the settings which control the behavior of Github pages. It should look something like this:

Sam Csik provides an excellent overview of the entire process of creating Quarto websites.

### Exercise 2

To use Github pages, we need to complete some set up work. The usethis package is designed to make this sort of work easier.

In the Console, run `library(usethis)`. CP/CR.

###

There are other free services you can use for hosting your websites, including Quarto Pub and Posit Cloud.

### Exercise 3

At the Console, run `use_github_pages()`. CP/CR.

###

You answer should look like:

    > use_github_pages()
    ✔ Setting active project to '/Users/dkane/Desktop/projects/first-website'
    ✔ Initializing empty, orphan 'gh-pages' branch in GitHub repo 'davidkane9/first-website'
    ✔ GitHub Pages is publishing from:
    • URL: 'https://davidkane9.github.io/first-website/'
    • Branch: 'gh-pages'
    • Path: '/'
    >

`use_github_pages()` has completed the set up for using Github pages. If you refresh the “Pages” page for your repo, it should look more like this:

Understanding the details of what these changes mean is beyond the scope of this tutorial.

### Exercise 4

As the “Pages” page indicates, you now have a website. Copy/paste its URL.

###

The URL should be something like this:

    https://davidkane9.github.io/first-website/

But, if you go to the URL, you will get an error message because you have not uploaded any of the necessary files.

### Exercise 5

Ensure that all the files in the project have been committed and pushed. (Recall that you have, at least, edited `about.qmd` and that doing so has caused changes in other downstream files.)

At the Terminal, run:

`quarto publish gh-pages`

You will then need to select “Yes” to accept the default settings.

CP/CR the first few lines of the output.

###

Your answer should look like this:

    Davids-MacBook-Pro-2:first-website dkane$ quarto publish gh-pages
    ? Update site at https://davidkane9.github.io/first-website/? (Y/n) › Yes
    From https://github.com/davidkane9/first-website
     * branch            gh-pages   -> FETCH_HEAD
     * [new branch]      gh-pages   -> origin/gh-pages
    Rendering for publish:

    [1/2] index.qmd
    [2/2] about.qmd

    Preparing worktree (new branch 'gh-pages')
    branch 'gh-pages' set up to track 'origin/gh-pages'.
    HEAD is now at 897554b Remove temp file
    fatal: pathspec '.' did not match any files
    [gh-pages 55c1b2a] Built site for gh-pages
     23 files changed, 6027 insertions(+)

    ...

    origin  https://github.com/davidkane9/first-website (push)
    To https://github.com/davidkane9/first-website
       897554b..55c1b2a  HEAD -> gh-pages

    NOTE: GitHub Pages sites use caching so you might need to click the refresh
    button within your web browser to see changes after deployment.

    [✓] Deploying gh-pages branch to website (this may take a few minutes)
    [✓] Published to https://davidkane9.github.io/first-website/

    Davids-MacBook-Pro-2:first-website dkane$

`quarto publish`, like `quarto preview`, first renders all the files on the project. Note the phrase “Rendering for publish” in the output. The URL for the website is provided at the end.

### Exercise 6

A link to your new website should be brought up in a browser. Copy/paste the URL for your website. (It is the same URL which produced an error when we used it earlier.)

###

It should look like:

    https://davidkane9.github.io/first-website/

When using GitHub Pages, the URL will always have the same base: your GitHub user name followed by `github.io`. The second part of the URL will be the name of the repo. So, use non-stupid names for your repos.

### Exercise 7

If you look closely in the Files tab, you will see a new directory, `.quarto`, in the Files tab. Neither this directory, nor any of the files within it, appear in the Git tab because of the `/.quarto/` line in the `.gitignore` file.

From the Console, run `list.files(".quarto")`. CP/CR.

###

The `.quarto` directory is like the `.git` and `.Rproj.user` directories. We will never look at or change the files inside of them. Only the relevant programs — Quarto, Git and RStudio — should work with the contents of these directories.

### Exercise 8

Open the `_quarto.yml` file in the Source pane. Change `title: "A New Website"` to `title: "A New Website, second edition"`. Save the file.

In the Console, run:

    show_file("_quarto.yml", start = 4, end = 5)

CP/CR.

###

Your answer should look like:

    > show_file("_quarto.yml", start = 4, end = 5)
    website:
      title: "A New Website, second edition"
    >

Keep track of the three different places that the title of our project now exists. First, it is present in `_quarto.yml`. We have changed it there. But we have not changed it in the `_site` files which constitute the website nor in files uploaded to Github Pages.

### Exercise 9

From the Terminal, run `quarto preview`. Copy and paste the text from the home page once it comes up on your browser.

###

Your answer should look like:

    A New Website, second edition

    Home
    About
    A New Website
    This is a Quarto website.

    To learn more about Quarto websites visit https://quarto.org/docs/websites.

But, if you look at the Github Pages version of your website, it still uses the “A New Website” title because we have not (yet) published our new version. We have, however, changed the files in the `_site` directory.

### Exercise 10

Stop the `quarto preview` command by hitting the red stop sign on the upper right of the Terminal tab. From the Terminal, run `quarto publish`. You may need to hit `return/enter` to confirm that you still want to use GitHub Pages.

CP/CR.

###

Your answer should look like:

    Davids-MacBook-Pro-2:first-website dkane$ quarto publish
    ? Publish update to: › https://davidkane9.github.io/first-website/ (GitHub Pages)
    From https://github.com/davidkane9/first-website
     * branch            gh-pages   -> FETCH_HEAD
    Rendering for publish:

    [1/2] index.qmd
    [2/2] about.qmd

    Preparing worktree (resetting branch 'gh-pages'; was at 2576ffd)
    branch 'gh-pages' set up to track 'origin/gh-pages'.
    HEAD is now at 2576ffd Built site for gh-pages
    [gh-pages f262006] Built site for gh-pages
     3 files changed, 5 insertions(+), 5 deletions(-)
    origin  https://github.com/davidkane9/first-website (fetch)
    origin  https://github.com/davidkane9/first-website (push)
    To https://github.com/davidkane9/first-website
       2576ffd..f262006  HEAD -> gh-pages

    NOTE: GitHub Pages sites use caching so you might need to click the refresh
    button within your web browser to see changes after deployment.

    [✓] Deploying gh-pages branch to website (this may take a few minutes)
    [✓] Published to https://davidkane9.github.io/first-website/

    Davids-MacBook-Pro-2:first-website dkane$

### Exercise 11

Commit and push all the files in the project. Run `git log -n 2` in the Terminal. CP/CR.

The `-n 2` option causes Git to just provide the information on the last two commits.

###

Note both the simplicity and the complexity of your project. It is simple in that, even if our computer blew up we would be able to recreate everything from the files on Github. It is complex in that there are a lot of files, interacting in a fairly sophisticated fashion.

## Summary

###

This tutorial covered material from Chapter 28 Quarto and Chapter 29 Quarto formats in R for Data Science (2e) by Hadley Wickham, Mine Çetinkaya-Rundel, and Garrett Grolemund, although much of the information from Chapter 28 has already appeared in the “RStudio and Github” tutorial in this package. You have learned the process of creating and organizing the Quarto websites using the Quarto CLI (command line interface) and commands like `quarto create project`, `quarto render`, `quarto preview` and `quarto publish`.

Sam Csik provides an excellent overview of the entire process of creating Quarto websites.

## Download answers

###

When you have completed this tutorial, follow these steps:

1. Click the button to download a file containing your answers.
2. Save the file onto your computer in a convenient location.

Download HTML
(If no file seems to download, try clicking with the alternative button on the download button and choose "Save link as...")

# Quarto Websites Introduction

#### David Kane