forked from ivelasq/2022-10-27_intro-to-quarto
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index.html
2958 lines (2824 loc) · 160 KB
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index.html
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<!DOCTYPE html>
<html lang="en"><head>
<script src="index_files/libs/clipboard/clipboard.min.js"></script>
<script src="index_files/libs/quarto-html/tabby.min.js"></script>
<script src="index_files/libs/quarto-html/popper.min.js"></script>
<script src="index_files/libs/quarto-html/tippy.umd.min.js"></script>
<link href="index_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="index_files/libs/quarto-html/light-border.css" rel="stylesheet">
<link href="index_files/libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
<link href="index_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<link href="index_files/libs/quarto-contrib/reveal-auto-agenda-0.0.1/reveal-auto-agenda.css" rel="stylesheet"><meta charset="utf-8">
<meta name="generator" content="quarto-1.3.353">
<title>index</title>
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no, minimal-ui">
<link rel="stylesheet" href="index_files/libs/revealjs/dist/reset.css">
<link rel="stylesheet" href="index_files/libs/revealjs/dist/reveal.css">
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
vertical-align: middle;
}
/* CSS for syntax highlighting */
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
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code.sourceCode > span { color: inherit; text-decoration: inherit; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
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-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ color: #007020; background-color: #f3f5f6; }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span { color: #007020; } /* Normal */
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { color: #008000; } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
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code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
</style>
<link rel="stylesheet" href="index_files/libs/revealjs/dist/theme/quarto.css">
<link href="index_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
<link href="index_files/libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
<style type="text/css">
.callout {
margin-top: 1em;
margin-bottom: 1em;
border-radius: .25rem;
}
.callout.callout-style-simple {
padding: 0em 0.5em;
border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
display: flex;
}
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border-left: solid #acacac .3rem;
border-right: solid 1px silver;
border-top: solid 1px silver;
border-bottom: solid 1px silver;
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flex-grow: 1;
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font-size: 1rem;
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font-size: 0.9rem;
font-weight: 400;
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margin-bottom: -0.2em;
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margin-top: 0.5em;
margin-bottom: 0.5em;
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margin-top: 0;
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margin-top: 0.7em;
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border-bottom: none;
font-size: .9rem;
font-weight: 600;
opacity: 75%;
}
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border-bottom: none;
font-weight: 600;
opacity: 85%;
font-size: 0.9rem;
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-default div.callout-content {
padding-left: 0.5em;
padding-right: 0.5em;
}
.callout.callout-style-simple .callout-icon::before {
height: 1rem;
width: 1rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 1rem 1rem;
}
.callout.callout-style-default .callout-icon::before {
height: 0.9rem;
width: 0.9rem;
display: inline-block;
content: "";
background-repeat: no-repeat;
background-size: 0.9rem 0.9rem;
}
.callout-title {
display: flex
}
.callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
.callout.no-icon::before {
display: none !important;
}
.callout.callout-titled .callout-body > .callout-content > :last-child {
margin-bottom: 0.5rem;
}
.callout.callout-titled .callout-icon::before {
margin-top: .5rem;
padding-right: .5rem;
}
.callout:not(.callout-titled) .callout-icon::before {
margin-top: 1rem;
padding-right: .5rem;
}
/* Callout Types */
div.callout-note {
border-left-color: #4582ec !important;
}
div.callout-note .callout-icon::before {
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}
div.callout-note.callout-style-default .callout-title {
background-color: #dae6fb
}
div.callout-important {
border-left-color: #d9534f !important;
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<div class="reveal">
<div class="slides">
<section id="section" class="slide level2 title">
<h2></h2>
<div class="r-fit-text">
<p>Intro to <span class="flow">Quarto</span></p>
</div>
<div style="font-size: 80px">
<p>Tracy Teal</p>
</div>
<p>From Isabella Velásquez’s R-Ladies St. Louis presentation</p>
<aside class="notes">
<p>Hi everybody! Thank you so much for joining today’s session. I am so excited to introduce Quarto and many thanks to Laura and the R-Ladies St. Louis co-organizers for having me today hi there.</p>
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</section>
<section>
<section class="title-slide slide level1 agenda-slide center">
<h1>Introduction</h1>
<div class="agenda-heading">
<p>Agenda</p>
</div>
<div class="agenda">
<ol>
<li><div class="agenda-active">
<p>Introduction</p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>About <span class="flow">Quarto</span></p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>How to use <span class="flow">Quarto</span></p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Get Started with <span class="flow">Quarto</span></p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Styling <span class="flow">Quarto</span></p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Publishing <span class="flow">Quarto</span></p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Conclusion</p>
</div></li>
</ol>
</div>
</section>
<section id="instructions" class="slide level2 small">
<h2>Instructions</h2>
<div>
<ul>
<li class="fragment">Slides: <a href="https://tracykteal.quarto.pub/intro-to-quarto/" class="uri">https://tracykteal.quarto.pub/intro-to-quarto/</a></li>
<li class="fragment">Session repo with instructions: <a href="https://github.com/tracykteal/2022-10-27_intro-to-quarto" class="uri">https://github.com/tracykteal/2022-10-27_intro-to-quarto</a></li>
<li class="fragment">Exercise repo: <a href="https://github.com/ivelasq/intro-to-quarto-exercises" class="uri">https://github.com/ivelasq/intro-to-quarto-exercises</a></li>
<li class="fragment">rstudio.cloud Project: <a href="https://rstudio.cloud/content/4823293" class="uri">https://rstudio.cloud/content/4823293</a></li>
</ul>
</div>
<div class="fragment">
<div class="callout callout-tip callout-titled callout-style-default">
<div class="callout-body">
<div class="callout-title">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<p><strong>Workshop Prep</strong></p>
</div>
<div class="callout-content">
<p>To follow along with the exercises, please be sure that you:</p>
<ul>
<li>Are on the latest version of RStudio v2022.07 or later and have cloned the exercise repo</li>
<li>Or, have a rstudio.cloud account and can access the project</li>
<li>And, have a <a href="https://quartopub.com/" class="uri">https://quartopub.com/</a> account.</li>
</ul>
</div>
</div>
</div>
<aside class="notes">
<p>You have a few options of how to attend this session. On the README file of the GitHub repo for this session is a list of instructions and a link to the exercise repo. One option is that you have a local copy of the exercises already, and when we get to the different sections you can follow along with what I am doing on your own RStudio. Another option is that you sign up for RStudio Cloud and go into the project to follow along. It is also linked in the instructions. One benefit of this is that you don’t have to have RStudio installed on your computer and the project is ready, the packages are installed for you, and you can save a copy of your work if you would like. But, please feel free to just watch the session and try things out on your own afterwards. The slides, repositories, and project will stay up so that you can try things out on your own time. One other thing to note is that Quarto has a lot of options for creating content, so I added some reference materials in the exercise repo README so that you can play around with other options other than the ones I show you.</p>
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</section></section>
<section>
<section class="title-slide slide level1 agenda-slide center">
<h1>About <span class="flow">Quarto</span></h1>
<div class="agenda-heading">
<p>Agenda</p>
</div>
<div class="agenda">
<ol>
<li><div class="agenda-inactive agenda-pre-active">
<p>Introduction</p>
</div></li>
<li><div class="agenda-active">
<p>About <span class="flow">Quarto</span></p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>How to use <span class="flow">Quarto</span></p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Get Started with <span class="flow">Quarto</span></p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Styling <span class="flow">Quarto</span></p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Publishing <span class="flow">Quarto</span></p>
</div></li>
<li><div class="agenda-inactive agenda-post-active">
<p>Conclusion</p>
</div></li>
</ol>
</div>
</section>
<section id="what-is-quarto" class="slide level2" data-auto-animate="true">
<h2 data-id="quarto-animate-title">What is Quarto®?</h2>
<center>
<p>Quarto® is an</p>
<div class="fragment grow semi-fade-out">
<p>open-source</p>
</div>
<div class="fragment grow semi-fade-out">
<p>scientific and technical</p>
</div>
<div class="fragment grow semi-fade-out">
<p>publishing system</p>
</div>
<div class="fragment grow semi-fade-out">
<p>built on Pandoc.</p>
</div>
</center>
<aside class="notes">
<p>Quarto is an open-source scientific and technical publishing system built on Pandoc. Let’s break this down: Open-source: RStudio believes that it’s better for everyone if the tools used for research and science are free and open. Free software means more reproducibility, widespread sharing of knowledge and techniques, and elimination of cost barriers. You can also see the source code and contribute, too. Scientific and technical: Scientific and technical means that Quarto has specific things for journal articles or scientific papers, like support for code execution, citations, footnotes, scientific markdown, equations, citations, crossrefs, so many things. We’ll be showing some of these later on, but Quarto definitely has the scientific publishing audience in mind. Publishing system: Quarto is a tool for writing dynamic documents that combine code, output, and text. It can embed output from Python, R, Julia, and Observable. Quarto can be rendered to create high-quality articles, reports, presentations, websites, blogs, and books in HTML, PDF, MS Word, ePub, and more formats. Pandoc is the tool working behind the scenes to change Quarto documents to their finalized format.Quarto documents are authored with markdown, which is a plain text format. But Pandoc markdown is very rich and lets you control your document in very specific ways while being easy to read and write. We’ll cover this as well.</p>
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</section>
<section id="quarto-origins" class="slide level2">
<h2>Quarto Origins</h2>
<div>
<ul>
<li class="fragment">Open source project sponsored by Posit Software, PBC (formerly RStudio)</li>
<li class="fragment">We’ve had 10 years of experience with R Markdown</li>
<li class="fragment">But there are a lot of other programming languages…</li>
</ul>
</div>
<div class="fragment">
<p>Can we reimplement R Markdown such that it’s not tied to R?</p>
<aside class="notes">
<p>R Markdown is a file format for making dynamic documents with R. However, you need to call it from R to use it, and it was depedentn on knitr. If you’re a Python user, it means you need to install R to use R Markdown. Quarto is a tool that you can call from the terminal or command line, and is independent from the computational systems. Quarto supports knitr, and can support others. So, you can think of Quarto as the next generation R Markdown that is fundamentally multilanguage and multiengine.</p>
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</div>
<aside><div>
<p>Check out <a href="https://www.youtube.com/watch?v=9jGc0TxoRco">JJ Allaire’s R Medicine Keynote</a>!</p>
</div></aside></section>
<section id="quarto-goals" class="slide level2">
<h2>Quarto Goals</h2>
<div>
<ul>
<li class="fragment">Create computational documents that hold source code for automation and reproducibility</li>
<li class="fragment">Reduce how difficult it is to make a scientific document</li>
<li class="fragment">Enable “single-source publishing” — create Word, PDFs, HTML, etc. from one source</li>
</ul>
</div>
<aside class="notes">
<p>So the goals are to create these dynamic documents that can be reproducible and automated. [story about building documents]. For single-source publishing, you often need to create all sorts of output, like things that are printed, on the web, on the mobile. The idea is to being able to make publications from one source.</p>
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<aside><div>
<p>Check out <a href="https://www.youtube.com/watch?v=9jGc0TxoRco">JJ Allaire’s R Medicine Keynote</a>!</p>
</div></aside></section>
<section id="a-new-tool-for-literate-programming" class="slide level2">
<h2>A new tool for literate programming</h2>
<div class="columns">
<div class="column" style="width:{50%";">
<div class="fragment fade-in">
<p><img data-src="images/rstudio-hello.png"></p>
</div>
</div><div class="column" style="width:{50%";">
<div class="fragment fade-in">
<p><img data-src="images/lit-program-tools.png" height="600"></p>
</div>
</div>
</div>
<aside class="notes">
<p>Quarto sits inside the big and broad literate programming world, which mixes narrative in text form with code for formatted outputs like documents and webpages and more. [click] There are lots of literate programming systems that support computation, like R Markdown, Org Mode, Jupyter Book, and now there is Quarto!</p>
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display:block!important;
}</style></aside>
<aside><div>
<p>Check out <a href="https://www.youtube.com/watch?v=9jGc0TxoRco">JJ Allaire’s R Medicine Keynote</a>!</p>
</div></aside></section>
<section id="why-a-new-system" class="slide level2">
<h2>Why a new system?</h2>
<div>
<ul>
<li class="fragment">At its core, Quarto is multilingual and independent of computational systems</li>
<li class="fragment">Has expanded upon R Markdown to add new languages and can add more in the future</li>
</ul>
</div>
<div class="fragment">
<p>Let’s bring R Markdown to everybody!</p>
<aside class="notes">
<p>So, if there already exist literate programming tools out there, why create a new one, especially since RStudio is also behind R Markdown? Like mentioned earlier, Quarto was built from the start to support multiple computational systems and ecosystems. This new system brings R Markdown to everybody.</p>
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</div>
</section>
<section id="why-is-it-called-quarto" class="slide level2">
<h2>Why is it called “Quarto”?</h2>
<div class="columns">
<div class="column" style="width:60%;">
<div style="font-size:28px">
<p>“Quarto is the format of a book or<br>pamphlet produced from full sheets<br>printed with eight pages of text, four to a<br>side, then folded twice to produce four leaves.”</p>
<p>— Wikipedia</p>
</div>
</div><div class="column" style="width:40%;">
<p><img data-src="images/quarto-book.png"></p>
</div>
</div>
<aside class="notes">
<p>According to the website, the developers wanted to use a name that had meaning in the history of publishing and ulitimately landed on Quarto. A quarto is an 8-page double-sided booklet, made by folding a single sheet of paper into four sections.</p>
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<aside><div>
<p>Image based on one from gutenberg.org</p>
</div></aside></section>
<section id="quarto-formats" class="slide level2">
<h2>Quarto Formats</h2>
<div class="panel-tabset">
<ul id="tabset-1" class="panel-tabset-tabby"><li><a data-tabby-default="" href="#tabset-1-1">Websites</a></li><li><a href="#tabset-1-2">Books</a></li><li><a href="#tabset-1-3">Blogs</a></li><li><a href="#tabset-1-4">Presentations</a></li><li><a href="#tabset-1-5">Journals</a></li></ul>
<div class="tab-content">
<div id="tabset-1-1">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/website.png" height="400"></p>
<figcaption>nbdev.fast.ai</figcaption>
</figure>
</div>
</div>
<div id="tabset-1-2">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/book.png" height="400"></p>
<figcaption>Python for Data Analysis, 3E by Wes McKinney</figcaption>
</figure>
</div>
</div>
<div id="tabset-1-3">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/blog.png" height="400"></p>
<figcaption>https://jollydata.blog/</figcaption>
</figure>
</div>
</div>
<div id="tabset-1-4">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="images/presentation.png" height="400"></p>
<figcaption>The untold story of palmerpenguins by Dr. Kristen Gorman, Dr. Allison Horst, and<br>Dr. Alison Hill</figcaption>
</figure>
</div>
</div>
<div id="tabset-1-5">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="https://user-images.githubusercontent.com/163582/42351114-e5deaa1c-8078-11e8-90de-2aff57bba255.png" height="400"></p>
<figcaption>Journal of Statistical Software (JSS)</figcaption>
</figure>
</div>
</div>
</div>
</div>
<aside class="notes">
<p>Quarto can make very flexible websites, or books which are a a Quarto website that can be rendered to Word, ePub, etc., blogs with listings and posts and RSS feeds, Quarto has deep feature set for presentations with reveal.js optimized for scientific content, and of course, publishing for journals. There is custom format systems and the ability to flexibly adapt LaTeX templates.</p>
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}</style></aside>
</section>
<section id="quarto-engines" class="slide level2">
<h2>Quarto Engines</h2>
<h3 id="knitr">knitr</h3>
<img data-src="images/knitr-engine.png" class="r-stretch"><aside class="notes">
<p>An engine is the tool that runs code. This is the underlying structure that creates documents from the source, the Quarto markdown file or the QMD file. When we render a Quarto document, first, the knitr engine executes all of the code chunks and generates an intermediary markdown file that includes both the code and code output. Then that markdown file is processed by pandoc to create the finished document. Since Quarto uses knitr, most Rmd files can be used unmodified.</p>
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}</style></aside>
</section>
<section id="knitr-1" class="slide level2 small">
<h2>knitr</h2>
<div class="columns">
<div class="column" style="width:50%;">
<div class="sourceCode" id="cb1"><pre class="sourceCode markdown code-with-copy"><code class="sourceCode markdown"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="an">title:</span><span class="co"> "ggplot2 demo"</span></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="an">format:</span><span class="co"> </span></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co"> html:</span></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co"> code-fold: true</span></span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="fu">## Meet Quarto</span></span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a>Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <span class="ot"><https://quarto.org></span>.</span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="co">#| label: plot-penguins</span></span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a><span class="co">#| echo: false</span></span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a><span class="co">#| message: false</span></span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a><span class="co">#| warning: false</span></span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyverse)</span>
<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(palmerpenguins)</span>
<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(penguins, </span>
<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a> <span class="fu">aes</span>(<span class="at">x =</span> flipper_length_mm, <span class="at">y =</span> bill_length_mm)) <span class="sc">+</span></span>
<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>(<span class="fu">aes</span>(<span class="at">color =</span> species, <span class="at">shape =</span> species)) <span class="sc">+</span></span>
<span id="cb1-24"><a href="#cb1-24" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_color_manual</span>(<span class="at">values =</span> <span class="fu">c</span>(<span class="st">"darkorange"</span>,<span class="st">"purple"</span>,<span class="st">"cyan4"</span>)) <span class="sc">+</span></span>
<span id="cb1-25"><a href="#cb1-25" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(</span>
<span id="cb1-26"><a href="#cb1-26" aria-hidden="true" tabindex="-1"></a> <span class="at">title =</span> <span class="st">"Flipper and bill length"</span>,</span>
<span id="cb1-27"><a href="#cb1-27" aria-hidden="true" tabindex="-1"></a> <span class="at">subtitle =</span> <span class="st">"Dimensions for penguins at Palmer Station LTER"</span>,</span>
<span id="cb1-28"><a href="#cb1-28" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> <span class="st">"Flipper length (mm)"</span>, <span class="at">y =</span> <span class="st">"Bill length (mm)"</span>,</span>
<span id="cb1-29"><a href="#cb1-29" aria-hidden="true" tabindex="-1"></a> <span class="at">color =</span> <span class="st">"Penguin species"</span>, <span class="at">shape =</span> <span class="st">"Penguin species"</span></span>
<span id="cb1-30"><a href="#cb1-30" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb1-31"><a href="#cb1-31" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_minimal</span>()</span>
<span id="cb1-32"><a href="#cb1-32" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column" style="width:50%;">
<p><img data-src="images/knitr-plot.png"></p>
</div>
</div>
<aside class="notes">
<p>This is a Quarto document with the extension .qmd (on the left) along with its rendered version as HTML (on the right). You could also choose to render it into other formats like PDF, MS Word, etc. This is the basic model for Quarto publishing—take a source document and render it to a variety of output formats.</p>
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overflow: hidden!important;
display:block!important;
}</style></aside>
</section>
<section id="quarto-engines-1" class="slide level2">
<h2>Quarto Engines</h2>
<h3 id="jupyter">Jupyter</h3>
<img data-src="images/jupyter-engine.png" class="r-stretch"><aside class="notes">
<p>The structure is similar for Jupyter, we just are running documents natively through the Jupyter engine. Like R Marukdown, you can render Jupyter notebooks with Quarto, too. Jupyter will support any other language that has a Jupyter kernal, and right now, there’s a lot of Quarto functionality for Python and Julia through Jupyter. But, this is part of the multilingualism that we discussed earlier, where you can keep adding languages if you swap out different engines. This also means you can have a shared syntax and format across languages, since the backend is the same.</p>
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position:absolute!important;
clip: rect(1px, 1px, 1px, 1px);
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overflow: hidden!important;
display:block!important;
}</style></aside>
</section>
<section id="jupyter-1" class="slide level2 small">
<h2>Jupyter</h2>
<div class="columns">
<div class="column" style="width:50%;">
<div class="sourceCode" id="cb2"><pre class="sourceCode markdown code-with-copy"><code class="sourceCode markdown"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="an">title:</span><span class="co"> "Palmer Penguins Demo"</span></span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="an">format:</span><span class="co"> </span></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="co"> html:</span></span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a><span class="co"> code-fold: true</span></span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="an">jupyter:</span><span class="co"> python3</span></span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a><span class="fu">## Meet Quarto</span></span>
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a>Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <span class="ot"><https://quarto.org></span>.</span>
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-13"><a href="#cb2-13" aria-hidden="true" tabindex="-1"></a><span class="in">```{python}</span></span>
<span id="cb2-14"><a href="#cb2-14" aria-hidden="true" tabindex="-1"></a><span class="co">#| echo: false</span></span>
<span id="cb2-15"><a href="#cb2-15" aria-hidden="true" tabindex="-1"></a><span class="co">#| message: false</span></span>
<span id="cb2-16"><a href="#cb2-16" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-17"><a href="#cb2-17" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
<span id="cb2-18"><a href="#cb2-18" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> seaborn <span class="im">as</span> sns </span>
<span id="cb2-19"><a href="#cb2-19" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> palmerpenguins <span class="im">import</span> load_penguins</span>
<span id="cb2-20"><a href="#cb2-20" aria-hidden="true" tabindex="-1"></a>sns.set_style(<span class="st">'whitegrid'</span>)</span>
<span id="cb2-21"><a href="#cb2-21" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-22"><a href="#cb2-22" aria-hidden="true" tabindex="-1"></a>penguins <span class="op">=</span> load_penguins()</span>
<span id="cb2-23"><a href="#cb2-23" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-24"><a href="#cb2-24" aria-hidden="true" tabindex="-1"></a>g <span class="op">=</span> sns.lmplot(x<span class="op">=</span><span class="st">"flipper_length_mm"</span>,</span>
<span id="cb2-25"><a href="#cb2-25" aria-hidden="true" tabindex="-1"></a> y<span class="op">=</span><span class="st">"body_mass_g"</span>,</span>
<span id="cb2-26"><a href="#cb2-26" aria-hidden="true" tabindex="-1"></a> hue<span class="op">=</span><span class="st">"species"</span>,</span>
<span id="cb2-27"><a href="#cb2-27" aria-hidden="true" tabindex="-1"></a> height<span class="op">=</span><span class="dv">7</span>,</span>
<span id="cb2-28"><a href="#cb2-28" aria-hidden="true" tabindex="-1"></a> data<span class="op">=</span>penguins,</span>
<span id="cb2-29"><a href="#cb2-29" aria-hidden="true" tabindex="-1"></a> palette<span class="op">=</span>[<span class="st">'#FF8C00'</span>,<span class="st">'#159090'</span>,<span class="st">'#A034F0'</span>])<span class="op">;</span></span>
<span id="cb2-30"><a href="#cb2-30" aria-hidden="true" tabindex="-1"></a>g.set_xlabels(<span class="st">'Flipper Length'</span>)<span class="op">;</span></span>
<span id="cb2-31"><a href="#cb2-31" aria-hidden="true" tabindex="-1"></a>g.set_ylabels(<span class="st">'Body Mass'</span>)<span class="op">;</span></span>
<span id="cb2-32"><a href="#cb2-32" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div><div class="column" style="width:50%;">
<p><img data-src="images/jupyter-plot.png"></p>
</div>
</div>
</section>
<section id="why-quarto" class="slide level2">
<h2>Why Quarto?</h2>
<h3 id="a-unified-ecosystem">A unified ecosystem</h3>
<div>
<ul>
<li class="fragment">R Markdown has a lot of packages doing lots of different things</li>
</ul>
<p><img data-src="images/hexes.png"></p>
<ul>
<li class="fragment">Quarto has a shared expression for core features</li>
</ul>
</div>
<p><img data-src="images/quarto.png"></p>
<aside class="notes">
<p>So this is all good and well, but you may be wondering should you switch to Quarto if you already have another tool that you really like, you may be wondering whether or not you should switch. Here are some considerations. Quarto has a shared expression for core features. If you used the packages from the R Markdown ecosystem, then you may have had to switch between different ways of doing the same thing. In Quarto, you have a shared core syntax that is the same across all formats. Things like tabset, code folding, cross references in the same way. Another example is that Quarto has a universal theming system based on SCSS for all HTML output where core variables defined by bslib and so it is compatible with Shiny, flexdashboard, and R Markdown themes. So, users can create very consistent and organized theming across content.</p>
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}</style></aside>
</section>
<section id="why-quarto-1" class="slide level2 scrollable">
<h2>Why Quarto?</h2>
<h3 id="new-features">New features</h3>
<ul>
<li>Cross references</li>
<li>Advanced layout</li>
<li>Figure/layout panels</li>
<li>Callouts</li>
<li>Diagrams</li>
<li>Extensions</li>
<li>Interactivity</li>
<li>YAML intelligence</li>
<li>Publishing</li>
<li>Conditional content</li>
<li>Notebook filters</li>
</ul>
<aside class="notes">
<p>R Markdown isn’t going away but big new features will be in Quarto, things like YAML intelligence, figure panels, layouts, which we’ll cover later in the session.</p>
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span.MJX_Assistive_MathML {
position:absolute!important;
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</section>
<section id="why-quarto-2" class="slide level2 small">
<h2>Why Quarto?</h2>
<h3 id="lua-based-extension-system">Lua-based extension system</h3>
<div class="panel-tabset">
<ul id="tabset-2" class="panel-tabset-tabby"><li><a data-tabby-default="" href="#tabset-2-1">Shortcodes</a></li><li><a href="#tabset-2-2">Journal</a></li><li><a href="#tabset-2-3">Formats</a></li><li><a href="#tabset-2-4">Revealjs</a></li></ul>
<div class="tab-content">
<div id="tabset-2-1">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="https://github.com/schochastics/quarto-nutshell/raw/main/nutshell.gif" height="400"></p>
<figcaption>nutshell shortcode by schochastics</figcaption>
</figure>
</div>
</div>
<div id="tabset-2-2">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="https://user-images.githubusercontent.com/163582/42351114-e5deaa1c-8078-11e8-90de-2aff57bba255.png" height="400"></p>
<figcaption>Journal of Statistical Software (JSS)</figcaption>
</figure>
</div>
</div>
<div id="tabset-2-3">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="https://user-images.githubusercontent.com/14034784/187721198-04400c7a-4432-4c90-9344-f1cf938be3b1.gif" height="400"></p>
<figcaption>nes-revealjs format by EmilHvitfeldt</figcaption>
</figure>
</div>
</div>
<div id="tabset-2-4">
<div class="quarto-figure quarto-figure-center">
<figure>
<p><img data-src="https://github.com/quarto-ext/attribution/raw/main/example.png" height="400"></p>
<figcaption>attribution Revealjs Extension</figcaption>
</figure>
</div>
</div>
</div>
</div>
<aside class="notes">
<p>Quarto also supports extensions. Quarto extensions are written in Lua, meaning that they are not language specific. So, you can use the same extension in a Jupyter file or a knitr file. Shortcodes let you add content, like fontawesome icons that you have seen in this presentation, or videos from YouTube. Filters let you add new markdown syntax for extended features. And formats are custom formats. There are built in extensions and then community built ones, if you search for Awesome Quarto, there are a list of them there.</p>
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</section></section>
<section>