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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.549">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<meta name="author" content="Quinn Asena">
<meta name="dcterms.date" content="2024-07-07">
<title>Example</title>
<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 { line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
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;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
}
pre.numberSource { margin-left: 3em; padding-left: 4px; }
div.sourceCode
{ }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
/* CSS for citations */
div.csl-bib-body { }
div.csl-entry {
clear: both;
}
.hanging-indent div.csl-entry {
margin-left:2em;
text-indent:-2em;
}
div.csl-left-margin {
min-width:2em;
float:left;
}
div.csl-right-inline {
margin-left:2em;
padding-left:1em;
}
div.csl-indent {
margin-left: 2em;
}</style>
<script src="template_complete_files/libs/clipboard/clipboard.min.js"></script>
<script src="template_complete_files/libs/quarto-html/quarto.js"></script>
<script src="template_complete_files/libs/quarto-html/popper.min.js"></script>
<script src="template_complete_files/libs/quarto-html/tippy.umd.min.js"></script>
<script src="template_complete_files/libs/quarto-html/anchor.min.js"></script>
<link href="template_complete_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="template_complete_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
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<link href="template_complete_files/libs/bootstrap/bootstrap-dark.min.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
</head>
<body>
<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<nav id="TOC" role="doc-toc" class="toc-active">
<h2 id="toc-title">Table of contents</h2>
<ul>
<li><a href="#introduction" id="toc-introduction" class="nav-link active" data-scroll-target="#introduction">Introduction</a>
<ul class="collapse">
<li><a href="#a-note-on-project-structure" id="toc-a-note-on-project-structure" class="nav-link" data-scroll-target="#a-note-on-project-structure">A note on project structure</a></li>
</ul></li>
<li><a href="#data-wrangling" id="toc-data-wrangling" class="nav-link" data-scroll-target="#data-wrangling">Data wrangling</a></li>
<li><a href="#visualisations" id="toc-visualisations" class="nav-link" data-scroll-target="#visualisations">Visualisations</a>
<ul class="collapse">
<li><a href="#plot-tabs" id="toc-plot-tabs" class="nav-link" data-scroll-target="#plot-tabs">Plot tabs</a></li>
</ul></li>
<li><a href="#to-do" id="toc-to-do" class="nav-link" data-scroll-target="#to-do">To do</a></li>
<li><a href="#final-remarks" id="toc-final-remarks" class="nav-link" data-scroll-target="#final-remarks">Final remarks</a></li>
<li><a href="#useful-links" id="toc-useful-links" class="nav-link" data-scroll-target="#useful-links">Useful links</a>
<ul class="collapse">
<li><a href="#references" id="toc-references" class="nav-link" data-scroll-target="#references">References</a></li>
</ul></li>
</ul>
</nav>
</div>
<main class="content" id="quarto-document-content">
<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title">Example</h1>
</div>
<div class="quarto-title-meta-author">
<div class="quarto-title-meta-heading">Author</div>
<div class="quarto-title-meta-heading">Affiliation</div>
<div class="quarto-title-meta-contents">
<p class="author">Quinn Asena </p>
</div>
<div class="quarto-title-meta-contents">
<p class="affiliation">
UW-Madison (Formaly University of Auckland)
</p>
</div>
</div>
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">July 7, 2024</p>
</div>
</div>
</div>
</header>
<section id="introduction" class="level1">
<h1>Introduction</h1>
<p>This template is designed to accompany the slide deck and to include most of the features you will need for hosting a collaborative research project. I’ve included a few extras that I find handy (e.g., YAML entries, and check out the plot loop!). Every research project needs to be taylored towards your preferred workflow, collaborators, data, data privacy, and the list goes on.</p>
<p>Some things are the same across projects like well commented code and a well documented version control history. I use documents like this (previously in Rmarkdown) to share results easily with a link hosted on GitHub.</p>
<p>This complete template has a structure that many projects roughly follow from intro inforation to colaborators through some data wrangling and visualisations.You can replace ths intro (and following sub-section) with a summary of your project and any useful links, references and content you desire.</p>
<section id="a-note-on-project-structure" class="level2">
<h2 class="anchored" data-anchor-id="a-note-on-project-structure">A note on project structure</h2>
<p>Today, we have cloned an existing project structure. It is important that you create a project structure that works for your particular case. A general framework is to create a primary directory that is your repo and contains your <code>.qmd</code> script, and sub directories for data, outputs.</p>
<ul>
<li><p>/primary_directory</p>
<ul>
<li><p>script.qmd</p></li>
<li><p>.git, .gitignore</p></li>
<li><p>/data</p>
<ul>
<li>data.csv</li>
</ul></li>
<li><p>/outputs</p>
<ul>
<li>results</li>
</ul></li>
</ul></li>
</ul>
<p>Plenty of tools exist for reproducibility (such as the <code>renv</code> package to record package versions used in your project).</p>
</section>
</section>
<section id="packages-and-libraries" class="level1 unlisted">
<h1 class="unlisted">Packages and libraries</h1>
<p>It is good practice to include a list of packages used as well as any source files or functions up front. <code>{.unlisted}</code> will exclude the section from the table of contents. You can hide the section completely with <code>{.unlisted .hidden}</code>. This is useful for sections like ‘packages’ which are included in the code for reproducibility and are necessary to execute but maybe unnecessary to display. If your sections are numbered (insert <code>number-sections: true</code> in <a href="https://quarto.org/docs/output-formats/html-basics.html#section-numbering">YAML</a>) then you will need <code>{.unlisted. unnumbered .hidden}</code> to hide the section.</p>
<p>You might also include sourcing any function scripts (e.g., <code>source("my_functions.R")</code>).</p>
</section>
<section id="you-cant-see-me" class="level1 unlisted hidden">
<h1 class="unlisted hidden">You can’t see me!</h1>
<p>Lah lah lah!</p>
<p>I’m here in spirit, code will still be executed.</p>
</section>
<section id="data-wrangling" class="level1">
<h1>Data wrangling</h1>
<p>Typically you need to do some tidying of your data. Each project will have different reqirements e.g., transforming data or generating new datasets. You probably want to dedicate a section just for wrangling but may want to hide it from the output. See <a href="https://r4ds.had.co.nz/introduction.html">R for Data Science</a> for more info.</p>
</section>
<section id="visualisations" class="level1 tabset">
<h1 class="tabset">Visualisations</h1>
<p>Sometimes I have a lot of plots (like, a lot!). Perhaps generated from a loop that outputs a list of related plots. It is possible to programatically generate panel tabsets rather that repeatedly writing out the heading <code>#</code> and inserting the plot (e.g., <code>plot_list[[1]]</code>). As an example, I’ve grabbed a couple of plots from <a href="https://allisonhorst.github.io/palmerpenguins/articles/examples.html">Alison Horst</a> again.</p>
<div class="cell">
<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co"># A list of plots:</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>plot_list <span class="ot"><-</span> penguins <span class="sc">|></span></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">split</span>(penguins<span class="sc">$</span>species) <span class="sc">|></span></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">lapply</span>(<span class="cf">function</span>(x){</span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(x, <span class="fu">aes</span>(<span class="at">x =</span> flipper_length_mm, <span class="at">y =</span> body_mass_g)) <span class="sc">+</span> </span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>() <span class="sc">+</span></span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_minimal</span>()</span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a> }) </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><span class="co"># Make some heading names:</span></span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a>headings <span class="ot"><-</span> <span class="fu">names</span>(plot_list)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<section id="plot-tabs" class="level2">
<h2 class="anchored" data-anchor-id="plot-tabs">Plot tabs</h2>
<p>The code might be a little complicated but useful to reduce the length and manual work if you have a lot of outputs.</p>
<div class="tabset-margin-container"></div><div class="panel-tabset">
<ul class="nav nav-tabs" role="tablist"><li class="nav-item" role="presentation"><a class="nav-link active" id="tabset-1-1-tab" data-bs-toggle="tab" data-bs-target="#tabset-1-1" role="tab" aria-controls="tabset-1-1" aria-selected="true" href="">Adelie</a></li><li class="nav-item" role="presentation"><a class="nav-link" id="tabset-1-2-tab" data-bs-toggle="tab" data-bs-target="#tabset-1-2" role="tab" aria-controls="tabset-1-2" aria-selected="false" href="">Chinstrap</a></li><li class="nav-item" role="presentation"><a class="nav-link" id="tabset-1-3-tab" data-bs-toggle="tab" data-bs-target="#tabset-1-3" role="tab" aria-controls="tabset-1-3" aria-selected="false" href="">Gentoo</a></li></ul>
<div class="tab-content">
<div id="tabset-1-1" class="tab-pane active" role="tabpanel" aria-labelledby="tabset-1-1-tab">
<p><img src="template_complete_files/figure-html/unnamed-chunk-2-1.png" class="img-fluid" width="672"></p>
</div>
<div id="tabset-1-2" class="tab-pane" role="tabpanel" aria-labelledby="tabset-1-2-tab">
<p><img src="template_complete_files/figure-html/unnamed-chunk-2-2.png" class="img-fluid" width="672"></p>
</div>
<div id="tabset-1-3" class="tab-pane" role="tabpanel" aria-labelledby="tabset-1-3-tab">
<p><img src="template_complete_files/figure-html/unnamed-chunk-2-3.png" class="img-fluid" width="672"></p>
</div>
</div>
</div>
</section>
</section>
<section id="to-do" class="level1">
<h1>To do</h1>
<p>I sometimes keep a project to-do list here</p>
<ul class="task-list">
<li><p><label><input type="checkbox" checked="">Get up</label></p></li>
<li><p><label><input type="checkbox" checked="">Put on pants</label></p></li>
<li><p><label><input type="checkbox">Present workshop</label></p></li>
</ul>
</section>
<section id="final-remarks" class="level1">
<h1>Final remarks</h1>
<p>This workshop is primarily designed to introduce you to tools and useful features in Quarto. Regardless of your workflow (which this template may not fit!), hopefully you will have the tools to make sharing results and colaborating with supervisors and researchers much easier.</p>
</section>
<section id="useful-links" class="level1">
<h1>Useful links</h1>
<p><a href="https://biostats-r.github.io/biostats/quarto/">Biostats</a> - very useful resource for authoring documents in Quarto.</p>
<p><a href="https://github.com/mcanouil/awesome-quarto">Awsome Quarto</a> - a big list of Quarto things.</p>
<p><a href="https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content">Generating a DOI using Zenodo</a></p>
<section id="references" class="level3">
<h3 class="anchored" data-anchor-id="references">References</h3>
<p>References will <a href="https://quarto.org/docs/authoring/citations.html#bibliography-generation">appear here</a>!</p>
<div id="refs" role="list">
</div>
</section>
</section>
</main>
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const manageTransitions = (selector, allowTransitions) => {
const els = window.document.querySelectorAll(selector);
for (let i=0; i < els.length; i++) {
const el = els[i];
if (allowTransitions) {
el.classList.remove('notransition');
} else {
el.classList.add('notransition');
}
}
}
const toggleGiscusIfUsed = (isAlternate, darkModeDefault) => {
const baseTheme = document.querySelector('#giscus-base-theme')?.value ?? 'light';
const alternateTheme = document.querySelector('#giscus-alt-theme')?.value ?? 'dark';
let newTheme = '';
if(darkModeDefault) {
newTheme = isAlternate ? baseTheme : alternateTheme;
} else {
newTheme = isAlternate ? alternateTheme : baseTheme;
}
const changeGiscusTheme = () => {
// From: https://github.com/giscus/giscus/issues/336
const sendMessage = (message) => {
const iframe = document.querySelector('iframe.giscus-frame');
if (!iframe) return;
iframe.contentWindow.postMessage({ giscus: message }, 'https://giscus.app');
}
sendMessage({
setConfig: {
theme: newTheme
}
});
}
const isGiscussLoaded = window.document.querySelector('iframe.giscus-frame') !== null;
if (isGiscussLoaded) {
changeGiscusTheme();
}
}
const toggleColorMode = (alternate) => {
// Switch the stylesheets
const alternateStylesheets = window.document.querySelectorAll('link.quarto-color-scheme.quarto-color-alternate');
manageTransitions('#quarto-margin-sidebar .nav-link', false);
if (alternate) {
enableStylesheet(alternateStylesheets);
for (const sheetNode of alternateStylesheets) {
if (sheetNode.id === "quarto-bootstrap") {
toggleBodyColorMode(sheetNode);
}
}
} else {
disableStylesheet(alternateStylesheets);
toggleBodyColorPrimary();
}
manageTransitions('#quarto-margin-sidebar .nav-link', true);
// Switch the toggles
const toggles = window.document.querySelectorAll('.quarto-color-scheme-toggle');
for (let i=0; i < toggles.length; i++) {
const toggle = toggles[i];
if (toggle) {
if (alternate) {
toggle.classList.add("alternate");
} else {
toggle.classList.remove("alternate");
}
}
}
// Hack to workaround the fact that safari doesn't
// properly recolor the scrollbar when toggling (#1455)
if (navigator.userAgent.indexOf('Safari') > 0 && navigator.userAgent.indexOf('Chrome') == -1) {
manageTransitions("body", false);
window.scrollTo(0, 1);
setTimeout(() => {
window.scrollTo(0, 0);
manageTransitions("body", true);
}, 40);
}
}
const isFileUrl = () => {
return window.location.protocol === 'file:';
}
const hasAlternateSentinel = () => {
let styleSentinel = getColorSchemeSentinel();
if (styleSentinel !== null) {
return styleSentinel === "alternate";
} else {
return false;
}
}
const setStyleSentinel = (alternate) => {
const value = alternate ? "alternate" : "default";
if (!isFileUrl()) {
window.localStorage.setItem("quarto-color-scheme", value);
} else {
localAlternateSentinel = value;
}
}
const getColorSchemeSentinel = () => {
if (!isFileUrl()) {
const storageValue = window.localStorage.getItem("quarto-color-scheme");
return storageValue != null ? storageValue : localAlternateSentinel;
} else {
return localAlternateSentinel;
}
}
const darkModeDefault = false;
let localAlternateSentinel = darkModeDefault ? 'alternate' : 'default';
// Dark / light mode switch
window.quartoToggleColorScheme = () => {
// Read the current dark / light value
let toAlternate = !hasAlternateSentinel();
toggleColorMode(toAlternate);
setStyleSentinel(toAlternate);
toggleGiscusIfUsed(toAlternate, darkModeDefault);
};
// Ensure there is a toggle, if there isn't float one in the top right
if (window.document.querySelector('.quarto-color-scheme-toggle') === null) {
const a = window.document.createElement('a');
a.classList.add('top-right');
a.classList.add('quarto-color-scheme-toggle');
a.href = "";
a.onclick = function() { try { window.quartoToggleColorScheme(); } catch {} return false; };
const i = window.document.createElement("i");
i.classList.add('bi');
a.appendChild(i);
window.document.body.appendChild(a);
}
// Switch to dark mode if need be
if (hasAlternateSentinel()) {
toggleColorMode(true);
} else {
toggleColorMode(false);
}
const icon = "";
const anchorJS = new window.AnchorJS();
anchorJS.options = {
placement: 'right',
icon: icon
};
anchorJS.add('.anchored');
const isCodeAnnotation = (el) => {
for (const clz of el.classList) {
if (clz.startsWith('code-annotation-')) {
return true;
}
}
return false;
}
const clipboard = new window.ClipboardJS('.code-copy-button', {
text: function(trigger) {
const codeEl = trigger.previousElementSibling.cloneNode(true);
for (const childEl of codeEl.children) {
if (isCodeAnnotation(childEl)) {
childEl.remove();
}
}
return codeEl.innerText;
}
});
clipboard.on('success', function(e) {
// button target
const button = e.trigger;
// don't keep focus
button.blur();
// flash "checked"
button.classList.add('code-copy-button-checked');
var currentTitle = button.getAttribute("title");
button.setAttribute("title", "Copied!");
let tooltip;
if (window.bootstrap) {
button.setAttribute("data-bs-toggle", "tooltip");
button.setAttribute("data-bs-placement", "left");
button.setAttribute("data-bs-title", "Copied!");
tooltip = new bootstrap.Tooltip(button,
{ trigger: "manual",
customClass: "code-copy-button-tooltip",
offset: [0, -8]});
tooltip.show();
}
setTimeout(function() {
if (tooltip) {
tooltip.hide();
button.removeAttribute("data-bs-title");
button.removeAttribute("data-bs-toggle");
button.removeAttribute("data-bs-placement");
}
button.setAttribute("title", currentTitle);
button.classList.remove('code-copy-button-checked');
}, 1000);
// clear code selection
e.clearSelection();
});
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp('/' + window.location.host + '/');
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// target, if specified
link.setAttribute("target", "_blank");
if (link.getAttribute("rel") === null) {
link.setAttribute("rel", "noopener");
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
maxWidth: 500,
delay: 100,
arrow: false,
appendTo: function(el) {
return el.parentElement;
},
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start',
};
if (contentFn) {
config.content = contentFn;
}
if (onTriggerFn) {
config.onTrigger = onTriggerFn;
}
if (onUntriggerFn) {
config.onUntrigger = onUntriggerFn;
}
window.tippy(el, config);
}
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
for (var i=0; i<noterefs.length; i++) {
const ref = noterefs[i];
tippyHover(ref, function() {
// use id or data attribute instead here
let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
const processXRef = (id, note) => {
// Strip column container classes
const stripColumnClz = (el) => {
el.classList.remove("page-full", "page-columns");
if (el.children) {
for (const child of el.children) {
stripColumnClz(child);
}
}
}
stripColumnClz(note)
if (id === null || id.startsWith('sec-')) {
// Special case sections, only their first couple elements
const container = document.createElement("div");
if (note.children && note.children.length > 2) {
container.appendChild(note.children[0].cloneNode(true));
for (let i = 1; i < note.children.length; i++) {
const child = note.children[i];
if (child.tagName === "P" && child.innerText === "") {
continue;
} else {
container.appendChild(child.cloneNode(true));
break;
}
}
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(container);
}
return container.innerHTML
} else {
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(note);
}
return note.innerHTML;
}
} else {
// Remove any anchor links if they are present
const anchorLink = note.querySelector('a.anchorjs-link');
if (anchorLink) {
anchorLink.remove();
}
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(note);
}
// TODO in 1.5, we should make sure this works without a callout special case
if (note.classList.contains("callout")) {
return note.outerHTML;
} else {
return note.innerHTML;
}
}
}
for (var i=0; i<xrefs.length; i++) {
const xref = xrefs[i];
tippyHover(xref, undefined, function(instance) {
instance.disable();
let url = xref.getAttribute('href');
let hash = undefined;
if (url.startsWith('#')) {
hash = url;
} else {
try { hash = new URL(url).hash; } catch {}
}
if (hash) {
const id = hash.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
if (note !== null) {
try {
const html = processXRef(id, note.cloneNode(true));
instance.setContent(html);
} finally {
instance.enable();
instance.show();
}
} else {
// See if we can fetch this
fetch(url.split('#')[0])
.then(res => res.text())
.then(html => {
const parser = new DOMParser();
const htmlDoc = parser.parseFromString(html, "text/html");
const note = htmlDoc.getElementById(id);
if (note !== null) {
const html = processXRef(id, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
} else {
// See if we can fetch a full url (with no hash to target)
// This is a special case and we should probably do some content thinning / targeting
fetch(url)
.then(res => res.text())
.then(html => {
const parser = new DOMParser();
const htmlDoc = parser.parseFromString(html, "text/html");
const note = htmlDoc.querySelector('main.content');
if (note !== null) {
// This should only happen for chapter cross references
// (since there is no id in the URL)
// remove the first header
if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
note.children[0].remove();
}
const html = processXRef(null, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
}, function(instance) {
});
}
let selectedAnnoteEl;
const selectorForAnnotation = ( cell, annotation) => {
let cellAttr = 'data-code-cell="' + cell + '"';
let lineAttr = 'data-code-annotation="' + annotation + '"';
const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
return selector;
}
const selectCodeLines = (annoteEl) => {
const doc = window.document;
const targetCell = annoteEl.getAttribute("data-target-cell");
const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
const lines = annoteSpan.getAttribute("data-code-lines").split(",");
const lineIds = lines.map((line) => {
return targetCell + "-" + line;
})
let top = null;
let height = null;
let parent = null;
if (lineIds.length > 0) {
//compute the position of the single el (top and bottom and make a div)
const el = window.document.getElementById(lineIds[0]);
top = el.offsetTop;
height = el.offsetHeight;
parent = el.parentElement.parentElement;
if (lineIds.length > 1) {
const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
const bottom = lastEl.offsetTop + lastEl.offsetHeight;
height = bottom - top;
}
if (top !== null && height !== null && parent !== null) {
// cook up a div (if necessary) and position it
let div = window.document.getElementById("code-annotation-line-highlight");
if (div === null) {
div = window.document.createElement("div");
div.setAttribute("id", "code-annotation-line-highlight");
div.style.position = 'absolute';
parent.appendChild(div);
}
div.style.top = top - 2 + "px";
div.style.height = height + 4 + "px";
div.style.left = 0;
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
if (gutterDiv === null) {
gutterDiv = window.document.createElement("div");
gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
gutterDiv.style.position = 'absolute';
const codeCell = window.document.getElementById(targetCell);
const gutter = codeCell.querySelector('.code-annotation-gutter');
gutter.appendChild(gutterDiv);
}
gutterDiv.style.top = top - 2 + "px";
gutterDiv.style.height = height + 4 + "px";
}
selectedAnnoteEl = annoteEl;
}
};
const unselectCodeLines = () => {
const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
elementsIds.forEach((elId) => {
const div = window.document.getElementById(elId);
if (div) {
div.remove();
}
});
selectedAnnoteEl = undefined;
};
// Handle positioning of the toggle
window.addEventListener(
"resize",
throttle(() => {
elRect = undefined;
if (selectedAnnoteEl) {
selectCodeLines(selectedAnnoteEl);
}
}, 10)
);
function throttle(fn, ms) {
let throttle = false;
let timer;
return (...args) => {
if(!throttle) { // first call gets through
fn.apply(this, args);
throttle = true;
} else { // all the others get throttled
if(timer) clearTimeout(timer); // cancel #2
timer = setTimeout(() => {
fn.apply(this, args);
timer = throttle = false;
}, ms);
}
};
}
// Attach click handler to the DT
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
for (const annoteDlNode of annoteDls) {
annoteDlNode.addEventListener('click', (event) => {
const clickedEl = event.target;
if (clickedEl !== selectedAnnoteEl) {
unselectCodeLines();
const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
if (activeEl) {
activeEl.classList.remove('code-annotation-active');
}
selectCodeLines(clickedEl);
clickedEl.classList.add('code-annotation-active');
} else {
// Unselect the line
unselectCodeLines();
clickedEl.classList.remove('code-annotation-active');
}
});
}
const findCites = (el) => {
const parentEl = el.parentElement;
if (parentEl) {
const cites = parentEl.dataset.cites;
if (cites) {
return {
el,
cites: cites.split(' ')
};
} else {
return findCites(el.parentElement)
}
} else {
return undefined;
}
};
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
const ref = bibliorefs[i];
const citeInfo = findCites(ref);
if (citeInfo) {
tippyHover(citeInfo.el, function() {
var popup = window.document.createElement('div');
citeInfo.cites.forEach(function(cite) {
var citeDiv = window.document.createElement('div');
citeDiv.classList.add('hanging-indent');
citeDiv.classList.add('csl-entry');
var biblioDiv = window.document.getElementById('ref-' + cite);
if (biblioDiv) {
citeDiv.innerHTML = biblioDiv.innerHTML;
}
popup.appendChild(citeDiv);
});
return popup.innerHTML;
});
}
}
});
</script>
</div> <!-- /content -->
</body></html>