Skip to content

Commit

Permalink
Built site for gh-pages
Browse files Browse the repository at this point in the history
  • Loading branch information
Quarto GHA Workflow Runner committed Feb 21, 2024
1 parent 6270525 commit c7cad58
Show file tree
Hide file tree
Showing 55 changed files with 4,121 additions and 650 deletions.
2 changes: 1 addition & 1 deletion .nojekyll
View file
Original file line number Diff line number Diff line change
@@ -1 +1 @@
77920e31
2da7e1a8
Binary file modified R-for-Clinical-Study-Reports-and-Submission.pdf
View file
Binary file not shown.
197 changes: 180 additions & 17 deletions index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.3.450">
<meta name="generator" content="quarto-1.4.550">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand Down Expand Up @@ -52,7 +52,13 @@
"collapse-after": 3,
"panel-placement": "start",
"type": "textbox",
"limit": 20,
"limit": 50,
"keyboard-shortcut": [
"f",
"/",
"s"
],
"show-item-context": false,
"language": {
"search-no-results-text": "No results",
"search-matching-documents-text": "matching documents",
Expand All @@ -61,6 +67,7 @@
"search-more-match-text": "more match in this document",
"search-more-matches-text": "more matches in this document",
"search-clear-button-title": "Clear",
"search-text-placeholder": "",
"search-detached-cancel-button-title": "Cancel",
"search-submit-button-title": "Submit",
"search-label": "Search"
Expand All @@ -80,7 +87,7 @@
<meta property="og:title" content="R for Clinical Study Reports and Submission">
<meta property="og:description" content="Learn how to prepare tables, listings, and figures for clinical study report and submit to regulatory agencies, the essential part of clinical trial development.">
<meta property="og:image" content="https://r4csr.org/images/preview.jpg">
<meta property="og:site-name" content="R for Clinical Study Reports and Submission">
<meta property="og:site_name" content="R for Clinical Study Reports and Submission">
<meta name="twitter:title" content="R for Clinical Study Reports and Submission">
<meta name="twitter:description" content="Learn how to prepare tables, listings, and figures for clinical study report and submit to regulatory agencies, the essential part of clinical trial development.">
<meta name="twitter:image" content="https://r4csr.org/images/preview.jpg">
Expand All @@ -89,17 +96,16 @@

<body class="nav-sidebar floating">


<div id="quarto-search-results"></div>
<header id="quarto-header" class="headroom fixed-top">
<nav class="quarto-secondary-nav">
<div class="container-fluid d-flex">
<button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
<button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
<i class="bi bi-layout-text-sidebar-reverse"></i>
</button>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./index.html">Welcome</a></li></ol></nav>
<a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
</a>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./index.html">Welcome</a></li></ol></nav>
<a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
</a>
<button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
<i class="bi bi-search"></i>
</button>
Expand All @@ -109,12 +115,12 @@
<!-- content -->
<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article">
<!-- sidebar -->
<nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
<nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
<div class="pt-lg-2 mt-2 text-left sidebar-header">
<div class="sidebar-title mb-0 py-0">
<a href="./">R for Clinical Study Reports and Submission</a>
<div class="sidebar-tools-main tools-wide">
<a href="https://github.com/elong0527/r4csr" rel="" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
<a href="https://github.com/elong0527/r4csr" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
<div class="dropdown">
<a href="" title="Share" id="quarto-navigation-tool-dropdown-0" class="quarto-navigation-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false" aria-label="Share"><i class="bi bi-share"></i></a>
<ul class="dropdown-menu" aria-labelledby="quarto-navigation-tool-dropdown-0">
Expand Down Expand Up @@ -291,7 +297,7 @@
</ul>
</div>
</nav>
<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
<!-- margin-sidebar -->
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<nav id="TOC" role="doc-toc" class="toc-active">
Expand All @@ -304,7 +310,7 @@ <h2 id="toc-title">Table of contents</h2>
<li><a href="#license" id="toc-license" class="nav-link" data-scroll-target="#license">License</a></li>
</ul></li>
</ul>
<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/elong0527/r4csr/edit/main/index.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/elong0527/r4csr/issues/new" class="toc-action">Report an issue</a></p><p><a href="https://github.com/elong0527/r4csr/blob/main/index.qmd" class="toc-action">View source</a></p></div></div></nav>
<div class="toc-actions"><ul><li><a href="https://github.com/elong0527/r4csr/edit/main/index.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/elong0527/r4csr/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li><li><a href="https://github.com/elong0527/r4csr/blob/main/index.qmd" class="toc-action"><i class="bi empty"></i>View source</a></li></ul></div></nav>
</div>
<!-- main -->
<main class="content" id="quarto-document-content">
Expand Down Expand Up @@ -338,9 +344,11 @@ <h1 class="title">R for Clinical Study Reports and Submission</h1>
</div>



</header>



<section id="welcome" class="level1 unnumbered">
<h1 class="unnumbered">Welcome</h1><p><img src="images/cover.png" title="R for Clinical Study Reports and Submission" class="quarto-cover-image img-fluid"></p>
<p>Welcome to R for Clinical Study Reports and Submission. Clinical study reports (CSR) are crucial components in clinical trial development. A CSR is an “integrated” full scientific report of an individual clinical trials.</p>
Expand Down Expand Up @@ -495,10 +503,9 @@ <h2 class="unnumbered anchored" data-anchor-id="license">License</h2>
// clear code selection
e.clearSelection();
});
function tippyHover(el, contentFn) {
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
content: contentFn,
maxWidth: 500,
delay: 100,
arrow: false,
Expand All @@ -508,8 +515,17 @@ <h2 class="unnumbered anchored" data-anchor-id="license">License</h2>
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start'
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"]');
Expand All @@ -523,6 +539,125 @@ <h2 class="unnumbered anchored" data-anchor-id="license">License</h2>
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) => {
Expand Down Expand Up @@ -565,6 +700,7 @@ <h2 class="unnumbered anchored" data-anchor-id="license">License</h2>
}
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");
Expand All @@ -590,6 +726,32 @@ <h2 class="unnumbered anchored" data-anchor-id="license">License</h2>
});
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) {
Expand Down Expand Up @@ -653,7 +815,7 @@ <h2 class="unnumbered anchored" data-anchor-id="license">License</h2>
<div class="nav-page nav-page-previous">
</div>
<div class="nav-page nav-page-next">
<a href="./preface.html" class="pagination-link">
<a href="./preface.html" class="pagination-link" aria-label="Preface">
<span class="nav-page-text">Preface</span> <i class="bi bi-arrow-right-short"></i>
</a>
</div>
Expand All @@ -662,4 +824,5 @@ <h2 class="unnumbered anchored" data-anchor-id="license">License</h2>



</body></html>

<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/elong0527/r4csr/edit/main/index.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/elong0527/r4csr/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li><li><a href="https://github.com/elong0527/r4csr/blob/main/index.qmd" class="toc-action"><i class="bi empty"></i>View source</a></li></ul></div></div></div></footer></body></html>
Loading

0 comments on commit c7cad58

Please sign in to comment.