Built site for gh-pages

elong0527 · Feb 21, 2024 · c7cad58 · c7cad58
1 parent 6270525
commit c7cad58
Show file tree

Hide file tree

Showing 55 changed files with 4,121 additions and 650 deletions.
diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-77920e31
+2da7e1a8
diff --git a/R-for-Clinical-Study-Reports-and-Submission.pdf b/R-for-Clinical-Study-Reports-and-Submission.pdf
diff --git a/index.html b/index.html
@@ -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">
 
@@ -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",
@@ -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"
@@ -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">
@@ -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>
@@ -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">
@@ -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">
@@ -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">
@@ -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>
@@ -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,
@@ -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"]');
@@ -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) => {
@@ -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");
@@ -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) {
@@ -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>
@@ -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>