2020-04-27 20:35:41 +00:00
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<!DOCTYPE html>
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<html>
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<head>
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<meta charset="utf-8" />
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<meta name="generator" content="pandoc" />
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<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
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<title>Oncology Extension</title>
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2023-03-28 16:28:17 +00:00
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<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
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2022-01-13 18:59:03 +00:00
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<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
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2020-04-27 20:35:41 +00:00
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
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<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
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<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
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2022-01-13 18:59:03 +00:00
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<style>h1 {font-size: 34px;}
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h1.title {font-size: 38px;}
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h2 {font-size: 30px;}
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h3 {font-size: 24px;}
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h4 {font-size: 18px;}
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h5 {font-size: 16px;}
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h6 {font-size: 12px;}
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code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
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pre:not([class]) { background-color: white }</style>
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2020-04-27 20:35:41 +00:00
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<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
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<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
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<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
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<script src="site_libs/navigation-1.1/tabsets.js"></script>
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<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
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<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
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<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
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<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
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<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
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2021-01-06 15:52:57 +00:00
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<style type="text/css">
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code{white-space: pre-wrap;}
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span.smallcaps{font-variant: small-caps;}
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span.underline{text-decoration: underline;}
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div.column{display: inline-block; vertical-align: top; width: 50%;}
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div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
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ul.task-list{list-style: none;}
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</style>
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2020-04-27 20:35:41 +00:00
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<style type="text/css">code{white-space: pre;}</style>
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<script type="text/javascript">
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if (window.hljs) {
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hljs.configure({languages: []});
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hljs.initHighlightingOnLoad();
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if (document.readyState && document.readyState === "complete") {
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window.setTimeout(function() { hljs.initHighlighting(); }, 0);
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}
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}
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</script>
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2021-01-06 15:52:57 +00:00
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2022-07-27 01:48:28 +00:00
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2020-04-27 20:35:41 +00:00
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<link rel="stylesheet" href="style.css" type="text/css" />
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<style type = "text/css">
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.main-container {
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max-width: 940px;
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margin-left: auto;
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margin-right: auto;
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}
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img {
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max-width:100%;
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}
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.tabbed-pane {
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padding-top: 12px;
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}
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.html-widget {
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margin-bottom: 20px;
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}
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button.code-folding-btn:focus {
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outline: none;
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}
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summary {
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display: list-item;
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}
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2022-07-27 01:48:28 +00:00
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details > summary > p:only-child {
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display: inline;
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}
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2022-01-13 18:59:03 +00:00
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pre code {
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padding: 0;
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}
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2020-04-27 20:35:41 +00:00
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</style>
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<style type="text/css">
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.dropdown-submenu {
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position: relative;
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}
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.dropdown-submenu>.dropdown-menu {
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top: 0;
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left: 100%;
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margin-top: -6px;
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margin-left: -1px;
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border-radius: 0 6px 6px 6px;
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}
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.dropdown-submenu:hover>.dropdown-menu {
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display: block;
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}
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.dropdown-submenu>a:after {
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display: block;
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content: " ";
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float: right;
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width: 0;
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height: 0;
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border-color: transparent;
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border-style: solid;
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border-width: 5px 0 5px 5px;
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border-left-color: #cccccc;
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margin-top: 5px;
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margin-right: -10px;
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}
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.dropdown-submenu:hover>a:after {
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2022-01-13 18:59:03 +00:00
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border-left-color: #adb5bd;
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2020-04-27 20:35:41 +00:00
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}
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.dropdown-submenu.pull-left {
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float: none;
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}
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.dropdown-submenu.pull-left>.dropdown-menu {
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left: -100%;
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margin-left: 10px;
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border-radius: 6px 0 6px 6px;
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}
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</style>
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2022-01-13 18:59:03 +00:00
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<script type="text/javascript">
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2020-04-27 20:35:41 +00:00
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// manage active state of menu based on current page
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$(document).ready(function () {
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// active menu anchor
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href = window.location.pathname
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href = href.substr(href.lastIndexOf('/') + 1)
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if (href === "")
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href = "index.html";
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var menuAnchor = $('a[href="' + href + '"]');
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2023-02-08 20:04:22 +00:00
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// mark the anchor link active (and if it's in a dropdown, also mark that active)
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var dropdown = menuAnchor.closest('li.dropdown');
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if (window.bootstrap) { // Bootstrap 4+
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menuAnchor.addClass('active');
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dropdown.find('> .dropdown-toggle').addClass('active');
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} else { // Bootstrap 3
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menuAnchor.parent().addClass('active');
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dropdown.addClass('active');
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}
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2022-01-13 18:59:03 +00:00
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// Navbar adjustments
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var navHeight = $(".navbar").first().height() + 15;
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var style = document.createElement('style');
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var pt = "padding-top: " + navHeight + "px; ";
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var mt = "margin-top: -" + navHeight + "px; ";
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var css = "";
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// offset scroll position for anchor links (for fixed navbar)
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for (var i = 1; i <= 6; i++) {
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css += ".section h" + i + "{ " + pt + mt + "}\n";
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}
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style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
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document.head.appendChild(style);
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2020-04-27 20:35:41 +00:00
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});
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</script>
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<!-- tabsets -->
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<style type="text/css">
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.tabset-dropdown > .nav-tabs {
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display: inline-table;
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max-height: 500px;
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min-height: 44px;
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overflow-y: auto;
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border: 1px solid #ddd;
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border-radius: 4px;
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}
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2023-03-28 16:28:17 +00:00
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.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
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content: "\e259";
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2020-04-27 20:35:41 +00:00
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font-family: 'Glyphicons Halflings';
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display: inline-block;
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padding: 10px;
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border-right: 1px solid #ddd;
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
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2023-03-28 16:28:17 +00:00
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content: "\e258";
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2020-04-27 20:35:41 +00:00
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font-family: 'Glyphicons Halflings';
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2023-03-28 16:28:17 +00:00
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border: none;
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2020-04-27 20:35:41 +00:00
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}
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.tabset-dropdown > .nav-tabs > li.active {
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display: block;
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}
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.tabset-dropdown > .nav-tabs > li > a,
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.tabset-dropdown > .nav-tabs > li > a:focus,
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.tabset-dropdown > .nav-tabs > li > a:hover {
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border: none;
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display: inline-block;
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border-radius: 4px;
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background-color: transparent;
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}
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.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
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display: block;
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float: none;
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}
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.tabset-dropdown > .nav-tabs > li {
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display: none;
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}
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</style>
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<!-- code folding -->
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<style type="text/css">
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#TOC {
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margin: 25px 0px 20px 0px;
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}
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@media (max-width: 768px) {
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#TOC {
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position: relative;
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width: 100%;
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}
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}
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@media print {
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.toc-content {
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/* see https://github.com/w3c/csswg-drafts/issues/4434 */
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float: right;
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}
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}
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.toc-content {
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padding-left: 30px;
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padding-right: 40px;
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}
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div.main-container {
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max-width: 1200px;
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}
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div.tocify {
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width: 20%;
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max-width: 260px;
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max-height: 85%;
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}
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@media (min-width: 768px) and (max-width: 991px) {
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div.tocify {
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width: 25%;
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}
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}
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@media (max-width: 767px) {
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div.tocify {
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width: 100%;
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max-width: none;
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}
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}
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.tocify ul, .tocify li {
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line-height: 20px;
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}
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.tocify-subheader .tocify-item {
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font-size: 0.90em;
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}
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.tocify .list-group-item {
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border-radius: 0px;
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}
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</style>
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Background
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CDM Versions
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<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
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How to
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<a href="cdmRPackage.html">Use the CDM R Package</a>
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<a href="drug_dose.html">Calculate Drug Dose</a>
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<a href="sqlScripts.html">SQL Scripts</a>
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2022-01-13 18:59:03 +00:00
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2020-04-27 20:35:41 +00:00
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<h1 class="title toc-ignore">Oncology Extension</h1>
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</div>
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2023-02-08 20:04:22 +00:00
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<div id="omop-common-data-model-oncology-extension-documentation"
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class="section level2">
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2020-04-27 20:35:41 +00:00
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<h2>OMOP Common Data Model Oncology Extension Documentation</h2>
|
2023-02-08 20:04:22 +00:00
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<p>This documentation details the ratified proposal of adding an
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oncology extension to the OMOP CDM. These tables and fields will become
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part of the next release (v6.1) of the Common Data Model. Below are
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their descriptions; showing <em>additions</em> to the model only. For
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example, two fields were added to the MEASUREMENT table as part of this
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extension so only those two fields are listed below for MEASUREMENT
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instead of the entire table. For more information, please see the <a
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href="https://github.com/OHDSI/OncologyWG/wiki">OMOP Oncology wiki
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site</a>.</p>
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<p>The DDLs for these tables are located on the Oncology github, as
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detailed in the <a
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href="https://github.com/OHDSI/OncologyWG/wiki/Oncology-CDM-Extension-Installation">installation
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instructions</a>.</p>
|
2023-03-28 16:28:17 +00:00
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<pre><code>## Warning in read.table(file = file, header = header, sep = sep, quote = quote, :
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## incomplete final line found by readTableHeader on
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## '../inst/csv/OMOP_CDM_Oncology_Ex_Table_Level.csv'</code></pre>
|
2020-04-27 20:35:41 +00:00
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<div id="episode" class="section level3 tabset tabset-pills">
|
2021-01-06 15:52:57 +00:00
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<h3 class="tabset tabset-pills">EPISODE</h3>
|
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<p><strong>Table Description</strong></p>
|
2023-02-08 20:04:22 +00:00
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<p>The EPISODE table aggregates lower-level clinical events
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(VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE)
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into a higher-level abstraction representing clinically and analytically
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relevant disease phases,outcomes and treatments. The EPISODE_EVENT table
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connects qualifying clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE,
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PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate EPISODE entry.
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For example cancers including their development over time, their
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treatment, and final resolution.</p>
|
2021-09-22 19:39:44 +00:00
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<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
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<p>Valid Episode Concepts belong to the ‘Episode’ domain. For cancer
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episodes please see [article], for non-cancer episodes please see
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[article]. If your source data does not have all episodes that are
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relevant to the therapeutic area, write only those you can easily derive
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from the data. It is understood that that table is not currently
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expected to be comprehensive.</p>
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2020-04-27 20:35:41 +00:00
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</div>
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<div id="episode_event" class="section level3 tabset tabset-pills">
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2021-01-06 15:52:57 +00:00
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<h3 class="tabset tabset-pills">EPISODE_EVENT</h3>
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2020-04-27 20:35:41 +00:00
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<p><strong>Table Description</strong></p>
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2023-02-08 20:04:22 +00:00
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<p>The EPISODE_EVENT table connects qualifying clinical events (such as
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CONDITION_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, MEASUREMENT)
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to the appropriate EPISODE entry. For example, linking the precise
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location of the metastasis (cancer modifier in MEASUREMENT) to the
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disease episode.</p>
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2021-09-22 19:39:44 +00:00
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<p><strong>User Guide</strong></p>
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2023-02-08 20:04:22 +00:00
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<p>This connecting table is used instead of the FACT_RELATIONSHIP table
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for linking low-level events to abstracted Episodes.</p>
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2020-04-27 20:35:41 +00:00
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<p><strong>ETL Conventions</strong></p>
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2023-02-08 20:04:22 +00:00
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<p>Some episodes may not have links to any underlying clinical events.
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For such episodes, the EPISODE_EVENT table is not populated.</p>
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2020-04-27 20:35:41 +00:00
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</div>
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<div id="measurement" class="section level3 tabset tabset-pills">
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2021-01-06 15:52:57 +00:00
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<h3 class="tabset tabset-pills">MEASUREMENT</h3>
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2020-04-27 20:35:41 +00:00
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<p><strong>Table Description</strong></p>
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2023-02-08 20:04:22 +00:00
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<p>The MEASUREMENT table contains records of Measurement,
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i.e. structured values (numerical or categorical) obtained through
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systematic and standardized examination or testing of a Person or
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Person’s sample. The MEASUREMENT table contains both orders and results
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of such Measurements as laboratory tests, vital signs, quantitative
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findings from pathology reports, etc. Measurements are stored as
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attribute value pairs, with the attribute as the Measurement Concept and
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the value representing the result. The value can be a Concept (stored in
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VALUE_AS_CONCEPT), or a numerical value (VALUE_AS_NUMBER) with a Unit
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(UNIT_CONCEPT_ID).</p>
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2020-04-27 20:35:41 +00:00
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<p><strong>User Guide</strong></p>
|
2023-02-08 20:04:22 +00:00
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<p>Measurements differ from Observations in that they require a
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standardized test or some other activity to generate a quantitative or
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qualitative result.</p>
|
2020-04-27 20:35:41 +00:00
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</div>
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</div>
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</div>
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</div>
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</div>
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<script>
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// add bootstrap table styles to pandoc tables
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function bootstrapStylePandocTables() {
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2021-01-06 15:52:57 +00:00
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$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
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2020-04-27 20:35:41 +00:00
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}
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$(document).ready(function () {
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bootstrapStylePandocTables();
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});
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</script>
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<!-- tabsets -->
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<script>
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$(document).ready(function () {
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window.buildTabsets("TOC");
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});
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$(document).ready(function () {
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$('.tabset-dropdown > .nav-tabs > li').click(function () {
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2022-01-13 18:59:03 +00:00
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$(this).parent().toggleClass('nav-tabs-open');
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2020-04-27 20:35:41 +00:00
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});
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});
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</script>
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<!-- code folding -->
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<script>
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$(document).ready(function () {
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|
2022-01-13 18:59:03 +00:00
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// temporarily add toc-ignore selector to headers for the consistency with Pandoc
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$('.unlisted.unnumbered').addClass('toc-ignore')
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2020-04-27 20:35:41 +00:00
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// move toc-ignore selectors from section div to header
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$('div.section.toc-ignore')
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.removeClass('toc-ignore')
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.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
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// establish options
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var options = {
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selectors: "h1,h2,h3,h4,h5",
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theme: "bootstrap3",
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context: '.toc-content',
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hashGenerator: function (text) {
|
2021-01-06 15:52:57 +00:00
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return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
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2020-04-27 20:35:41 +00:00
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},
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ignoreSelector: ".toc-ignore",
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scrollTo: 0
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};
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options.showAndHide = true;
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options.smoothScroll = true;
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// tocify
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var toc = $("#TOC").tocify(options).data("toc-tocify");
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});
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</script>
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<!-- dynamically load mathjax for compatibility with self-contained -->
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<script>
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(function () {
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var script = document.createElement("script");
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script.type = "text/javascript";
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script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
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document.getElementsByTagName("head")[0].appendChild(script);
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})();
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</script>
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</body>
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</html>
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