2021-09-22 19:39:44 +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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2021-11-19 14:22:53 +00:00
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<title>CDM R Package Demo</title>
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2021-09-22 19:39:44 +00:00
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2023-10-26 18:13:30 +00:00
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<script src="site_libs/header-attrs-2.25/header-attrs.js"></script>
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2021-11-19 14:22:53 +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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2021-09-22 19:39:44 +00:00
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<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
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2021-11-19 14:22:53 +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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2021-09-22 19:39:44 +00:00
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<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
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2023-10-26 18:13:30 +00:00
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<link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
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<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />
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2021-09-22 19:39:44 +00:00
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<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
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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 type="text/css">code{white-space: pre;}</style>
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2022-07-27 01:48:28 +00:00
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2021-09-22 19:39:44 +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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2021-11-19 14:22:53 +00:00
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pre code {
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padding: 0;
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}
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2021-09-22 19:39:44 +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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border-left-color: #adb5bd;
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2021-09-22 19:39:44 +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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2021-11-19 14:22:53 +00:00
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<script type="text/javascript">
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2021-09-22 19:39:44 +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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2021-11-19 14:22:53 +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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2021-09-22 19:39:44 +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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2023-10-26 18:13:30 +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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2021-09-22 19:39:44 +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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2023-10-26 18:13:30 +00:00
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content: "\e258";
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2021-09-22 19:39:44 +00:00
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font-family: 'Glyphicons Halflings';
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2023-10-26 18:13:30 +00:00
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border: none;
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2021-09-22 19:39:44 +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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</head>
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<body>
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<div class="container-fluid main-container">
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<div class="navbar navbar-default navbar-fixed-top" role="navigation">
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<div class="container">
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<div class="navbar-header">
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2022-07-27 01:48:28 +00:00
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
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2021-09-22 19:39:44 +00:00
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
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</button>
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<a class="navbar-brand" href="index.html"><div><img src="ohdsi16x16.png"></img> OMOP Common Data Model </div></a>
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</div>
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<div id="navbar" class="navbar-collapse collapse">
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<ul class="nav navbar-nav">
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<li>
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<a href="index.html">
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2023-02-08 20:04:22 +00:00
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<span class="fa fa-house"></span>
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2021-09-22 19:39:44 +00:00
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</a>
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</li>
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<li class="dropdown">
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2022-07-27 01:48:28 +00:00
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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2021-11-19 14:22:53 +00:00
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<span class="fa fa-landmark"></span>
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2021-09-22 19:39:44 +00:00
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Background
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="background.html">Model Background</a>
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</li>
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<li>
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<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
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</li>
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<li>
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<a href="vocabulary.html">How the Vocabulary is Built</a>
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</li>
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</ul>
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</li>
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<li class="dropdown">
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2022-07-27 01:48:28 +00:00
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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2021-11-19 14:22:53 +00:00
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<span class="fa fa-list-alt"></span>
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2021-09-22 19:39:44 +00:00
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Conventions
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="dataModelConventions.html">General Conventions</a>
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</li>
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<li>
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<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
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</li>
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<li>
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<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
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</li>
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</ul>
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</li>
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<li class="dropdown">
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2022-07-27 01:48:28 +00:00
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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2021-11-19 14:22:53 +00:00
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<span class="fa fa-history"></span>
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2021-09-22 19:39:44 +00:00
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CDM Versions
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="cdm30.html">CDM v3.0</a>
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</li>
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<li>
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<a href="cdm53.html">CDM v5.3</a>
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</li>
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<li class="dropdown-submenu">
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2021-09-22 19:39:44 +00:00
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2021-09-22 19:39:44 +00:00
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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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<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
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2021-09-22 19:39:44 +00:00
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How to
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2021-11-19 14:22:53 +00:00
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2021-09-22 19:39:44 +00:00
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2021-11-19 14:22:53 +00:00
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<h1 class="title toc-ignore"><strong>CDM R Package Demo</strong></h1>
|
2021-09-22 19:39:44 +00:00
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</div>
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|
2023-02-08 20:04:22 +00:00
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<p>Below is an example showing two different ways the CDM R package can
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be used to create the tables in your environment. First, it uses the
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<code>buildRelease</code> function to create the DDL files on your
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machine. Once you have these downloaded you can then run them in your
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SQL client to set up the empty CDM tables. Second, the script shows the
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<code>executeDdl</code> function that will connect up to your SQL client
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directly (assuming your dbms is one of the supported dialects) and
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instantiate the tables through R.</p>
|
2021-11-19 14:22:53 +00:00
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<pre class="r"><code>## First, install the package from GitHub
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install.packages("devtools")
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devtools::install_github("OHDSI/CommonDataModel")
|
2021-09-22 19:39:44 +00:00
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|
2021-11-19 14:22:53 +00:00
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## List the currently supported SQL dialects
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CommonDataModel::listSupportedDialects()
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## List the currently supported CDM versions
|
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|
CommonDataModel::listSupportedVersions()
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|
## There are multiple ways to generate the DDLs
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## 1. Use the buildRelease function to generate the text files in the dialect you choose.
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## This function will put the output files in the folder you specify
|
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CommonDataModel::buildRelease(cdmVersions = "5.4",
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targetDialects = "postgresql",
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outputfolder = "/pathToOutput")
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## 2. If you have an empty schema ready to go, the package will connect and instantiate
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## the tables for you.
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### 2a. To start, you need to download DatabaseConnector in order to connect to your database.
|
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devtools::install_github("DatabaseConnector")
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cd <- DatabaseConnector::createConnectionDetails(dbms = "postgresql",
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server = "localhost/ohdsi",
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user = "postgres",
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password = "postgres",
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pathToDriver = "/pathToDriver"
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)
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CommonDataModel::executeDdl(connectionDetails = cd,
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|
cdmVersion = "5.4",
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cdmDatabaseSchema = "ohdsi_demo"
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)</code></pre>
|
2021-09-22 19:39:44 +00:00
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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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$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
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}
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$(document).ready(function () {
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bootstrapStylePandocTables();
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});
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