adding index.html file

analysis/index.Rmd

+---
+title: "index"
+author: "Ruqian Lyu"
+date: "11/28/2021"
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## Introduction
+
+Application of `comapr` on public dataset 
+
+1 [comapr application](Crossover-identification-with-sscocaller-and-comapr.html)
\ No newline at end of file

public/site_libs/header-attrs-2.11/header-attrs.js

+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});

public/site_libs/navigation-1.1/codefolding.js

@@ -23,7 +23,6 @@ window.initializeCodeFolding = function(show) {
     // create a collapsable div to wrap the code in
     var div = $('<div class="collapse r-code-collapse"></div>');
     var showThis = (show || $(this).hasClass('fold-show')) && !$(this).hasClass('fold-hide');
-    if (showThis) div.addClass('in');
     var id = 'rcode-643E0F36' + currentIndex++;
     div.attr('id', id);
     $(this).before(div);
@@ -31,7 +30,7 @@ window.initializeCodeFolding = function(show) {
 
     // add a show code button right above
     var showCodeText = $('<span>' + (showThis ? 'Hide' : 'Code') + '</span>');
-    var showCodeButton = $('<button type="button" class="btn btn-default btn-xs code-folding-btn pull-right"></button>');
+    var showCodeButton = $('<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm code-folding-btn pull-right float-right"></button>');
     showCodeButton.append(showCodeText);
     showCodeButton
         .attr('data-toggle', 'collapse')
@@ -47,13 +46,27 @@ window.initializeCodeFolding = function(show) {
 
     div.before(buttonRow);
 
+    // show the div if necessary
+    if (showThis) div.collapse('show');
+
     // update state of button on show/hide
-    div.on('hidden.bs.collapse', function () {
+    //   * Change text
+    //   * add a class for intermediate states styling
+    div.on('hide.bs.collapse', function () {
       showCodeText.text('Code');
+      showCodeButton.addClass('btn-collapsing');
+    });
+    div.on('hidden.bs.collapse', function () {
+      showCodeButton.removeClass('btn-collapsing');
     });
     div.on('show.bs.collapse', function () {
       showCodeText.text('Hide');
+      showCodeButton.addClass('btn-expanding');
+    });
+    div.on('shown.bs.collapse', function () {
+      showCodeButton.removeClass('btn-expanding');
     });
+
   });
 
 }

public/site_libs/tocify-1.9.1/jquery.tocify.js

@@ -176,7 +176,7 @@
         self._setEventHandlers();
 
         // Binding to the Window load event to make sure the correct scrollTop is calculated
-        $(window).load(function() {
+        $(window).on("load", function() {
 
           // Sets the active TOC item
           self._setActiveElement(true);