Starting structure of gh-pages

index.md and the mneu bars are present

.gitignore

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+### R stuff to ignore
+.Rproj.user
+.Rhistory
+.RData
+
+
+### Jekyll stuff to ignore
+# "Add _site to .gitignore. The generated site should not be uploaded to GitHub since its gets generated by GitHub (https://gist.github.com/jedschneider/2890453)
+_site

Gemfile

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+source 'https://rubygems.org'
+gem 'github-pages'

Makefile

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+HTML_FILES := $(patsubst %.Rmd, %.html ,$(wildcard *.Rmd)) \
+              $(patsubst %.md, %.html ,$(wildcard *.md))
+
+all: clean html
+
+
+html: $(HTML_FILES)
+
+%.html: %.Rmd
+	R --vanilla --slave -e "rmarkdown::render('$<')"
+
+%.html: %.md
+	R --vanilla --slave -e "rmarkdown::render('$<')"
+
+.PHONY: clean
+clean:
+	$(RM) $(HTML_FILES)

NlsyLinks.Rproj

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+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: No
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+BuildType: Makefile

_config.yml

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+encoding: UTF-8
+
+permalink: pretty
+highlighter: rouge
+safe: false
+
+# Site details
+lang: en-US
+
+# Jekyll config
+exclude:
+  - Makefile
+  - README.md
+  - Gemfile
+  - Gemfile.lock
+
+logo: ./images/favicon.png

_output.yaml

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+html_document:
+  self_contained: false
+  theme: cerulean
+  highlight: textmate
+  css: include/custom.css
+  mathjax: null
+  toc: true
+  toc_depth: 2
+  lib_dir: libs
+  includes:
+    in_header: include/in_header.html
+    before_body: include/before_body.html
+    after_body: include/after_body.html
+
+md_document:
+  variant: markdown_github
+  toc: true
+  toc_depth: 2

include/after_body.html

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+<!-- start of after_body material from RMarkdown example http://rmarkdown.rstudio.com/ -->
+
+<!-- some extra javascript for older browsers -->
+<script type="text/javascript" src="libs/polyfill.js"></script>
+
+<script>
+
+// manage active state of menu based on current page
+$(document).ready(function () {
+
+    // active menu
+    href = window.location.pathname
+    href = href.substr(href.lastIndexOf('/') + 1)
+    $('a[href="' + href + '"]').parent().addClass('active');
+
+    // manage active menu header
+    if (href.startsWith('authoring_'))
+      $('a[href="' + 'authoring' + '"]').parent().addClass('active');
+    else if (href.endsWith('_format.html'))
+      $('a[href="' + 'formats' + '"]').parent().addClass('active');
+    else if (href.startsWith('developer_'))
+      $('a[href="' + 'developer' + '"]').parent().addClass('active');
+
+});
+
+</script>
+
+<!-- disqus -->
+<!--
+<div id="disqus_thread"></div>
+<script type="text/javascript">
+    /* * * CONFIGURATION VARIABLES: EDIT BEFORE PASTING INTO YOUR WEBPAGE * * */
+    var disqus_shortname = 'mreportingpublic'; // required: replace example with your forum shortname
+
+    /* * * DON'T EDIT BELOW THIS LINE * * */
+    (function() {
+        var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true;
+        dsq.src = '//' + disqus_shortname + '.disqus.com/embed.js';
+        (document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq);
+    })();
+</script>
+<noscript>Please enable JavaScript to view the <a href="http://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
+-->
+<!-- end of after_body material from RMarkdown example http://rmarkdown.rstudio.com/ -->

include/before_body.html

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+<!-- start of before_body material from RMarkdown example http://rmarkdown.rstudio.com/ -->
+<div class="navbar navbar-inverse navbar-default">
+  <div class="navbar-inner">
+    <div class="container">
+      <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
+        <!-- navbar will automatically collapse into a button when the screen size is too small–which is much friendlier to mobile devices: http://brizzled.clapper.org/blog/2012/03/05/using-twitter-bootstrap-with-jekyll/ -->
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <a class="brand" href="/NlsyLinks/">NlsyLinks</a>
+      <div class="nav-collapse collapse">
+        <ul class="nav">
+
+          <li class="dropdown">
+            <a href="funding" class="dropdown-toggle" data-toggle="dropdown">Description<b class="caret"></b></a>
+            <ul class="dropdown-menu">
+
+               <li><a href="history.html">History</a></li>
+               <li><a href="facilitating_research.html">Facilitating Research</a></li>
+
+            </ul>
+          </li>
+
+          <li class="dropdown">
+            <a href="funding" class="dropdown-toggle" data-toggle="dropdown">Datasets<b class="caret"></b></a>
+            <ul class="dropdown-menu">
+               <li class="nav-header">Kinship</li>
+               <li><a href="links_79_pair.html">Links79Pair</a></li>
+               <li><a href="links_79_pair_expanded.html">Links79PairExpanded</a></li>
+               <li class="divider"/>
+               <li class="nav-header">Nongenetic</li>
+               <li><a href="subject_details_79.html">SubjectDetails79</a></li>
+               <li><a href="extra_outcomes_79.html">ExtraOutcomes79</a></li>
+            </ul>
+          </li>
+
+          <li class="dropdown">
+            <a href="funding" class="dropdown-toggle" data-toggle="dropdown">Funding<b class="caret"></b></a>
+          </li>
+
+          <li class="dropdown">
+            <a href="funding" class="dropdown-toggle" data-toggle="dropdown">About<b class="caret"></b></a>
+            <ul class="dropdown-menu">
+               <li><a href="about_collaborators.html">Collaborators</a></li>
+               <li><a href="about_site.html">This Site</a></li>
+            </ul>
+          </li>
+
+        </ul>
+        <ul class="nav pull-right">
+          <a class="btn btn-primary" href="https://github.com/LiveOak/NlsyLinks">
+            <i class="fa fa-github fa-lg"></i>
+            Source Code
+          </a>
+        </ul>
+      </div><!--/.nav-collapse -->
+    </div>
+  </div>
+</div>
+<!-- end of before_body material from RMarkdown example http://rmarkdown.rstudio.com/ -->

include/custom.css

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+/* Beasley thought the link text was a little too faint, so switched its color with the hover & focus color */
+a {
+  color: #157ab5;
+  text-decoration: none;
+}
+a:hover,
+a:focus {
+  color: #2fa4e7;
+}
+
+/*  
+.navbar-inverse .navbar-brand {
+  background-color: #ffaaaa;
+}
+.navbar-inverse,
+.navbar-inverse {
+  background-color: #ff00ff;
+}
+.navbar-brand,
+.navbar-inverse {
+  background-color: #ff00ff;
+  border-color: #022f5a;
+}
+*/

include/in_header.html

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+<!-- adding icons with troubleshooting with Andriy Koval https://github.com/andkov -->
+<link rel="icon" href="./images/favicon.png" type="image/png"/>
+<link rel="shortcut icon" href="./images/favicon.ico"/>
+
+<!-- start of in-header material from RMarkdown example http://rmarkdown.rstudio.com/ -->
+<style type="text/css">
+
+/* padding for bootstrap navbar */
+body {
+  padding-top: 50px;
+  padding-bottom: 40px;
+}
+@media (max-width: 979px) {
+  body {
+    padding-top: 0;
+  }
+}
+
+/* offset scroll position for anchor links (for fixed navbar)  */
+@media (min-width: 980px) {
+  .section h2 {
+    padding-top: 52px;
+    margin-top: -52px;
+  }
+  .section h3 {
+    padding-top: 52px;
+    margin-top: -52px;
+  }
+}
+
+
+/* don't use link color in navbar */
+.dropdown-menu>li>a {
+  color: black;
+}
+
+/* some padding for disqus */
+#disqus_thread {
+  margin-top: 45px;
+}
+
+</style>
+
+<link rel="stylesheet" href="libs/font-awesome-4.1.0/css/font-awesome.min.css"/>
+<!-- end of in-header material from RMarkdown example http://rmarkdown.rstudio.com/ -->