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websites.html
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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>Simple Websites from Rmds</title>
<script src="site_libs/header-attrs-2.7/header-attrs.js"></script>
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/readable.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<link rel="shortcut icon" href="favicon.ico" type="image/x-icon">
<style type="text/css">
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>
<style type="text/css">code{white-space: pre;}</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<link rel="stylesheet" href="styles.css" type="text/css" />
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
pre code {
padding: 0;
}
</style>
<style type="text/css">
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
<style type="text/css">
#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}
@media print {
.toc-content {
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
float: right;
}
}
.toc-content {
padding-left: 30px;
padding-right: 40px;
}
div.main-container {
max-width: 1200px;
}
div.tocify {
width: 20%;
max-width: 260px;
max-height: 85%;
}
@media (min-width: 768px) and (max-width: 991px) {
div.tocify {
width: 25%;
}
}
@media (max-width: 767px) {
div.tocify {
width: 100%;
max-width: none;
}
}
.tocify ul, .tocify li {
line-height: 20px;
}
.tocify-subheader .tocify-item {
font-size: 0.90em;
}
.tocify .list-group-item {
border-radius: 0px;
}
.tocify-subheader {
display: inline;
}
.tocify-subheader .tocify-item {
font-size: 0.95em;
}
</style>
</head>
<body>
<div class="container-fluid main-container">
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row">
<div class="col-sm-12 col-md-4 col-lg-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-sm-12 col-md-8 col-lg-9">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">RWorkflow</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="set-up.html">
<span class="fas fa-clone"></span>
Set-up
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fab fa-git"></span>
Git
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="intro-git.html">
<span class="fab fa-github"></span>
Intro to Git + GitHub
</a>
</li>
<li>
<a href="more-git.html">
<span class="fab fa-github-alt"></span>
More Git + GitHub
</a>
</li>
<li>
<a href="gitlab-to-github.html">
<span class="fas fa-truck-moving"></span>
GitLab to GitHub
</a>
</li>
<li>
<a href="websites.html">
<span class="fab fa-chrome"></span>
Websites with GitHub
</a>
</li>
<li>
<a href="jekyll.html">
<span class="fas fa-sitemap"></span>
Dynamic Websites with Jekyll and GitHub
</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-file"></span>
RMarkdown
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="week3-RMarkdown.html">
<span class="fas fa-file"></span>
R Markdown for Reports
</a>
</li>
<li>
<a href="bookdown.html">
<span class="fas fa-book"></span>
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</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-archive"></span>
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<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="week4-packages.html">
<span class="fas fa-archive"></span>
R Packaging with RStudio
</a>
</li>
<li>
<a href="week5-roxygen.html">
<span class="fas fa-question-circle"></span>
Roxygen documentation
</a>
</li>
<li>
<a href="week6-more-packages.html">
<span class="fas fa-folder"></span>
More package stuff
</a>
</li>
<li>
<a href="shiny.html">
<span class="fas fa-gamepad"></span>
Shiny GUIs
</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-broom"></span>
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</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="week8-ggplot2.html">
<span class="fas fa-image"></span>
ggplot2
</a>
</li>
<li>
<a href="week9-data-wrangling.html">
<span class="fas fa-broom"></span>
tidyr
</a>
</li>
</ul>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
More
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</a>
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<li>
<a href="links.html">Tutorials</a>
</li>
</ul>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/RVerse-Tutorials/RWorkflow">
<span class="fab fa-github"></span>
Repo
</a>
</li>
<li>
<a href="search.html">Search</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div id="header">
<h1 class="title toc-ignore">Simple Websites from Rmds</h1>
</div>
<p>This will show you how to make a very simple website with R Markdown and put that online via GitHub Pages. When you are ready to learn more go to the <a href="links.html">Links</a> page for more tutorials.</p>
<div id="simple-website-template" class="section level2">
<h2>Simple website template</h2>
<p>Clone the <a href="https://github.com/RVerse-Tutorials/Test-Website">RVerse-Tutorials-Website</a> repository.</p>
<ul>
<li>Copy the URL.</li>
<li>Open GitHub and click the “+” in top right for new repo. Select ‘Import repository’, then select import from URL and paste in the URL.</li>
<li>Once it is imported (might take awhile), copy the URL for <strong>your</strong> new repository.</li>
<li>Open RStudio. Click the blue cube with R in top right. Select New Project > Version Control > Git and paste in the URL.</li>
</ul>
<p>Now you’ll have a copy of Test-Website on GitHub and a copy on your computer that is linked to your remote repository (on GitHub).</p>
</div>
<div id="build-the-website" class="section level2">
<h2>Build the website</h2>
<ol start="2" style="list-style-type: decimal">
<li>From RStudio, click ‘Build’ from upper right and then ‘Build Website’. Your website should open. You can select ‘View in browser’.</li>
</ol>
<ul>
<li>You can also right click on ‘index.html’ from the files, and select ‘open in browser’.</li>
</ul>
<p><a href="https://youtu.be/94iHk0UnxJc">Watch a video of this step</a></p>
</div>
<div id="overview" class="section level2">
<h2>Overview</h2>
<p>There are two required files for a website plus your content (your R Markdown files).</p>
<p>The first required file is <code>_site.yml</code> which is your configuration file.</p>
<p>The second required file is <code>index.Rmd</code> which is your landing page or page #1.</p>
<p>Your content is specified in additional R Markdown files. Not required, but your website is not very interesting without content.</p>
</div>
<div id="site.yml" class="section level2">
<h2>_site.yml</h2>
<p>The <code>_site.yml</code> specifies the basic info about your site and the navigation bar at top.</p>
<pre><code>name: "my-website"
output_dir: "."
navbar:
title: "My Website"
left:
- text: "Home"
icon: fa-home
href: index.html
- text: "About"
icon: fa-bullhorn
href: about.html
menu:
- text: "Page A"
href: page_a.html
- text: "Page B"
href: page_b.html
output:
html_document:
theme: readable
toc_depth: 3
toc_float:
collapsed: false</code></pre>
</div>
<div id="index.rmd" class="section level2">
<h2>index.Rmd</h2>
<p><code>index.Rmd</code> is just your landing page. You can have as little or as much content as you want here. When readers click on your site, they will see this page first.</p>
<p>A minimal <code>index.Rmd</code> would look like:</p>
<pre><code>---
title: "My website"
---
Here is my website.</code></pre>
</div>
<div id="content" class="section level2">
<h2>Content</h2>
<p>You can now add as many Rmarkdown files as you want for your content. Each one will be processed into an html file. For example in <code>Test Website</code>, we have two files, <code>about.Rmd</code> and <code>contact.Rmd</code>. Your Rmd files should have the yaml at top and then your Rmarkdown content.</p>
<p>Here is a simple example.</p>
<pre><code>---
title: Simple Rmd File
---
Here is a simple file.</code></pre>
<p><code>about.Rmd</code> is a fuller Rmd file with R code and figures.</p>
<p>If you want the file linked to in your top nav bar, then add it to <code>_site.yml</code>.</p>
<pre><code>name: "my-website"
output_dir: "."
navbar:
title: "My Website"
left:
- text: "About"
href: about.html
- text: "Contact"
icon: fa-user-circle
href: contact.html
output:
html_document:
theme: readable
toc_depth: 3
toc_float:
collapsed: false</code></pre>
</div>
<div id="make-your-website-live" class="section level2">
<h2>Make your website live</h2>
<p><a href="https://youtu.be/eHWi5XmTO8U">Watch a video of this step</a></p>
<p>Here is how to make your website live on GitHub.</p>
<p>First you need to add this as a repository on GitHub.</p>
<ol style="list-style-type: decimal">
<li><p>Open GitHub Desktop and select File > New Repository. Type ‘Test-Website’ (or if you renamed it, then whatever you renamed it to). Leave everything else blank (for now).</p></li>
<li><p>This adds your repository to GitHub Desktop. Now click ‘Publish’ in the top right corner. If ‘private’ is checked, uncheck that.</p></li>
</ol>
<p>Next you need to open your repository on GitHub and set it up to serve a webpage.</p>
<ol style="list-style-type: decimal">
<li>Go to your GitHub account.</li>
<li>Click on the new Test-Website repository.</li>
<li>Click on Settings. <img src="images/GitHub_pages_1.png" alt="Settings" /></li>
<li>Scroll down to GitHub Pages and change source from ‘none’ to ‘master branch’. <img src="images/GitHub_pages_2.png" alt="Source" /></li>
<li>Wait a few minutes and then go to your new webpage. The link will appear just above where your changed the source.</li>
</ol>
</div>
<div id="extras" class="section level2">
<h2>Extras</h2>
<div id="table-of-contents" class="section level3">
<h3>Table of Contents</h3>
<p>If you want to see table of contents for your Rmd files, you specify toc properties in your <code>_site.yml</code> file.</p>
<pre><code>output:
html_document:
theme: readable
toc_depth: 3
toc_float:
collapsed: false</code></pre>
<p>and specify <code>toc: true</code> in your yaml at the top of your Rmd file.</p>
<pre><code>output:
html_document:
toc: true</code></pre>
<p>See the <code>about.Rmd</code> file for an example.</p>
</div>
<div id="themes" class="section level3">
<h3>Themes</h3>
<p>Your <code>_site.yml</code> file has a line that specifies the theme.</p>
<pre><code>output:
html_document:
theme: readable</code></pre>
<p>The following are automatically available to you: bootstrap, cerulean, cosmo, flatly, journal, lumen, paper, readable, sandstone, simplex, spacelab, united and yeti. Try changing the theme to one of these and rebuilding your website.</p>
<p>You can download other bootstrap css files and put in site_libs if you want other themes. Do a search for ‘bootstrap themes free’.</p>
</div>
<div id="icons" class="section level3">
<h3>Icons</h3>
<p>You can easily add icons to your navigation tabs. The <code>icon:</code> line specifies the icon. See the FontAwesome website for icons available. Put <code>fa-</code> in front of the name. For example a photo icon would be specified <code>fa-picture-o</code>.</p>
<pre><code> left:
- text: "Set-up"
icon: fa-picture-o
href: setup.html</code></pre>
</div>
<div id="customizing" class="section level3">
<h3>Customizing</h3>
<p>You can add your own css file to customize the html. Add to your <code>_site.yml</code> file:</p>
<pre><code>output:
html_document:
theme: cosmo
highlight: textmate
include:
after_body: footer.html
css: styles.css</code></pre>
<p>And then add a <code>styles.css</code> file to your folder. You can change all the h1 headers to green.</p>
<pre><code>h1 {
font-color: green
}</code></pre>
<p>Change the font-family and add some more space.</p>
<pre><code>body {
font-family: "Helvetica Neue",Helvetica,Arial,sans-serif;
line-height: 2;
}</code></pre>
<p>Add more spacing between the sections.</p>
<pre><code>.section {
padding-bottom: 2em;
}</code></pre>
<p>Etc, etc, etc, etc.</p>
</div>
<div id="fixing-a-navbar-that-wraps" class="section level3">
<h3>Fixing a navbar that wraps</h3>
<p>The bootstrap css doesn’t handle navbars with many tabs very well. It wraps and covers up the text. Adding the following to your <code>styles.css</code> file will fix that.</p>
<pre><code>/* Need to adjust the navbar behaviour so the navbar doesn't wrap */
.navbar-nav {
position: fixed;
left: 150px;
width: 700px;
}
.navbar-header {
position: fixed;
left: 30px;
width: 97%;
}</code></pre>
</div>
</div>
<hr>
<div style="text-align: center">
<i class="fas fa-cubes"></i> NWFSC Math Bio Program <i class="fas fa-cubes"></i>
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