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Separate intro slides.

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1 parent 88bf1ac commit 24de902cddb62ce78ec13ac522a7050d36ee134c @trvrb committed Apr 26, 2016
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@@ -1,5 +1,6 @@
## Viral phylodynamics
+* [Introduction](http://bedford.io/projects/phylodynamics-lecture/intro.html): These slides give an introduction to what is meant by phylodynamics.
* [Influenza](http://bedford.io/projects/phylodynamics-lecture/flu.html): These slides describe influenza dynamics and antigenic evolution.
* [The Coalescent](http://bedford.io/projects/phylodynamics-lecture/coalescent.html): These slides introduce the coalescent, demographic inference and selection.
-* [Phylogenetics](http://bedford.io/projects/phylodynamics-lecture/phylogenetics.html): These slides introduce phylogenetic inference via parsimony, maximum likelihood and Bayesian approaches.
+* [Phylogenetics](http://bedford.io/projects/phylodynamics-lecture/phylogenetics.html): These slides introduce phylogenetic inference via parsimony, maximum likelihood and Bayesian approaches.
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@@ -4,7 +4,7 @@
<head>
<meta charset="utf-8">
- <title>Viral phylodynamics</title>
+ <title>The coalescent</title>
<meta name="author" content="Trevor Bedford">
@@ -36,63 +36,6 @@
<!-- Any section element inside of this container is displayed as a slide -->
<div class="slides">
-
- <section data-background="#5097BA">
- <h2 class="title">Phylogenies</h2>
- </section>
-
- <section>
- <h3>Phylogenies describe history</h3>
- <img class="stretch" src="images/phylogenies_tudors.jpg">
- </section>
-
- <section>
- <h3>Phylogenies describe history</h3>
- <img class="stretch" src="images/phylogenies_haeckel.jpg">
- <div class="citation">
- Haeckel 1879
- </div>
- </section>
-
- <section>
- <h3>Phylogenies describe history</h3>
- <img class="stretch" src="images/phylogenies_pace.png">
- <div class="citation">
- <a href="http://www.sciencemag.org/content/276/5313/734.short">Pace 1997</a>
- </div>
- </section>
-
- <section>
- <h3>Phylogenies reveal process</h3>
- <img class="stretch" src="images/phylogenies_darwin.png">
- <div class="citation">
- Darwin 1859
- </div>
- </section>
-
- <section data-background="#5BA6A7">
- <h2 class="title">Epidemic process</h2>
- </section>
-
- <section data-transition="none">
- <h3>Epidemic process</h3>
- <img class="stretch" src="images/infection_tree_1.png">
- </section>
-
- <section data-transition="none">
- <h3>Sample some individuals</h3>
- <img class="stretch" src="images/infection_tree_2.png">
- </section>
-
- <section data-transition="none">
- <h3>Sequence and determine phylogeny</h3>
- <img class="stretch" src="images/infection_tree_3.png">
- </section>
-
- <section data-transition="none">
- <h3>Sequence and determine phylogeny</h3>
- <img class="stretch" src="images/infection_tree_4.png">
- </section>
<section data-background="#69B091">
<h2 class="title">The coalescent</h2>
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@@ -0,0 +1,130 @@
+<!doctype html>
+<html lang="en">
+
+ <head>
+ <meta charset="utf-8">
+
+ <title>Viral phylodynamics</title>
+
+ <meta name="author" content="Trevor Bedford">
+
+ <meta name="apple-mobile-web-app-capable" content="yes" />
+ <meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
+
+ <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
+
+ <link rel="stylesheet" href="reveal/css/reveal.min.css">
+ <link rel="stylesheet" href="reveal/css/theme/trvrb.css" id="theme">
+ <link rel="stylesheet" href="reveal/css/font-awesome/css/font-awesome.min.css">
+
+ <!-- For syntax highlighting -->
+ <link rel="stylesheet" href="reveal/lib/css/zenburn.css">
+
+ </head>
+
+ <body>
+
+ <div style="position: absolute; top:10px; left:10px; z-index:100;">
+ <a href="http://bedford.io/projects/phylodynamics-lecture/">
+ <i class="fa fa-times-circle" style="color: #bbb;"></i>
+ </a>
+ </div>
+
+ <div class="reveal">
+
+ <!-- Color ramp: ["#5097BA", "#5BA6A7", "#69B091", "#79B77D", "#8BBB6A", "#9EBE5A", "#B2BD4D", "#C4B945", "#D4B13F", "#DFA43B"] -->
+
+ <!-- Any section element inside of this container is displayed as a slide -->
+ <div class="slides">
+
+ <section data-background="#5097BA">
+ <h2 class="title">Phylogenies</h2>
+ </section>
+
+ <section>
+ <h3>Phylogenies describe history</h3>
+ <img class="stretch" src="images/phylogenies_tudors.jpg">
+ </section>
+
+ <section>
+ <h3>Phylogenies describe history</h3>
+ <img class="stretch" src="images/phylogenies_haeckel.jpg">
+ <div class="citation">
+ Haeckel 1879
+ </div>
+ </section>
+
+ <section>
+ <h3>Phylogenies describe history</h3>
+ <img class="stretch" src="images/phylogenies_pace.png">
+ <div class="citation">
+ <a href="http://www.sciencemag.org/content/276/5313/734.short">Pace 1997</a>
+ </div>
+ </section>
+
+ <section>
+ <h3>Phylogenies reveal process</h3>
+ <img class="stretch" src="images/phylogenies_darwin.png">
+ <div class="citation">
+ Darwin 1859
+ </div>
+ </section>
+
+ <section data-background="#5BA6A7">
+ <h2 class="title">Epidemic process</h2>
+ </section>
+
+ <section data-transition="none">
+ <h3>Epidemic process</h3>
+ <img class="stretch" src="images/infection_tree_1.png">
+ </section>
+
+ <section data-transition="none">
+ <h3>Sample some individuals</h3>
+ <img class="stretch" src="images/infection_tree_2.png">
+ </section>
+
+ <section data-transition="none">
+ <h3>Sequence and determine phylogeny</h3>
+ <img class="stretch" src="images/infection_tree_3.png">
+ </section>
+
+ <section data-transition="none">
+ <h3>Sequence and determine phylogeny</h3>
+ <img class="stretch" src="images/infection_tree_4.png">
+ </section>
+
+ <section>
+ <h3>Localized Middle Eastern MERS-CoV phylogeny</h3>
+ <img class="stretch" src="images/pathogen_phylogeny_mers.jpg">
+ <div class="citation">
+ <a href="http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(13)61887-5/abstract">Cotten et al 2013</a>
+ </div>
+ </section>
+
+ <section>
+ <h3>Regional West African Ebola phylogeny</h3>
+ <img class="stretch" src="images/pathogen_phylogeny_ebola.png">
+ <div class="citation">
+ <a href="http://bedford.io/papers/park-ebola-transmission/">Park et al 2015</a>
+ </div>
+ </section>
+
+ <section>
+ <h3>Global influenza phylogeny</h3>
+ <img class="stretch" src="images/pathogen_phylogeny_flu.png">
+ <div class="citation">
+ <a href="http://bedford.io/papers/bedford-global-circulation/">Bedford et al 2015</a>
+ </div>
+ </section>
+
+ </div>
+
+ </div>
+
+ <script src="reveal/lib/js/head.min.js"></script>
+ <script src="reveal/js/reveal.min.js"></script>
+ <script src="reveal/js/config.js"></script>
+
+ </body>
+</html>

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