There's a lot going on with the epidemiology and evolution of influenza; I've made a model that attempts capture all the salient details. This includes things like the yearly attack rates, rate of antigenic evolution, genetic diversity, and geographic spread. At it's core, the model assumes that the antigenic phenotype of the virus can be adequately explained as a point in a Euclidean space. Mutation serves to jostle the location of the virus in this space and infection by one virus confers immunity to subsequent infection by nearby viruses in this antigenic space. The geometric basis of the model stems from empirical studies of influenza's antigenic phenotype (see Smith et al. 2004). In this study, I find that evolution in such a space results in a "canalized" trajectory. The best move for a virus is to move as far away from its past as possible, resulting in linear antigenic movement and a distinctive single-trunked phylogenic tree.

The manuscript is written in LaTeX. I've included everything necessary to compile to PDF and to HTML. Here I have canal.bbl which includes all my references all run through bibtex. In this case, to compile run:

pdflatex canal
pdflatex canal

This will produce a PDF entitled canal.pdf. If you want HTML output, run:

htlatex canal ms

This uses ms.cfg and ms.css to style the resulting HTML output. This produces a file entitled canal.html. There were a couple of styling issues that I couldn't take care of through the stylesheet and so I added a small Ruby script to do some post-hoc styling and file cleanup. Run:

ruby clean.rb canal

Additionally, I've made use of GitHub pages. This repository is stored in the branch gh-pages.
This causes files to be published at trvrb.github.com/canalization/. Here, I've renamed canal.html to index.html. A full compile is possible with:

pdflatex canal
pdflatex canal
htlatex canal ms
ruby clean.rb canal
mv canal.html index.html

Alternatively:

ruby textile.rb canal

will do all the above.

All text is copyright Bedford, Rambaut and Pascual 2011. Distributed under the GPL v3.