Refactored big messy test file to
* separate into 4 separate tests
* abstract away some functions
* produce nice output tables using knitr and xtable
* carry out some meta-analysis of results
This is refactored so that the titv test is executed by itself in this doc, and results are reported in a table separate from other results.
replaced custom functions with functions in survcomp package
Rewrote the processing due to an error discovered in conversation with Tim Palzkill.  The publisher's web site mixes up the supplementary data files in such a way that I was using a set of preferences based on alignments of natural sequences, rather than a set based on the mutant effects.

This has now been fixed.
fixed to ignore template file