Numerical fix for OU (pruning) models with very small alpha.
Added numerical tweak to the OU/VCV calculation, too.
Fix Mk2 ASR error when transition rates are zero.

Reported by Anna Rice on r-sig-phylo
http://www.mail-archive.com/r-sig-phylo@r-project.org/msg02928.html
Fix coef.mcmcsamples for constrained likelihoods
Simple PGLS implementation

Probably not actually very useful for least squares fitting now, as
little support for testing different models.  But could be useful
for Bayesian fitting.  No transformations yet.
Support for extracting fitted values and residuals from PGLS functions
Extract fitted and residual values from PGLS ML fit
Run tests on source version, not package version
Restore save of likelihood functions with mle output.
Updated mcmc to save the likelihood function with the samples.

Approximately the same interface as find.mle().  The function is saved
as "func", even though mcmc takes the argument "lik".  Not very pretty,
but I can't really change the argument names at this point.
Update the likelihood extraction functions (now exported as get.likelihood)
Update PGLS code to use saved likelihood functions.
More options for coef.mcmcsamples

Can now drop "burn-in" as well as sample with replacement.
Allow specificiation of burnin by fraction in coef.mcmcsamples
Add configure script

This should remove the requirement of installing autotools to install from
source, which is a bit of a hassle.
Classing of mcmcsamples objects works the same as find.mle
OU calculations on non-ultrametric trees are suspect.  Add a warning.
Fitted and residual values from mcmcsamples.pgls objects
Fix typos in help file.

Reported by Natalie Cooper.
Added support for time-varying GeoSSE (contributed by Jonathan Rolland)