NEW IN VERSION 2.6-1

o   In the 'hansen' function, the use of the argument 'alpha' was confusing.
    This vector parameterizes the "selection" portion of the OU model, which since version 2 has been assumed to be a positive-definite matrix (corresponding to stabilizing selection).
    In particular, it contains the entries of the lower-triangular matrix square root of this positive definite matrix.
    To make the name more mnemonic, this argument has been renamed 'sqrt.alpha'.
    This is a superficial change meant to improve intelligibility: the algorithm itself has not changed.
    To prevent loss of backward compatibility, use of argument 'alpha' will continue to work, though it will generate a warning.
    In some future release, use of 'alpha' as an argument to 'hansen' will no longer generate a warning but will instead be passed through to the control list for 'optim' if method='optim' and will otherwise generate an error.

NEW IN VERSION 2

Version 2 of ouch represents a major revision.  
ouch's capabilities have been substantially extended.
In particular,

o   support is now provided for multivariate characters.  
    Inference based on multivariate Ornstein-Uhlenbeck and multivariate Brownian motion models is now provided.

o   nonultrametric trees are supported.

o   the root character state need no longer be estimated.  
    Instead, the root state is assumed to be distributed according to the stationary distribution of the OU process.

o   convenience functions for parametric bootstrap confidence intervals are provided.

o   the new function 'paint' simplifies the specification of adaptive regimes in complex phylogenies.

o   the new function 'ape2ouch' translates trees in the 'phylo' format of the ape package into 'ouchtree' format (thanks to Dan Ackerly).

The new package is a complete rewrite, using S4 classes.  
The old functionality from ouch v. 1 remains available, but is now deprecated.
