normalizing constant b

git-svn-id: http://beast-mcmc.googlecode.com/svn@6571 ca793f91-a31e-0410-b540-2769d408b6a1
add likelihood, because we are not testing

git-svn-id: http://beast-mcmc.googlecode.com/svn@6572 ca793f91-a31e-0410-b540-2769d408b6a1
XML can contain never-infected cases which will be taken account of in likelihood calcs

git-svn-id: http://beast-mcmc.googlecode.com/svn@6573 ca793f91-a31e-0410-b540-2769d408b6a1
Attempting to normalize latent rate densities

git-svn-id: http://beast-mcmc.googlecode.com/svn@6574 ca793f91-a31e-0410-b540-2769d408b6a1
Implements MatrixMatrixProduct class
Removes IntermediateReturnLikelihood class
LFM is now an abstract likelihood again
Attempts to implement a transposition of BlockUpperTriangularMatrixParameter

git-svn-id: http://beast-mcmc.googlecode.com/svn@6575 ca793f91-a31e-0410-b540-2769d408b6a1
Fixed normalization in LatentStateBranchRateModel and added necessary Jacobian for sampling over proportion of branch instead of reward value.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6576 ca793f91-a31e-0410-b540-2769d408b6a1
Debugged last commit

git-svn-id: http://beast-mcmc.googlecode.com/svn@6577 ca793f91-a31e-0410-b540-2769d408b6a1