Latent Factor Model now can do proper integrations using latent liabilities for specific transition kernels

git-svn-id: http://beast-mcmc.googlecode.com/svn@6544 ca793f91-a31e-0410-b540-2769d408b6a1
Latent Factor Model now can do proper integrations using latent liabilities for all transition kernels

git-svn-id: http://beast-mcmc.googlecode.com/svn@6545 ca793f91-a31e-0410-b540-2769d408b6a1
Fixes bug from previous commit, removes erroneous residual computation.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6546 ca793f91-a31e-0410-b540-2769d408b6a1
Various minor speedups. LFM no longer computes likelihood for discrete values. Various functions added to DiagonalMatrixParameter

git-svn-id: http://beast-mcmc.googlecode.com/svn@6547 ca793f91-a31e-0410-b540-2769d408b6a1
New connection between MultidimensionalScaling and TraitLikelihood

git-svn-id: http://beast-mcmc.googlecode.com/svn@6548 ca793f91-a31e-0410-b540-2769d408b6a1