added cardinality-dependent extinciton to grm
Modifications to the RootedTripletDistribution to move towards a working MPest. Now some branch length information can be saved in the RootedTripletDistribution. Compiles, but not tested.
Now the rooted triplet distribution works when branch length information needs to be kept (as for MPest). Had to change the birth death simulate function, because it did not keep species information at the tips, and added clone and "=" function to the Taxon class. Not sure the "==" function in the Taxon class works by the way (I have not changed it though).
Corrected the "==" function in Taxon. In doing so I had to start implementing the class TimeAndDate, but it is far from finished.
Implementation of branch-heterogeneous Ornstein-Uhlenbeck processes. Not tested, but compiles.
Added RealNodeValTree to RbRegister, and added a tutorial file for Ornstein-Uhlenbeck models.
earth23 tests
Merge branch '130924_bgdate' into development
Updated fnBiogeoDE to work with fnFreeBinary
Now we can get the tip values from a RealNodeContainer and RlRealNodeValTree, and we can also write continuous values to a Nexus file. We can't do the same to a Fasta file (in case someone's interested in implementing this).
Merge branch 'development' of github.com:revbayes/code into development
Merging character history simulate and initialization code
bg sim working from rev console
basic GeneralTreeHistoryCtmc simulation working through Rev CLI
corrected scaling factor in computeProposal density for PUSP
added Move_CharacterHistory/mvCharacterHistory with charType/proposalType options
minimum working examples for simulation and inference using CH model
Merge branch 'development' of github.com:revbayes/revbayes into development
Work on freeK GeneralRateMatrix
freeK rate matrix core object