StatSVN - Directory src/dr/app/beagle/evomodel/branchmodel/

Lines of Code

src/dr/app/beagle/evomodel/branchmodel/ Lines of Code

Developers

Author	Changes	Lines of Code	Lines per Change
Totals	36 (100.0%)	941 (100.0%)	26.1
rambaut	23 (63.9%)	868 (92.2%)	37.7
msuchard	11 (30.6%)	69 (7.3%)	6.2
fbielejec	2 (5.6%)	4 (0.4%)	2.0

Most Recent Commits

msuchard 2013-01-15 12:01 Rev.: 5324

Can pass arbitrary root FrequencyModel to HomogeneousBranchModel.

14 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/branchmodel: HomogeneousBranchModel.java (new)

msuchard 2013-01-15 11:50 Rev.: 5323

Added getRootFrequencyModel to BranchModel interface. Consider deprecating getRootSubstitutionModel() as there are no substitutions occurring at the root. Also commented out @Override to interface functions since this is not Java 1.5 compatible.

55 lines of code changed in 9 files:

src/dr/app/beagle/evomodel/branchmodel: BranchModel.java (+8 -2), BranchSpecificBranchModel.java (+14 -10), EpochBranchModel.java (new), ExternalInternalBranchModel.java (+9 -5), HomogeneousBranchModel.java (+9 -4)

fbielejec 2012-11-16 21:15

switching the simulator to new interfaces

4 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/branchmodel: EpochBranchModel.java (+3 -9)

rambaut 2012-11-15 14:45 Rev.: 5230

Updated copyright messages.

30 lines of code changed in 5 files:

src/dr/app/beagle/evomodel/branchmodel: BranchModel.java (+1 -1), BranchSpecificBranchModel.java (+1 -1), EpochBranchModel.java (+2 -2), ExternalInternalBranchModel.java (+25), HomogeneousBranchModel.java (+1 -1)

rambaut 2012-11-15 14:41 Rev.: 5229

Branch specific substitution models now working. NewTreeLikelihood will replace BeagleTreeLikelihood in a future commit. AncestralStateTL and MarkovJumpsTL now descend from NewTreeLikelihood. EpochBranchModel uses a different XML format from EpochBranchSubstitutionModel (now depreciated). Also implemented a branch-specific substitution model.

311 lines of code changed in 5 files:

src/dr/app/beagle/evomodel/branchmodel: BranchModel.java (+29 -2), BranchSpecificBranchModel.java (+259), EpochBranchModel.java (+9), ExternalInternalBranchModel.java (+6), HomogeneousBranchModel.java (+8 -1)

rambaut 2012-11-10 00:11 Rev.: 5224

NewBeagleTreeLikelihood evaluation seems to work for Epoch models.

2 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/branchmodel: EpochBranchModel.java (+2 -2)

rambaut 2012-11-09 22:40 Rev.: 5219

Finished first implementation of new SubstitutionModelDelegate for BranchModels (which allow changing substitution model by branch).

81 lines of code changed in 4 files:

src/dr/app/beagle/evomodel/branchmodel: BranchModel.java (+10 -1), EpochBranchModel.java (+10), ExternalInternalBranchModel.java (+14), HomogeneousBranchModel.java (+47 -1)

rambaut 2012-11-08 04:11 Rev.: 5216

Epoch model in new form...

287 lines of code changed in 5 files:

src/dr/app/beagle/evomodel/branchmodel: BranchModel.java (+52), BranchSpecificModel.java (del), EpochBranchModel.java (+208), ExternalInternalBranchModel.java (+1 -3), HomogeneousBranchModel.java (+26 -1)

rambaut 2012-11-08 03:47 Rev.: 5215

Beginnings of a new branch specific substitution model interface. Homogenous and Ext/Int examples implemented.

157 lines of code changed in 3 files:

src/dr/app/beagle/evomodel/branchmodel: BranchSpecificModel.java (new 52), ExternalInternalBranchModel.java (+91), HomogeneousBranchModel.java (+14)