StatSVN - Directory src/test/dr/app/beagle/

Lines of Code

src/test/dr/app/beagle/ Lines of Code

Developers

Author	Changes	Lines of Code	Lines per Change
Totals	16 (100.0%)	479 (100.0%)	29.9
msuchard	7 (43.8%)	464 (96.9%)	66.2
rambaut	9 (56.3%)	15 (3.1%)	1.6

Most Recent Commits

rambaut 2012-11-16 00:50 Rev.: 5231

Renamed BeagleTreeLikelihood to OldBeagleTreeLikelihood

2 lines of code changed in 2 files:

src/test/dr/app/beagle: TinyTest.java (+2 -2)

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.

10 lines of code changed in 4 files:

src/test/dr/app/beagle: AncestralStateBeagleTreeLikelihoodTest.java (new), MarkovJumpsTest.java (+5 -5)

msuchard 2012-03-08 07:09 Rev.: 4789

Implemented TN93 under BEAGLE.

70 lines of code changed in 1 file:

src/test/dr/app/beagle: TN93Test.java (new 70)

rambaut 2011-11-16 05:17

Ported sequence error models to BeagleTreeLikelihood and implemented a variant model that emits tip states rather than tip partials.

3 lines of code changed in 3 files:

src/test/dr/app/beagle: AncestralStateBeagleTreeLikelihoodTest.java (+1), MarkovJumpsTest.java (+1), TinyTest.java (+1)

msuchard 2010-10-27 12:09 Rev.: 3684

Refactored BranchSiteModel to BranchSubstitutionModel to better reflect that this class specifies a substitution model for each branch, while SiteRateModel gives the site-specitic rate multiplier information.

12 lines of code changed in 3 files:

src/test/dr/app/beagle: AncestralStateBeagleTreeLikelihoodTest.java (+4 -4), MarkovJumpsTest.java (+4 -4), TinyTest.java (+4 -4)

msuchard 2010-07-13 23:46 Rev.: 3308

BEAST-BEAGLE JUnits (require BEAGLE, can disable on Hudson if necessary).

296 lines of code changed in 2 files:

src/test/dr/app/beagle: AncestralStateBeagleTreeLikelihoodTest.java (+129), MarkovJumpsTest.java (+167)

msuchard 2010-07-13 23:45 Rev.: 3307

Add several wrappers to convert automatically between different reductions of TreeTraits (sum over tree, sum across sites, etc.). One can even double-wrap to get sum over tree + sum across sites. This should reduce substantial code-duplication and earn me a gold star.

86 lines of code changed in 1 file:

src/test/dr/app/beagle: TinyTest.java (+86)