StatSVN - Directory src/dr/app/beast/

Author	Changes	Lines of Code	Lines per Change
Totals	679 (100.0%)	9176 (100.0%)	13.5
rambaut	239 (35.2%)	3086 (33.6%)	12.9
msuchard	135 (19.9%)	1905 (20.8%)	14.1
dong.w.xie	122 (18.0%)	1372 (15.0%)	11.2
alexei.drummond	38 (5.6%)	949 (10.3%)	24.9
alexander.alekseyenko	13 (1.9%)	378 (4.1%)	29.0
Sebastian.Hoehna	4 (0.6%)	364 (4.0%)	91.0
dong.w.xie@gmail.com	3 (0.4%)	343 (3.7%)	114.3
Michael.DefoinPLatel	3 (0.4%)	271 (3.0%)	90.3
jheled	32 (4.7%)	172 (1.9%)	5.3
akaruiws	14 (2.1%)	128 (1.4%)	9.1
graham853@gmail.com	6 (0.9%)	33 (0.4%)	5.5
bloomquist	17 (2.5%)	31 (0.3%)	1.8
graham853	2 (0.3%)	20 (0.2%)	10.0
mdhall272@gmail.com	11 (1.6%)	18 (0.2%)	1.6
Sibon.Li@gmail.com	4 (0.6%)	18 (0.2%)	4.5
tbcbedford@gmail.com	10 (1.5%)	13 (0.1%)	1.3
mtholder	1 (0.1%)	13 (0.1%)	13.0
fbielejec	6 (0.9%)	13 (0.1%)	2.1
aaron.darling	1 (0.1%)	13 (0.1%)	13.0
gcybis@yahoo.com.br	2 (0.3%)	8 (0.1%)	4.0
philippe.lemey@gmail.com	3 (0.4%)	7 (0.1%)	2.3
julia.pal.r@gmail.com	4 (0.6%)	5 (0.1%)	1.2
higgs.ml	1 (0.1%)	4 (0.0%)	4.0
baele.guy@gmail.com	3 (0.4%)	4 (0.0%)	1.3
gerton.lunter	3 (0.4%)	3 (0.0%)	1.0
benjamin.redelings	1 (0.1%)	3 (0.0%)	3.0
danny.wilson@gmail.com	1 (0.1%)	2 (0.0%)	2.0

Most Recent Commits

julia.pal.r@gmail.com 2013-05-09 05:42 Rev.: 5641

Latest version with new operator for joint--TODO: let Parameters.restore for vectors with different sizes. Tracer analysis doesn't read log files with {num,num,..}

2 lines of code changed in 2 files:

src/dr/app/beast: development_parsers.properties (new)

mdhall272@gmail.com 2013-05-09 00:22 Rev.: 5639

efficiency improvements & other misc small fixes

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1)

msuchard 2013-05-03 07:25 Rev.: 5628

Fixed log determine of a matrix and positive-definite check in WishartDistribution; there is still an error in LUPDecomposition.isPD()

1 lines of code changed in 2 files:

src/dr/app/beast: release_parsers.properties (new)

rambaut 2013-05-03 02:58 Rev.: 5627

A couple of minor fixes to the main(). -version now works. -beagle_info on the command line doesn't throw up the options dialog but prints the info and quits.

2 lines of code changed in 2 files:

src/dr/app/beast: BeastMain.java (+2 -1)

msuchard 2013-04-25 06:38 Rev.: 5610

Implemented a scaled mixture of Wishart distribution for precision matrix inference.

2 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+2)

msuchard 2013-04-15 09:25 Rev.: 5590

Fixed Jacobian for log-transforms under new adaptive multivariate transition kernel for mixture models.

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1 -1)

mdhall272@gmail.com 2013-04-10 23:57 Rev.: 5578

Finished combining the classes.

0 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (-1)

mdhall272@gmail.com 2013-04-08 20:41 Rev.: 5562

Nomenclature change

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1 -1)

mdhall272@gmail.com 2013-04-06 03:48 Rev.: 5557

Made the case class an inner class of the case set class, which is much neater.

0 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (-1)

julia.pal.r@gmail.com 2013-03-23 04:33 Rev.: 5529

added the "tracer" analysis similar to EBSP

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1)

msuchard 2013-03-19 18:02 Rev.: 5509

Fixed log determinate for large diagonal matrices; refactored transforms.

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1)

rambaut 2013-03-14 00:00 Rev.: 5482

Created an 'AttributeBranchRateModel' which exposes an attribute embedded in a tree as a branch rate model.

1 lines of code changed in 1 file:

src/dr/app/beast: release_parsers.properties (+1)

rambaut 2013-03-07 21:56 Rev.: 5472

EmpiricalTreeDistributionModel can now read a rate attribute and expose it as a branchRateModel (it now implements that interface).

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1)

msuchard 2013-03-03 15:46 Rev.: 5465

Prototype Parameter.class to constraint equality among parameters; seems more consistent with usage than a Model.class

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1)

msuchard 2013-03-01 16:40 Rev.: 5461

Prototype Model.class to constraint equality among parameters.

4 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+4 -1)

mdhall272@gmail.com 2013-02-21 21:43 Rev.: 5444

Cleaning up

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1)

rambaut 2013-02-16 07:17 Rev.: 5418

Merging version stuff and copyright dates with 1.7 branch.

7 lines of code changed in 1 file:

src/dr/app/beast: BeastMain.java (+7)

mdhall272@gmail.com 2013-02-14 23:46 Rev.: 5397

Updating parser list to match.

2 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+2 -2)

baele.guy@gmail.com 2013-02-07 01:48 Rev.: 5378

First version of an independent sampler from a gamma distribution.

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1)

rambaut 2013-01-29 22:14 Rev.: 5356

Porting fixes for issue http://code.google.com/p/beast-mcmc/issues/detail?id=671 to trunk.

5 lines of code changed in 2 files:

src/dr/app/beast: BeastVersion.java (new)

tbcbedford@gmail.com 2013-01-18 05:38 Rev.: 5332

Change AntigenicDistancePrior to take new Offsets parameter (rather than Dates parameter) and remove deprecated AntigenicJumpPrior.

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1)

mdhall272@gmail.com 2013-01-17 04:53 Rev.: 5328

Un-mothballing the label-switching version (Felsenstein very slow) and renaming to reflect this.

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1 -1)

mdhall272@gmail.com 2013-01-15 06:04 Rev.: 5321

Added parser to list.

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1)

mdhall272@gmail.com 2013-01-15 06:03 Rev.: 5320

Began work on new version using modified Felsenstein pruning algorithm rather than sampling the network simultaneously.

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1 -1)

rambaut 2013-01-13 22:20 Rev.: 5319

Renaming a class that doesn't conform to Java naming (camel case starting with a capital). Also general aversion to arbitrary acronyms in class names as this makes finding them and browsing code difficult. Added authors to comments.

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1 -1)

tbcbedford@gmail.com 2013-01-13 08:16 Rev.: 5317

Include drifted traits logger in dev parsers.

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1 -6)

tbcbedford@gmail.com 2013-01-12 03:05 Rev.: 5313

Include DriftedLocationStatistic in dev parsers.

1 lines of code changed in 1 file:

src/dr/app/beast: development_parsers.properties (+1 -1)

msuchard 2013-01-10 05:20 Rev.: 5302

Added unit-IntervalLatentLiabilityLikelihood for VNTRs; plan to refactor to remove duplicated code once more fully tested.

3 lines of code changed in 1 file:

src/dr/app/beast: release_parsers.properties (+3 -2)

msuchard 2012-12-05 12:41 Rev.: 5275

Added transition kernel for disjoint geographic regions

1 lines of code changed in 1 file:

src/dr/app/beast: release_parsers.properties (+1 -1)

msuchard 2012-12-04 06:11 Rev.: 5271

Extra level of indirection to stay off NoClassDefinition errors for MPI

79 lines of code changed in 2 files:

src/dr/app/beast: BeastMPI.java (new 75), BeastMain.java (+4 -6)

msuchard 2012-12-01 11:50 Rev.: 5266

Added MPI ranking of output for embarrassingly parallel use on Keeneland.

30 lines of code changed in 1 file:

src/dr/app/beast: BeastMain.java (+30)

msuchard 2012-11-29 11:06 Rev.: 5261

Composition parameters; should really be a Statistic with signaling ability

1 lines of code changed in 1 file:

src/dr/app/beast: release_parsers.properties (+1)

rambaut 2012-11-27 10:41 Rev.: 5257

Old TL/ASTL/MJTL in parser list.

2 lines of code changed in 2 files:

src/dr/app/beast: beagle_parsers.properties (+2)

alexander.alekseyenko 2012-11-20 09:35 Rev.: 5244

renamed integratedMixtureModel to MixtureModelLikelihood. Preserved an alias parser <integratedMixtureModel> per Marc's request. Updated the class, such that the mixtures are always normalized internally when likelihood is calculated.

1 lines of code changed in 1 file:

src/dr/app/beast: release_parsers.properties (+1 -1)

rambaut 2012-11-16 00:57 Rev.: 5233

Final swapping of the parser names

1 lines of code changed in 1 file:

src/dr/app/beast: beagle_parsers.properties (+1 -1)

rambaut 2012-11-16 00:54 Rev.: 5232

Renamed NewTreeLikelihood to BeagleTreeLikelihood

1 lines of code changed in 1 file:

src/dr/app/beast: beagle_parsers.properties (+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.

2 lines of code changed in 1 file:

src/dr/app/beast: beagle_parsers.properties (+2 -1)

rambaut 2012-11-10 03:30 Rev.: 5226

Parsers for the new epoch implementations.

2 lines of code changed in 1 file:

src/dr/app/beast: beagle_parsers.properties (+2)

msuchard 2012-11-08 10:08 Rev.: 5217

Attempting a first-order MRF prior for VNTR diffusion

1 lines of code changed in 1 file:

src/dr/app/beast: release_parsers.properties (+1)

msuchard 2012-11-03 14:44 Rev.: 5213

Added missing multivariate distribution likelihood model; opens up so many possibilities for rate models. Caution: may have broken Brownian diffusion precision Gibbs sampler.

1 lines of code changed in 1 file:

src/dr/app/beast: release_parsers.properties (+1)

(527 more)

Directory src/dr/app/beast/

Lines of Code

Developers

Most Recent Commits