September 2011 Commit Log

Number of Commits:
65
Number of Active Developers:
9
msuchard 2011-09-29 04:58 Rev.: 4338

Improved user-friendliness of robust counting errors

17 lines of code changed in 3 files:

msuchard 2011-09-28 06:40 Rev.: 4337

MatrixParameters now return valid names even if underlying parameters are unnamed

15 lines of code changed in 3 files:

rambaut 2011-09-28 01:38 Rev.: 4336

Parser replace warnings not shown for additional parser lists (i.e., BEAGLE) unless verbose is on.

2 lines of code changed in 1 file:

rambaut 2011-09-28 01:23 Rev.: 4335

duplicated parser warnings are no only visible with verbose errors (these were appearing for BEAGLE parsers)

2 lines of code changed in 1 file:

graham853@gmail.com 2011-09-27 02:04 Rev.: 4334

Separated out AlloppMulLabTree from AlloppSpeciesNetworkModel. Logging of MUL-tree. New network prior implementation. Other minor changes.

1548 lines of code changed in 5 files:

msuchard 2011-09-26 10:31 Rev.: 4333

Can specify non-integer degrees-of-freedom for Wishart distributions

24 lines of code changed in 3 files:

msuchard 2011-09-24 14:39 Rev.: 4332

Fixed degrees-of-freedom in Wishart statistics for NonPhylogeneticMultivariateTraitLikelihood

29 lines of code changed in 2 files:

msuchard 2011-09-24 11:56 Rev.: 4331

Enabled Gibbs sampling of precision matrix in NonPhylogeneticMultivariateTraitLikelihood

113 lines of code changed in 4 files:

msuchard 2011-09-22 10:36 Rev.: 4330

Fixed integer overflow (when prior sampling) and mixed-math in RandomWalkOperator

27 lines of code changed in 7 files:

msuchard 2011-09-21 22:54 Rev.: 4329

Fixed store/restore in WeightedMixtureModel

80 lines of code changed in 5 files:

msuchard 2011-09-21 14:37 Rev.: 4328

Better handling of limiting (0,1) cases in WeightedMixtureModel

7 lines of code changed in 1 file:

msuchard 2011-09-21 13:44 Rev.: 4327

Improved stability for finite mixture models.

103 lines of code changed in 1 file:

fbielejec 2011-09-20 23:47 Rev.: 4326

changed dependency to commons-math-2.2

20 lines of code changed in 1 file:

rambaut 2011-09-20 20:54 Rev.: 4325

Fixed issue with generating taxon lists when partitions have different taxa.

7 lines of code changed in 1 file:

rambaut 2011-09-20 20:40 Rev.: 4324

More 1.7 work

69 lines of code changed in 10 files:

baele.guy@gmail.com 2011-09-20 01:31 Rev.: 4323

Include the parser for the stepping-stone analysis in the development_parsers.properties

1 lines of code changed in 1 file:

baele.guy@gmail.com 2011-09-20 01:29 Rev.: 4322

Code to calculate the marginal likelihood using stepping-stone sampling (Xie et al., 2011), after the marginal likelihood estimator code has been run.

200 lines of code changed in 1 file:

dong.w.xie 2011-09-19 16:02 Rev.: 4321

trunk: update xml to compare BEAST 2.

372 lines of code changed in 1 file:

rambaut 2011-09-16 21:42 Rev.: 4320

Line wrapping of message

8 lines of code changed in 2 files:

rambaut 2011-09-16 21:29 Rev.: 4319

Improvements to the StarBEAST interface and how it asks for a species designation.

72 lines of code changed in 3 files:

msuchard 2011-09-16 13:42 Rev.: 4318

Playing with rescaling for the non-phylogenetic model

27 lines of code changed in 1 file:

rambaut 2011-09-16 04:23 Rev.: 4317

Fixing up discrete/continuous trait generation..

120 lines of code changed in 9 files:

rambaut 2011-09-16 03:04 Rev.: 4316

Continuous traits nearly working. Separated discrete traits out into a 'component' but will have broken things probably. Fixing up now.

1844 lines of code changed in 49 files:

dong.w.xie 2011-09-15 17:18 Rev.: 4315

trunk: update my tool with rescale height in starting tree.

14 lines of code changed in 2 files:

dong.w.xie 2011-09-15 14:37 Rev.: 4314

trunk: add Junit test for GF81

139 lines of code changed in 1 file:

dong.w.xie 2011-09-14 17:26 Rev.: 4313

trunk: update my tool

84 lines of code changed in 1 file:

dong.w.xie 2011-09-14 12:29 Rev.: 4311

trunk: solve Issue 500: remove RandomWalkIntegerOperator operator from relaxed clocks xml

3 lines of code changed in 1 file:

dong.w.xie 2011-09-14 11:14

trunk: rename a tool to generate relaxed clock xml by given data

343 lines of code changed in 3 files:

dong.w.xie 2011-09-13 17:31 Rev.: 4308

trunk: create program to beat Battistuzzi et al who are slandering BEAST

0 lines of code changed in 1 file:

mandevsgill 2011-09-13 05:35 Rev.: 4307

Latest version of GMRFMultilocusSkyrideLikelihood.

125 lines of code changed in 1 file:

msuchard 2011-09-12 21:59 Rev.: 4306

Implemented a null model to test for phylogenetic correlation of continuous traits

418 lines of code changed in 10 files:

msuchard 2011-09-12 21:57 Rev.: 4305

Fixes to HPM specification in BEAUti

66 lines of code changed in 8 files:

jheled@gmail.com 2011-09-12 16:25 Rev.: 4304

fix setting of pop sizes with constant

2 lines of code changed in 1 file:

dong.w.xie 2011-09-12 15:54 Rev.: 4302

trunk: solve Issue 499: Strip out should be false in the patterns when using binary Covarion Model

17 lines of code changed in 1 file:

rambaut 2011-09-09 22:55 Rev.: 4301

Adding continuous traits in BEAUti

659 lines of code changed in 8 files:

rambaut 2011-09-09 21:51 Rev.: 4300

Adding continuous traits in BEAUti

152 lines of code changed in 12 files:

msuchard 2011-09-09 06:05 Rev.: 4299

Fixed prior graphs in BEAUti, inverse gamma cdf and started stochastic Dollo

362 lines of code changed in 10 files:

rambaut 2011-09-09 04:50 Rev.: 4298

Fixed an issue with parameter table not being updated after a change to TreePrior.

19 lines of code changed in 2 files:

fbielejec 2011-09-09 01:33 Rev.: 4297

moved the getActiveFrame method to PanelUtils class

5 lines of code changed in 1 file:

fbielejec 2011-09-09 01:33 Rev.: 4296

method to return active frame

53 lines of code changed in 1 file:

fbielejec 2011-09-09 01:09 Rev.: 4295

dNdS robust counting model is now set in the check box

51 lines of code changed in 1 file:

fbielejec 2011-09-09 00:44 Rev.: 4294

working on dNdS robust counting UI

40 lines of code changed in 1 file:

rambaut 2011-09-08 23:57 Rev.: 4293

UI alterations...

22 lines of code changed in 2 files:

msuchard 2011-09-08 23:54 Rev.: 4292

Removed some conflicts in XML parsers

1 lines of code changed in 2 files:

msuchard 2011-09-08 23:49 Rev.: 4291

Changing user experience with MarkovJumps

80 lines of code changed in 6 files:

fbielejec 2011-09-08 22:42 Rev.: 4290

dNdS robust counting model is now set in the combo-box

65 lines of code changed in 1 file:

rambaut 2011-09-08 11:10 Rev.: 4289

Started to implement continuous traits in BEAUti. Needed extensive cleaning up and streamlining of code.

210 lines of code changed in 17 files:

msuchard 2011-09-07 22:43 Rev.: 4288

Promoted stochastic Dollo to basic BEAUti-enabled

2 lines of code changed in 1 file:

msuchard 2011-09-07 22:41 Rev.: 4287

Cleaning labels for robust counting

7 lines of code changed in 1 file:

msuchard 2011-09-06 09:38 Rev.: 4286

Re-added a matrix inversion statistic that quietly fell out of use

5 lines of code changed in 3 files:

dong.w.xie 2011-09-05 17:59 Rev.: 4285

add xml to compare with BEAST 2

0 lines of code changed in 1 file:

tbcbedford@gmail.com 2011-09-03 20:41 Rev.: 4284

Fixed calculation of thresholded likelihoods in MDS likelihood. MDS distance for a thresholded observation can often be zero (because of clustering).

22 lines of code changed in 3 files:

graham853@gmail.com 2011-09-03 20:28 Rev.: 4283

Allopolyploid model: Made code compatible with Java 1.5 (removed @Override's). Added citation. More sensible implementation of debugging logger.

143 lines of code changed in 24 files:

tbcbedford@gmail.com 2011-09-03 04:10 Rev.: 4282

Removing cruft from ClusterSingleMoveOperator.

4 lines of code changed in 1 file:

tbcbedford@gmail.com 2011-09-03 01:59 Rev.: 4281

Fixed issue with Hasting's ratio of clusterClusterSingleMoveOperator. The easiest solution was to remove location jitter entirely and instead pick a random unoccupied cluster when splitting.

20 lines of code changed in 2 files:

graham853@gmail.com 2011-09-02 21:18

Remove debugging class intended for my use only.

0 lines of code changed in 2 files:

tbcbedford@gmail.com 2011-09-02 00:35 Rev.: 4278

(I think) fixed the bug in indexing of MDS likelihood.

10 lines of code changed in 2 files:

graham853@gmail.com 2011-09-02 00:01 Rev.: 4277

5667 lines of code changed in 24 files:

dong.w.xie 2011-09-01 17:35 Rev.: 4276

update bsp xml

11 lines of code changed in 4 files:

dong.w.xie 2011-09-01 13:55 Rev.: 4275

add bsp xml to compare to BEAST 2 bsp

364 lines of code changed in 2 files:

dong.w.xie 2011-09-01 11:42 Rev.: 4274

struggling svn

0 lines of code changed in 7 files:

dong.w.xie 2011-09-01 11:41 Rev.: 4273

0 lines of code changed in 1 file:

dong.w.xie 2011-09-01 11:22 Rev.: 4272

struggling svn

814 lines of code changed in 2 files:

dong.w.xie 2011-09-01 11:14 Rev.: 4271

struggling svn

0 lines of code changed in 26 files:

dong.w.xie 2011-09-01 11:04 Rev.: 4270

0 lines of code changed in 1 file:

August 2011 »

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