October 2011 Commit Log

Number of Commits:
36
Number of Active Developers:
6
dong.w.xie 2011-10-31 15:19 Rev.: 4375

trunk: solve Issue 523: BEAUti Traits panel buttons enable/disable should adapt to data and traits

20 lines of code changed in 1 file:

dong.w.xie 2011-10-31 14:45 Rev.: 4374

trunk: correct *BEAST calibration and solve Issue 520: BEAUti tmrca parameter not sync with prior panel.

1 lines of code changed in 1 file:

dong.w.xie 2011-10-28 12:48 Rev.: 4373

update testSRD06 xml

289 lines of code changed in 2 files:

msuchard 2011-10-25 09:17 Rev.: 4372

Skeleton for Gaussian Process coalescent model

300 lines of code changed in 5 files:

rambaut 2011-10-25 01:35 Rev.: 4371

Start towards implementing Volz et al (2009) Genetics

246 lines of code changed in 4 files:

mandevsgill 2011-10-21 07:40 Rev.: 4370

Latest version of GMRFMultilocusSkyrideLikelihood. Needs to be cleaned up.

17 lines of code changed in 1 file:

dong.w.xie 2011-10-19 13:49 Rev.: 4369

trunk: correct *BEAST calibration and solve Issue 520: BEAUti tmrca parameter not sync with prior panel.

25 lines of code changed in 8 files:

dong.w.xie 2011-10-19 12:45 Rev.: 4368

trunk: correct *BEAST calibration on species tree XML generator in BEAUti.

109 lines of code changed in 4 files:

msuchard 2011-10-19 07:45 Rev.: 4367

Fixed optional parameter settings in GMRFSkyrideLikelihoodParser

1 lines of code changed in 2 files:

dong.w.xie 2011-10-18 15:17 Rev.: 4366

trunk: implement *BEAST calibration on species tree XML generator in BEAUti.

187 lines of code changed in 5 files:

msuchard 2011-10-18 08:34 Rev.: 4365

Better way to handle star trees via a derived TreeModel

661 lines of code changed in 4 files:

baele.guy@gmail.com 2011-10-17 20:10 Rev.: 4364

Update to allow multiple input files with marginal likelihood samples to be processed.

67 lines of code changed in 1 file:

baele.guy@gmail.com 2011-10-17 19:56 Rev.: 4363

Removed some unnecessary comments.

0 lines of code changed in 1 file:

baele.guy@gmail.com 2011-10-17 19:47 Rev.: 4362

Update to allow multiple input files with marginal likelihood samples to be processed.

57 lines of code changed in 1 file:

dong.w.xie 2011-10-17 16:43 Rev.: 4361

trunk: update Species Set panel GUI part to take Taxa object instead, and ready to implement XML generator next time.

315 lines of code changed in 5 files:

msuchard 2011-10-17 03:49 Rev.: 4360

Preliminary star tree implementation as an alternative to the correlated trait models; would function better as a subclass of TreeModel than TreeLikelihood.

553 lines of code changed in 6 files:

rambaut 2011-10-15 09:13 Rev.: 4359

Can still edit a trait called 'species' if it is not currently being used for *BEAST

1 lines of code changed in 2 files:

dong.w.xie 2011-10-14 14:40 Rev.: 4358

trunk: Issue 514: NullPointerException when setting prior to tree model in BEAUti Prior panel

1 lines of code changed in 1 file:

mandevsgill 2011-10-13 15:16 Rev.: 4357

Updated the multilocus gmrf model so that we have a proper prior. Still needs to be cleaned up a little bit.

265 lines of code changed in 2 files:

dong.w.xie 2011-10-13 12:00 Rev.: 4356

trunk: Issue 513: *BEAST constraint of the 'species' trait

2 lines of code changed in 1 file:

dong.w.xie 2011-10-12 15:39 Rev.: 4355

trunk: finish Species Set panel GUI part, and wait for XML example to implement XML generator.

65 lines of code changed in 1 file:

rambaut 2011-10-12 05:09 Rev.: 4354

Fixed an issue with repeatedly added listeners for Prior Dialog components.

7 lines of code changed in 2 files:

rambaut 2011-10-12 03:16 Rev.: 4353

Added drag and drop of XML file to input file text of main beast dialog boxl.

12 lines of code changed in 1 file:

rambaut 2011-10-12 03:12 Rev.: 4352

Fixed an issue with creating a 'species' trait when *BEAST was already on. Now checks that the user actually loads a species trait when asked to when switching on *BEAST.

Also, reinstated UCLN and UCED as clock options. UCGD and UCCD (Chauchy) are not currently implemented but could be. Also autocorrelated?

132 lines of code changed in 4 files:

rambaut 2011-10-12 00:20 Rev.: 4351

Fixed warning messages

2 lines of code changed in 1 file:

rambaut 2011-10-12 00:16 Rev.: 4350

Removed certain special cases that weren't necessary

2 lines of code changed in 1 file:

dong.w.xie 2011-10-11 18:20 Rev.: 4349

trunk: initial dev for Species Set panel when *BEAST calibration that is only allowed on species tree

839 lines of code changed in 4 files:

rambaut 2011-10-11 03:46 Rev.: 4348

A slight modification to the thread pooling. Rather than just threading the 'likelihood' compoundLikelihood, it now threads the 'posterior'. To do this it flattens out all the compoundLikelihoods (i.e., 'likelihood' and 'prior'). Should allow the prior calculations to help pad some of the unused thread and load balance a bit better. Tested and works but would like to do some benchmarking.

38 lines of code changed in 4 files:

rambaut 2011-10-10 21:36 Rev.: 4347

Refined the interface for turning on and off *BEAST. 'species' is not a special trait until *BEAST is turned on.

61 lines of code changed in 16 files:

dong.w.xie 2011-10-10 14:24 Rev.: 4346

trunk: solve Issue 510: BEAUti uncheck *BEAST but cannot reverse to normal BEAST properly

30 lines of code changed in 6 files:

dong.w.xie 2011-10-10 10:51 Rev.: 4345

trunk: solve Issue 506: The gamma prior is not reverted to what it was previously if *BEAST in unselected.

0 lines of code changed in 2 files:

dong.w.xie 2011-10-10 10:13 Rev.: 4344

trunk: solve Issue 503: BEAUti operator analysis should be chosen as default

1 lines of code changed in 1 file:

msuchard 2011-10-08 21:01 Rev.: 4343

BEAUti generates discrete trait XMLs that run.

137 lines of code changed in 4 files:

msuchard 2011-10-08 19:39 Rev.: 4342

Adding binary stochastic Dollo to BEAUti. Now can read Ringe dataset and generate an XML that runs.

499 lines of code changed in 11 files:

alexei.drummond 2011-10-07 22:17 Rev.: 4341

added parser for IntermediateExchange.

64 lines of code changed in 1 file:

dong.w.xie 2011-10-06 15:39

trunk: update xml to compare BEAST 2.

318 lines of code changed in 3 files:

September 2011 »

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