November 2012 Commit Log

Number of Commits:
52
Number of Active Developers:
6
rambaut 2012-11-30 22:06 Rev.: 5265

Pathogen - you can now copy names of selected taxa to the clipboard.

60 lines of code changed in 9 files:

rambaut 2012-11-30 21:58 Rev.: 5264

New BeagleTreeLikelihood was not updating correctly for a rescale after an underflow.

1 lines of code changed in 1 file:

msuchard 2012-11-30 06:37 Rev.: 5263

Fixed zero-branch length bug in IntegratedMultivariateTraitLikelihood and harmonized behavior of NonPhylogeneticMultivariateTraitLikelihood for model selection.

53 lines of code changed in 3 files:

mdhall272@gmail.com 2012-11-30 04:28 Rev.: 5262

More tip date shenaningans. Also added method to dump the current transmission tree to a file.

44 lines of code changed in 2 files:

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

Composition parameters; should really be a Statistic with signaling ability

207 lines of code changed in 5 files:

msuchard 2012-11-28 10:34 Rev.: 5260

Incomplete implementation of multi-state stochastic Dollo under BEAGLE. Needs considerably more work.

660 lines of code changed in 11 files:

mdhall272@gmail.com 2012-11-28 04:08 Rev.: 5259

Fixed (hopefully) an issue that was causing systematic under-estimation of incubation periods

154 lines of code changed in 3 files:

msuchard 2012-11-27 11:01 Rev.: 5258

Fix for complete history logging; this may break code elsewhere

8 lines of code changed in 1 file:

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

Old TL/ASTL/MJTL in parser list.

4 lines of code changed in 3 files:

rambaut 2012-11-27 09:43 Rev.: 5256

Forgot to change the parser name.

1 lines of code changed in 2 files:

rambaut 2012-11-27 09:33 Rev.: 5255

Inserting the old MJTL back in to the deep inheritance chain of OTL. For testing purposes only. If it has a line through it - it is going to go at some point.

815 lines of code changed in 2 files:

rambaut 2012-11-27 09:23 Rev.: 5254

Inserting the old ASTL back in to the deep inheritance chain of OTL. MJTL next.

683 lines of code changed in 4 files:

mdhall272@gmail.com 2012-11-27 02:33 Rev.: 5253

Various improvements and bugfixes to starting transmission trees

14 lines of code changed in 1 file:

rambaut 2012-11-22 04:11 Rev.: 5252

Cleaned up the format of the complete history logging. Now has {{SITE,TIME,FROM_STATE,TO_STATE},...}. I am aware this will mess up people's processing scripts but it was a mess before (unnecessary nesting of parentheses and '-1's all over the place).

3 lines of code changed in 1 file:

rambaut 2012-11-22 01:29 Rev.: 5251

Cleaned up the format of the complete history logging. Now has {SITE,{TIME,FROM_STATE,TO_STATE},...}. I am aware this will mess up people's processing scripts but it was a mess before (unnecessary nesting of parentheses and '-1's all over the place).

12 lines of code changed in 5 files:

fbielejec 2012-11-21 06:50 Rev.: 5250

starting to work on XML generator

137 lines of code changed in 13 files:

mdhall272@gmail.com 2012-11-21 05:11 Rev.: 5249

Now repeatedly tries to find a starting transmission tree with nonzero likelihood rather than giving up after one try

25 lines of code changed in 1 file:

fbielejec 2012-11-21 02:15 Rev.: 5248

set tree for partition using hash map

31 lines of code changed in 5 files:

fbielejec 2012-11-21 01:54 Rev.: 5247

adding multiple trees

202 lines of code changed in 10 files:

mdhall272@gmail.com 2012-11-20 22:24 Rev.: 5246

Implemented user-specified starting transmission trees

56 lines of code changed in 4 files:

alexander.alekseyenko 2012-11-20 11:02 Rev.: 5245

resolving Issue 630.

3 lines of code changed in 1 file:

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.

254 lines of code changed in 7 files:

msuchard 2012-11-20 08:36 Rev.: 5243

Binomial likelihood now takes non-fixed counts.

36 lines of code changed in 3 files:

mdhall272@gmail.com 2012-11-20 04:24 Rev.: 5242

Fixed a bug regarding tip dates

5 lines of code changed in 3 files:

fbielejec 2012-11-20 03:05 Rev.: 5241

working on UI

93 lines of code changed in 5 files:

mdhall272@gmail.com 2012-11-20 02:44 Rev.: 5240

Fixed a problem with normal incubation periods

67 lines of code changed in 4 files:

fbielejec 2012-11-20 01:32 Rev.: 5239

switching to new interfaces for epoch model

5 lines of code changed in 1 file:

alexander.alekseyenko 2012-11-17 11:24 Rev.: 5238

Started on a model to compute mixtures of likelihoods.

147 lines of code changed in 3 files:

mdhall272@gmail.com 2012-11-17 04:00 Rev.: 5237

Will accept a wider value of distributions on incubation periods

19 lines of code changed in 3 files:

fbielejec 2012-11-16 21:15

switching the simulator to new interfaces

387 lines of code changed in 10 files:

fbielejec 2012-11-16 07:17 Rev.: 5234

preparing to switch to new interface

28 lines of code changed in 2 files:

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

Final swapping of the parser names

241 lines of code changed in 4 files:

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

Renamed NewTreeLikelihood to BeagleTreeLikelihood

1545 lines of code changed in 20 files:

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

Renamed BeagleTreeLikelihood to OldBeagleTreeLikelihood

1349 lines of code changed in 16 files:

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

Updated copyright messages.

1441 lines of code changed in 167 files:

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.

775 lines of code changed in 33 files:

Sibon.Li@gmail.com 2012-11-15 11:24 Rev.: 5228

Updated InstantiableTracerApp to include an option to load a System exitable instance of Tracer

54 lines of code changed in 2 files:

rambaut 2012-11-10 05:19 Rev.: 5227

Debuggin'

20 lines of code changed in 3 files:

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

Parsers for the new epoch implementations.

366 lines of code changed in 4 files:

rambaut 2012-11-10 01:43 Rev.: 5225

Implemented eventuality where the delegate runs out of spare buffers - it now shunts of what it has so far and then continues.

99 lines of code changed in 1 file:

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

NewBeagleTreeLikelihood evaluation seems to work for Epoch models.

32 lines of code changed in 3 files:

rambaut 2012-11-09 23:39 Rev.: 5223

Stuff

35 lines of code changed in 1 file:

rambaut 2012-11-09 23:24 Rev.: 5222

Test main for NewBeagleTreeLikelihood

91 lines of code changed in 1 file:

fbielejec 2012-11-09 23:08 Rev.: 5221

working on UI

35 lines of code changed in 2 files:

fbielejec 2012-11-09 23:07 Rev.: 5220

commititng recent changes

2 lines of code changed in 1 file:

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

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

1591 lines of code changed in 8 files:

fbielejec 2012-11-08 23:58 Rev.: 5218

some more work on the UI

159 lines of code changed in 12 files:

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

Attempting a first-order MRF prior for VNTR diffusion

187 lines of code changed in 3 files:

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

Epoch model in new form...

287 lines of code changed in 5 files:

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:

msuchard 2012-11-03 14:45 Rev.: 5214

Updated testMNV for Gibbs sampling of precision parameter

126 lines of code changed in 2 files:

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.

511 lines of code changed in 8 files:

October 2012 »

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