January 2013 Commit Log

Number of Commits:
59
Number of Active Developers:
6
rambaut 2013-01-31 04:42 Rev.: 5367

Porting some fixes from 1.7 branch

25 lines of code changed in 13 files:

fbielejec 2013-01-30 22:17 Rev.: 5363

report element generation. Moving to multiple partitions

34 lines of code changed in 1 file:

fbielejec 2013-01-30 20:49 Rev.: 5362

split the condition to avoid compiler warnings

24 lines of code changed in 2 files:

msuchard 2013-01-30 10:26 Rev.: 5361

Added a flag to debug and profile epoch models in series; option should probably be elevated to a system property.

53 lines of code changed in 1 file:

mdhall272@gmail.com 2013-01-30 07:18 Rev.: 5360

Moving on to the next tree operator.

159 lines of code changed in 8 files:

mdhall272@gmail.com 2013-01-30 05:19 Rev.: 5359

Finished off transmission tree operators and began on special cases of the existing phylogenetic tree operators

151 lines of code changed in 6 files:

fbielejec 2013-01-30 04:55 Rev.: 5357

simulator element generation

108 lines of code changed in 7 files:

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.

30 lines of code changed in 6 files:

mdhall272@gmail.com 2013-01-29 06:57 Rev.: 5353

Cleaned up comments.

12 lines of code changed in 2 files:

mdhall272@gmail.com 2013-01-29 06:36 Rev.: 5352

Silly mistake rectified.

3 lines of code changed in 2 files:

mdhall272@gmail.com 2013-01-29 06:03

Further work on TT>=TMRCA. Sacrificing efficiency for more intuitive code for now.

258 lines of code changed in 3 files:

rambaut 2013-01-29 04:45 Rev.: 5349

The code as written requires at least eigenCount extra buffers to be able to guarantee to convolve matrices along a branch. Put a check in for this if convolution is being used. Also fixed a possible error where we run out of buffers midway through compiling a set of convolutions for a branch. Now if it knows it will not have enough buffers, it computes the current list and then continues, rather than waiting until it runs out.

36 lines of code changed in 1 file:

fbielejec 2013-01-29 03:57 Rev.: 5348

minor changes to Utils and partition element parser

10 lines of code changed in 4 files:

fbielejec 2013-01-29 03:54

starting to work on reportable timers for update and convolve operations

64 lines of code changed in 2 files:

baele.guy@gmail.com 2013-01-29 02:19 Rev.: 5345

bug fix

1 lines of code changed in 1 file:

mdhall272@gmail.com 2013-01-28 22:41 Rev.: 5344

Finished rewriting for TT>=TMRCA version (needs testing).

16 lines of code changed in 1 file:

mdhall272@gmail.com 2013-01-28 22:14 Rev.: 5343

Rewriting for TT>=TMRCA version

30 lines of code changed in 1 file:

fbielejec 2013-01-27 01:11 Rev.: 5342

site rate model element generation, changes to naming scheme, util methods

474 lines of code changed in 5 files:

rambaut 2013-01-27 00:52 Rev.: 5341

I think the convolution buffer issue is now fixed. Had to create a single extra reserve buffer that was used to free up the convolution list when all the other buffers had been used. Now runs - can't promise correctness so probably ought to be compared to older implementation.

59 lines of code changed in 1 file:

rambaut 2013-01-27 00:17 Rev.: 5340

Towards making the spare buffer stack working. The convolveMatrices() was not completing the convolution operation that it had interrupted to free up some buffers. There is still a bug though - if this method runs out of buffers on the first convolution then it has nothing to free up. More thinking required.

8 lines of code changed in 1 file:

msuchard 2013-01-26 09:34 Rev.: 5339

Can now set BEAGLE extra buffer count from system properties

20 lines of code changed in 2 files:

msuchard 2013-01-26 09:15 Rev.: 5338

Some buffers not returned to pool; but error still persists in code.

14 lines of code changed in 1 file:

mdhall272@gmail.com 2013-01-25 04:56 Rev.: 5337

Started adding the operators to allow the transmission times to occur after TMRCAs.

179 lines of code changed in 3 files:

msuchard 2013-01-23 09:47 Rev.: 5335

Added hard bounds for ancient DNA studies involving EmpiricalDistributionLikelihood

35 lines of code changed in 3 files:

fbielejec 2013-01-19 11:28 Rev.: 5334

moved XML generation to a separate generator class

671 lines of code changed in 3 files:

msuchard 2013-01-18 06:54 Rev.: 5333

Fixing jitter in IMTL

5 lines of code changed in 1 file:

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.

216 lines of code changed in 4 files:

fbielejec 2013-01-18 02:18 Rev.: 5331

frequency model element in XML

299 lines of code changed in 8 files:

fbielejec 2013-01-18 01:05 Rev.: 5330

implemented data type selection

289 lines of code changed in 5 files:

msuchard 2013-01-17 09:56 Rev.: 5329

Fixed normalization of CTMC reference prior

31 lines of code changed in 2 files:

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

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

917 lines of code changed in 7 files:

msuchard 2013-01-16 10:50 Rev.: 5327

Eigendecomposition check uses anonymous subclass that turns off condition number evaluation.

8 lines of code changed in 2 files:

mdhall272@gmail.com 2013-01-16 02:36 Rev.: 5326

Done but not tested.

118 lines of code changed in 1 file:

mdhall272@gmail.com 2013-01-15 23:01 Rev.: 5325

Added some other matrices that don't work.

47 lines of code changed in 1 file:

msuchard 2013-01-15 12:01 Rev.: 5324

Can pass arbitrary root FrequencyModel to HomogeneousBranchModel.

15 lines of code changed in 4 files:

msuchard 2013-01-15 11:50 Rev.: 5323

Added getRootFrequencyModel to BranchModel interface. Consider deprecating getRootSubstitutionModel() as there are no substitutions occurring at the root. Also commented out @Override to interface functions since this is not Java 1.5 compatible.

79 lines of code changed in 15 files:

mdhall272@gmail.com 2013-01-15 06:05 Rev.: 5322

Cleaning up.

60 lines of code changed in 2 files:

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

Added parser to list.

1 lines of code changed in 1 file:

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.

822 lines of code changed in 6 files:

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.

602 lines of code changed in 4 files:

rambaut 2013-01-13 22:13 Rev.: 5318

Cosmetics

27 lines of code changed in 6 files:

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:

tbcbedford@gmail.com 2013-01-13 07:38 Rev.: 5316

Implement logging of drifted tree traits.

155 lines of code changed in 2 files:

tbcbedford@gmail.com 2013-01-13 03:43 Rev.: 5315

Improving caching by tracking column effect and row effect updates.

24 lines of code changed in 1 file:

tbcbedford@gmail.com 2013-01-12 03:37 Rev.: 5314

Small change to parameter syntax (virusOffset to virusOffsets).

30 lines of code changed in 2 files:

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

Include DriftedLocationStatistic in dev parsers.

1 lines of code changed in 1 file:

tbcbedford@gmail.com 2013-01-12 03:04 Rev.: 5312

Implement statistic that records drifted locations. This required storing virusDates and serumDates parameters from AntigenicLikelihood and passing these, plus the locationDriftParameter, to the new DriftedLocationsStatistic.

162 lines of code changed in 2 files:

tbcbedford@gmail.com 2013-01-11 23:01 Rev.: 5311

Depecrate antigenic drift priors. Now incorporated directly into antigenicLikelihood.

49 lines of code changed in 4 files:

tbcbedford@gmail.com 2013-01-11 10:17 Rev.: 5310

Streamline antigenic likelihood a bit, removing virusDates parameter.

19 lines of code changed in 1 file:

tbcbedford@gmail.com 2013-01-10 12:18 Rev.: 5309

Reinstate linear initial conditions.

4 lines of code changed in 1 file:

tbcbedford@gmail.com 2013-01-10 11:55 Rev.: 5308

Fix bug in assigning dates.

10 lines of code changed in 1 file:

tbcbedford@gmail.com 2013-01-10 11:20 Rev.: 5307

Implement antigenic drift on map distances.

48 lines of code changed in 1 file:

tbcbedford@gmail.com 2013-01-10 09:36 Rev.: 5306

Include antigenic drift parameter. Doesn't do anything yet.

20 lines of code changed in 1 file:

rambaut 2013-01-10 05:40 Rev.: 5305

Important copyright homogenization

1 lines of code changed in 1 file:

rambaut 2013-01-10 05:36 Rev.: 5304

Drifting

107 lines of code changed in 6 files:

rambaut 2013-01-10 05:31 Rev.: 5303

Drifting

239 lines of code changed in 5 files:

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

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

583 lines of code changed in 8 files:

fbielejec 2013-01-10 03:02 Rev.: 5301

working on XML generator

234 lines of code changed in 2 files:

tbcbedford@gmail.com 2013-01-09 01:02 Rev.: 5300

Fix numerical bug. If an interval likelihood is in the far tail of the distribution cdf1 == cdf2. Should return a point likelihood here, rather than 0.0, as had been the case.

16 lines of code changed in 1 file:

December 2012 »

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