December 2012 Commit Log

Number of Commits:
32
Number of Active Developers:
8
jheled@gmail.com 2012-12-23 12:48 Rev.: 5299

Add '-heights ca' option to set heights which do not suffer from the "negative branches" problem. citation later ....

149 lines of code changed in 3 files:

fbielejec 2012-12-22 04:53 Rev.: 5298

XML generating

94 lines of code changed in 3 files:

fbielejec 2012-12-22 04:09 Rev.: 5297

working on XML generation

5 lines of code changed in 6 files:

rambaut 2012-12-22 02:13 Rev.: 5296

Grammar

1 lines of code changed in 2 files:

tbcbedford@gmail.com 2012-12-22 00:15 Rev.: 5295

Fixed calculation of intervalLikelihood to properly use intervalWidth (rather than assuming 1.0).

1 lines of code changed in 1 file:

tbcbedford@gmail.com 2012-12-21 23:18 Rev.: 5294

Remove truncation and make likelihood in terms of titre H_ij rather than immunological distance d_ij

28 lines of code changed in 1 file:

msuchard 2012-12-21 11:28 Rev.: 5293

Standardizing output for markov jumps

75 lines of code changed in 7 files:

msuchard 2012-12-21 05:39 Rev.: 5292

Improving ease to subclass ComplexSubstitutionModel for varying conditioning restrictions

27 lines of code changed in 4 files:

msuchard 2012-12-21 05:22 Rev.: 5291

Increased max iterations and largest allowable condition number for complex diagonalizable substitution models; may change inference in BSSVS models.

107 lines of code changed in 2 files:

mdhall272@gmail.com 2012-12-21 02:07 Rev.: 5290

changed to take a user-specified matrix

157 lines of code changed in 1 file:

rambaut 2012-12-20 22:07 Rev.: 5289

SubstitutionModelDelegate returns the root substitution model's frequencies.

2 lines of code changed in 1 file:

alexei.drummond 2012-12-20 10:37 Rev.: 5288

Added warning about single-child internal nodes that is suppressed in TreeStat but active in BEAST-MCMC and other programs.

14 lines of code changed in 3 files:

alexei.drummond 2012-12-20 10:10 Rev.: 5287

Added SingleChildCountStatistic to TreeStat to support e.g. the counting of direct ancestors and nodes representing migration events.

91 lines of code changed in 3 files:

msuchard 2012-12-20 10:00 Rev.: 5286

Standardizing format for complete histories with single events

11 lines of code changed in 4 files:

alexei.drummond 2012-12-20 08:51 Rev.: 5285

Relaxed nexus importer to allow internal nodes with 1 or more children. This is to allow TreeStat to analyze direct ancestor trees and migration trees where migrations events are defined by internal nodes.

11 lines of code changed in 1 file:

msuchard 2012-12-20 07:49 Rev.: 5284

Modified NexusImporter to handle nested arrays. May cause unforeseen bugs in important other traits.

41 lines of code changed in 2 files:

msuchard 2012-12-19 16:06 Rev.: 5283

Preliminary test unit for failure of eigen decompositions

249 lines of code changed in 1 file:

msuchard 2012-12-18 06:51 Rev.: 5282

Consistently clearing complete histories within CodonPartitionedRobustCounting

41 lines of code changed in 3 files:

baele.guy@gmail.com 2012-12-08 23:21 Rev.: 5281

Small correction in keeping track of the number of steps.

3 lines of code changed in 1 file:

msuchard 2012-12-08 08:56 Rev.: 5280

Delegated handling of missing values in IntegratedMultivariateTraitLikelihood with a view towards enabling partially missing values

184 lines of code changed in 5 files:

msuchard 2012-12-06 10:37 Rev.: 5279

ARGAddRemoveEventOperator updated to handle two partitions

373 lines of code changed in 2 files:

msuchard 2012-12-05 13:35 Rev.: 5276

Fixed bug in PrecisionMatrixGibbsOperator under power posterior

1 lines of code changed in 1 file:

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

Added transition kernel for disjoint geographic regions

250 lines of code changed in 7 files:

rambaut 2012-12-04 19:37 Rev.: 5274

A better solution to the multithreading issue with trees that avoids thread syncs. The problem was only for empirical trees for which the branch lengths were known but not the node heights. Thus it had to compute the node heights when asked and this caused the thread conflict. Now the EmpiricalTrees object forces a node height calculation prior to evaluation.

14 lines of code changed in 4 files:

rambaut 2012-12-04 11:21 Rev.: 5273

There was an issue when multiple BTL tried to get node heights from the same tree in different threads giving negative branch length errors. Synchronizing on the tree fixes this - might have other implications.

10 lines of code changed in 1 file:

msuchard 2012-12-04 08:11 Rev.: 5272

Updated PrecisionMatrixGibbsOperator for functionality within path sampling from posterior to prior. Should still cause errors in path sampling between two arbitrary models.

37 lines of code changed in 6 files:

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:

mdhall272@gmail.com 2012-12-03 22:12 Rev.: 5270

Another small tip date-related modification.

12 lines of code changed in 2 files:

rambaut 2012-12-03 03:04 Rev.: 5269

Removed the canReturnComplexDiagonalization() method which was always returning false even if there was a complex diagonalization. This method is correctly returned by the substitution model.

0 lines of code changed in 2 files:

rambaut 2012-12-03 02:59 Rev.: 5268

Removing a debug exit()

5 lines of code changed in 1 file:

msuchard 2012-12-03 02:51 Rev.: 5267

Fixed bug in SubstitutionModelDelegate; new and old BeagleTreeLikelihood now return same values.

15 lines of code changed in 1 file:

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

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

46 lines of code changed in 3 files:

November 2012 »

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