February 2013 Commit Log

Number of Commits:
65
Number of Active Developers:
9
dong.w.xie@gmail.com 2013-02-28 14:58 Rev.: 5459

tracer: doWork in EBSP needs to be reviewed, it seems a copy of BSP.

14 lines of code changed in 5 files:

dong.w.xie@gmail.com 2013-02-25 10:31 Rev.: 5458

trunk: merge Issue 677

124 lines of code changed in 14 files:

akaruiws 2013-02-22 16:49 Rev.: 5456

Missed correction.

17 lines of code changed in 2 files:

dong.w.xie@gmail.com 2013-02-22 11:25 Rev.: 5454

trunk: merge Issue 677 : Using Microsatellite loci for inferring one phylogenetic tree that uses all the loci.

126 lines of code changed in 13 files:

fbielejec 2013-02-22 04:28 Rev.: 5452

working on main menu bar

178 lines of code changed in 8 files:

baele.guy@gmail.com 2013-02-22 04:04 Rev.: 5451

Remove old version of the operator.

0 lines of code changed in 1 file:

baele.guy@gmail.com 2013-02-22 03:56 Rev.: 5450

Refactoring.

396 lines of code changed in 1 file:

baele.guy@gmail.com 2013-02-21 22:40 Rev.: 5449

Added option to specify the number of iterations using the initial covariance.

66 lines of code changed in 1 file:

baele.guy@gmail.com 2013-02-21 22:38 Rev.: 5448

Fixed citation error.

1 lines of code changed in 2 files:

baele.guy@gmail.com 2013-02-21 22:37 Rev.: 5447

Fixed typo.

1 lines of code changed in 2 files:

mdhall272@gmail.com 2013-02-21 22:19 Rev.: 5446

Working as intended. All classes necessary for TT=TMRCA model (sans geography) now complete.

3 lines of code changed in 1 file:

mdhall272@gmail.com 2013-02-21 21:46 Rev.: 5445

Cleaning up (fixing SVN tree conflict?)

32 lines of code changed in 1 file:

mdhall272@gmail.com 2013-02-21 21:43 Rev.: 5444

Cleaning up

3 lines of code changed in 2 files:

msuchard 2013-02-21 07:13 Rev.: 5443

Porting typo fix from 1.7

6 lines of code changed in 2 files:

baele.guy@gmail.com 2013-02-21 02:33 Rev.: 5442

Cleaning up.

11 lines of code changed in 1 file:

baele.guy@gmail.com 2013-02-21 01:29 Rev.: 5441

Remaining part of an adaptive Metropolis (AM) algorithm/operator. Seems to be working but needs more testing. Also needs a rewrite to exploit symmetry and avoid redundant calculations.

156 lines of code changed in 1 file:

mdhall272@gmail.com 2013-02-20 23:30 Rev.: 5440

Added method to check transmission network makes sense

27 lines of code changed in 2 files:

mdhall272@gmail.com 2013-02-20 22:15 Rev.: 5439

Parser done

62 lines of code changed in 2 files:

mdhall272@gmail.com 2013-02-20 06:36 Rev.: 5438

Operator wrapping a phylogenetic tree operator that changes transmission tree accordingly (TT=TMRCA only). Still needs testing and parser.

98 lines of code changed in 2 files:

fbielejec 2013-02-20 01:57 Rev.: 5437

get the save paths right

35 lines of code changed in 4 files:

graham853@gmail.com 2013-02-20 00:01

Allopolyploid model. Added diploidRootIsRoot flag (but only tested code when true), changed formula for network prior, added error check relating to oneHybridization flag, improved debug output.

AlloppChangeNumHybridizations: added error check relating to oneHybridization flag.
AlloppChangeNumHybridizationsParser: added error relating to oneHybridization flag.
AlloppDiploidHistory.java: nicer debug output, changes for diploidRootIsRoot flag.
AlloppLeggedTree: simpler debug output.
AlloppMulLabTree: nicer debug output.
AlloppNetworkNodeSlide: Changed operateOneNodeInDiploidHistory() for diploidRootIsRoot flag.
AlloppNetworkPrior: Changed formula for prior (9.0 -> 7.0*sqrt(#diploids))
AlloppSpeciesBindings: nicer debug output.
AlloppSpeciesNetworkModel: changes for diploidRootIsRoot flag, debug output.
AlloppSpeciesNetworkModelParser: changes for diploidRootIsRoot flag.

173 lines of code changed in 22 files:

fbielejec 2013-02-19 22:31 Rev.: 5434

had to manually repair org.virion.jam imports to fix ant build problem

25 lines of code changed in 10 files:

akaruiws 2013-02-19 16:32 Rev.: 5433

Modify to handle ambiguity.

3 lines of code changed in 2 files:

fbielejec 2013-02-19 10:04 Rev.: 5432

updated buildfile

5 lines of code changed in 1 file:

fbielejec 2013-02-19 09:39 Rev.: 5431

updated buildfile

125 lines of code changed in 4 files:

fbielejec 2013-02-19 03:36

cleaning up

1583 lines of code changed in 9 files:

fbielejec 2013-02-19 03:21 Rev.: 5428

Display taxa height

11 lines of code changed in 5 files:

fbielejec 2013-02-19 02:20 Rev.: 5427

Display taxa height

455 lines of code changed in 4 files:

baele.guy@gmail.com 2013-02-19 01:52 Rev.: 5426

First part of an adaptive Metropolis (AM) algorithm/operator.

290 lines of code changed in 1 file:

fbielejec 2013-02-18 23:13 Rev.: 5425

Generate for multiple trees option done. Some extra error checking.

144 lines of code changed in 6 files:

mdhall272@gmail.com 2013-02-18 22:32 Rev.: 5424

ProductStatistics now take the ID of the relevant XML object as a name if they do not otherwise have one (so the relevant columns in the log file and hence in Tracer will not simply be called "productStatistic"). This is how SumStatistic already works.

9 lines of code changed in 2 files:

fbielejec 2013-02-18 05:36 Rev.: 5423

aligned radio buttons with GridBagConstraints

31 lines of code changed in 2 files:

fbielejec 2013-02-18 04:32 Rev.: 5422

working on simulating from multiple trees

186 lines of code changed in 6 files:

fbielejec 2013-02-18 03:15 Rev.: 5421

working on simulating from multiple trees

302 lines of code changed in 7 files:

rambaut 2013-02-17 01:05 Rev.: 5420

Retrospectively added a couple of bug fixes to the version list for completeness.

3 lines of code changed in 2 files:

msuchard 2013-02-16 07:58 Rev.: 5419

Keep Colt flag off unless shown to provide more reliable simulants.

7 lines of code changed in 2 files:

rambaut 2013-02-16 07:17 Rev.: 5418

Merging version stuff and copyright dates with 1.7 branch.

80 lines of code changed in 22 files:

baele.guy@gmail.com 2013-02-16 00:48 Rev.: 5411

- nextGamma(alpha, lambda) in Colt needs to be called with 1/scale instead of scale
- also replaced log(x/scale) by log(x) - log(scale) to avoid numerical errors when evaluating very small values from a gamma distribution

23 lines of code changed in 1 file:

fbielejec 2013-02-16 00:10 Rev.: 5410

generate number of simulations fasta files

334 lines of code changed in 4 files:

rambaut 2013-02-15 13:13 Rev.: 5409

Ported recent updates from 1.7 branch

7 lines of code changed in 2 files:

rambaut 2013-02-15 12:47 Rev.: 5406

Ported recent updates from 1.7 branch

27 lines of code changed in 5 files:

rambaut 2013-02-15 03:19 Rev.: 5400

Erroneous import giving a warning in Hudson

0 lines of code changed in 2 files:

mdhall272@gmail.com 2013-02-15 03:14 Rev.: 5399

Efficiency savings

11 lines of code changed in 2 files:

mdhall272@gmail.com 2013-02-15 02:49 Rev.: 5398

Efficiency savings

56 lines of code changed in 1 file:

mdhall272@gmail.com 2013-02-14 23:46 Rev.: 5397

Updating parser list to match.

2 lines of code changed in 1 file:

mdhall272@gmail.com 2013-02-14 23:44 Rev.: 5396

New case and case set classes with likelihood functions borrowed from Morelli et al, PLoS Comp Biol, 2012

597 lines of code changed in 6 files:

philippe.lemey@gmail.com 2013-02-14 08:04 Rev.: 5395

text message changes for the renaissance counting method in AncestralStatesOptionsPanel

8 lines of code changed in 2 files:

fbielejec 2013-02-14 01:36 Rev.: 5394

Tree model element and idrefs now set. XML generation almost done

228 lines of code changed in 3 files:

baele.guy@gmail.com 2013-02-13 01:25 Rev.: 5390

First version of an independent sampler from a normal distribution model.

177 lines of code changed in 1 file:

baele.guy@gmail.com 2013-02-12 21:27 Rev.: 5389

Forgot to include the actual parameter in the XML rules.

8 lines of code changed in 2 files:

fbielejec 2013-02-12 02:43 Rev.: 5388

fixed a bug in frequency model editor

2 lines of code changed in 1 file:

fbielejec 2013-02-12 01:28 Rev.: 5387

Set idrefs for xml elements. Need to rewrite the tree model element with a more elegant solution

368 lines of code changed in 3 files:

fbielejec 2013-02-11 21:52 Rev.: 5386

Set idrefs for clock model

55 lines of code changed in 3 files:

fbielejec 2013-02-09 01:43 Rev.: 5385

write model only if unique. Moving to idrefs

154 lines of code changed in 2 files:

msuchard 2013-02-08 05:11 Rev.: 5384

Implemented bounds and negative offsets for empirical distributions; improved normalization.

9 lines of code changed in 2 files:

msuchard 2013-02-07 06:29 Rev.: 5383

Side-stepping trouble with Gamma RV generation

16 lines of code changed in 1 file:

fbielejec 2013-02-07 04:36 Rev.: 5382

add only unique taxa to the list

65 lines of code changed in 5 files:

baele.guy@gmail.com 2013-02-07 02:28 Rev.: 5381

Operator reporting and citation fix.

5 lines of code changed in 1 file:

fbielejec 2013-02-07 02:11 Rev.: 5380

direct call to updateUI not needed

6 lines of code changed in 3 files:

fbielejec 2013-02-07 02:02 Rev.: 5379

taxa list updates call taxa table model to repaint table. This fixes previous problem

38 lines of code changed in 4 files:

baele.guy@gmail.com 2013-02-07 01:48 Rev.: 5378

First version of an independent sampler from a gamma distribution.

164 lines of code changed in 2 files:

fbielejec 2013-02-06 22:16 Rev.: 5377

BSS gui allows for multiple trees now. Problems with taxa panel not getting updated

155 lines of code changed in 5 files:

rambaut 2013-02-02 05:17 Rev.: 5376

Porting changes from 1.7

32 lines of code changed in 3 files:

msuchard 2013-02-01 05:20 Rev.: 5371

BEAUti generates coalescent trees with matching opening and closing tags, a good property to have.

30 lines of code changed in 1 file:

msuchard 2013-02-01 05:08 Rev.: 5370

Proposed solution for handling multiple ambiguity codes in stochastic Dollo BEAUti generator

4 lines of code changed in 2 files:

January 2013 »

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