August 2007 Commit Log

Number of Commits:
69
Number of Active Developers:
6
rambaut 2007-08-31 04:09 Rev.: 532

Added a synonymous rate statistic to the codon model (in discussion with Danny Wilson).

41 lines of code changed in 2 files:

rambaut 2007-08-29 01:07 Rev.: 531

Add ability to display BFs in log10, ln & untransformed ratios.

92 lines of code changed in 2 files:

alexei.drummond 2007-08-28 21:43 Rev.: 530

Still fighting with the covarion models -- I *think* I have some Scilab code that I can rely on now...

130 lines of code changed in 2 files:

alexei.drummond 2007-08-27 00:53 Rev.: 529

Still fighting with the covarion models -- they are tricky little things. More than one way to normalize them for a start. I have also added possibility of unequal equilibrium frequencies for the hidden rate classes.

1388 lines of code changed in 8 files:

rambaut 2007-08-24 04:31 Rev.: 528

Transmission history stuff progressing...

186 lines of code changed in 7 files:

rambaut 2007-08-23 22:29 Rev.: 527

Made Attribute & Attribute.Default a generic class. So use Attribute.Default<Double> rather than Attribute.Double.

379 lines of code changed in 1 file:

rambaut 2007-08-23 22:24 Rev.: 526

29 lines of code changed in 2 files:

rambaut 2007-08-23 03:37 Rev.: 525

Renamed Attribute.Double to avoid name overlap with Double

101 lines of code changed in 4 files:

alexei.drummond 2007-08-21 14:27 Rev.: 524

Covarion HKY model successfully validated against independent matlab code by David Bryant (included in comment)

147 lines of code changed in 2 files:

alexei.drummond 2007-08-21 12:40 Rev.: 523

TwoStateCovarion is now confirmed to be working correctly -- working on test for nucleotide covarion models now...

237 lines of code changed in 4 files:

msuchard 2007-08-21 08:38 Rev.: 522

288 lines of code changed in 5 files:

msuchard 2007-08-21 08:32 Rev.: 521

Hacked TreeAnnotator to report the model trait value for discrete outcomes on the nodes/branches. Can use in conjunction with the AncestralTreeLikelihood to do ancestral state reconstructions. I apologize if I broke anything with my hack.

73 lines of code changed in 1 file:

alexei.drummond 2007-08-20 17:19 Rev.: 520

Two state covarion model successfully validated against independent matlab code by David Bryant (included in comment)

143 lines of code changed in 2 files:

alexei.drummond 2007-08-19 21:06 Rev.: 519

Still can't get the analytical results to match the numerical ones in TwoStateCovarion. I believe in numerical results so the analytical ones must have something wrong. Will confirm with David Bryant...

18 lines of code changed in 2 files:

alexei.drummond 2007-08-19 21:01 Rev.: 518

Changed operator weights from ints to doubles (touched a lot of files so I may have missed one or two operators but I was pretty careful). I also took the opportunity to tighten up SimpleMCMCOperator and remove some copy/paste code for handling weights in various operators. This change means that it is a bit easier to adjust the relative rates of operators without having to scale every other operator up when you just want to scale one of the weight=1 operators down. For example: hky.kappa should probably be set to ~ 0.25 for most runs -- it is getting called too often...

4872 lines of code changed in 46 files:

rambaut 2007-08-18 04:27 Rev.: 517

Fixed problem finding MCC trees in TreeAnnotator

1 lines of code changed in 1 file:

msuchard 2007-08-17 11:20 Rev.: 514

Removed some overhead associated with setParameterValues in GMRF operators

36 lines of code changed in 3 files:

rambaut 2007-08-17 03:18 Rev.: 513

Added Suchard citation on BF window

7 lines of code changed in 1 file:

rambaut 2007-08-17 03:12 Rev.: 512

Completed Bayes Factor calculations in Tracer

279 lines of code changed in 4 files:

alexei.drummond 2007-08-16 20:48 Rev.: 509

JUnit test for twoStateCovarionModel

51 lines of code changed in 1 file:

rambaut 2007-08-16 20:10 Rev.: 508

Trying to add BFs to tracer. Opens a frame with a table of BFs

319 lines of code changed in 5 files:

rambaut 2007-08-16 10:52 Rev.: 507

Trying to add BFs to tracer. May have fixed a problem with the MarginalLikelihoodAnalysis ignoring specified burnins.

465 lines of code changed in 6 files:

rambaut 2007-08-16 03:38 Rev.: 505

Ported a few BEAUti fixes over from 1.4 branch

270 lines of code changed in 4 files:

rambaut 2007-08-16 03:38 Rev.: 504

Fixed Taxa so it can only add taxa that are not already present. Hence removed unionTaxons and renamed addTaxons and removeTaxons to addTaxa and removeTaxa. This means that taxa

23 lines of code changed in 2 files:

rambaut 2007-08-16 02:41 Rev.: 503

Fixed a few class renaming issues that had spread into various strings (namely Trace being renamed to TraceOld).

7 lines of code changed in 4 files:

rambaut 2007-08-14 21:04 Rev.: 502

Copied additions to delta model to Trunk

4 lines of code changed in 3 files:

bloomquist 2007-08-14 15:16 Rev.: 501

Added in the gibbs operator for the fixed effects in GMRF
skyline model. Still need to test more, but fairly sure is
working.

41 lines of code changed in 2 files:

msuchard 2007-08-14 12:59

Started Gibbs operator for fixed effects in the GMRF

1450 lines of code changed in 11 files:

bloomquist 2007-08-14 09:28 Rev.: 498

Temporary commit for Marc. Working on GMRF block update class.

712 lines of code changed in 4 files:

rambaut 2007-08-14 09:05 Rev.: 497

Fixed a problem with Tracer not showing loaded trace files. The problem was with rounding burnins that were not integer - in one place they were rounded up, in the other rounded down. This cause an array to be allocated too small for the trace to be copied to.

5 lines of code changed in 2 files:

rambaut 2007-08-14 08:45 Rev.: 496

Fixed a problem with Tracer not show loaded trace files.

2 lines of code changed in 1 file:

alexei.drummond 2007-08-13 19:56 Rev.: 495

JUnit test for twoStateCovarionModel

77 lines of code changed in 1 file:

alexei.drummond 2007-08-12 23:25 Rev.: 494

fixed a couple of bugs in twoStateCovarionModel and wrote a JUnit test to ensure that normalization of the matrix works (I normalized the matrix so that the total number of substitutions (not including switching events) was on average 1.0 per unit time). Also added some pretty matrix toString code.

218 lines of code changed in 8 files:

alexei.drummond 2007-08-12 16:52 Rev.: 493

fixed some obvious bugs in covarion HKY -- it appears to work now...

96 lines of code changed in 3 files:

alexei.drummond 2007-08-11 23:48 Rev.: 492

covarion models are bizarre...

77 lines of code changed in 3 files:

alexei.drummond 2007-08-11 22:35 Rev.: 491

still working on genrea dna covarion model -- the parameters seem to be in the wrong cells of the matrix...

739 lines of code changed in 10 files:

alexei.drummond 2007-08-11 21:18 Rev.: 490

organizing examples folder

2512 lines of code changed in 34 files:

alexei.drummond 2007-08-11 19:49 Rev.: 489

implemented general DNA covarion models - untested!

1382 lines of code changed in 12 files:

msuchard 2007-08-11 06:46 Rev.: 488

Had to modify TreeLogger so that a Likelihood.class can provide likelihood information and be a Node/Branch-AttributeProvider

270 lines of code changed in 1 file:

msuchard 2007-08-11 06:34 Rev.: 487

207 lines of code changed in 1 file:

msuchard 2007-08-11 06:25 Rev.: 486

Extended TreeLikelihood to AncestralStateTreeLikelihood. This class provides an ancestral reconstruction of the internal node states when the tree is logged. The class implements NodeAttribute(something) and performs a pre-traversal order simulation of the internal node states. To save on computations, I added a few public accessors to AbstractLikelihoodCore; these should probably be moved elsewhere, as they may conflict with the native likelihoodCores. There's a simple example in testAncestralReconstruction.xml. TreeAnnotator will need some patching to return the modal internal node states.

I apologize if ancestral reconstruction is already handled elsewhere, but in my defense, I could not find it!

BEAST users will probably enjoy doing lots of reconstruction, so let's write some sort of quick paper to inform users.

1373 lines of code changed in 5 files:

rambaut 2007-08-11 00:31 Rev.: 485

Copied additions to delta model to Trunk

2 lines of code changed in 1 file:

alexei.drummond 2007-08-10 16:49 Rev.: 483

126 lines of code changed in 3 files:

msuchard 2007-08-10 10:52 Rev.: 482

57 lines of code changed in 1 file:

msuchard 2007-08-10 10:01 Rev.: 481

Removed dependence on colt by using sparse matrix algorithms in mtj, results in several order of magnitude speed increase.

879 lines of code changed in 5 files:

rambaut 2007-08-10 02:50 Rev.: 480

Copied additions to delta model to Trunk

43 lines of code changed in 1 file:

rambaut 2007-08-10 02:47 Rev.: 478

Ported further improvements to TreeAnnotator (MCC tree) to Trunk

9 lines of code changed in 2 files:

rambaut 2007-08-09 01:25 Rev.: 476

Ported improvements to TreeAnnotator (MCC tree) to Trunk

87 lines of code changed in 2 files:

rambaut 2007-08-09 01:24 Rev.: 475

Synonym parser 'log' conflicts with the 'log' parser for logging. Changed to logarithm.

1 lines of code changed in 1 file:

rambaut 2007-08-09 01:16 Rev.: 473

Cleaned up all the expression statistics (mainly porting from 1.4 branch)

374 lines of code changed in 14 files:

alexei.drummond 2007-08-08 21:50 Rev.: 469

tidying

1185 lines of code changed in 9 files:

jheled 2007-08-08 20:10 Rev.: 468

add support for non monophyletic constraints. The logic is not proven to be 100% but hopefully will take care of almost all reasonable usage.

275 lines of code changed in 6 files:

alexei.drummond 2007-08-08 18:10 Rev.: 467

139 lines of code changed in 2 files:

alexei.drummond 2007-08-07 20:59 Rev.: 462

refactored coalgen to use same trace classes as tracer, added missing library

1039 lines of code changed in 11 files:

msuchard 2007-08-07 08:37 Rev.: 458

Starting to implement Rue's block updator for the GMRF classes

1017 lines of code changed in 4 files:

rambaut 2007-08-07 00:27 Rev.: 454

Removed vestigal 'adoptState' methods that had been proliferating like endogenous retroviruses dispite that the method had been removed from the interface.

0 lines of code changed in 1 file:

rambaut 2007-08-07 00:26 Rev.: 453

2 lines of code changed in 1 file:

rambaut 2007-08-07 00:23 Rev.: 452

Removed vestigal 'adoptState' methods that had been proliferating like endogenous retroviruses dispite that the method had been removed from the interface.

62 lines of code changed in 42 files:

rambaut 2007-08-07 00:12 Rev.: 451

Added a difference and ratio statistic (these can be done using negate and reciprocal but this seem to add consistency). Fixed ProductStatistic to work like SumStatistic (elementwise attribute added).

330 lines of code changed in 4 files:

alexei.drummond 2007-08-06 22:48 Rev.: 450

tidying

40 lines of code changed in 2 files:

alexei.drummond 2007-08-06 22:07 Rev.: 449

Default to Jeffreys prior for all scale parameters

1265 lines of code changed in 2 files:

alexei.drummond 2007-08-06 20:16 Rev.: 448

tidying work towards improving log outputs

99 lines of code changed in 4 files:

alexei.drummond 2007-08-06 18:35 Rev.: 447

Refactoring to consolidate Tracer and trace analysis and log analyzer code - part 1

4442 lines of code changed in 35 files:

alexei.drummond 2007-08-06 07:46 Rev.: 446

tidying work towards improving log outputs (time stamps, versions et cetera)

352 lines of code changed in 8 files:

jheled 2007-08-05 20:15 Rev.: 445

new version for mrca constraints and test files

922 lines of code changed in 16 files:

jheled 2007-08-05 20:13 Rev.: 444

operator name

8 lines of code changed in 4 files:

jheled 2007-08-05 20:12 Rev.: 443

cosmetic java warnings

18 lines of code changed in 1 file:

jheled 2007-08-05 20:11 Rev.: 442

cosmetic java

2 lines of code changed in 1 file:

Sebastian.Hoehna 2007-08-01 02:42

Added a Branch-Score Metric and the NNI, SPR and ECR moves.

1080 lines of code changed in 12 files:

July 2007 »

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