August 2011 Commit Log

Number of Commits:
81
Number of Active Developers:
9
dong.w.xie 2011-08-31 15:45 Rev.: 4267

trunk: add EBSP virus version tutorial, but tracer analysis part is incomplete yet.

1089 lines of code changed in 14 files:

rambaut 2011-08-31 03:51 Rev.: 4266

Catch a exception and throw an explanation...

13 lines of code changed in 1 file:

msuchard 2011-08-31 03:43 Rev.: 4265

Small tweak for reversibility

21 lines of code changed in 2 files:

tbcbedford@gmail.com 2011-08-31 03:29 Rev.: 4264

Commenting out code for modifying hastings ratio based on location jitter. Current code perfectly recovers Dirichlet distribution when sampling from the prior.

10 lines of code changed in 1 file:

tbcbedford@gmail.com 2011-08-31 02:22 Rev.: 4263

Implemented a cluster operator that takes single elements and moves them to a different / new cluster.

271 lines of code changed in 2 files:

rambaut 2011-08-30 21:15 Rev.: 4262

Added some more comments and set the [log] Hastings ratio to 0.0

16 lines of code changed in 1 file:

dong.w.xie 2011-08-30 15:55 Rev.: 4261

trunk: add EBSP analysis in Tracer, but doWork() not working yet.

945 lines of code changed in 5 files:

rambaut 2011-08-30 11:04 Rev.: 4260

Starting with N=40

1 lines of code changed in 1 file:

rambaut 2011-08-30 10:42 Rev.: 4259

Fixed another issue with the operator

18 lines of code changed in 1 file:

dong.w.xie 2011-08-30 10:41 Rev.: 4258

Add xml to compare with BEAST 2

330 lines of code changed in 1 file:

rambaut 2011-08-30 10:18 Rev.: 4257

Assumed it would be easy to keep the clusters arranged such that the first K are occupied. Easier not to do this.

25 lines of code changed in 1 file:

rambaut 2011-08-30 09:17 Rev.: 4256

Simplified some logic

4 lines of code changed in 1 file:

tbcbedford@gmail.com 2011-08-30 08:59 Rev.: 4255

Fixed bug in ClusterSplitMergeOperator. Infinite loop when asking for a split with K=1.

7 lines of code changed in 1 file:

rambaut 2011-08-30 08:32 Rev.: 4254

Added parser to parser list

7 lines of code changed in 2 files:

rambaut 2011-08-30 08:13 Rev.: 4253

22 lines of code changed in 1 file:

msuchard 2011-08-30 06:20 Rev.: 4252

Made split/merge operation stochastically reversible, i.e. the augmented parameter space gains/losses exactly two dimensions.

15 lines of code changed in 1 file:

tbcbedford@gmail.com 2011-08-30 05:35 Rev.: 4251

I found a bug in the calculate of the MultidimensionalScalingLikelihood.

It had been:
double logLikelihood = (0.5 * Math.log(precision) * pointObservationCount) - (0.5 * sumOfSquaredResiduals / (precision * precision));

I've changed it to:
double logLikelihood = (0.5 * Math.log(precision) * pointObservationCount) - (0.5 * precision * sumOfSquaredResiduals);

Precision had been swapped for sigma. This fixes the problem of everything moving to a single cluster with very high estimated precision.

I'm pretty sure there is a problem with the way truncated likelihoods are calculated, however.

I also reverted cluster initialization to start with a single cluster.

8 lines of code changed in 2 files:

rambaut 2011-08-30 03:58 Rev.: 4250

Created an operator to split and merge occupied clusters

523 lines of code changed in 5 files:

rambaut 2011-08-28 11:53 Rev.: 4249

Random starting clustering

2 lines of code changed in 1 file:

rambaut 2011-08-28 11:20 Rev.: 4248

Might be working now.

46 lines of code changed in 3 files:

rambaut 2011-08-28 08:46 Rev.: 4247

More tweaks

11 lines of code changed in 2 files:

rambaut 2011-08-28 08:13 Rev.: 4246

Fixed up the caching in DiscreteATL.

789 lines of code changed in 6 files:

rambaut 2011-08-28 04:15 Rev.: 4245

Dirichlet stuff

14 lines of code changed in 2 files:

rambaut 2011-08-27 20:43 Rev.: 4244

Added parser option for Gibbs sampling of Dirichlet process from posterior

11 lines of code changed in 1 file:

rambaut 2011-08-27 12:26 Rev.: 4243

Fixed an indexing bug

7 lines of code changed in 2 files:

msuchard 2011-08-25 11:52 Rev.: 4242

Tidying up DP operations.

67 lines of code changed in 3 files:

baele.guy@gmail.com 2011-08-25 01:59 Rev.: 4241

Added more extensive logging for the PathLikelihood class

30 lines of code changed in 1 file:

rambaut 2011-08-25 01:52 Rev.: 4240

An operator that draws item allocations to clusters under the Dirichlet process.

5 lines of code changed in 1 file:

rambaut 2011-08-24 23:18 Rev.: 4239

An operator that draws item allocations to clusters under the Dirichlet process.

212 lines of code changed in 5 files:

msuchard 2011-08-24 12:38 Rev.: 4238

Latent liability model appears to work well.

427 lines of code changed in 5 files:

rambaut 2011-08-24 04:17 Rev.: 4237

Added a uniform operator on indexes of N items allocated to K clusters. This is an attempt to get the correct Hastings ratio.

0 lines of code changed in 1 file:

rambaut 2011-08-24 04:16 Rev.: 4236

Added a prior on distances based on Coulombs law of charged particles repelling

158 lines of code changed in 2 files:

rambaut 2011-08-24 04:15 Rev.: 4235

Moved antigenic stuff into its own package.

1576 lines of code changed in 7 files:

rambaut 2011-08-24 01:27

Test suit for the DirichletProcessLikelihood

8 lines of code changed in 3 files:

rambaut 2011-08-24 01:13 Rev.: 4232

Test suit for the DirichletProcessLikelihood

101 lines of code changed in 2 files:

rambaut 2011-08-23 18:18 Rev.: 4231

Very minor language improvements.

89 lines of code changed in 2 files:

dong.w.xie 2011-08-23 14:41 Rev.: 4230

trunk: merge Issue 495 from branch 1.6

25 lines of code changed in 3 files:

dong.w.xie 2011-08-22 15:28 Rev.: 4228

trunk: merge Issue 494 from branch 1.6

2 lines of code changed in 1 file:

msuchard 2011-08-21 11:51 Rev.: 4224

Bug fix; null pointer exception

1 lines of code changed in 1 file:

rambaut 2011-08-20 20:18 Rev.: 4223

At some point, when sampling from the prior, BEAUti stopped generating dummy alignments consisting of a full codon (NNN) and instead just a single nucleotide (N). This causes problems when using codon-partitioning. If only using a single partition this gets compressed down to a single partition anyway.

2 lines of code changed in 1 file:

msuchard 2011-08-20 14:02 Rev.: 4222

Implemented Joe Felsenstein's latent liability model with a single new class to BEAST.

490 lines of code changed in 5 files:

rambaut 2011-08-20 10:29 Rev.: 4221

Fixed up a few things.

565 lines of code changed in 4 files:

rambaut 2011-08-20 08:37 Rev.: 4220

Fix for DPL parser. (also added 'scale' attribute to exponential as alternative to 'mean').

22 lines of code changed in 4 files:

rambaut 2011-08-20 07:11 Rev.: 4219

Couldn't resist implementing the log factorials as a look-up table.

17 lines of code changed in 1 file:

rambaut 2011-08-20 07:04 Rev.: 4218

Parser for the Dirichlet process likelihood

80 lines of code changed in 2 files:

rambaut 2011-08-20 06:34 Rev.: 4217

Spelling mistake and a fix to the formula.

129 lines of code changed in 2 files:

rambaut 2011-08-20 03:58 Rev.: 4216

Various bits

47 lines of code changed in 5 files:

rambaut 2011-08-20 03:57 Rev.: 4215

First stab at a Dirichlet process likelihood (no parser yet).

0 lines of code changed in 1 file:

dong.w.xie 2011-08-19 15:48 Rev.: 4214

trunk: update version history and update native NucleotideLikelihoodCore into 64 bit

77 lines of code changed in 5 files:

dong.w.xie 2011-08-19 15:40 Rev.: 4213

trunk: merge from branch 1.6

11 lines of code changed in 8 files:

rambaut 2011-08-19 00:53 Rev.: 4201

Work on discrete Antigenic MDS

58 lines of code changed in 6 files:

fbielejec 2011-08-18 02:31 Rev.: 4196

method for generating ancestralTreeLikelihood XML block

1 lines of code changed in 1 file:

dong.w.xie 2011-08-16 11:18 Rev.: 4189

trunk: I think Issue 463 is solved, but cannot test because of Issue 485

4 lines of code changed in 2 files:

dong.w.xie 2011-08-15 12:11 Rev.: 4187

trunk: update example xml for beast 1 vs beast 2

6 lines of code changed in 2 files:

dong.w.xie 2011-08-15 12:04 Rev.: 4186

trunk: update example xml for beast 1 vs beast 2

43 lines of code changed in 1 file:

dong.w.xie 2011-08-12 13:21 Rev.: 4185

trunk: merge from branch 1.6

8 lines of code changed in 1 file:

sibon.li 2011-08-12 11:51 Rev.: 4183

Fixed a bug that made AncestralSequenceAnnotator not work properly for BAli-Phy files. Now provided it an option to take in BEAST input tree files

498 lines of code changed in 1 file:

sibon.li 2011-08-12 11:17 Rev.: 4182

Work in progress on AncestralSequenceAnnotator, will be fixed by end of today

239 lines of code changed in 1 file:

philippe.lemey@gmail.com 2011-08-11 07:06 Rev.: 4181

adding custom burn-in to DnDsPerSiteAnalysis

27 lines of code changed in 1 file:

rambaut 2011-08-10 23:59 Rev.: 4180

Test script for multivariate normal prior

0 lines of code changed in 1 file:

rambaut 2011-08-10 23:50 Rev.: 4179

Some refactoring of MatrixParameter (renamed getNumberOfParameters to getParameterCount). Also allowed MultivariateNormalPrior take a matrix parameter and assume the individual parameters within this represent independent draws from the MVN.

224 lines of code changed in 24 files:

rambaut 2011-08-10 04:21 Rev.: 4172

Discrete AG model...

100 lines of code changed in 2 files:

rambaut 2011-08-09 22:39 Rev.: 4171

First attempt at a discrete antigenic cluster classifier.

447 lines of code changed in 5 files:

fbielejec 2011-08-08 20:17 Rev.: 4169

moved per site analysis report after mcmc block

1 lines of code changed in 1 file:

fbielejec 2011-08-08 20:07 Rev.: 4168

parser for ancestralTreeLikelihood

1 lines of code changed in 1 file:

fbielejec 2011-08-08 20:06 Rev.: 4167

method for generating ancestralTreeLikelihood XML block

71 lines of code changed in 1 file:

fbielejec 2011-08-08 20:04 Rev.: 4166

moved xml blocks around

13 lines of code changed in 1 file:

msuchard 2011-08-08 11:40 Rev.: 4165

Added flexibility to check numerical stability of BSSVS substitution models

51 lines of code changed in 4 files:

msuchard 2011-08-06 10:15 Rev.: 4164

Numerically stability improvement for simulating uniformized CTMCs with BSSVS.

1 lines of code changed in 1 file:

fbielejec 2011-08-05 20:10 Rev.: 4163

new constructor

7 lines of code changed in 2 files:

fbielejec 2011-08-05 20:09 Rev.: 4162

added option to SRD06 model settings

71 lines of code changed in 1 file:

rambaut 2011-08-05 14:22 Rev.: 4159

Fix for AG plotter

1 lines of code changed in 1 file:

dong.w.xie 2011-08-05 13:31 Rev.: 4158

trunk: merge from branch 1.6: Issue 478 TipDates table cell editor large the text font size when changing the value

1 lines of code changed in 1 file:

rambaut 2011-08-05 04:24 Rev.: 4156

22 lines of code changed in 3 files:

fbielejec 2011-08-03 13:13 Rev.: 4154

added default tags

0 lines of code changed in 1 file:

fbielejec 2011-08-03 13:12 Rev.: 4153

added option to remove dnds counting

51 lines of code changed in 1 file:

rambaut 2011-08-03 05:05 Rev.: 4152

Some additions to the tools for plotting antigenic maps.

108 lines of code changed in 3 files:

rambaut 2011-08-02 19:00 Rev.: 4151

Improvements and tweaks to Antigenic MDS

31 lines of code changed in 2 files:

alexei.drummond 2011-08-02 14:53 Rev.: 4150

added handling for multi-block partitions

191 lines of code changed in 4 files:

rambaut 2011-08-01 21:27 Rev.: 4149

Improvements and tweaks to Antigenic MDS

188 lines of code changed in 3 files:

dong.w.xie 2011-08-01 14:11 Rev.: 4148

update VirusPractical to use BEAST 1.6.1

1007 lines of code changed in 47 files:

July 2011 »

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