March 2012 Commit Log

« Development Statistics for /trunk

Commit Logs

Number of Commits:: 145
Number of Active Developers:: 10

fbielejec 2012-03-31 02:56 #145 Rev.: 4911

cleaning the code

54 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+54 -68)

rambaut 2012-03-31 02:48 #144 Rev.: 4910

Sets all the tip locations now but something is still wrong.

10 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+10 -8)

fbielejec 2012-03-31 02:25 #143 Rev.: 4909

hide the debugging messages

14 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+14 -14)

fbielejec 2012-03-31 02:12 #142 Rev.: 4908

only do the neccessary operations

23 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+23 -11)

rambaut 2012-03-30 12:06 #141 Rev.: 4907

Failed to fix error.

43 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+43 -33)

fbielejec 2012-03-30 08:26 #140 Rev.: 4906

sequential routine

46 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+46 -25)

fbielejec 2012-03-30 01:00 #139 Rev.: 4905

...has been discontinued

3 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+3 -22)

fbielejec 2012-03-30 00:52 #138 Rev.: 4904

Due to a shortage of devoted followers, the production of great leaders

37 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+37 -70)

fbielejec 2012-03-29 23:10 #137 Rev.: 4903

Howe's Law: Everyone has a scheme that will not work

55 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+55 -15)

fbielejec 2012-03-29 08:50 #136 Rev.: 4902

almost there

27 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+27 -32)

fbielejec 2012-03-29 01:49 #135 Rev.: 4901

not to be used just yet

105 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+105 -30)

rambaut 2012-03-28 05:49 #134 Rev.: 4900

Hooks up with tree traits.

14 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+14 -5)

tbcbedford@gmail.com 2012-03-28 04:56 #133 Rev.: 4899

Negatively impact the likelihood is a strain known to be top branch is assigned to bottom branch. Many bit flip operations will be rejected. This appears to be working (maybe).

53 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicSplitPrior.java (+53 -8)

tbcbedford@gmail.com 2012-03-27 21:59 #132 Rev.: 4898

Parsing topBranch strains and bottomBranch strains and assigning {0,1} based on this.

40 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicSplitPrior.java (+40 -7)

tbcbedford@gmail.com 2012-03-27 21:30 #131 Rev.: 4897

Basics of split prior implemented. There is an assignment vector that assigns strains to top branch (0) or bottom branch (1). This is operated on with bitFlipOperator. Currently not converging nicely. Will try to help the assignment by including definite Yamagata (0) or Victoria (1) isolates.

86 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicSplitPrior.java (+86 -35)

msuchard 2012-03-27 10:28 #130 Rev.: 4896

Pinpointing Filip's bug

18 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+18 -2)

msuchard 2012-03-27 07:45 #129 Rev.: 4895

Implementing transformed trees and Pagel's lambda estimator

208 lines of code changed in 4 files:

src/dr/app/beast: development_parsers.properties (+1)
src/dr/evomodel/continuous: IntegratedMultivariateTraitLikelihood.java (+29 -4)
src/dr/evomodel/tree: TransformedTreeModel.java (+89)
src/dr/evomodelxml/tree: TransformedTreeModelParser.java (+89)

msuchard 2012-03-27 06:41 #128 Rev.: 4894

Improved ability to co-opt an existing root height in StarTreeModel

390 lines of code changed in 5 files:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+353 -357)
src/dr/evomodel/tree: StarTreeModel.java (new)
src/dr/evomodelxml/tree: StarTreeModelParser.java (new)

baele.guy@gmail.com 2012-03-27 01:08 #127 Rev.: 4893

Added an XML parser for MixtureModelLogAnalyser.

71 lines of code changed in 2 files:

src/dr/app/tools: MixtureModelLogAnalyser.java (+71 -3)

tbcbedford@gmail.com 2012-03-27 00:32 #126 Rev.: 4892

Adding three additional parameters to control antigenic split.

36 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicSplitPrior.java (+36 -4)

tbcbedford@gmail.com 2012-03-27 00:02 #125 Rev.: 4891

Starting on a prior for flu B. Should produce a 'Y' in antigenic space. Currently just a copy of the '|' prior.

242 lines of code changed in 2 files:

src/dr/app/beast: development_parsers.properties (+1)
src/dr/evomodel/antigenic: AntigenicSplitPrior.java (+241)

rambaut 2012-03-26 23:14 #124 Rev.: 4889

Fixed an issue in BEAUti with robust counting XML generated where completely gapped sites were being stripped (these are sometimes used to maintain reading frame).

14 lines of code changed in 4 files:

build.xml (+2 -2)
src/dr/app/beauti/generator: PatternListGenerator.java (+11 -10)
src/dr/evoxml: SitePatternsParser.java (new)

msuchard 2012-03-26 15:04 #123 Rev.: 4888

Added ability to co-opt an existing root height in StarTreeModel

46 lines of code changed in 3 files:

src/dr/evomodel/tree: StarTreeModel.java (+29 -12)
src/dr/evomodelxml/tree: StarTreeModelParser.java (+8 -8)
src/dr/inference/markovchain: MarkovChain.java (+9 -9)

fbielejec 2012-03-26 05:18 #122 Rev.: 4887

cleaning the code

1 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+1 -1)

fbielejec 2012-03-26 04:55 #121 Rev.: 4886

cleaning the code

6 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+6 -99)

msuchard 2012-03-25 09:24 #120 Rev.: 4885

Fixed store/restore error in BeagleTreeLikelihood

29 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: HomogenousBranchSubstitutionModel.java (+29 -33)

rambaut 2012-03-24 05:08 #119 Rev.: 4884

Created a new GUI app for plotting antigenic maps (and other multivariate traits). Starting to diverge from tracer.

68 lines of code changed in 1 file:

src/dr/app/mapper/application/mapper: MapperPanel.java (+68 -1)

rambaut 2012-03-24 03:20 #118 Rev.: 4883

Created a new GUI app for plotting antigenic maps (and other multivariate traits). Starting to diverge from tracer.

159 lines of code changed in 13 files:

src/dr/app/mapper/application: AnalysisMenuFactory.java (del), AnalysisMenuHandler.java (del), GeneralPreferencesSection.java (+1 -1), MapperApp.java (+1), MapperDefaultFileMenuFactory.java (+1), MapperFileMenuHandler.java (+1), MapperFrame.java (+55 -846), MapperMacFileMenuFactory.java (+1), MapperMenuBarFactory.java (+1 -2)
src/dr/app/mapper/application/mapper: Layer.java (new 40), LayerType.java (new 11), MapperPanel.java (+46)
src/dr/app/tracer/application: TracerFrame.java (+1 -1)

rambaut 2012-03-23 23:50 #117

Created a new GUI app for plotting antigenic maps (and other multivariate traits). Currently just a copy of Tracer.

2254 lines of code changed in 14 files:

src/dr/app/mapper/application: AnalysisMenuFactory.java (+148), AnalysisMenuHandler.java (new 10), GeneralPreferencesSection.java (+41), MapperApp.java (+127), MapperDefaultFileMenuFactory.java (+77), MapperFileMenuHandler.java (+14), MapperFrame.java (+1658), MapperMacFileMenuFactory.java (+102), MapperMenuBarFactory.java (+29)
src/dr/app/mapper/application/images: Mapper.png (changed), prefsGeneral.png (new)
src/dr/app/tracer/application: TracerApp.java (+1 -1)

baele.guy@gmail.com 2012-03-23 21:55 #116 Rev.: 4880

Bug fix for beta quantile integrator scheme.

5 lines of code changed in 1 file:

src/dr/inference/mcmc: MarginalLikelihoodEstimator.java (+5 -1)

rambaut 2012-03-23 05:04 #115 Rev.: 4879

Implemented the setting of tip trait parameter in the rewritten AGL.

123 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+123 -69)

fbielejec 2012-03-21 01:08 #114 Rev.: 4878

reverting

122 lines of code changed in 4 files:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+107 -91)
src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+15 -1), EasyPeasy.java (del), EpochModelSequenceSimulator.java (del)

fbielejec 2012-03-20 22:39 #113 Rev.: 4877

renaming

453 lines of code changed in 2 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+143 -271), EpochModelSequenceSimulator.java (new 310)

fbielejec 2012-03-20 21:40 #112 Rev.: 4876

we need other way

0 lines of code changed in 1 file:

src/dr/app/beagle/tools: EasyPeasy.java (new)

rambaut 2012-03-20 11:01 #111 Rev.: 4875

Minor 1.5/1.6 issue

0 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (-3)

rambaut 2012-03-20 04:18 #110 Rev.: 4874

Fixing main().

4 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+4 -4)

rambaut 2012-03-20 04:17 #109 Rev.: 4873

Turning on USE_INTERVALS (can still be switched to point densities by omitting intervalWidth attribute).

6 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+6 -6)

fbielejec 2012-03-20 03:29 #108 Rev.: 4872

new beagle sequence simulator

121 lines of code changed in 1 file:

src/dr/app/beagle/tools: EasyPeasy.java (+121)

tbcbedford@gmail.com 2012-03-20 02:54 #107 Rev.: 4871

I've moved thresholded and interval values to use the non-normalized titres. I checked this and MDS precision is good for both. Andrew, feel free to revert this if you don't like this strategy.

32 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+32 -44)

tbcbedford@gmail.com 2012-03-20 02:00 #106 Rev.: 4870

Believe I've fixed the MDS-precision-going-to-0 bug. There was a problem in the normalization. I've replace the code with a non-normalizing version that appears to work.

13 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+13 -4)

rambaut 2012-03-20 01:22 #105 Rev.: 4869

USE_THRESHOLD switch now just treats them as missing.

13 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+13 -12)

rambaut 2012-03-20 00:58 #104 Rev.: 4868

Serum dates were not being set correctly

3 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+3 -3)

rambaut 2012-03-20 00:16 #103 Rev.: 4867

Thresholds switches on/off

12 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+12 -6)

fbielejec 2012-03-19 07:46 #102 Rev.: 4866

I always forget

1 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+1 -1)

fbielejec 2012-03-19 06:02 #101 Rev.: 4865

non-beagle implementation

338 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+96 -11)
src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+242 -170)

fbielejec 2012-03-16 20:55 #100 Rev.: 4864

stub of a new generic simulator

235 lines of code changed in 2 files:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+235), EpochBranchSubstitutionModelSimulator.java (del)

gcybis@yahoo.com.br 2012-03-16 18:15 #99 Rev.: 4863

Hierarchical model for discrete trait

432 lines of code changed in 5 files:

src/dr/app/beast: development_parsers.properties (+6)
src/dr/inference/distribution: HierarchicalGraphLikelihood.java (+162)
src/dr/inference/operators: HierarchicalBitFlipOperator.java (+108)
src/dr/inferencexml/distribution: HierarchicalGraphLikelihoodParser.java (new 79)
src/dr/inferencexml/operators: HierarchicalBitFlipOperatorParser.java (new 77)

rambaut 2012-03-16 05:22 #98 Rev.: 4859

Now column/row effect parameters are optional.

10 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+10 -5)

rambaut 2012-03-16 05:17 #97 Rev.: 4858

Fixing ADP for row/column confusion in matrix parameter

1 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+1 -1)

rambaut 2012-03-16 05:15 #96 Rev.: 4857

If row effect parameter is there then use it otherwise just scale by column maximum or column effect if given.

21 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+21 -16)

rambaut 2012-03-16 04:29 #95 Rev.: 4856

Fixing AL for row/column confusion in matrix parameter

1 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+1 -1)

rambaut 2012-03-16 04:17 #94 Rev.: 4855

Fixing ADP for row/column confusion in matrix parameter

2 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+2 -2)

rambaut 2012-03-16 04:11 #93 Rev.: 4854

Simplifying AL and fixing ADP for row/column confusion in matrix parameter

70 lines of code changed in 2 files:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+1 -1), AntigenicLikelihood.java (+69 -104)

rambaut 2012-03-16 03:46 #92 Rev.: 4853

Fixed issues with upper/lower/intervals - maybe?

43 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+43 -11)

fbielejec 2012-03-16 02:22 #91 Rev.: 4852

merging Guys changes

75 lines of code changed in 1 file:

src/dr/app/beagle/tools: EpochBranchSubstitutionModelSimulator.java (new 75)

baele.guy@gmail.com 2012-03-16 02:17 #90 Rev.: 4851

Parsing from XML should be fine (in theory). Now we need to fix the getTransitionProbabilities method ...

5 lines of code changed in 1 file:

src/dr/app/beagle/tools: EpochBranchSubstitutionModelSimulator.java (+5 -5)

baele.guy@gmail.com 2012-03-16 01:49 #89 Rev.: 4850

Fixed a number of XML parsing problems.

3 lines of code changed in 1 file:

src/dr/app/beagle/tools: EpochBranchSubstitutionModelSimulator.java (+3 -2)

fbielejec 2012-03-16 01:42 #88 Rev.: 4849

set substitution model just to parse frequency model

78 lines of code changed in 1 file:

src/dr/app/beagle/tools: EpochBranchSubstitutionModelSimulator.java (+78 -76)

tbcbedford@gmail.com 2012-03-15 23:06 #87 Rev.: 4848

AntigenicDistancePrior is now a regression of time vs location on AG1. Each year's locations are drawn from a bivariate normal (with equal X and Y precision) centered on the expected value from the regression. This eliminates the need for Procrustes.

10 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+10 -14)

fbielejec 2012-03-15 22:04 #86 Rev.: 4847

merging Guys suggestions

62 lines of code changed in 1 file:

src/dr/app/beagle/tools: EpochBranchSubstitutionModelSimulator.java (+62 -25)

baele.guy@gmail.com 2012-03-15 21:52 #85 Rev.: 4846

Added additional constructor and XML parser for the epoch sequence simulator.

78 lines of code changed in 1 file:

src/dr/app/beagle/tools: EpochBranchSubstitutionModelSimulator.java (+78)

tbcbedford@gmail.com 2012-03-15 21:13 #84 Rev.: 4845

Back to Euclidean distance from origin scaling with time.

27 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+27 -26)

gcybis@yahoo.com.br 2012-03-15 12:56 #83 Rev.: 4844

1084 lines of code changed in 3 files:

src/dr/app/beast: development_parsers.properties (+2)
src/dr/evomodel/antigenic: NPAntigenicLikelihood.java (+487), ddCRPGibbsOperator.java (new 595)

tbcbedford@gmail.com 2012-03-15 10:38 #82 Rev.: 4843

Reverted row and columns. Fixed bug with handleVariableChanged.

5 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+5 -5)

tbcbedford@gmail.com 2012-03-15 10:27 #81 Rev.: 4842

Fixed bug that swapped row and column dimensions.

4 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+4 -3)

tbcbedford@gmail.com 2012-03-15 10:16 #80 Rev.: 4841

AntigenicDistancePrior from pairwise regression of distance vs time.

23 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+23 -25)

tbcbedford@gmail.com 2012-03-15 09:07 #79 Rev.: 4840

Trying a distance prior where Euclidean distance from origin is linear with time

14 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+14 -10)

msuchard 2012-03-15 04:26 #78 Rev.: 4839

Reverting dimension accessors to be consistent with getParameterValue() in MatrixParameter.

28 lines of code changed in 1 file:

src/dr/inference/model: MatrixParameter.java (+28 -3)

fbielejec 2012-03-15 00:40 #77 Rev.: 4838

deleting

0 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (del)

fbielejec 2012-03-15 00:40 #76 Rev.: 4837

working on an explicit simulator for epoch model

272 lines of code changed in 1 file:

src/dr/app/beagle/tools: EpochBranchSubstitutionModelSimulator.java (+272)

philippe.lemey@gmail.com 2012-03-14 23:00 #75 Rev.: 4836

tweaking dnds trace analysis

72 lines of code changed in 2 files:

src/dr/inference/trace: DnDsPerSiteAnalysis.java (+72 -14)

fbielejec 2012-03-14 22:31 #74 Rev.: 4835

TODO pass epoch model to site model

184 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (new 184)

fbielejec 2012-03-14 21:13 #73 Rev.: 4834

setting substModel

78 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+78 -81)

fbielejec 2012-03-14 20:26 #72 Rev.: 4833

setting substModel

6 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+6 -4)

fbielejec 2012-03-14 02:57 #71 Rev.: 4832

working on seq simulator for Beagle

257 lines of code changed in 1 file:

src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+257)

tbcbedford@gmail.com 2012-03-14 01:53 #70 Rev.: 4831

Replacing Log(NormalPDF) with NormalLogPDF to fix -INF likelihoods. Also, temporarily switched HI distance to only take columnEffects. This allows direct comparison with prior model.

3 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+3 -2)

tbcbedford@gmail.com 2012-03-14 00:34 #69 Rev.: 4830

Fixed: only fire rawTitres if minTitre and maxTitre are absent.

17 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+17 -15)

tbcbedford@gmail.com 2012-03-14 00:30 #68 Rev.: 4829

Modified parsing of HI pairs to be able to except raw titres as point measurements (kicks in if minTitre and maxTitre columsn are left empty).

41 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+41 -10)

tbcbedford@gmail.com 2012-03-13 05:05 #67 Rev.: 4828

Initial locations sorted according to date.

19 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+19 -10)

tbcbedford@gmail.com 2012-03-13 03:34 #66 Rev.: 4827

Store and restore implemented. Not throwing run time errors anymore.

13 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+13 -15)

rambaut 2012-03-13 03:10 #65 Rev.: 4826

Fixed issue with date parameter

28 lines of code changed in 4 files:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+12 -7)
src/dr/evomodel/substmodel: MultivariateOUModel.java (+5)
src/dr/inference/model: Statistic.java (+11 -1)

rambaut 2012-03-13 02:56 #64 Rev.: 4825

Problem with parser not picking up dates parameter

1 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+1 -1)

tbcbedford@gmail.com 2012-03-13 02:49 #63 Rev.: 4824

Regression of antigenic location along AG1 with time. System err messages demonstrate problem with dateParameter.

46 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+46 -5)

rambaut 2012-03-13 02:40 #62 Rev.: 4823

Reverting changes prior to Trevor's merge

4 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+4 -23)

rambaut 2012-03-13 02:33 #61 Rev.: 4822

Regression on date difference as prior.

24 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+24 -4)

tbcbedford@gmail.com 2012-03-13 00:32 #60 Rev.: 4821

Including slope and precision parameters in AntigenicDistancePrior

24 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+24 -4)

rambaut 2012-03-13 00:23 #59 Rev.: 4820

Merging a couple of changes from 1.7 branch

11 lines of code changed in 4 files:

src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (new), PriorsPanel.java (new)

dong.w.xie@gmail.com 2012-03-12 11:11 #58 Rev.: 4817

trunk: fix Junit test

1 lines of code changed in 2 files:

src/test/dr/distibutions: LogNormalDistributionTest.java (+1)

dong.w.xie@gmail.com 2012-03-12 09:24 #57 Rev.: 4816

trunk: merge prior dialog and distribution changes to trunk

212 lines of code changed in 17 files:

release/common: VERSION HISTORY.txt (+34 -2)
src/dr/app/beauti/priorsPanel: HierarchicalPriorDialog.java (new), PriorDialog.java (+24 -15), PriorOptionsPanel.java (+92 -8), PriorsPanel.java (+1 -1)
src/dr/app/gui/components: RealNumberField.java (+9 -5)
src/dr/math/distributions: GammaDistribution.java (+5 -2), InverseGammaDistribution.java (+2 -3), LaplaceDistribution.java (new), LogNormalDistribution.java (+6), TruncatedDistribution.java (new)

rambaut 2012-03-12 00:03 #56 Rev.: 4815

Merging from 1.7 branch

6 lines of code changed in 1 file:

src/dr/app/beauti/components/continuous: ContinuousComponentGenerator.java (+6 -5)

rambaut 2012-03-11 22:59 #55 Rev.: 4813

Porting fix for Issue 605 to trunk

32 lines of code changed in 1 file:

src/dr/app/beauti/util: BEAUTiImporter.java (+32 -8)

rambaut 2012-03-10 03:49 #54 Rev.: 4811

More fixes

12 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+12 -7)

rambaut 2012-03-10 03:44 #53 Rev.: 4810

Double logging.

0 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (-1)

rambaut 2012-03-10 03:14 #52 Rev.: 4809

Scale max titres into log2

4 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+4 -3)

rambaut 2012-03-10 03:10 #51 Rev.: 4808

Initializes the row and column effect parameters with the maximum observed titre for the rows and columns

43 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+43 -16)

rambaut 2012-03-10 02:54 #50 Rev.: 4807

Added caching - 10 fold speed increase

60 lines of code changed in 2 files:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+57 -25)
src/dr/inference/model: MatrixParameter.java (+3 -3)

rambaut 2012-03-09 23:30 #49 Rev.: 4806

Work on AG.

255 lines of code changed in 4 files:

src/dr/app/beast: development_parsers.properties (+1)
src/dr/evomodel/antigenic: AntigenicDistancePrior.java (+193), AntigenicLikelihood.java (+43 -8)
src/dr/inference/model: Parameter.java (+18 -1)

msuchard 2012-03-09 08:33 #48 Rev.: 4803

Implemented a "not statistics" for boolean stats (like monophylyl). NotStatistic is now deprecated.

130 lines of code changed in 3 files:

src/dr/app/beast: release_parsers.properties (+2 -1)
src/dr/inference/model: NotBooleanStatistic.java (new 60)
src/dr/inferencexml/model: NotBooleanStatisticParser.java (new 68)

rambaut 2012-03-09 05:09 #47 Rev.: 4802

Merged changes from 1.7

8 lines of code changed in 2 files:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+3 -3)
src/dr/app/beauti/priorsPanel: PriorsPanel.java (+5 -3)

rambaut 2012-03-09 05:08 #46 Rev.: 4801

Antigenic

27 lines of code changed in 1 file:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+27 -8)

rambaut 2012-03-09 00:34 #45 Rev.: 4797

Few more fixes to truncation of prior distributions

14 lines of code changed in 2 files:

src/dr/app/beauti/options: PartitionTreeModel.java (+10 -8)
src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+4 -1)

rambaut 2012-03-08 23:56 #44 Rev.: 4796

Fix to last commit.

1 lines of code changed in 1 file:

src/dr/math/distributions: TruncatedDistribution.java (+1 -1)

rambaut 2012-03-08 22:09 #43 Rev.: 4795

TruncatedDistribution now adjusts its bounds to be inside the source distribution's (i.e., if it is an OffsetPositive). LogNormalDistribution had a lower bound of -Inf, now set to zero.

9 lines of code changed in 2 files:

src/dr/math/distributions: LogNormalDistribution.java (+1 -1), TruncatedDistribution.java (+8)

rambaut 2012-03-08 21:51 #42 Rev.: 4794

Don't use a truncated distribution unless this option is selected.

2 lines of code changed in 1 file:

src/dr/app/beauti/priorsPanel: PriorOptionsPanel.java (+2 -2)

rambaut 2012-03-08 21:41 #41 Rev.: 4793

Added BEAGLE rescaling options to BEAST UI dialog. Added command line option to control the rescaling frequency in dynamic scaling.

37 lines of code changed in 3 files:

src/dr/app/beagle/evomodel/treelikelihood: BeagleTreeLikelihood.java (+18 -5)
src/dr/app/beast: BeastDialog.java (+10 -1), BeastMain.java (+9 -9)

msuchard 2012-03-08 07:09 #40 Rev.: 4789

Implemented TN93 under BEAGLE.

327 lines of code changed in 6 files:

src/dr/app/beagle/evomodel/parsers: TN93Parser.java (+84)
src/dr/app/beagle/evomodel/substmodel: TN93.java (+152)
src/dr/app/beast: beagle_parsers.properties (+2 -2)
src/dr/evomodel/substmodel: TN93.java (+19 -19)
src/test/dr/app/beagle: TN93Test.java (new 70)

rambaut 2012-03-08 05:30 #39 Rev.: 4788

Runtime errors galore.

62 lines of code changed in 3 files:

src/dr/evomodel/antigenic: AntigenicLikelihood.java (+43 -32)
src/dr/math/distributions: NormalDistribution.java (new)

rambaut 2012-03-08 04:52 #38 Rev.: 4787

Finally fixed the diagnostics strings displayed after an incorrect restore so that they are genuinely before and after (as opposed to both after).

9 lines of code changed in 1 file:

src/dr/inference/markovchain: MarkovChain.java (+9 -5)

rambaut 2012-03-08 04:40 #37 Rev.: 4786

Commented out a couple of debug printfs

6 lines of code changed in 5 files:

src/dr/inference/markovchain: MarkovChain.java (+4 -1)
src/dr/inference/operators: NormalGammaPrecisionGibbsOperator.java (new), NormalNormalMeanGibbsOperator.java (+1 -1)

rambaut 2012-03-08 04:39 #36 Rev.: 4785

Added a total to the diagnostic string of compound likelihood

8 lines of code changed in 1 file:

src/dr/inference/model: CompoundLikelihood.java (+8 -3)

rambaut 2012-03-08 04:38 #35 Rev.: 4784

BEAST version for trunk changed to 1.8.

2 lines of code changed in 1 file:

src/dr/app/beast: BeastVersion.java (+2 -2)

rambaut 2012-03-08 04:37 #34 Rev.: 4783

Initial, horribly slow, inefficient re-write of antigenic likelihood.

240 lines of code changed in 5 files:

src/dr/app/beast: development_parsers.properties (+1)
src/dr/evomodel/antigenic: AntigenicLikelihood.java (+142 -55)
src/dr/math/distributions: NormalDistribution.java (+5)
src/dr/util: DataTable.java (new)

rambaut 2012-03-08 02:29 #33 Rev.: 4782

Corrected spelling and simplified error XML reporting (commented out public ID and System ID).

3 lines of code changed in 1 file:

src/dr/xml: XMLParser.java (+3 -3)

msuchard 2012-03-07 13:32 #32 Rev.: 4781

Reverting more silly changes

29 lines of code changed in 2 files:

src/dr/evomodelxml/coalescent/operators: GMRFSkyrideBlockUpdateOperatorParser.java (+29 -7)

msuchard 2012-03-07 12:09 #31 Rev.: 4780

Reverting inadvertent changes from Julia

35 lines of code changed in 5 files:

src/dr/inference/loggers: MCLogger.java (new)
src/dr/inferencexml: MCMCParser.java (+4 -6)
src/dr/xml: AbstractXMLObjectParser.java (+25 -40)

julia.pal.r@gmail.com 2012-03-07 11:42 #30 Rev.: 4779

Not finished but descent version of GPOperator - fixing imports :S

23 lines of code changed in 5 files:

src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (-1)
src/dr/evomodelxml/coalescent/operators: GMRFSkyrideBlockUpdateOperatorParser.java (+2)
src/dr/inference/loggers: MCLogger.java (+3)
src/dr/inferencexml: MCMCParser.java (+2)
src/dr/xml: AbstractXMLObjectParser.java (+16 -1)

julia.pal.r@gmail.com 2012-03-07 11:39 #29 Rev.: 4778

Not finished but descent version of GPOperator

117 lines of code changed in 1 file:

src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+117 -32)

rambaut 2012-03-07 04:17 #28 Rev.: 4776

Merged changes in 1.7 - fixes generation of MarkovJumps.

69 lines of code changed in 2 files:

src/dr/app/beauti/components/ancestralstates: AncestralStatesComponentGenerator.java (+47 -1)
src/dr/app/beauti/generator: TreeLikelihoodGenerator.java (+22 -16)

rambaut 2012-03-07 01:58 #27 Rev.: 4773

Default scaling returns to 'dynamic'. 'oldSchool' is renamed 'delayed'.

7 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/treelikelihood: BeagleTreeLikelihood.java (+7 -3)

baele.guy@gmail.com 2012-03-06 22:25 #26 Rev.: 4772

Allow for a parameter value to be obtained by calculating the mean for that parameter from a log file, using the name of the column (and excluding a burn-in), if a file name is given in the XML element. If a file name is not given, nothing is changed.

65 lines of code changed in 2 files:

src/dr/inference/model: ParameterParser.java (new)

rambaut 2012-03-06 00:28 #25 Rev.: 4771

Default scaling returns to 'dynamic'. 'oldSchool' is renamed 'delayed'.

10 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/treelikelihood: BeagleTreeLikelihood.java (+3 -3), PartialsRescalingScheme.java (+7 -7)

rambaut 2012-03-05 23:49 #24 Rev.: 4770

Made full set of scaling options available to command line.

13 lines of code changed in 3 files:

src/dr/app/beagle/evomodel/treelikelihood: PartialsRescalingScheme.java (+4)
src/dr/app/beast: BeastMain.java (+9 -2)
src/dr/evomodel/treelikelihood: TreeLikelihood.java (-1)

rambaut 2012-03-05 21:45 #23 Rev.: 4769

Cleaned up code.

10 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: TreeLikelihoodParser.java (+10 -7)

rambaut 2012-03-05 21:40 #22 Rev.: 4768

Double negative in the check for SequenceError model and -beagle_instances giving opposite of intended behaviour.

1 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: TreeLikelihoodParser.java (+1 -1)

rambaut 2012-03-05 21:37 #21 Rev.: 4767

Java 1.5 doesn't allow @override on interface methods

13 lines of code changed in 1 file:

src/dr/app/beagle/evomodel/parsers: BeagleSubstitutionEpochModelParser.java (+13 -14)

msuchard 2012-03-05 04:46 #20 Rev.: 4766

Implementing classic BEAST rescaling option (no rescaling until first underflow) in BEAGLE

58 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/treelikelihood: BeagleTreeLikelihood.java (+31 -36), PartialsRescalingScheme.java (+27 -1)

baele.guy@gmail.com 2012-03-05 01:52 #19 Rev.: 4765

Added additional prior parsers (for future use with generalized stepping-stone sampling).

194 lines of code changed in 1 file:

src/dr/inferencexml/distribution: PriorParsers.java (+194)

baele.guy@gmail.com 2012-03-05 01:50 #18 Rev.: 4764

Minor change (mainly for testing purposes).

26 lines of code changed in 2 files:

src/dr/inference/trace: KernelDensityEstimate.java (new)

fbielejec 2012-03-05 00:57 #17 Rev.: 4763

lets keep it hidden

4 lines of code changed in 2 files:

src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+1 -1)
src/dr/app/beagle/evomodel/treelikelihood: BeagleTreeLikelihood.java (+3 -3)

fbielejec 2012-03-05 00:51 #16 Rev.: 4762

commiting everything

43 lines of code changed in 5 files:

src/dr/app/beagle/evomodel/parsers: BeagleSubstitutionEpochModelParser.java (+1 -7), GammaSiteModelParser.java (+3 -2)
src/dr/app/beagle/evomodel/sitemodel: EpochBranchSubstitutionModel.java (+36 -46)
src/dr/app/seqgen: SequenceSimulator.java (+3 -2)

rambaut 2012-03-04 01:01 #15 Rev.: 4761

Removing wrongly located files.

0 lines of code changed in 4 files:

src/dr/inference/markovchain: BlueBeastMarkovChain.java (del)
src/dr/inference/mcmc: BlueBeastMCMC.java (del)
src/dr/inferencexml: BlueBeastMCMCParser.java (del)
src/dr/inferencexml/loggers: BlueBeastLoggerParser.java (del)

rambaut 2012-03-04 00:59 #14 Rev.: 4760

Reverting changes in 4754 - MarkovChain is not designed for subclassing.

19 lines of code changed in 1 file:

src/dr/inference/markovchain: MarkovChain.java (+19 -19)

rambaut 2012-03-03 23:50 #13 Rev.: 4759

Removing 'blue.jar' from lib folder. Need to work out other solution - either it is part of BEAST or it isn't.

1 lines of code changed in 4 files:

build.xml (-1), build_eclipse.xml (+1 -2)
lib: blue.jar (del)

sibon.li 2012-03-03 21:38 #12 Rev.: 4758

Commented out all of my last commit until issues resolved

1202 lines of code changed in 9 files:

build.xml (+1 -1), build_eclipse.xml (+1 -1)
lib: blue-beast.jar (del), blue.jar (new)
src/dr/evolution/alignment: SimpleAlignment.java (+4 -4)
src/dr/inference/markovchain: BlueBeastMarkovChain.java (new 536)
src/dr/inference/mcmc: BlueBeastMCMC.java (new 199)
src/dr/inferencexml: BlueBeastMCMCParser.java (new 294)
src/dr/inferencexml/loggers: BlueBeastLoggerParser.java (new 167)

sibon.li 2012-03-03 18:40 #11 Rev.: 4757

Test build

1 lines of code changed in 1 file:

src/dr/inferencexml: BlueBeastMCMCParser.java (+1 -1)

sibon.li 2012-03-03 18:14 #10 Rev.: 4756

Added blue-beast.jar and modified build xmls

3 lines of code changed in 4 files:

.classpath (+1), build.xml (+1), build_eclipse.xml (+1)
lib: blue-beast.jar (new)

sibon.li 2012-03-03 16:23 #9 Rev.: 4755

Added classes to enable implicit convergence assessment checks using BLUE

1255 lines of code changed in 4 files:

src/dr/inference/markovchain: BlueBeastMarkovChain.java (+595)
src/dr/inference/mcmc: BlueBeastMCMC.java (+200)
src/dr/inferencexml: BlueBeastMCMCParser.java (+294 -294)
src/dr/inferencexml/loggers: BlueBeastLoggerParser.java (+166 -165)

sibon.li 2012-03-03 16:18 #8 Rev.: 4754

Changes to encapsulation in MCMC.java and MarkovChain.java. MarkovChain.java no longer final and some private variables changed to protected

33 lines of code changed in 2 files:

src/dr/inference/markovchain: MarkovChain.java (+20 -20)
src/dr/inference/mcmc: MCMC.java (+13 -13)

fbielejec 2012-03-03 02:33 #7

setter for count report - safe

3 lines of code changed in 2 files:

src/dr/evolution/alignment: SimpleAlignment.java (+2 -1)

fbielejec 2012-03-03 02:28 #6 Rev.: 4751

setter for count report

1 lines of code changed in 1 file:

src/dr/evolution/alignment: SimpleAlignment.java (+1 -1)

fbielejec 2012-03-03 02:06 #5 Rev.: 4750

setter for count report

6 lines of code changed in 1 file:

src/dr/evolution/alignment: SimpleAlignment.java (+6 -1)

fbielejec 2012-03-03 00:11 #4

Sequence simulator accepts ancestral sequence now

98 lines of code changed in 2 files:

src/dr/app/seqgen: SequenceSimulator.java (+98 -30)

julia.pal.r@gmail.com 2012-03-02 12:10 #3 Rev.: 4747

still working on GPOperator

472 lines of code changed in 1 file:

src/dr/evomodel/coalescent/operators: GaussianProcessSkytrackBlockUpdateOperator.java (+472 -64)

rambaut 2012-03-02 05:02 #2 Rev.: 4746

Fixed some issues with APOBEC error model generation.

7 lines of code changed in 6 files:

src/dr/app/beauti/ancestralStatesPanel: AncestralStatesOptionsPanel.java (+2 -2)
src/dr/app/beauti/components/sequenceerror: SequenceErrorModelComponentGenerator.java (+4 -4), SequenceErrorModelComponentOptions.java (new)
src/dr/app/beauti/siteModelsPanel: SiteModelsPanel.java (-20)

rambaut 2012-03-01 22:09 #1 Rev.: 4744

Fixed some issues with LogCombiner that had been introduced in v1.7. Thanks to Matthew Hall for suggesting code fixes. Needs testing.

70 lines of code changed in 3 files:

src/dr/app/tools: LogCombiner.java (+67 -23), LogCombinerDialog.java (new)

February 2012 »

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