StatSVN - Directory src/dr/evomodelxml/treelikelihood/

Author	Changes	Lines of Code	Lines per Change
Totals	43 (100.0%)	1020 (100.0%)	23.7
msuchard	12 (27.9%)	461 (45.2%)	38.4
dong.w.xie	9 (20.9%)	390 (38.2%)	43.3
rambaut	19 (44.2%)	93 (9.1%)	4.8
aaron.darling	1 (2.3%)	50 (4.9%)	50.0
akaruiws	1 (2.3%)	25 (2.5%)	25.0
fbielejec	1 (2.3%)	1 (0.1%)	1.0

Most Recent Commits

msuchard 2013-05-07 07:43 Rev.: 5635

Fixing transformed trees when random

27 lines of code changed in 2 files:

src/dr/evomodelxml/treelikelihood: TreeTraitParserUtilities.java (+27 -2)

rambaut 2013-01-31 04:42 Rev.: 5367

Porting some fixes from 1.7 branch

5 lines of code changed in 4 files:

src/dr/evomodelxml/treelikelihood: AncestralStateTreeLikelihoodParser.java (new), MarkovJumpsTreeLikelihoodParser.java (new)

rambaut 2012-11-16 00:54 Rev.: 5232

Renamed NewTreeLikelihood to BeagleTreeLikelihood

3 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: AncestralStateTreeLikelihoodParser.java (+3 -3)

rambaut 2012-08-20 21:05 Rev.: 5148

Fix for Issue 660: For trait specification errors, error messages should include name of taxon.

8 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: TreeTraitParserUtilities.java (+8 -7)

rambaut 2012-04-26 07:20 Rev.: 4930

Demoted the non-beagle form of AncestralTreeLikelihood (parser now specifies BEAGLE is required).

24 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: AncestralStateTreeLikelihoodParser.java (+24 -23)

rambaut 2012-02-15 09:59 Rev.: 4695

Very very minor thing - TreeLikelihoodParser was looking at the wrong system property to see whether to use the Java core. This means that the advertised '-java' option wasn't working.

1 lines of code changed in 2 files:

src/dr/evomodelxml/treelikelihood: TreeLikelihoodParser.java (new)

rambaut 2011-11-16 05:16 Rev.: 4433

Ported sequence error models to BeagleTreeLikelihood and implemented a variant model that emits tip states rather than tip partials.

10 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: TreeLikelihoodParser.java (+10 -6)

rambaut 2011-11-15 00:50 Rev.: 4418

Fixed a few issues with BSSVS generation. Also robust counting. Also unified the RECONSTRUCTION_TAG_NAME for the BEAGLE and non-BEAGLE versions of ASTL.

3 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: AncestralStateTreeLikelihoodParser.java (+3 -3)

msuchard 2011-09-08 23:49 Rev.: 4291

Changing user experience with MarkovJumps

42 lines of code changed in 2 files:

src/dr/evomodelxml/treelikelihood: AncestralStateTreeLikelihoodParser.java (+1 -2), MarkovJumpsTreeLikelihoodParser.java (+41)

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

Bug fix; null pointer exception

1 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: TreeLikelihoodParser.java (+1 -1)

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

Various bits

3 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: TreeLikelihoodParser.java (+3)

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.

2 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: TreeTraitParserUtilities.java (+2 -2)

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

parser for ancestralTreeLikelihood

1 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: TreeLikelihoodParser.java (+1)

msuchard 2011-06-04 04:01 Rev.: 4002

Implemented ascertainment correction for continous, integrated diffusion models

7 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: TreeTraitParserUtilities.java (+7 -1)

dong.w.xie 2011-03-30 16:45 Rev.: 3907

Trunk: continue to work on BEAUti microsat, but writing different taxa function still has a bug.

5 lines of code changed in 2 files:

src/dr/evomodelxml/treelikelihood: MicrosatelliteSamplerTreeLikelihoodParser.java (+5 -4)

msuchard 2011-03-03 05:44 Rev.: 3847

Add functionality to read plink SNP frequencies and run continuous diffusion models

22 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: TreeTraitParserUtilities.java (+22 -12)

rambaut 2010-11-15 21:45 Rev.: 3717

TreeTraitParserUtilities now picks up trait parameters that are either simply called the taxon name or have the trait name appended.

8 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: TreeTraitParserUtilities.java (+8 -4)

rambaut 2010-11-13 08:33 Rev.: 3714

AntigenicTraitLikelihood runs! Unlikely to work though. Changed MatrixParameter to set dimensions lazily. TreeTraitParserUtility now labels the individual rows of the compound parameter just as taxon labels so that ATL can pick them up.

7 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: TreeTraitParserUtilities.java (+7 -4)

dong.w.xie 2010-10-04 10:56 Rev.: 3596

Trunk: @Override is JDK1.6 code.

3 lines of code changed in 2 files:

src/dr/evomodelxml/treelikelihood: HiddenLinkageLikelihoodParser.java (new)

aaron.darling 2010-10-02 15:11 Rev.: 3588

Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is commit phase 1: adding new files. Phase 2 comes next, committing related changes to existing files.

50 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: HiddenLinkageLikelihoodParser.java (+50)

rambaut 2010-09-02 01:35 Rev.: 3479

Added an optional indicator parameter into the sequence error model to try to identify damaged sequences.

9 lines of code changed in 2 files:

src/dr/evomodelxml/treelikelihood: SequenceErrorModelParser.java (new)

msuchard 2010-08-25 12:15 Rev.: 3443

Fixed parsing of multidimensional continuous traits when trait parameter is first defined in likelihood (and not TreeModel), i.e. for Pagelesque type models

14 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: TreeTraitParserUtilities.java (+14 -11)

msuchard 2010-07-31 07:11 Rev.: 3355

Backwards compatibility so MarkovJumps XML blocks do not crash BEAST without BEAGLE.

2 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: AncestralStateTreeLikelihoodParser.java (+2 -1)

msuchard 2010-07-02 22:03 Rev.: 3299

Fix with traitName in SampledMultivariateTraitLikelihood

7 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: TreeTraitParserUtilities.java (+7 -3)

msuchard 2010-06-22 05:50 Rev.: 3277

Refactoring attribute to trait (for likelihood) parsing for use in other models

338 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: TreeTraitParserUtilities.java (+338)

msuchard 2010-06-14 14:20 Rev.: 3264

DiscreteTraitBranchRateModel now works again for ancestral state reconstructions. Something is still wrong with AncestralStateBeagleTreeLikelihood however.

1 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: AncestralStateTreeLikelihoodParser.java (+1 -1)

akaruiws 2010-06-06 22:12 Rev.: 3233

Misc changes to classes for msat likelihood calculation.

25 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: MicrosatelliteSamplerTreeLikelihoodParser.java (+25 -6)

rambaut 2010-06-02 23:10 Rev.: 3216

In the interests of generalization, AncestralState has been improved to optionally take a trait name, renamed AncestralTrait, moved to dr.evomodel.tree. It has a parser synonym of AncestralState and defaults to getting the 'state' trait so it is backwards compatible with existing XML (namely testAncestralSequenceReconstuction.xml).

0 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: AncestralStateParser.java (del)

rambaut 2010-06-02 22:53 Rev.: 3215

TreeTraits commit number 2. This one is a bit more wide ranging with potential to break things. 1) BranchAttributeProvider and NodeAttributeProvider have been deleted and replaced with a combination of TreeTraits and TreeTraitProviders. Sources implement TreeTraitProvider to say that they can provide information about nodes and branches. A good example of a class which has been generalized is AncestralState (in evomodel.treelikelihood) - this now just takes a TreeTrait and logs the trait for a given MRCA (the trait can be anything at all - whereas previously it took an AncestralStateTreeLikelihood).

10 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: AncestralStateParser.java (new 10)

dong.w.xie 2010-02-23 09:35 Rev.: 2959

Trunk refactoring: finish tree likihood model (split parsers)..

333 lines of code changed in 4 files:

src/dr/evomodelxml/treelikelihood: AncestralStateParser.java (+59), AncestralStateTreeLikelihoodParser.java (+87), SequenceErrorModelParser.java (+100), TreeLikelihoodParser.java (+87)

dong.w.xie 2010-02-22 10:42 Rev.: 2954

Trunk refactoring: organize tree and treelikelihood parsers.

49 lines of code changed in 1 file:

src/dr/evomodelxml/treelikelihood: MicrosatelliteSamplerTreeLikelihoodParser.java (+49)

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