Directory src/dr/evomodelxml/operators/

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graham853@gmail.com 2013-02-20 00:05 Rev.: 5436

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.

3 lines of code changed in 2 files:

• src/dr/evomodelxml/operators: AlloppChangeNumHybridizationsParser.java (+3)

rambaut 2013-01-10 05:31 Rev.: 5303

Drifting

1 lines of code changed in 2 files:

• src/dr/evomodelxml/operators: MoveLinkageGroupParser.java (+1)

rambaut 2012-12-22 02:13 Rev.: 5296

Grammar

1 lines of code changed in 2 files:

• src/dr/evomodelxml/operators: ExchangeOperatorParser.java (new)

graham853@gmail.com 2012-09-02 04:49 Rev.: 5149

Allopolyploid model: adding code for arbitrary numbers of diploids, tetraploids, hybridizations.

110 lines of code changed in 2 files:

• src/dr/evomodelxml/operators: AlloppChangeNumHybridizationsParser.java (+55), AlloppHybPopSizesScaleParser.java (new 55)

rambaut 2012-08-04 03:49 Rev.: 5097

Porting fixes from 1.7.3 back into the trunk

0 lines of code changed in 2 files:

• src/dr/evomodelxml/operators: PopsIOTreeNodeSlideParser.java (new)

graham853@gmail.com 2012-07-17 02:28 Rev.: 5071

Code for n diploids, one hybridization now working. Experimental code (PopsIO) added for multispecies coalescent with population size parameters integrated out.

50 lines of code changed in 1 file:

• src/dr/evomodelxml/operators: PopsIOTreeNodeSlideParser.java (+50)

graham853@gmail.com 2012-01-09 23:59 Rev.: 4571

Adding multiply-labelled tree model. MulSpeciesTreeModel, MulMSCoalescent, MulSpeciesBindings, MulSpeciesTreePrior. Operators MulTreeNodeSlide, MulTreeSequenceReassignment. Plus parsers.

Minor updates to AlloppSpeciesBindings, AlloppSpeciesNetworkModel, the latter dues to changes in logging behaviour.

112 lines of code changed in 2 files:

• src/dr/evomodelxml/operators: MulTreeNodeSlideParser.java (new 54), MulTreeSequenceReassignmentParser.java (new 58)

alexei.drummond 2011-10-07 22:17 Rev.: 4341

added parser for IntermediateExchange.

64 lines of code changed in 1 file:

• src/dr/evomodelxml/operators: ExchangeOperatorParser.java (+64 -2)

graham853@gmail.com 2011-09-03 20:28 Rev.: 4283

Allopolyploid model: Made code compatible with Java 1.5 (removed @Override's). Added citation. More sensible implementation of debugging logger.

2 lines of code changed in 6 files:

• src/dr/evomodelxml/operators: AlloppMoveLegsParser.java (new), AlloppNetworkNodeSlideParser.java (+1 -1), AlloppSequenceReassignmentParser.java (-1)

graham853@gmail.com 2011-09-02 00:01 Rev.: 4277

187 lines of code changed in 3 files:

• src/dr/evomodelxml/operators: AlloppMoveLegsParser.java (+60), AlloppNetworkNodeSlideParser.java (+68), AlloppSequenceReassignmentParser.java (+59)

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.

48 lines of code changed in 1 file:

• src/dr/evomodelxml/operators: MoveLinkageGroupParser.java (+48)

jheled 2010-09-24 13:14 Rev.: 3570

Catch errors which lead to beast infinite loop or failure in parsers. more detailed error messages.

5 lines of code changed in 3 files:

• src/dr/evomodelxml/operators: ExchangeOperatorParser.java (+3), SubtreeSlideOperatorParser.java (new)

msuchard 2010-09-04 04:04 Rev.: 3487

Add several wrappers to convert automatically between different reductions of TreeTraits (sum over tree, sum across sites, etc.). One can even double-wrap to get sum over tree + sum across sites. This should reduce substantial code-duplication and earn me a gold star.

3 lines of code changed in 2 files:

• src/dr/evomodelxml/operators: FunkyPriorMixerOperatorParser.java (+3 -1)

msuchard 2010-08-11 13:11 Rev.: 3380

Placeholders for an awesome new transition kernel to hopefully solve the uniform internal node prior issues

66 lines of code changed in 1 file:

• src/dr/evomodelxml/operators: FunkyPriorMixerOperatorParser.java (+66)

dong.w.xie 2010-02-24 15:20 Rev.: 2973

Trunk refactoring: finish rate operators (split parsers)..

192 lines of code changed in 3 files:

• src/dr/evomodelxml/operators: RateSampleOperatorParser.java (new 58), RateScaleOperatorParser.java (new 66), RateVarianceScaleOperatorParser.java (new 68)

dong.w.xie 2010-02-24 14:50 Rev.: 2972

Trunk refactoring: finish tree operators (split parsers)..

441 lines of code changed in 8 files:

• src/dr/evomodelxml/operators: GibbsPruneAndRegraftParser.java (new 56), GibbsSubtreeSwapParser.java (new 50), ImportanceNarrowExchangeParser.java (new 58), RateExchangeOperatorParser.java (new 54), TreeBitMoveOperatorParser.java (new 58), TreeBitRandomWalkOperatorParser.java (new 63), TreeNodeSlideParser.java (new 50), TreeUniformParser.java (new 52)

dong.w.xie 2010-02-24 11:53 Rev.: 2970

Trunk refactoring: correct ExchangeOperatorParser in operators (split parsers)..

87 lines of code changed in 3 files:

• src/dr/evomodelxml/operators: ExchangeOperatorParser.java (+87), NarrowExchangeOperatorParser.java (del), WideExchangeOperatorParser.java (del)

dong.w.xie 2010-02-24 11:18 Rev.: 2969

Trunk refactoring: 1st part of operators (split parsers)..

422 lines of code changed in 8 files:

• src/dr/evomodelxml/operators: FNPRParser.java (new 47), ImportancePruneAndRegraftParser.java (new 50), ImportanceSubtreeSwapParser.java (new 52), NNIParser.java (new 48), NarrowExchangeOperatorParser.java (new 46), SubtreeSlideOperatorParser.java (+84), WideExchangeOperatorParser.java (new 47), WilsonBaldingParser.java (new 48)