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graham853@gmail.com 2013-02-20 00:01

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.

173 lines of code changed in 22 files:

• src/dr/evomodel/operators: AlloppChangeNumHybridizations.java (new), AlloppNetworkNodeSlide.java (new), AlloppSequenceReassignment.java (new)
• src/dr/evomodel/speciation: AlloppDiploidHistory.java (+30 -22), AlloppLeggedTree.java (+2 -3), AlloppMulLabTree.java (new), AlloppNetworkPrior.java (new), AlloppSpeciesBindings.java (new), AlloppSpeciesNetworkModel.java (new)
• src/dr/evomodelxml/operators: AlloppChangeNumHybridizationsParser.java (+3)
• src/dr/evomodelxml/speciation: AlloppSpeciesNetworkModelParser.java (new)

graham853@gmail.com 2012-10-10 00:19 Rev.: 5192

Allopolyploid model. Added MCMC operator to flip legs and sequences of tetraploid tree to improve mixing. Improved sampling for initial state of network. Added statistic for number of hybridizations.

1287 lines of code changed in 12 files:

• src/dr/app/beast: development_parsers.properties (+1)
• src/dr/evomodel/operators: AlloppChangeNumHybridizations.java (+4 -2), AlloppNetworkNodeSlide.java (+195 -193), AlloppSequenceReassignment.java (+22 -5)
• src/dr/evomodel/speciation: AlloppDiploidHistory.java (+192 -160), AlloppLeggedTree.java (+16 -2), AlloppMulLabTree.java (+451 -450), AlloppNetworkPrior.java (+2 -2), AlloppNumHybsStatistic.java (new 30), AlloppSpeciesBindings.java (+37 -19), AlloppSpeciesNetworkModel.java (+278 -225)
• src/dr/evomodelxml/speciation: AlloppNumHybsStatisticParser.java (new 59)

graham853@gmail.com 2012-09-15 02:40 Rev.: 5162

Allopolyploid model: new version of ChangeNumHybridizations move and bug fixes.

523 lines of code changed in 14 files:

• src/dr/evolution/tree: SlidableTree.java (+5 -6)
• src/dr/evomodel/operators: AlloppChangeNumHybridizations.java (+82 -25), AlloppNetworkNodeSlide.java (+1 -1), AlloppSequenceReassignment.java (+1)
• src/dr/evomodel/speciation: AlloppDiploidHistory.java (+79 -24), AlloppLeggedTree.java (+3 -4), AlloppMulLabTree.java (+22), AlloppSpeciesBindings.java (+5 -11), AlloppSpeciesNetworkModel.java (+153 -28), PopsIOSpeciesTreeModel.java (+154 -102)
• src/test/dr/evomodel/speciation: AlloppSpeciesNetworkModelTEST.java (+18 -1)

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

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

3294 lines of code changed in 39 files:

• src/dr/app/beast: development_parsers.properties (+3)
• src/dr/evomodel/operators: AlloppChangeNumHybridizations.java (+237), AlloppHybPopSizesScale.java (new 52), AlloppMoveLegs.java (+1 -1), AlloppNetworkNodeSlide.java (+84 -79)
• src/dr/evomodel/speciation: AlloppDiploidHistory.java (+720 -560), AlloppFootLinks.java (del), AlloppLegLink.java (del), AlloppLeggedTree.java (+449 -751), AlloppMSCoalescent.java (new), AlloppMulLabTree.java (+479 -487), AlloppNetworkPrior.java (+81 -161), AlloppNetworkPriorModel.java (new), AlloppNode.java (+32 -128), AlloppSpeciesBindings.java (+111 -167), AlloppSpeciesNetworkModel.java (+604 -987), AlloppTreeLeg.java (del), MulMSCoalescent.java (+1 -1), MulSpeciesBindings.java (new), MulSpeciesTreeModel.java (new), PopsIOMSCoalescent.java (new), PopsIOSpeciesBindings.java (+1 -1)
• src/dr/evomodelxml/operators: AlloppChangeNumHybridizationsParser.java (+55), AlloppHybPopSizesScaleParser.java (new 55)
• src/dr/evomodelxml/speciation: AlloppNetworkPriorModelParser.java (new), AlloppSpeciesNetworkModelParser.java (+50 -26)
• src/dr/util: AlloppMisc.java (new)
• src/test/dr/evomodel/speciation: AlloppSpeciesNetworkModelTEST.java (+100 -415)

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.

2393 lines of code changed in 35 files:

• src/dr/app/beast: development_parsers.properties (+8)
• src/dr/evolution/tree: SlidableTree.java (+131 -111)
• src/dr/evomodel/operators: AlloppNetworkNodeSlide.java (+16 -25), AlloppSequenceReassignment.java (-1), PopsIOTreeNodeSlide.java (new 84)
• src/dr/evomodel/speciation: AlloppDiploidHistory.java (+25 -32), AlloppLeggedTree.java (+257 -243), AlloppMSCoalescent.java (+1), AlloppMulLabTree.java (+13 -37), AlloppNetworkPriorModel.java (+1 -3), AlloppNode.java (+41 -32), AlloppSpeciesBindings.java (+14 -42), AlloppSpeciesNetworkModel.java (+14 -35), AlloppTreeLeg.java (new 2), MulSpeciesBindings.java (+13 -21), PopsIOMSCoalescent.java (+54), PopsIOSpeciesBindings.java (+442), PopsIOSpeciesTreeModel.java (+832), PopsIOSpeciesTreePrior.java (new 29)
• src/dr/evomodelxml/operators: PopsIOTreeNodeSlideParser.java (+50)
• src/dr/evomodelxml/speciation: AlloppNetworkPriorParser.java (+1 -15), AlloppSpeciesBindingsApSpInfoParser.java (new), AlloppSpeciesBindingsParser.java (+3 -10), AlloppSpeciesNetworkModelParser.java (+3 -11), MulSpeciesTreePriorParser.java (+9 -12), PopsIOMSCoalescentParser.java (+49), PopsIOSpeciesBindingsParser.java (+102), PopsIOSpeciesBindingsSpInfoParser.java (+45), PopsIOSpeciesTreeModelParser.java (+81), PopsIOSpeciesTreePriorParser.java (+63)
• src/test/dr/evomodel/speciation: AlloppSpeciesNetworkModelTEST.java (+10 -11)

graham853@gmail.com 2012-05-10 00:51 Rev.: 4946

Extending allopolyploid model to deal with arbitrary numbers of diploids. Most new code is in new class AlloppDiploidHistory and old class AlloppNetworkNodeSlide.

2353 lines of code changed in 13 files:

• src/dr/evolution/tree: SlidableTree.java (+135)
• src/dr/evomodel/operators: AlloppNetworkNodeSlide.java (+162 -206)
• src/dr/evomodel/speciation: AlloppDiploidHistory.java (+737), AlloppFootLinks.java (new 28), AlloppLegLink.java (new 51), AlloppLeggedTree.java (+78 -62), AlloppMulLabTree.java (+146 -188), AlloppNode.java (+224), AlloppSpeciesBindings.java (+95 -8), AlloppSpeciesNetworkModel.java (+361 -25), AlloppTreeLeg.java (+42)
• src/dr/util: AlloppMisc.java (+60)
• src/test/dr/evomodel/speciation: AlloppSpeciesNetworkModelTEST.java (+234 -31)

graham853@gmail.com 2012-01-23 01:15 Rev.: 4600

Improved MCMC moves for allopolyploid model (diploid root, moves of legs).

234 lines of code changed in 4 files:

• src/dr/evomodel/operators: AlloppNetworkNodeSlide.java (+27 -5)
• src/dr/evomodel/speciation: AlloppLeggedTree.java (+172 -71), AlloppSpeciesNetworkModel.java (+18 -3)
• src/dr/util: AlloppMisc.java (+17 -1)

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.

3530 lines of code changed in 15 files:

• src/dr/app/beast: development_parsers.properties (+8)
• src/dr/evomodel/operators: MulTreeNodeSlide.java (new 222), MulTreeSequenceReassignment.java (new 59)
• src/dr/evomodel/speciation: AlloppSpeciesBindings.java (+5 -5), AlloppSpeciesNetworkModel.java (+1 -1), MulMSCoalescent.java (+290), MulSpeciesBindings.java (+944), MulSpeciesTreeModel.java (+1528), MulSpeciesTreePrior.java (new 30)
• src/dr/evomodelxml/operators: MulTreeNodeSlideParser.java (new 54), MulTreeSequenceReassignmentParser.java (new 58)
• src/dr/evomodelxml/speciation: MulMSCoalescentParser.java (new 41), MulSpeciesBindingsParser.java (new 146), MulSpeciesTreeModelParser.java (new 75), MulSpeciesTreePriorParser.java (+69)

graham853@gmail.com 2011-12-20 04:19 Rev.: 4553

Randomized initialisation of sequence assignments in AlloppSpeciesBindings. Less strict numerical test in AlloppNetworkPrior.

10 lines of code changed in 2 files:

• src/dr/evomodel/speciation: AlloppNetworkPrior.java (+1 -1), AlloppSpeciesBindings.java (+9 -3)

graham853@gmail.com 2011-09-27 02:04 Rev.: 4334

Separated out AlloppMulLabTree from AlloppSpeciesNetworkModel. Logging of MUL-tree. New network prior implementation. Other minor changes.

1548 lines of code changed in 5 files:

• src/dr/evomodel/speciation: AlloppLeggedTree.java (+25 -9), AlloppMulLabTree.java (+1080), AlloppNetworkPrior.java (+162 -11), AlloppSpeciesBindings.java (+2 -8), AlloppSpeciesNetworkModel.java (+279 -1085)

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.

143 lines of code changed in 24 files:

• src/dr/app/beast: development_parsers.properties (-1)
• src/dr/evomodel/operators: AlloppMoveLegs.java (-1), AlloppNetworkNodeSlide.java (-1), AlloppSequenceReassignment.java (-1)
• src/dr/evomodel/speciation: AlloppLeggedTree.java (+60 -70), AlloppMSCoalescent.java (-2), AlloppNetworkPriorModel.java (-2), AlloppSpeciesBindings.java (+5 -6), AlloppSpeciesNetworkModel.java (+71 -35)
• src/dr/evomodelxml/operators: AlloppMoveLegsParser.java (new), AlloppNetworkNodeSlideParser.java (+1 -1), AlloppSequenceReassignmentParser.java (-1)
• src/dr/evomodelxml/speciation: AlloppMSCoalescentParser.java (new), AlloppNetworkPriorModelParser.java (-1), AlloppNetworkPriorParser.java (+1 -1), AlloppSpeciesBindingsApSpInfoParser.java (-1), AlloppSpeciesBindingsIndividualParser.java (new), AlloppSpeciesBindingsParser.java (+2 -2), AlloppSpeciesNetworkModelParser.java (-1)

graham853@gmail.com 2011-09-02 21:18

Remove debugging class intended for my use only.

0 lines of code changed in 2 files:

• src/dr/inference/loggers: AlloppDBUGTUNELogger.java (del)
• src/dr/inferencexml/loggers: AlloppDBUGTUNELoggerParser.java (del)

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

5667 lines of code changed in 24 files:

• src/dr/app/beast: development_parsers.properties (+13)
• src/dr/evomodel/operators: AlloppMoveLegs.java (+49), AlloppNetworkNodeSlide.java (+331), AlloppSequenceReassignment.java (+58)
• src/dr/evomodel/speciation: AlloppLeggedTree.java (+784), AlloppMSCoalescent.java (+119), AlloppNetworkPrior.java (+49), AlloppNetworkPriorModel.java (+85), AlloppSpeciesBindings.java (+1015), AlloppSpeciesNetworkModel.java (+1821)
• src/dr/evomodelxml/operators: AlloppMoveLegsParser.java (+60), AlloppNetworkNodeSlideParser.java (+68), AlloppSequenceReassignmentParser.java (+59)
• src/dr/evomodelxml/speciation: AlloppMSCoalescentParser.java (+56), AlloppNetworkPriorModelParser.java (+63), AlloppNetworkPriorParser.java (+94), AlloppSpeciesBindingsApSpInfoParser.java (+72), AlloppSpeciesBindingsIndividualParser.java (+66), AlloppSpeciesBindingsParser.java (+148), AlloppSpeciesNetworkModelParser.java (+138)
• src/dr/inference/loggers: AlloppDBUGTUNELogger.java (new 54)
• src/dr/inferencexml/loggers: AlloppDBUGTUNELoggerParser.java (new 60)
• src/dr/util: AlloppMisc.java (+66)
• src/test/dr/evomodel/speciation: AlloppSpeciesNetworkModelTEST.java (+339)