Directory src/dr/evomodel/speciation/

Total Files:
39
Deleted Files:
8
Lines of Code:
781

[root]/src/dr/evomodel/speciation
                    directory in repo ModelAveragingResearch (4 files, 448 lines)

Lines of Code

src/dr/evomodel/speciation/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 376 (100.0%) 27635 (100.0%) 73.4
graham853@gmail.com 100 (26.6%) 16112 (58.3%) 161.1
jheled 98 (26.1%) 4948 (17.9%) 50.4
alexei.drummond 87 (23.1%) 3748 (13.6%) 43.0
rambaut 29 (7.7%) 1440 (5.2%) 49.6
jheled@gmail.com 15 (4.0%) 738 (2.7%) 49.2
dong.w.xie 36 (9.6%) 343 (1.2%) 9.5
msuchard 7 (1.9%) 237 (0.9%) 33.8
denise.kuehnert@gmail.com 1 (0.3%) 60 (0.2%) 60.0
dong.w.xie@gmail.com 3 (0.8%) 9 (0.0%) 3.0

Most Recent Commits

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.

93 lines of code changed in 12 files:

  • src/dr/evomodel/speciation: AlloppDiploidHistory.java (+30 -22), AlloppLeggedTree.java (+2 -3), AlloppMulLabTree.java (new), AlloppNetworkPrior.java (new), AlloppSpeciesBindings.java (+4 -2), AlloppSpeciesNetworkModel.java (+52 -24)
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.

1006 lines of code changed in 7 files:

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

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

416 lines of code changed in 7 files:

  • 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 (new)
graham853@gmail.com 2012-09-02 04:49 Rev.: 5149

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

2542 lines of code changed in 25 files:

  • 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)
dong.w.xie@gmail.com 2012-08-10 13:05 Rev.: 5121

trunk: merge Issue 637: birth-death sampling model seems to not work smoothly

2 lines of code changed in 2 files:

  • src/dr/evomodel/speciation: BirthDeathSerialSamplingModel.java (+2 -2)
jheled@gmail.com 2012-07-23 14:13 Rev.: 5077

Improve report sent by BEAST when initial posterior is infinite

11 lines of code changed in 2 files:

  • src/dr/evomodel/speciation: SpeciationLikelihood.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.

1738 lines of code changed in 14 files:

  • 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)
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.

1762 lines of code changed in 9 files:

  • 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)
dong.w.xie@gmail.com 2012-02-07 10:20 Rev.: 4641

trunk:solve Issue 569: BirthDeathEpidemiologyModel bug

7 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: BirthDeathSerialSamplingModel.java (+7 -5)
graham853@gmail.com 2012-01-23 01:15 Rev.: 4600

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

190 lines of code changed in 2 files:

  • src/dr/evomodel/speciation: AlloppLeggedTree.java (+172 -71), AlloppSpeciesNetworkModel.java (+18 -3)
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.

2798 lines of code changed in 6 files:

  • 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)
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)
rambaut 2011-12-07 10:49 Rev.: 4518

New parameterization of Tanja's BDSSM for epidemiology

65 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: BirthDeathSerialSamplingModel.java (+65 -13)
rambaut 2011-11-16 03:13 Rev.: 4430

Loggers weren't logging if they overrode the base class log(int state) - because it had been changed to log(long state). Put a final int version in the base class to prevent overriding.

3 lines of code changed in 4 files:

  • src/dr/evomodel/speciation: AlloppLeggedTree.java (+1 -1), AlloppSpeciesNetworkModel.java (+1 -1), SpeciesTreeModel.java (new)
dong.w.xie 2011-11-09 11:59 Rev.: 4401

improve enum CorrectionType to suit for BEAUti, and finish Calibrated Yule GUI part, but need further work on xml generator.

149 lines of code changed in 2 files:

  • src/dr/evomodel/speciation: CalibrationPoints.java (+149 -140)
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)
jheled@gmail.com 2011-09-12 16:25 Rev.: 4304

fix setting of pop sizes with constant

2 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: SpeciesTreeModel.java (+2 -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.

136 lines of code changed in 5 files:

  • src/dr/evomodel/speciation: AlloppLeggedTree.java (+60 -70), AlloppMSCoalescent.java (-2), AlloppNetworkPriorModel.java (-2), AlloppSpeciesBindings.java (+5 -6), AlloppSpeciesNetworkModel.java (+71 -35)
graham853@gmail.com 2011-09-02 00:01 Rev.: 4277

3873 lines of code changed in 6 files:

  • src/dr/evomodel/speciation: AlloppLeggedTree.java (+784), AlloppMSCoalescent.java (+119), AlloppNetworkPrior.java (+49), AlloppNetworkPriorModel.java (+85), AlloppSpeciesBindings.java (+1015), AlloppSpeciesNetworkModel.java (+1821)
jheled@gmail.com 2011-07-19 11:47 Rev.: 4112

Add an alternative exact marginal

101 lines of code changed in 3 files:

  • src/dr/evomodel/speciation: CalibrationLineagesIterator.java (+2 -2), CalibrationPoints.java (+99 -51)
dong.w.xie 2011-07-08 11:24 Rev.: 4103

comment out system print in BDSS

1 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: BirthDeathSerialSamplingModel.java (+1 -1)
jheled@gmail.com 2011-07-04 13:40 Rev.: 4098

more fixes to calibration code

31 lines of code changed in 4 files:

  • src/dr/evomodel/speciation: BirthDeathGernhard08Model.java (+1 -68), CalibrationLineagesIterator.java (+1 -1), CalibrationPoints.java (+29 -40)
jheled@gmail.com 2011-07-04 13:39 Rev.: 4097

species tree taxa references in XML work now

2 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: SpeciesTreeModel.java (+2 -1)
alexei.drummond 2011-07-02 08:48 Rev.: 4093

Tidied up parsers and added option to specify epoch widths from the origin rather than the tips.

53 lines of code changed in 3 files:

  • src/dr/evomodel/speciation: BirthDeathSerialSamplingModel.java (+4 -5), BirthDeathSerialSkylineModel.java (new)
alexei.drummond 2011-07-01 06:56 Rev.: 4085

likelihoods correct! phew! Late night debugging with Denise and Tanja in Zurich ;-)

177 lines of code changed in 2 files:

  • src/dr/evomodel/speciation: BirthDeathSerialSamplingModel.java (+18 -12), BirthDeathSerialSkylineModel.java (+159 -100)
alexei.drummond 2011-06-30 22:32 Rev.: 4079

removed final time interval

37 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: BirthDeathSerialSamplingModel.java (+37 -25)
jheled@gmail.com 2011-06-24 21:33 Rev.: 4064

Add first version for exact marginal for the general case of N monophyletic clades

591 lines of code changed in 4 files:

  • src/dr/evomodel/speciation: CalibrationLineagesIterator.java (+266), CalibrationPoints.java (+323 -60), UltrametricSpeciationModel.java (+2 -1)
dong.w.xie 2011-06-13 21:27 Rev.: 4026

TRUNK: update my tool and BDSS log transf

3 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: BirthDeathSerialSamplingModel.java (+3 -6)
dong.w.xie 2011-06-09 17:13 Rev.: 4020

Trunk: add log transformation into BDSS

22 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: BirthDeathSerialSamplingModel.java (+22 -11)
jheled 2011-06-08 18:24 Rev.: 4016


Re-organize calibration code. add experimental "approximate" marginal.

390 lines of code changed in 6 files:

  • src/dr/evomodel/speciation: BirthDeathGernhard08Model.java (+75 -61), CalibrationPoints.java (+286), SpeciationLikelihood.java (+12 -48), SpeciationModel.java (+10 -10), UltrametricSpeciationModel.java (+7 -58)
jheled 2011-06-06 13:56 Rev.: 4011

add all worked out closed form calibration marginals: parent of clade, two nested clades, clade and root.

102 lines of code changed in 4 files:

  • src/dr/evomodel/speciation: BirthDeathGernhard08Model.java (+45 -38), SpeciationLikelihood.java (+23 -15), SpeciationModel.java (+5 -4), UltrametricSpeciationModel.java (+29 -14)
dong.w.xie 2011-05-27 14:50 Rev.: 3989

Trunk: fix a bug of BDSS parser, and correct attribute name

2 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: BirthDeathSerialSamplingModel.java (+2 -2)
msuchard 2011-05-09 09:29 Rev.: 3972

Re-implemented logging of random local clock indicators in tree log files; this ability was lost when we converted over to tree traits.

5 lines of code changed in 2 files:

  • src/dr/evomodel/speciation: RandomLocalYuleModel.java (new)
jheled 2011-04-07 09:23 Rev.: 3927

Correctly handle calibration on root

14 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: BirthDeathGernhard08Model.java (+14 -3)
denise.kuehnert@gmail.com 2011-03-25 17:45 Rev.: 3903

some testing / debugging (unfinished)

60 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: BirthDeathSerialSkylineModel.java (+60 -47)
alexei.drummond 2011-02-12 17:51 Rev.: 3793

birth/death skyline

334 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: BirthDeathSerialSkylineModel.java (+334)
dong.w.xie 2011-02-04 12:48 Rev.: 3788

Trunk: change Model Averaging indexVariable initial values from all 0 into i+1.

1 lines of code changed in 2 files:

  • src/dr/evomodel/speciation: ModelAveragingSpeciationLikelihood.java (new)
dong.w.xie 2010-12-15 16:57 Rev.: 3759

Trunk: annother correction of MA

2 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: ModelAveragingSpeciationLikelihood.java (+2 -1)
dong.w.xie 2010-12-15 15:58 Rev.: 3758

Trunk: fix test and parser of MA

2 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: ModelAveragingSpeciationLikelihood.java (+2 -2)
dong.w.xie 2010-12-15 14:46 Rev.: 3756

Trunk: revert an incorrect change on uniform and random walk integer operator on integer parameter part

73 lines of code changed in 1 file:

  • src/dr/evomodel/speciation: ModelAveragingSpeciationLikelihood.java (+73 -15)

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