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alexander.alekseyenko 2012-11-20 09:35 Rev.: 5244

renamed integratedMixtureModel to MixtureModelLikelihood. Preserved an alias parser <integratedMixtureModel> per Marc's request. Updated the class, such that the mixtures are always normalized internally when likelihood is calculated.

7 lines of code changed in 2 files:

• examples/unrelease: testMVPolyaLikelihood2.xml (+7 -2)

alexander.alekseyenko 2012-11-17 11:24 Rev.: 5238

Started on a model to compute mixtures of likelihoods.

26 lines of code changed in 1 file:

• examples/unrelease: testMVPolyaLikelihood2.xml (+26 -6)

alexander.alekseyenko 2012-10-26 09:33 Rev.: 5209

Updated Compound DirichletMultinomial distribution to use both the rates and frequencies + dispersion parametrization. New example XML included.

86 lines of code changed in 1 file:

• examples/unrelease: testMVPolyaLikelihood2.xml (+86)

msuchard 2010-10-28 03:38 Rev.: 3685

Enabling tipBranchSubstitutionModel for ancestral state reconstruction

334 lines of code changed in 2 files:

• examples/unrelease: testBranchSiteModel.xml (del), testBranchSubstitutionModel.xml (new 334)

msuchard 2010-10-27 12:02 Rev.: 3683

Added example files

91 lines of code changed in 2 files:

• examples/unrelease: testBranchSiteModel.xml (new), testIntegratedConstantCoalescent.xml (new 91)

aaron.darling 2010-10-02 15:30 Rev.: 3595

Adding a very hackish and trivial example XML for using the metagenome HiddenLinkageModel.
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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 one part of commit phase 2.

1880 lines of code changed in 1 file:

• examples/unrelease: bushSausageUnknown.xml (new 1880)

alexander.alekseyenko 2010-09-25 04:58 Rev.: 3571

Started MV Polya Likelihood model

93 lines of code changed in 1 file:

• examples/unrelease: testMVPolyaLikelihood.xml (new 93)

alexander.alekseyenko 2010-09-24 04:20 Rev.: 3567

fix and move a few example files of my making

2 lines of code changed in 2 files:

• examples/unrelease: testIBDweights.xml (new), testPathSampling.xml (new 2)

dong.w.xie 2010-08-27 16:15 Rev.: 3467

Trunk: refactory xml examples

0 lines of code changed in 2 files:

• examples/unrelease: Msat (del), Phylogeography (del)

dong.w.xie 2010-08-27 16:03 Rev.: 3465

Trunk: refactory xml examples

0 lines of code changed in 25 files:

• examples/unrelease: testAlignmentStatistics.xml (del), testAutocorrelatedRelaxedClock.xml (del), testBinaryDollo.xml (del), testCTMCMap.xml (del), testCompleteHistorySimulator.xml (del), testConjugateTraitLikelihood.xml (del), testDiscreteMapDiffusion.xml (del), testIntegratedTraitLikelihood.xml (del), testLewisMk.xml (del), testLinearRegression.xml (del), testMLCalculator.xml (del), testMSSD.xml (del), testMarkovJumps.xml (del), testMissingIntegratedTraitLikelihood.xml (del), testMultivariateComparativeMethod.xml (del), testNewLikelihood.xml (del), testOTFPCLikelihood.xml (del), testPopTreeModel.xml (del), testRestrictedAncestralReconstruction.xml (del), testRobustCounting.xml (del), testSimplePathSampling.xml (del), testTransmission.xml (del), testTreePathSampling.xml (del), testUniformizedMarkovJumps.xml (del), testYuleOneSite.xml (del)

dong.w.xie 2010-08-27 13:28 Rev.: 3463

Trunk: refactory xml examples

0 lines of code changed in 35 files:

• examples/unrelease: Mdor phygeo ages1.xml (del), arg-ecoli.xml (del), arg-lepto.xml (del), arg-rokas.xml (del), benchmark.xml (del), benchmark2.xml (del), demoCodonHistorySimulator.xml (del), new_benchmark.xml (del), testAncestralReconstruction.xml (del), testAscertainment.xml (del), testBSP.xml (del), testCodonLikelihood.xml (del), testComparativeMethod.xml (del), testCovarionHKY.xml (del), testGeneralSubstitutionModel.xml (del), testIA.xml (del), testIBDweights.xml (del), testLikelihood.xml (del), testLocalClock.xml (del), testLognormalPrior.xml (del), testMC3.xml (del), testMCMC.xml (del), testML.xml (del), testMVOU.xml (del), testMixedModel.xml (del), testMultiThreading.xml (del), testNormalModelGibbs.xml (del), testPMD.xml (del), testPathSampling.xml (del), testPosteriorIBD.xml (del), testRandomLocalClock.xml (del), testSequenceSimulator.xml (del), testStrictClock.xml (del), testTransmissionStatistic.xml (del), testUncorrelatedRelaxedClock.xml (del)

dong.w.xie 2010-08-27 11:20 Rev.: 3462

Trunk: refactory xml examples

0 lines of code changed in 1 file:

• examples/unrelease: calibrations (del)

dong.w.xie 2010-08-27 11:12 Rev.: 3460

Trunk: refactory xml examples

0 lines of code changed in 1 file:

• examples/unrelease: treePriors (del)

dong.w.xie 2010-08-26 16:43 Rev.: 3459

Trunk: refactory xml examples

0 lines of code changed in 1 file:

• examples/unrelease: Data (del)

dong.w.xie 2010-08-26 16:11

Trunk: refactory xml examples

17429 lines of code changed in 65 files:

• examples/unrelease: Data (new), Mdor phygeo ages1.xml (new 1475), Msat (new), Phylogeography (new), arg-ecoli.xml (new), arg-lepto.xml (new), arg-rokas.xml (new), benchmark.xml (new), benchmark2.xml (new), calibrations (new), demoCodonHistorySimulator.xml (new 88), new_benchmark.xml (new 371), testAlignmentStatistics.xml (new 23), testAncestralReconstruction.xml (new 245), testAscertainment.xml (new 174), testAutocorrelatedRelaxedClock.xml (new 460), testBSP.xml (new 324), testBinaryDollo.xml (new 148), testCTMCMap.xml (new 312), testCodonLikelihood.xml (new 1183), testComparativeMethod.xml (new 292), testCompleteHistorySimulator.xml (new 200), testConjugateTraitLikelihood.xml (new 124), testCovarionHKY.xml (new 339), testDiscreteMapDiffusion.xml (new 112), testGeneralSubstitutionModel.xml (new 183), testIA.xml (new 120), testIBDweights.xml (new 166), testIntegratedTraitLikelihood.xml (new 115), testLewisMk.xml (new 31), testLikelihood.xml (new 727), testLinearRegression.xml (new 126), testLocalClock.xml (new 413), testLognormalPrior.xml (new 62), testMC3.xml (new 300), testMCMC.xml (new 175), testML.xml (new 165), testMLCalculator.xml (new 6), testMSSD.xml (new 203), testMVOU.xml (new 302), testMarkovJumps.xml (new 150), testMissingIntegratedTraitLikelihood.xml (new 115), testMixedModel.xml (new 148), testMultiThreading.xml (new 423), testMultivariateComparativeMethod.xml (new 310), testNewLikelihood.xml (new 477), testNormalModelGibbs.xml (new 109), testOTFPCLikelihood.xml (new 477), testPMD.xml (new 1550), testPathSampling.xml (new 236), testPopTreeModel.xml (new 39), testPosteriorIBD.xml (new 194), testRandomLocalClock.xml (new 321), testRestrictedAncestralReconstruction.xml (new 255), testRobustCounting.xml (new 452), testSequenceSimulator.xml (new 143), testSimplePathSampling.xml (new 251), testStrictClock.xml (new 334), testTransmission.xml (new 742), testTransmissionStatistic.xml (new 682), testTreePathSampling.xml (new 262), testUncorrelatedRelaxedClock.xml (new 418), testUniformizedMarkovJumps.xml (new 152), testYuleOneSite.xml (new 225), treePriors (new)