[med-svn] [beast-mcmc] branch master updated (69ceacf -> edb1ba5)
Andreas Tille
tille at debian.org
Tue Jun 28 08:03:38 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository beast-mcmc.
from 69ceacf Upload to experimental
new b477f08 Imported Upstream version 1.8.4+dfsg
new 079f026 Merge tag 'upstream/1.8.4+dfsg'
new 8a181ee New upstream version
new faf5ed1 export LC_ALL=C.UTF-8 to cope with encoding issues
new edb1ba5 Upload to unstable (main)
The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.idea/uiDesigner.xml | 124 ++++
README.md | 2 +-
build.xml | 7 +-
build_tempest.xml | 18 +-
debian/changelog | 8 +
debian/patches/fix_encoding.patch | 4 +-
debian/rules | 2 +
release/common/README.txt | 4 +-
release/common/VERSION HISTORY.txt | 28 +-
release_tempest/Linux/icons/pathogen.png | Bin 34709 -> 0 bytes
release_tempest/Linux/scripts/pathogen | 27 -
release_tempest/common/README.txt | 71 ++-
.../evomodel/branchmodel/EpochBranchModel.java | 24 +-
.../branchmodel/ExternalInternalBranchModel.java | 23 +-
.../lineagespecific/BeagleBranchLikelihood.java | 2 +-
.../LineageSpecificBranchModel.java | 25 +-
.../NewBeagleSequenceLikelihood.java | 4 +-
.../evomodel/parsers/ALSTreeLikelihoodParser.java | 2 +
.../AncestralStateTreeLikelihoodParser.java | 7 +-
.../BalancedBeagleTreeLikelihoodParser.java | 21 +-
.../parsers/BeagleTreeLikelihoodParser.java | 9 +
.../parsers/MarkovJumpsTreeLikelihoodParser.java | 2 +
.../OptimizedBeagleTreeLikelihoodParser.java | 103 +++-
.../sitemodel/EpochBranchSubstitutionModel.java | 21 +-
.../ExternalInternalBranchSubstitutionModel.java | 19 +-
.../evomodel/sitemodel/GammaSiteRateModel.java | 41 +-
.../substmodel/ComplexSubstitutionModel.java | 21 +-
.../evomodel/substmodel/GLMSubstitutionModel.java | 15 +
src/dr/app/beagle/evomodel/substmodel/GTR.java | 33 +-
.../beagle/evomodel/substmodel/GY94CodonModel.java | 35 +-
src/dr/app/beagle/evomodel/substmodel/HKY.java | 38 +-
.../beagle/evomodel/substmodel/MG94CodonModel.java | 34 +-
.../MarkovModulatedSubstitutionModel.java | 20 +-
.../substmodel/ProductChainSubstitutionModel.java | 19 +-
.../substmodel/SVSComplexSubstitutionModel.java | 2 +-
.../substmodel/SVSGeneralSubstitutionModel.java | 31 +-
src/dr/app/beagle/evomodel/substmodel/TN93.java | 34 +-
.../treelikelihood/ALSBeagleTreeLikelihood.java | 3 +-
.../AncestralStateBeagleTreeLikelihood.java | 28 +-
.../treelikelihood/BeagleTreeLikelihood.java | 142 +++--
.../MarkovJumpsBeagleTreeLikelihood.java | 16 +-
.../treelikelihood/OldBeagleTreeLikelihood.java | 12 +-
.../treelikelihood/SplitBySiteTraitLogger.java | 22 +-
.../evomodel/utilities/CompleteHistoryLogger.java | 22 +-
src/dr/app/beagle/mm/MMAlgorithm.java | 125 ++++
.../app/beagle/mm/MultiDimensionalScalingMM.java | 269 ++++++++
.../MassivelyParallelMDSImpl.java | 21 +-
.../MultiDimensionalScalingCore.java | 5 +
.../MultiDimensionalScalingCoreImpl2.java | 294 +++------
.../MultiDimensionalScalingLikelihood.java | 34 +-
.../NativeMDSSingleton.java | 15 +-
src/dr/app/beast/BeastMain.java | 29 +-
src/dr/app/beast/BeastParser.java | 47 +-
src/dr/app/beast/BeastVersion.java | 43 +-
src/dr/app/beast/beast.properties | 4 +-
src/dr/app/beast/development_parsers.properties | 24 +-
src/dr/app/beast/release_parsers.properties | 11 +-
src/dr/app/beauti/BeautiApp.java | 33 +-
src/dr/app/beauti/BeautiFrame.java | 2 -
.../clockModelsPanel/OldClockModelsPanel.java | 681 ---------------------
.../AncestralStatesComponentGenerator.java | 2 +-
.../continuous/ContinuousComponentOptions.java | 3 +-
.../discrete/DiscreteTraitsComponentGenerator.java | 12 +-
.../components/dollo/DolloComponentGenerator.java | 2 +-
.../hpm/HierarchicalModelComponentGenerator.java | 4 +-
.../MarginalLikelihoodEstimationGenerator.java | 4 +-
src/dr/app/beauti/datapanel/DataPanel.java | 12 +-
src/dr/app/beauti/generator/BeastGenerator.java | 56 +-
...odelGenerator.java => ClockModelGenerator.java} | 52 +-
src/dr/app/beauti/generator/Generator.java | 12 +-
.../app/beauti/generator/InitialTreeGenerator.java | 2 +-
src/dr/app/beauti/generator/LogGenerator.java | 142 ++---
.../app/beauti/generator/OperatorsGenerator.java | 230 ++++---
.../beauti/generator/ParameterPriorGenerator.java | 10 +-
.../app/beauti/generator/STARBEASTGenerator.java | 4 +-
.../generator/SubstitutionModelGenerator.java | 49 +-
.../beauti/generator/TreeLikelihoodGenerator.java | 6 +-
.../app/beauti/generator/TreePriorGenerator.java | 12 +-
src/dr/app/beauti/mcmcpanel/MCMCPanel.java | 2 +
.../app/beauti/operatorspanel/OperatorsPanel.java | 33 +-
.../app/beauti/options/AbstractPartitionData.java | 2 +-
src/dr/app/beauti/options/BeautiOptions.java | 84 +--
src/dr/app/beauti/options/ClockModelGroup.java | 96 ---
src/dr/app/beauti/options/ClockModelOptions.java | 622 +------------------
src/dr/app/beauti/options/ModelOptions.java | 20 +-
src/dr/app/beauti/options/Operator.java | 111 +++-
src/dr/app/beauti/options/Parameter.java | 64 +-
src/dr/app/beauti/options/PartitionClockModel.java | 243 +++-----
.../options/PartitionClockModelTreeModelLink.java | 78 +--
src/dr/app/beauti/options/PartitionData.java | 5 +-
src/dr/app/beauti/options/PartitionOptions.java | 294 ++++-----
.../beauti/options/PartitionSubstitutionModel.java | 83 +--
src/dr/app/beauti/options/PartitionTreeModel.java | 54 +-
src/dr/app/beauti/options/PartitionTreePrior.java | 6 +-
src/dr/app/beauti/options/TraitGuesser.java | 2 +-
src/dr/app/beauti/options/TreeModelOptions.java | 22 +-
.../priorsPanel/HierarchicalPriorDialog.java | 6 +-
.../app/beauti/priorsPanel/PriorOptionsPanel.java | 12 +-
.../app/beauti/priorsPanel/PriorSettingsPanel.java | 8 +-
src/dr/app/beauti/priorsPanel/PriorsPanel.java | 24 +-
.../siteModelsPanel/PartitionModelPanel.java | 2 +-
src/dr/app/beauti/tipdatepanel/TipDatesPanel.java | 5 +-
.../beauti/treespanel/PartitionTreeModelPanel.java | 11 -
src/dr/app/beauti/treespanel/TreesPanel.java | 5 -
src/dr/app/beauti/types/FixRateType.java | 2 +-
src/dr/app/beauti/types/OldClockType.java | 95 ---
src/dr/app/beauti/types/PriorType.java | 18 +-
src/dr/app/beauti/types/RelativeRatesType.java | 45 --
src/dr/app/beauti/util/BEAUTiImporter.java | 2 +-
src/dr/app/beauti/util/BeautiTemplate.java | 434 -------------
src/dr/app/beauti/util/CommandLineBeauti.java | 267 --------
src/dr/app/beauti/util/XMLWriter.java | 24 +-
src/dr/app/bss/test/BeagleSeqSimTest.java | 2 +-
src/dr/app/tempest/TempEstApp.java | 5 +-
src/dr/app/tempest/TempestFrame.java | 19 +-
src/dr/app/tools/AncestralSequenceAnnotator.java | 1 +
src/dr/app/tools/TreeAnnotatorDialog.java | 2 +-
.../alignment/AscertainedSitePatterns.java | 19 +-
src/dr/evolution/alignment/UncertainSiteList.java | 101 +++
.../coalescent/MultiEpochExponential.java | 16 +-
src/dr/evomodel/MSSD/CTMCScalePrior.java | 37 +-
src/dr/evomodel/antigenic/AntigenicDriftPrior.java | 45 +-
src/dr/evomodel/antigenic/AntigenicLikelihood.java | 30 +-
src/dr/evomodel/antigenic/AntigenicSplitPrior.java | 30 +-
.../ContinuousAntigenicTraitLikelihood.java | 24 +-
.../DiscreteAntigenicTraitLikelihood.java | 24 +-
.../misc/obsolete/AGLikelihoodCluster.java | 435 ++++++-------
.../misc/obsolete/AGLikelihoodTreeCluster.java | 43 +-
.../branchratemodel/CompoundBranchRateModel.java | 6 +-
.../CountableBranchCategoryProvider.java | 59 +-
.../branchratemodel/DiscretizedBranchRates.java | 37 +-
.../evomodel/branchratemodel/LocalClockModel.java | 31 +-
.../branchratemodel/RandomLocalClockModel.java | 34 +-
.../coalescent/BayesianSkylineLikelihood.java | 34 +-
.../coalescent/CataclysmicDemographicModel.java | 34 +-
src/dr/evomodel/coalescent/ConstExpConstModel.java | 35 +-
.../coalescent/ConstantExponentialModel.java | 34 +-
.../evomodel/coalescent/ConstantLogisticModel.java | 34 +-
.../coalescent/ExpConstExpDemographicModel.java | 34 +-
src/dr/evomodel/coalescent/ExpansionModel.java | 34 +-
.../coalescent/ExponentialConstantModel.java | 34 +-
.../coalescent/ExponentialLogisticModel.java | 34 +-
.../GMRFMultilocusSkyrideLikelihood.java | 402 ++++++++++--
.../evomodel/coalescent/GMRFSkyrideLikelihood.java | 78 ++-
.../evomodel/coalescent/LogisticGrowthModel.java | 34 +-
src/dr/evomodel/coalescent/SkylineLikelihood.java | 36 +-
.../coalescent/VariableDemographicModel.java | 35 +-
.../coalescent/VariableSkylineLikelihood.java | 33 +-
.../GMRFMultilocusSkyrideBlockUpdateOperator.java | 64 +-
.../AbstractMultivariateTraitLikelihood.java | 258 ++++----
.../BinaryLatentLiabilityLikelihood.java | 17 +-
.../continuous/ContinuousDiffusionStatistic.java | 119 +++-
.../FullyConjugateMultivariateTraitLikelihood.java | 264 ++++++--
.../continuous/GaussianProcessFromTree.java | 55 ++
.../IntegratedMultivariateTraitLikelihood.java | 229 +++----
.../IntervalLatentLiabilityLikelihood.java | 17 +-
.../MultinomialLatentLiabilityLikelihood.java | 17 +-
...NonPhylogeneticMultivariateTraitLikelihood.java | 17 +-
.../OrderedLatentLiabilityLikelihood.java | 17 +-
.../SampledMultivariateTraitLikelihood.java | 5 +-
.../SemiConjugateMultivariateTraitLikelihood.java | 4 +-
.../evomodel/continuous/plink/PlinkImporter.java | 15 +-
.../epidemiology/casetocase/AbstractCase.java | 13 +-
.../epidemiology/casetocase/AbstractOutbreak.java | 10 +-
.../epidemiology/casetocase/BranchMapModel.java | 2 +-
.../CaseToCaseTransmissionLikelihood.java | 49 +-
.../casetocase/CaseToCaseTreeLikelihood.java | 514 +++++-----------
.../epidemiology/casetocase/CategoryOutbreak.java | 90 ++-
.../casetocase/PartitionedTreeLogger.java | 5 +-
.../casetocase/PartitionedTreeModel.java | 493 +++++++++++++--
.../casetocase/PartitionedTreeModelParser.java | 21 +-
.../casetocase/WithinCaseCoalescent.java | 164 +----
.../operators/InfectionBranchMovementOperator.java | 105 ++--
.../operators/TransmissionSubtreeSlideA.java | 15 +-
.../operators/TransmissionSubtreeSlideB.java | 11 +-
.../operators/TransmissionWilsonBaldingA.java | 21 +-
.../operators/TransmissionWilsonBaldingB.java | 10 +-
.../operators/LatentFactorHamiltonianMC.java | 102 +--
.../evomodel/operators/LoadingsHamiltonianMC.java | 155 +++++
src/dr/evomodel/operators/SubtreeLeapOperator.java | 6 +-
.../speciation/AlloppSpeciesNetworkModel.java | 57 +-
.../speciation/BirthDeathCollapseModel.java | 45 +-
.../speciation/BirthDeathGernhard08Model.java | 52 +-
.../speciation/BirthDeathSerialSamplingModel.java | 32 +-
.../evomodel/speciation/MulSpeciesTreeModel.java | 210 ++++---
.../speciation/PopsIOSpeciesTreeModel.java | 13 +-
src/dr/evomodel/speciation/SpeciesTreeModel.java | 33 +-
src/dr/evomodel/substmodel/Blosum62.java | 22 +-
src/dr/evomodel/substmodel/CPREV.java | 20 +-
.../substmodel/ComplexSubstitutionModel.java | 24 +-
src/dr/evomodel/substmodel/Dayhoff.java | 22 +-
src/dr/evomodel/substmodel/FLU.java | 25 +-
.../evomodel/substmodel/GLMSubstitutionModel.java | 18 +-
src/dr/evomodel/substmodel/GTR.java | 34 +-
src/dr/evomodel/substmodel/HKY.java | 40 +-
src/dr/evomodel/substmodel/JTT.java | 21 +-
src/dr/evomodel/substmodel/LG.java | 23 +-
src/dr/evomodel/substmodel/MTREV.java | 28 +-
.../substmodel/MarginalVarianceStatistic.java | 2 +-
.../substmodel/SVSGeneralSubstitutionModel.java | 28 +-
src/dr/evomodel/substmodel/TN93.java | 34 +-
src/dr/evomodel/substmodel/WAG.java | 22 +-
.../tree}/ConditionalCladeProbability.java | 4 +-
.../tree/ProgressiveScalarTreeTransform.java | 7 +
...Statistic.java => TerminalBranchStatistic.java} | 32 +-
src/dr/evomodel/tree/TransformedTreeModel.java | 30 +-
src/dr/evomodel/tree/TreeModel.java | 56 +-
src/dr/evomodel/tree/TreeTransform.java | 28 +-
.../treelikelihood/HypermutantErrorModel.java | 44 +-
.../treelikelihood/SequenceErrorModel.java | 46 +-
src/dr/evomodelxml/MSSD/CTMCScalePriorParser.java | 4 +-
src/dr/evomodelxml/TreeWorkingPriorParsers.java | 2 +-
.../branchratemodel/LocalClockModelParser.java | 4 +-
.../coalescent/GMRFSkyrideLikelihoodParser.java | 84 ++-
...arser.java => LoadingsHamiltonianMCParser.java} | 36 +-
.../operators/SubtreeLeapOperatorParser.java | 12 +-
.../substmodel/MultivariateOUModelParser.java | 2 +-
.../evomodelxml/tree/MonophylyStatisticParser.java | 6 +-
...ser.java => TerminalBranchStatisticParser.java} | 16 +-
src/dr/evoxml/NewickParser.java | 10 +-
.../evoxml/UncertainAttributePatternsParser.java | 230 +++++++
.../distribution/GeneralizedLinearModel.java | 16 +-
.../distribution/MomentDistributionModel.java | 27 +-
.../MultivariateDistributionLikelihood.java | 1 -
.../MultivariateNormalDistributionModel.java | 10 +
.../distribution}/MultivariateOUModel.java | 6 +-
.../distribution/NormalDistributionModel.java | 12 +-
.../mcmc/MarginalLikelihoodEstimator.java | 85 ++-
src/dr/inference/mcmcmc/MCMCMC.java | 15 -
...ductParameter.java => ComplementParameter.java} | 53 +-
src/dr/inference/model/CompoundLikelihood.java | 23 +-
.../ElementWiseMatrixMultiplicationParameter.java | 69 +++
.../model/EqualityConstrainedParameter.java | 17 +-
...iangularMatrixParameter.java => FastBUTMP.java} | 112 ++--
src/dr/inference/model/FastMatrixParameter.java | 7 +
...trixParameter.java => FastTransposedBUTMP.java} | 52 +-
.../inference/model/IndianBuffetProcessPrior.java | 4 +-
src/dr/inference/model/LatentFactorModel.java | 93 ++-
src/dr/inference/model/MaskedParameter.java | 34 +-
.../inference/model/MatrixParameterInterface.java | 2 +-
src/dr/inference/model/MixtureModelLikelihood.java | 19 +-
src/dr/inference/model/Parameter.java | 4 +-
.../inference/model/TransposedMatrixParameter.java | 5 +
src/dr/inference/model/WeightedMixtureModel.java | 18 +-
.../operators/EllipticalSliceOperator.java | 8 +-
.../inference/operators/FactorGibbsOperator.java | 13 +-
.../operators/FactorIndependenceOperator.java | 13 +-
src/dr/inference/operators/FactorOperator.java | 13 +-
src/dr/inference/operators/GibbsOperator.java | 4 +-
.../LatentFactorModelPrecisionGibbsOperator.java | 7 +-
.../inference/operators/LoadingsGibbsOperator.java | 9 +-
...or.java => LoadingsGibbsTruncatedOperator.java} | 131 ++--
.../operators/LoadingsIndependenceOperator.java | 7 +-
src/dr/inference/operators/MaskMoveOperator.java | 182 ++++++
...Operator.java => ModeIndependenceOperator.java} | 15 +-
...bbsOperator.java => PathDependentOperator.java} | 16 +-
src/dr/inference/trace/CnCsPerSiteAnalysis.java | 87 ++-
.../inference/trace/CnCsToDnDsPerSiteAnalysis.java | 28 +-
src/dr/inference/trace/DnDsPerSiteAnalysis.java | 29 +-
.../distribution/GammaDistributionModelParser.java | 44 +-
.../distribution/GeneralizedLinearModelParser.java | 15 +-
.../MomentDistributionModelParser.java | 8 +-
...rParser.java => ComplementParameterParser.java} | 141 ++---
.../model/CompoundLikelihoodParser.java | 6 +-
.../ElementWiseMatrixMultiplicationParser.java | 48 ++
...ixParameterParser.java => FastBUTMPParser.java} | 39 +-
.../model/ImmutableParameterParser.java | 5 +
.../model/IndianBuffetProcessPriorParser.java | 2 +-
.../model/LatentFactorModelParser.java | 23 +-
.../operators/LoadingsGibbsOperatorParser.java | 15 +
.../operators/MaskMoveOperatorParser.java | 129 ++++
.../distributions/CompoundGaussianProcess.java | 154 ++++-
.../math/distributions/DirichletDistribution.java | 33 +-
.../GaussianProcessRandomGenerator.java | 4 +
.../MultivariateNormalDistribution.java | 9 +
src/dr/math/distributions/NormalDistribution.java | 1 +
src/dr/util/Citable.java | 14 +-
src/dr/util/Citation.java | 168 ++++-
src/dr/util/CommonCitations.java | 201 +++++-
src/dr/util/MessageLogHandler.java | 8 +-
src/dr/{geo/Location.java => util/Pair.java} | 39 +-
src/dr/util/Transform.java | 30 +-
src/dr/xml/AbstractXMLObjectParser.java | 7 +-
src/dr/xml/XMLObjectParser.java | 4 +-
src/dr/xml/XMLParser.java | 126 ++--
.../AncestralStateBeagleTreeLikelihoodTest.java | 1 +
src/test/dr/app/beagle/MarkovJumpsTest.java | 1 +
287 files changed, 8544 insertions(+), 6401 deletions(-)
create mode 100644 .idea/uiDesigner.xml
delete mode 100644 release_tempest/Linux/icons/pathogen.png
delete mode 100755 release_tempest/Linux/scripts/pathogen
create mode 100644 src/dr/app/beagle/mm/MMAlgorithm.java
create mode 100644 src/dr/app/beagle/mm/MultiDimensionalScalingMM.java
delete mode 100644 src/dr/app/beauti/clockModelsPanel/OldClockModelsPanel.java
rename src/dr/app/beauti/generator/{BranchRatesModelGenerator.java => ClockModelGenerator.java} (95%)
delete mode 100644 src/dr/app/beauti/options/ClockModelGroup.java
delete mode 100644 src/dr/app/beauti/types/OldClockType.java
delete mode 100644 src/dr/app/beauti/types/RelativeRatesType.java
delete mode 100644 src/dr/app/beauti/util/BeautiTemplate.java
delete mode 100755 src/dr/app/beauti/util/CommandLineBeauti.java
create mode 100644 src/dr/evolution/alignment/UncertainSiteList.java
create mode 100644 src/dr/evomodel/operators/LoadingsHamiltonianMC.java
rename src/dr/{inference/distribution => evomodel/tree}/ConditionalCladeProbability.java (94%)
copy src/dr/evomodel/tree/{TreeLengthStatistic.java => TerminalBranchStatistic.java} (69%)
copy src/dr/evomodelxml/operators/{LatentFactorHamiltonianMCParser.java => LoadingsHamiltonianMCParser.java} (58%)
copy src/dr/evomodelxml/tree/{TreeLengthStatisticParser.java => TerminalBranchStatisticParser.java} (77%)
create mode 100644 src/dr/evoxml/UncertainAttributePatternsParser.java
rename src/dr/{evomodel/substmodel => inference/distribution}/MultivariateOUModel.java (98%)
copy src/dr/inference/model/{ProductParameter.java => ComplementParameter.java} (67%)
create mode 100644 src/dr/inference/model/ElementWiseMatrixMultiplicationParameter.java
copy src/dr/inference/model/{BlockUpperTriangularMatrixParameter.java => FastBUTMP.java} (64%)
copy src/dr/inference/model/{TransposedBlockUpperTriangularMatrixParameter.java => FastTransposedBUTMP.java} (70%)
copy src/dr/inference/operators/{LoadingsGibbsOperator.java => LoadingsGibbsTruncatedOperator.java} (72%)
create mode 100644 src/dr/inference/operators/MaskMoveOperator.java
copy src/dr/inference/operators/{MultivariateNormalOperator.java => ModeIndependenceOperator.java} (92%)
copy src/dr/inference/operators/{GibbsOperator.java => PathDependentOperator.java} (79%)
copy src/dr/inferencexml/model/{DuplicatedParameterParser.java => ComplementParameterParser.java} (61%)
create mode 100644 src/dr/inferencexml/model/ElementWiseMatrixMultiplicationParser.java
copy src/dr/inferencexml/model/{BlockUpperTriangularMatrixParameterParser.java => FastBUTMPParser.java} (69%)
create mode 100644 src/dr/inferencexml/operators/MaskMoveOperatorParser.java
copy src/dr/{geo/Location.java => util/Pair.java} (54%)
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