[med-svn] [beast-mcmc] branch upstream updated (8fc8789 -> 8de73ae)
Andreas Tille
tille at debian.org
Thu Jun 2 19:01:55 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository beast-mcmc.
from 8fc8789 Imported Upstream version 1.8.2
new 8de73ae Imported Upstream version 1.8.3+dfsg
The 1 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/libraries/lib.xml | 4 +-
.idea/libraries/lib1.xml | 23 -
.idea/libraries/phylogeography.xml | 9 -
.idea/libraries/quaqua.xml | 9 -
.idea/libraries/tracer.xml | 9 -
.idea/libraries/tracer1.xml | 9 -
README.md | 2 +-
build.xml | 20 +-
build_coalsim.xml | 8 +-
build_pathogen.xml | 4 +
build_pathogen.xml => build_tempest.xml | 72 +-
build_tracer.xml | 1 +
examples/release/clockModels/testStrictClock.xml | 634 ++--
...stUCRelaxedClockContinuousQuantileLogNormal.xml | 375 ++
.../clockModels/testUCRelaxedClockGamma.xml | 377 ++
.../clockModels/testUCRelaxedClockLogNormal.xml | 651 ++--
.../clockModels/testUncorrelatedRelaxedClock.xml | 418 ---
release/common/README.txt | 22 +-
release/common/VERSION HISTORY.txt | 39 +-
.../Linux/icons/pathogen.png | Bin
.../Linux/scripts/pathogen | 0
.../common/README.txt | 0
.../branchmodel/BranchAssignmentModel.java | 19 +
.../lineagespecific/BeagleBranchLikelihood.java | 9 +-
.../lineagespecific/BranchLikelihood.java | 8 +-
.../lineagespecific/DirichletProcessOperator.java | 190 +-
.../DirichletProcessOperatorParser.java | 21 +-
.../NewAbstractLikelihoodOnTree.java | 640 ++++
.../NewAbstractSequenceLikelihood.java | 125 +
...ihood.java => NewBeagleSequenceLikelihood.java} | 984 +++--
.../NewFullyConjugateTraitLikelihood.java | 105 +
.../AncestralStateTreeLikelihoodParser.java | 41 +-
.../evomodel/parsers/FrequencyModelParser.java | 354 +-
.../parsers/MarkovJumpsTreeLikelihoodParser.java | 4 +
.../parsers/NewBeagleTreeLikelihoodParser.java | 232 ++
.../substmodel/ComplexSubstitutionModel.java | 28 +-
.../evomodel/substmodel/EmpiricalCodonModel.java | 4 -
.../substmodel/GeneralSubstitutionModel.java | 34 +
.../beagle/evomodel/substmodel/MG94CodonModel.java | 8 +-
.../evomodel/substmodel/MG94HKYCodonModel.java | 5 +-
.../beagle/evomodel/substmodel/PCACodonModel.java | 4 -
.../substmodel/SVSComplexSubstitutionModel.java | 27 +-
.../substmodel/SVSGeneralSubstitutionModel.java | 24 +
.../treelikelihood/BeagleTreeLikelihood.java | 17 +-
.../EvolutionaryProcessDelegate.java} | 21 +-
.../treelikelihood/SubstitutionModelDelegate.java | 2 +-
.../MassivelyParallelMDSImpl.java | 16 +-
.../MultiDimensionalScalingCore.java | 9 +-
.../MultiDimensionalScalingCoreImpl.java | 482 +--
.../MultiDimensionalScalingCoreImpl2.java | 6 +-
.../MultiDimensionalScalingLikelihood.java | 164 +-
.../NativeMDSSingleton.java | 30 +-
.../app/beagle/tools/BeagleSequenceSimulator.java | 8 +-
src/dr/app/beast/BeastMain.java | 21 +-
src/dr/app/beast/BeastVersion.java | 6 +-
src/dr/app/beast/RBeastMain.java | 63 +
src/dr/app/beast/development_parsers.properties | 47 +-
src/dr/app/beast/release_parsers.properties | 20 +-
src/dr/app/beauti/BeautiFrame.java | 9 +-
.../AncestralStatesOptionsPanel.java | 86 +-
.../beauti/clockModelsPanel/ClockModelsPanel.java | 408 +--
.../beauti/clockModelsPanel/CloneModelDialog.java | 94 +
.../clockModelsPanel/OldClockModelsPanel.java | 1 +
.../clockModelsPanel/PartitionClockModelPanel.java | 78 +-
.../AncestralStatesComponentGenerator.java | 7 +-
.../AncestralStatesComponentOptions.java | 10 +
.../discrete/DiscreteTraitsComponentGenerator.java | 24 +-
.../marginalLikelihoodEstimation/MLEGSSDialog.java | 33 +-
.../MarginalLikelihoodEstimationGenerator.java | 193 +-
.../beauti/generator/BaseComponentGenerator.java | 5 +
src/dr/app/beauti/generator/BeastGenerator.java | 272 +-
.../generator/BranchRatesModelGenerator.java | 155 +-
.../app/beauti/generator/ComponentGenerator.java | 8 +
src/dr/app/beauti/generator/Generator.java | 6 +
src/dr/app/beauti/generator/LogGenerator.java | 33 +-
.../app/beauti/generator/OperatorsGenerator.java | 22 +-
.../beauti/generator/ParameterPriorGenerator.java | 13 +
.../generator/SubstitutionModelGenerator.java | 2 -
.../beauti/generator/TreeLikelihoodGenerator.java | 33 +-
.../app/beauti/generator/TreePriorGenerator.java | 6 +-
src/dr/app/beauti/mcmcpanel/MCMCPanel.java | 2 +
.../app/beauti/operatorspanel/OperatorsPanel.java | 27 +
src/dr/app/beauti/options/BeautiOptions.java | 7 +-
src/dr/app/beauti/options/DateGuesser.java | 80 +-
src/dr/app/beauti/options/ModelOptions.java | 24 +-
src/dr/app/beauti/options/Parameter.java | 9 +
src/dr/app/beauti/options/PartitionClockModel.java | 61 +-
.../options/PartitionClockModelTreeModelLink.java | 31 +-
src/dr/app/beauti/options/PartitionOptions.java | 4 -
.../beauti/options/PartitionSubstitutionModel.java | 87 +-
src/dr/app/beauti/options/PartitionTreeModel.java | 62 +-
.../siteModelsPanel/PartitionModelPanel.java | 8 +-
.../app/beauti/tipdatepanel/GuessDatesDialog.java | 121 +-
src/dr/app/beauti/tipdatepanel/TipDatesPanel.java | 166 +-
.../beauti/treespanel/PartitionTreePriorPanel.java | 6 +-
src/dr/app/beauti/types/ClockType.java | 2 +-
.../types/OperatorSetType.java} | 24 +-
src/dr/app/beauti/types/OperatorType.java | 2 +
src/dr/app/beauti/types/PriorType.java | 6 +-
src/dr/app/beauti/types/TreePriorType.java | 4 +-
src/dr/app/bss/BeagleSequenceSimulatorApp.java | 21 +-
src/dr/app/bss/Changelog | 4 +-
src/dr/app/bss/PartitionData.java | 9 +-
src/dr/app/bss/README.textile | 5 +-
src/dr/app/bss/Utils.java | 12 +-
src/dr/app/bss/test/BeagleSeqSimTest.java | 4 +-
src/dr/app/gui/chart/JChart.java | 3 +-
src/dr/app/oldbeauti/BeastGenerator.java | 3007 ----------------
src/dr/app/oldbeauti/BeautiApp.java | 136 -
src/dr/app/oldbeauti/BeautiFrame.java | 656 ----
src/dr/app/oldbeauti/BeautiOptions.java | 1933 ----------
src/dr/app/oldbeauti/BeautiTester.java | 417 ---
src/dr/app/oldbeauti/CommandLineBeauti.java | 261 --
src/dr/app/oldbeauti/DataPanel.java | 699 ----
src/dr/app/oldbeauti/DiscretePriorDialog.java | 169 -
src/dr/app/oldbeauti/MCMCPanel.java | 219 --
src/dr/app/oldbeauti/ModelPanel.java | 484 ---
src/dr/app/oldbeauti/NexusApplicationImporter.java | 416 ---
src/dr/app/oldbeauti/OperatorsPanel.java | 285 --
src/dr/app/oldbeauti/PriorDialog.java | 419 ---
src/dr/app/oldbeauti/PriorType.java | 140 -
src/dr/app/oldbeauti/PriorsPanel.java | 509 ---
src/dr/app/oldbeauti/TaxaPanel.java | 816 -----
src/dr/app/oldbeauti/XMLWriter.java | 138 -
src/dr/app/pathogen/TemporalRooting.java | 15 +-
src/dr/app/tempest/ParentPlot.java | 129 +
src/dr/app/tempest/RootToTip.java | 328 ++
src/dr/app/tempest/SamplesPanel.java | 461 +++
src/dr/app/tempest/TempEstApp.java | 141 +
.../TempestDefaultFileMenuFactory.java} | 58 +-
src/dr/app/tempest/TempestFrame.java | 371 ++
.../TempestMacFileMenuFactory.java} | 112 +-
.../TempestMenuBarFactory.java} | 15 +-
src/dr/app/tempest/TempestPanel.java | 907 +++++
.../app/{pathogen => tempest}/TemporalRooting.java | 19 +-
src/dr/app/tempest/TemporalStress.java | 149 +
src/dr/app/{oldbeauti => tempest}/TreeUtils.java | 8 +-
.../app/{oldbeauti => tempest}/images/beauti.png | Bin
.../{pathogen => tempest}/images/coloursTool.png | Bin
.../app/{oldbeauti => tempest}/images/exclude.png | Bin
src/dr/app/{oldbeauti => tempest}/images/gear.png | Bin
.../app/{oldbeauti => tempest}/images/include.png | Bin
.../dr/app/tempest/images/tempest.png | Bin
src/dr/app/tools/TreeAnnotator.java | 62 +-
.../application/TracerMacFileMenuFactory.java | 41 +-
.../tracer/application/TracerMenuBarFactory.java | 2 +-
src/dr/evolution/alignment/Alignment.java | 8 +-
src/dr/evolution/alignment/PairedSitePatterns.java | 5 +
src/dr/evolution/alignment/PatternList.java | 6 +
src/dr/evolution/alignment/Patterns.java | 5 +
src/dr/evolution/alignment/ResamplePatterns.java | 7 +-
src/dr/evolution/alignment/SimpleAlignment.java | 5 +
src/dr/evolution/alignment/SimpleSiteList.java | 7 +-
src/dr/evolution/alignment/SitePatterns.java | 5 +
.../coalescent/CataclysmicDemographic.java | 4 +-
.../coalescent/MultiEpochExponential.java | 195 +
src/dr/evolution/datatype/Microsatellite.java | 7 +-
src/dr/evolution/io/NexusImporter.java | 38 +-
src/dr/evomodel/antigenic/AntigenicLikelihood.java | 1 -
.../evomodel/antigenic/NPAntigenicLikelihood.java | 4 -
.../Mu1ScaleActiveScaledMu1IntactOperator.java | 277 ++
.../Mu2ScaleActiveScaledMu2IntactOperator.java | 278 ++
.../ProbGenericSiteGibbsOperator.java | 193 +
.../MCMCOperators/ProbSitesGibbsOperator.java | 184 +
.../MCMCOperators/RandomWalkOnActiveMu.java | 247 ++
.../TreeClusterAlgorithmOperator.java | 3801 ++++++++++++++++++++
.../muMeanTranslateInactiveMu1Operator.java | 219 ++
.../muPrecisionInactiveMuOperator.java | 224 ++
.../MCMCOperators/randomWalkSerumDriftAndMu.java | 232 ++
.../serumDriftActiveScaledMu1Operator.java | 289 ++
.../serumPrecisionSerumLocOperator.java | 199 +
.../TreeClusteringVirusesPrior.java | 1778 +++++++++
.../Tree_Clustering_Shared_Routines.java | 224 ++
.../misc/mergeAdjacencyMatrixPlots.java | 276 ++
.../misc/obsolete/AGLikelihoodCluster.java} | 287 +-
.../misc/obsolete/AGLikelihoodTreeCluster.java} | 782 +++-
.../misc/obsolete/ClusterAlgorithmOperator.java | 619 ++++
.../misc/obsolete/ClusterComparison.java | 8 +
.../misc/obsolete/ClusterOperator.java | 443 +++
.../misc/obsolete/ClusterViruses.java | 619 ++++
.../misc/obsolete/ClusterWalkOperator.java | 225 ++
.../misc/obsolete/ClusterWalkOperatorParser.java | 92 +
.../phyloClustering/misc/obsolete/OrderDouble.java | 52 +
.../misc/obsolete/TiterImporter.java | 344 ++
.../misc/obsolete/TreeClusterGibbsOperator.java | 1090 ++++++
.../obsolete/TreeClusterSequentialSampling.java | 1482 ++++++++
.../misc/obsolete/serumDriftScalingMuOperator.java | 214 ++
.../phyloClustering/misc/simulateClusters.java | 689 ++++
.../statistics/ActiveIndicatorsStatistic.java | 125 +
.../AnnotateLocationParameterTreeTrait.java | 214 ++
.../statistics/AnnotateMuTreeTrait.java | 215 ++
.../statistics/CausalMutationsLogger.java | 133 +
.../statistics/ClusterLabelsVirusesStatistic.java | 345 ++
.../statistics/ClusterLabelsVirusesTreeTrait.java | 158 +
.../statistics/DriftedMuStatistic.java | 168 +
.../DriftedTreeClusterLocationsStatistic.java | 158 +
.../statistics/DriverCountStatistic.java | 122 +
.../phyloClustering/statistics/KStatistic.java | 98 +
.../statistics/MutationsTreeTrait.java | 275 ++
.../statistics/NodeNumberTreeTrait.java | 126 +
.../phyloClustering/statistics/PathStatistic.java | 288 ++
.../statistics/indicatorsStatistic.java | 94 +
.../phyloClustering/statistics/muStatistic.java | 118 +
src/dr/evomodel/arg/ARGRelaxedClock.java | 2 -
.../branchratemodel/ContinuousBranchRates.java | 180 +-
.../branchratemodel/DecayingRateModel.java | 1 -
.../DiscreteTraitBranchRateModel.java | 1 -
.../branchratemodel/DiscretizedBranchRates.java | 21 +-
.../branchratemodel/RateEpochBranchRateModel.java | 1 -
.../branchratemodel/ScaledTreeLengthRateModel.java | 1 -
.../branchratemodel/StrictClockBranchRates.java | 1 -
.../branchratemodel/TipBranchRateModel.java | 1 -
src/dr/evomodel/clock/RateEvolutionLikelihood.java | 2 -
src/dr/evomodel/clock/UniversalClock.java | 2 -
.../coalescent/AbstractCoalescentLikelihood.java | 26 +
.../evomodel/coalescent/AsymptoticGrowthModel.java | 1 -
.../coalescent/CataclysmicDemographicModel.java | 24 +-
.../coalescent/CoalescentEventsStatistic.java | 198 +-
.../coalescent/CoalescentIntervalProvider.java | 14 +-
.../coalescent/CoalescentIntervalStatistic.java | 16 +-
.../evomodel/coalescent/CoalescentLikelihood.java | 2 +-
.../evomodel/coalescent/EmergingEpidemicModel.java | 1 -
.../coalescent/ExponentialConstantModel.java | 2 -
.../coalescent/ExponentialExponentialModel.java | 3 -
...ExponentialProductPosteriorMeansLikelihood.java | 2 +-
.../coalescent/ExponentialSkythingLikelihood.java | 2 -
.../evomodel/coalescent/GMRFDensityComponent.java | 9 +
.../GMRFMultilocusSkyrideLikelihood.java | 57 +-
.../evomodel/coalescent/GMRFSkyrideLikelihood.java | 12 +-
...aussianProcessMultilocusSkytrackLikelihood.java | 1 -
src/dr/evomodel/coalescent/LinearGrowthModel.java | 2 -
...tModel.java => MultiEpochExponentialModel.java} | 71 +-
.../evomodel/coalescent/PeakAndDeclineModel.java | 2 -
.../evomodel/coalescent/PowerLawGrowthModel.java | 2 -
.../coalescent/TwoEpochDemographicModel.java | 4 +-
.../AbstractMultivariateTraitLikelihood.java | 2 -
.../FullyConjugateMultivariateTraitLikelihood.java | 191 +-
.../continuous/GaussianProcessFromTree.java | 63 +-
.../IntegratedMultivariateTraitLikelihood.java | 2 +-
src/dr/evomodel/epidemiology/SIRModel.java | 9 +
.../epidemiology/casetocase/AbstractOutbreak.java | 5 +
.../CaseToCaseTransmissionLikelihood.java | 603 ++--
.../casetocase/CaseToCaseTreeLikelihood.java | 323 +-
.../epidemiology/casetocase/CategoryOutbreak.java | 63 +-
.../casetocase/PartitionedTreeModel.java | 263 +-
.../casetocase/WithinCaseCoalescent.java | 107 +-
.../operators/InfectionBranchGibbsOperator.java | 235 --
.../operators/InfectionBranchMovementOperator.java | 44 +-
.../operators/TransmissionExchangeOperatorA.java | 14 +-
.../operators/TransmissionExchangeOperatorB.java | 4 -
.../operators/TransmissionSubtreeSlideA.java | 5 +-
.../operators/TransmissionSubtreeSlideB.java | 7 +-
.../operators/TransmissionWilsonBaldingA.java | 15 +-
.../operators/TransmissionWilsonBaldingB.java | 4 +-
...KnownVarianceNormalPeriodPriorDistribution.java | 1 -
.../NormalPeriodPriorDistribution.java | 1 -
src/dr/evomodel/lineage/LineageSitePatterns.java | 5 +
.../operators/LatentFactorHamiltonianMC.java | 161 +
.../evomodel/operators/LatentLiabilityGibbs.java | 47 +-
.../operators/MicrosatUpDownOperator.java | 325 +-
.../MicrosatelliteModelSelectOperator.java | 141 +-
.../operators/MsatBitFlipOperator.java | 315 +-
...MsatFullAncestryImportanceSamplingOperator.java | 253 +-
.../MsatSingleAncestralStateGibbsOperator.java | 250 +-
...andomWalkIntegerNodeHeightWeightedOperator.java | 177 +-
.../RandomWalkIntegerSetSizeWeightedOperator.java | 229 +-
src/dr/evomodel/operators/SubtreeJumpOperator.java | 41 +-
src/dr/evomodel/operators/SubtreeLeapOperator.java | 321 ++
.../substmodel/ComplexSubstitutionModel.java | 7 +
.../evomodel/substmodel/EmpiricalCodonModel.java | 2 -
src/dr/evomodel/substmodel/HKY.java | 1 -
src/dr/evomodel/substmodel/PCACodonModel.java | 3 -
.../substmodel/SVSGeneralSubstitutionModel.java | 13 +-
.../substmodel/SubstitutionEpochModel.java | 3 -
src/dr/evomodel/tree/HiddenLinkageModel.java | 11 +-
src/dr/evomodel/tree/TreeModel.java | 2 +-
src/dr/evomodel/tree/TreeParameterModel.java | 29 +-
.../EmpiricalTreeDistributionModelParser.java | 2 +-
src/dr/evomodelxml/TreeWorkingPriorParsers.java | 157 +-
.../ContinuousBranchRatesParser.java | 36 +-
.../DiscretizedBranchRatesParser.java | 9 +-
.../CataclysmicDemographicModelParser.java | 27 +-
....java => MultiEpochExponentialModelParser.java} | 190 +-
.../operators/LatentFactorHamiltonianMCParser.java | 65 +
.../operators/MicrosatUpDownOperatorParser.java | 201 +-
.../MicrosatelliteModelSelectOperatorParser.java | 144 +-
.../operators/MsatBitFlipOperatorParser.java | 170 +-
...llAncestryImportanceSamplingOperatorParser.java | 148 +-
...satSingleAncestralStateGibbsOperatorParser.java | 144 +-
...alkIntegerNodeHeightWeightedOperatorParser.java | 167 +-
...omWalkIntegerSetSizeWeightedOperatorParser.java | 172 +-
.../operators/SubtreeLeapOperatorParser.java | 83 +
.../treelikelihood/TreeTraitParserUtilities.java | 7 +-
src/dr/evoxml/AttributePatternsParser.java | 5 +-
src/dr/evoxml/MicrosatellitePatternParser.java | 37 +-
.../inference/distribution/BinomialLikelihood.java | 2 -
.../distribution/GammaDistributionModel.java | 106 +-
.../InverseGammaDistributionModel.java | 3 -
.../distribution/LogNormalDistributionModel.java | 1 -
.../MultivariateDistributionLikelihood.java | 13 +-
.../MultivariateNormalDistributionModel.java | 18 +-
.../distribution/NormalDistributionModel.java | 13 +-
.../TruncatedNormalDistributionModel.java | 2 +-
src/dr/inference/markovchain/MarkovChain.java | 21 +-
.../markovjumps/TwoStateOccupancyMarkovReward.java | 133 +-
src/dr/inference/mcmc/DebugUtils.java | 102 +-
src/dr/inference/mcmc/MCMC.java | 14 +-
src/dr/inference/model/AbstractModel.java | 7 +-
.../inference/model/AbstractModelLikelihood.java | 9 +
.../model/BlockUpperTriangularMatrixParameter.java | 10 +-
.../model/CompoundFastMatrixParameter.java | 210 ++
src/dr/inference/model/CompoundLikelihood.java | 13 +-
src/dr/inference/model/CompoundParameter.java | 20 +-
src/dr/inference/model/DesignMatrix.java | 9 +-
src/dr/inference/model/DiagonalMatrix.java | 2 +
src/dr/inference/model/FastMatrixParameter.java | 276 ++
src/dr/inference/model/LatentFactorModel.java | 471 ++-
src/dr/inference/model/Likelihood.java | 12 +
src/dr/inference/model/MatrixParameter.java | 50 +-
.../model/MatrixParameterInterface.java} | 41 +-
src/dr/inference/model/Model.java | 3 +-
src/dr/inference/model/Parameter.java | 32 +-
src/dr/inference/model/PathLikelihood.java | 10 +
src/dr/inference/model/SumParameter.java | 129 +
.../model/TestThreadedCompoundLikelihood.java | 13 +
.../model/ThreadedCompoundLikelihood.java | 12 +
.../operators/AbstractHamiltonianMCOperator.java | 30 +
...daptableVarianceMultivariateNormalOperator.java | 156 +-
.../operators/EllipticalSliceOperator.java | 152 +-
.../inference/operators/LoadingsGibbsOperator.java | 3 +-
src/dr/inference/operators/OperatorSchedule.java | 22 +-
.../operators/SimpleOperatorSchedule.java | 15 +-
.../CompoundGaussianProcessParser.java | 126 +
.../distribution/DistributionLikelihoodParser.java | 1 +
.../distribution/DistributionModelParser.java | 1 +
.../distribution/GammaDistributionModelParser.java | 63 +-
.../distribution/GeneralizedLinearModelParser.java | 32 +-
src/dr/inferencexml/distribution/PriorParsers.java | 54 +-
.../distribution/WorkingPriorParsers.java | 214 +-
src/dr/inferencexml/loggers/LoggerParser.java | 4 +-
.../model/CompoundLikelihoodParser.java | 5 +-
.../model/ImmutableParameterParser.java | 85 +
.../model/LatentFactorModelParser.java | 25 +-
src/dr/inferencexml/model/SumParameterParser.java | 79 +
.../operators/SimpleOperatorScheduleParser.java | 9 +-
src/dr/math/MathUtils.java | 197 +-
src/dr/math/MersenneTwisterFast.java | 447 +--
.../distributions/CompoundGaussianProcess.java | 99 +
.../math/distributions/DirichletDistribution.java | 73 +-
src/dr/math/distributions/GammaDistribution.java | 7 +
.../distributions/InverseGaussianDistribution.java | 3 +-
.../distributions/MultivariateKDEDistribution.java | 5 +-
.../MultivariateNormalDistribution.java | 43 +-
.../MultivariatePolyaDistributionLikelihood.java | 9 +
src/dr/math/distributions/RandomGenerator.java | 4 +-
src/dr/util/NumberFormatter.java | 8 +-
src/dr/util/Transform.java | 198 +-
src/dr/xml/Report.java | 2 +-
src/test/dr/distibutions/InvGammaTest.java | 26 +-
.../UncorrelatedRelaxedClockTest.java | 546 +--
.../coalescent/MultiEpochExponentialTest.java | 171 +
.../TwoStateOccupancyMarkovRewardsTest.java | 137 +-
362 files changed, 33734 insertions(+), 18375 deletions(-)
delete mode 100644 .idea/libraries/lib1.xml
delete mode 100644 .idea/libraries/phylogeography.xml
delete mode 100644 .idea/libraries/quaqua.xml
delete mode 100644 .idea/libraries/tracer.xml
delete mode 100644 .idea/libraries/tracer1.xml
copy build_pathogen.xml => build_tempest.xml (78%)
create mode 100644 examples/release/clockModels/testUCRelaxedClockContinuousQuantileLogNormal.xml
create mode 100644 examples/release/clockModels/testUCRelaxedClockGamma.xml
delete mode 100644 examples/release/clockModels/testUncorrelatedRelaxedClock.xml
copy {release_pathogen => release_tempest}/Linux/icons/pathogen.png (100%)
copy {release_pathogen => release_tempest}/Linux/scripts/pathogen (100%)
copy {release_pathogen => release_tempest}/common/README.txt (100%)
create mode 100644 src/dr/app/beagle/evomodel/newtreelikelihood/NewAbstractLikelihoodOnTree.java
create mode 100644 src/dr/app/beagle/evomodel/newtreelikelihood/NewAbstractSequenceLikelihood.java
rename src/dr/app/beagle/evomodel/newtreelikelihood/{NewBeagleTreeLikelihood.java => NewBeagleSequenceLikelihood.java} (55%)
create mode 100644 src/dr/app/beagle/evomodel/newtreelikelihood/NewFullyConjugateTraitLikelihood.java
create mode 100644 src/dr/app/beagle/evomodel/parsers/NewBeagleTreeLikelihoodParser.java
copy src/dr/{evomodel/coalescent/CoalescentIntervalProvider.java => app/beagle/evomodel/treelikelihood/EvolutionaryProcessDelegate.java} (69%)
create mode 100644 src/dr/app/beast/RBeastMain.java
create mode 100644 src/dr/app/beauti/clockModelsPanel/CloneModelDialog.java
rename src/dr/app/{oldbeauti/GuessDatesException.java => beauti/types/OperatorSetType.java} (71%)
delete mode 100644 src/dr/app/oldbeauti/BeastGenerator.java
delete mode 100644 src/dr/app/oldbeauti/BeautiApp.java
delete mode 100644 src/dr/app/oldbeauti/BeautiFrame.java
delete mode 100644 src/dr/app/oldbeauti/BeautiOptions.java
delete mode 100644 src/dr/app/oldbeauti/BeautiTester.java
delete mode 100755 src/dr/app/oldbeauti/CommandLineBeauti.java
delete mode 100644 src/dr/app/oldbeauti/DataPanel.java
delete mode 100644 src/dr/app/oldbeauti/DiscretePriorDialog.java
delete mode 100644 src/dr/app/oldbeauti/MCMCPanel.java
delete mode 100644 src/dr/app/oldbeauti/ModelPanel.java
delete mode 100644 src/dr/app/oldbeauti/NexusApplicationImporter.java
delete mode 100644 src/dr/app/oldbeauti/OperatorsPanel.java
delete mode 100644 src/dr/app/oldbeauti/PriorDialog.java
delete mode 100644 src/dr/app/oldbeauti/PriorType.java
delete mode 100644 src/dr/app/oldbeauti/PriorsPanel.java
delete mode 100644 src/dr/app/oldbeauti/TaxaPanel.java
delete mode 100644 src/dr/app/oldbeauti/XMLWriter.java
create mode 100644 src/dr/app/tempest/ParentPlot.java
create mode 100644 src/dr/app/tempest/RootToTip.java
create mode 100644 src/dr/app/tempest/SamplesPanel.java
create mode 100644 src/dr/app/tempest/TempEstApp.java
rename src/dr/app/{oldbeauti/BeautiDefaultFileMenuFactory.java => tempest/TempestDefaultFileMenuFactory.java} (59%)
create mode 100644 src/dr/app/tempest/TempestFrame.java
rename src/dr/app/{oldbeauti/BeautiMacFileMenuFactory.java => tempest/TempestMacFileMenuFactory.java} (53%)
rename src/dr/app/{oldbeauti/BeautiMenuBarFactory.java => tempest/TempestMenuBarFactory.java} (80%)
create mode 100644 src/dr/app/tempest/TempestPanel.java
copy src/dr/app/{pathogen => tempest}/TemporalRooting.java (98%)
create mode 100644 src/dr/app/tempest/TemporalStress.java
rename src/dr/app/{oldbeauti => tempest}/TreeUtils.java (95%)
rename src/dr/app/{oldbeauti => tempest}/images/beauti.png (100%)
copy src/dr/app/{pathogen => tempest}/images/coloursTool.png (100%)
rename src/dr/app/{oldbeauti => tempest}/images/exclude.png (100%)
rename src/dr/app/{oldbeauti => tempest}/images/gear.png (100%)
rename src/dr/app/{oldbeauti => tempest}/images/include.png (100%)
copy release_pathogen/Linux/icons/pathogen.png => src/dr/app/tempest/images/tempest.png (100%)
create mode 100644 src/dr/evolution/coalescent/MultiEpochExponential.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/MCMCOperators/Mu1ScaleActiveScaledMu1IntactOperator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/MCMCOperators/Mu2ScaleActiveScaledMu2IntactOperator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/MCMCOperators/ProbGenericSiteGibbsOperator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/MCMCOperators/ProbSitesGibbsOperator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/MCMCOperators/RandomWalkOnActiveMu.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/MCMCOperators/TreeClusterAlgorithmOperator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/MCMCOperators/muMeanTranslateInactiveMu1Operator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/MCMCOperators/muPrecisionInactiveMuOperator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/MCMCOperators/randomWalkSerumDriftAndMu.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/MCMCOperators/serumDriftActiveScaledMu1Operator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/MCMCOperators/serumPrecisionSerumLocOperator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/TreeClusteringVirusesPrior.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/Tree_Clustering_Shared_Routines.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/misc/mergeAdjacencyMatrixPlots.java
copy src/dr/evomodel/antigenic/{AntigenicLikelihood.java => phyloClustering/misc/obsolete/AGLikelihoodCluster.java} (78%)
copy src/dr/evomodel/antigenic/{AntigenicLikelihood.java => phyloClustering/misc/obsolete/AGLikelihoodTreeCluster.java} (57%)
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/misc/obsolete/ClusterAlgorithmOperator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/misc/obsolete/ClusterComparison.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/misc/obsolete/ClusterOperator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/misc/obsolete/ClusterViruses.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/misc/obsolete/ClusterWalkOperator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/misc/obsolete/ClusterWalkOperatorParser.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/misc/obsolete/OrderDouble.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/misc/obsolete/TiterImporter.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/misc/obsolete/TreeClusterGibbsOperator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/misc/obsolete/TreeClusterSequentialSampling.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/misc/obsolete/serumDriftScalingMuOperator.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/misc/simulateClusters.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/ActiveIndicatorsStatistic.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/AnnotateLocationParameterTreeTrait.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/AnnotateMuTreeTrait.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/CausalMutationsLogger.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/ClusterLabelsVirusesStatistic.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/ClusterLabelsVirusesTreeTrait.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/DriftedMuStatistic.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/DriftedTreeClusterLocationsStatistic.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/DriverCountStatistic.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/KStatistic.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/MutationsTreeTrait.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/NodeNumberTreeTrait.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/PathStatistic.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/indicatorsStatistic.java
create mode 100644 src/dr/evomodel/antigenic/phyloClustering/statistics/muStatistic.java
copy src/dr/evomodel/coalescent/{ExponentialConstantModel.java => MultiEpochExponentialModel.java} (54%)
delete mode 100644 src/dr/evomodel/epidemiology/casetocase/operators/InfectionBranchGibbsOperator.java
create mode 100644 src/dr/evomodel/operators/LatentFactorHamiltonianMC.java
rename src/dr/{inference => evomodel}/operators/MicrosatUpDownOperator.java (96%)
rename src/dr/{inference => evomodel}/operators/MicrosatelliteModelSelectOperator.java (95%)
rename src/dr/{inference => evomodel}/operators/MsatBitFlipOperator.java (94%)
rename src/dr/{inference => evomodel}/operators/MsatFullAncestryImportanceSamplingOperator.java (96%)
rename src/dr/{inference => evomodel}/operators/MsatSingleAncestralStateGibbsOperator.java (95%)
rename src/dr/{inference => evomodel}/operators/RandomWalkIntegerNodeHeightWeightedOperator.java (91%)
rename src/dr/{inference => evomodel}/operators/RandomWalkIntegerSetSizeWeightedOperator.java (93%)
create mode 100644 src/dr/evomodel/operators/SubtreeLeapOperator.java
copy src/dr/evomodelxml/coalescent/{CataclysmicDemographicModelParser.java => MultiEpochExponentialModelParser.java} (58%)
create mode 100644 src/dr/evomodelxml/operators/LatentFactorHamiltonianMCParser.java
rename src/dr/{inferencexml => evomodelxml}/operators/MicrosatUpDownOperatorParser.java (94%)
rename src/dr/{inferencexml => evomodelxml}/operators/MicrosatelliteModelSelectOperatorParser.java (94%)
rename src/dr/{inferencexml => evomodelxml}/operators/MsatBitFlipOperatorParser.java (95%)
rename src/dr/{inferencexml => evomodelxml}/operators/MsatFullAncestryImportanceSamplingOperatorParser.java (94%)
rename src/dr/{inferencexml => evomodelxml}/operators/MsatSingleAncestralStateGibbsOperatorParser.java (94%)
rename src/dr/{inferencexml => evomodelxml}/operators/RandomWalkIntegerNodeHeightWeightedOperatorParser.java (92%)
rename src/dr/{inferencexml => evomodelxml}/operators/RandomWalkIntegerSetSizeWeightedOperatorParser.java (94%)
create mode 100644 src/dr/evomodelxml/operators/SubtreeLeapOperatorParser.java
create mode 100644 src/dr/inference/model/CompoundFastMatrixParameter.java
create mode 100644 src/dr/inference/model/FastMatrixParameter.java
copy src/dr/{evomodel/coalescent/CoalescentIntervalProvider.java => inference/model/MatrixParameterInterface.java} (51%)
create mode 100644 src/dr/inference/model/SumParameter.java
create mode 100644 src/dr/inference/operators/AbstractHamiltonianMCOperator.java
create mode 100644 src/dr/inferencexml/distribution/CompoundGaussianProcessParser.java
create mode 100644 src/dr/inferencexml/model/ImmutableParameterParser.java
create mode 100644 src/dr/inferencexml/model/SumParameterParser.java
create mode 100644 src/dr/math/distributions/CompoundGaussianProcess.java
create mode 100644 src/test/dr/evomodel/coalescent/MultiEpochExponentialTest.java
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