[med-svn] [beast-mcmc] branch master updated (98d6828 -> 69ceacf)
Andreas Tille
tille at debian.org
Thu Jun 2 19:01:51 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 98d6828 Upload to unstable
new e9840a1 Add compression and mangling to debian/watch
new 8de73ae Imported Upstream version 1.8.3+dfsg
new 6872011 Merge tag 'upstream/1.8.3+dfsg'
new 8d45dec New upstream version
new 76a80ad Upload to official Debian (experimental)
new 0181e7d Adapt patches
new edfaa23 Fix version number which should have +dfsg
new 73f2052 cme fix dpkg-control
new 69ceacf Upload to experimental
The 9 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 +
debian/changelog | 8 +
debian/control | 12 +-
.../fix_classpath_in_build_tracer_xml.patch | 3 +-
debian/patches/fix_encoding.patch | 4 +-
debian/rules | 3 -
debian/watch | 2 +-
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 +-
368 files changed, 33753 insertions(+), 18388 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
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delete mode 100644 src/dr/app/oldbeauti/PriorDialog.java
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delete mode 100644 src/dr/app/oldbeauti/TaxaPanel.java
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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
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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
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rename src/dr/app/{oldbeauti => tempest}/images/beauti.png (100%)
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rename src/dr/app/{oldbeauti => tempest}/images/include.png (100%)
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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
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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
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copy src/dr/evomodel/antigenic/{AntigenicLikelihood.java => phyloClustering/misc/obsolete/AGLikelihoodTreeCluster.java} (57%)
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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
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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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