[med-svn] [beast-mcmc] 03/09: Merge tag 'upstream/1.8.3+dfsg'
Andreas Tille
tille at debian.org
Thu Jun 2 19:01:52 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository beast-mcmc.
commit 68720111f5e310f1ea8f90b2ecd0cba4f9b75314
Merge: e9840a1 8de73ae
Author: Andreas Tille <tille at debian.org>
Date: Thu Jun 2 13:49:57 2016 +0200
Merge tag 'upstream/1.8.3+dfsg'
Upstream version 1.8.3+dfsg
.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 +-
release_tempest/Linux/icons/pathogen.png | Bin 0 -> 34709 bytes
release_tempest/Linux/scripts/pathogen | 27 +
release_tempest/common/README.txt | 92 +
.../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
src/dr/app/tempest/images/coloursTool.png | Bin 0 -> 1915 bytes
.../app/{oldbeauti => tempest}/images/exclude.png | Bin
src/dr/app/{oldbeauti => tempest}/images/gear.png | Bin
.../app/{oldbeauti => tempest}/images/include.png | Bin
src/dr/app/tempest/images/tempest.png | Bin 0 -> 34709 bytes
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, 33853 insertions(+), 18375 deletions(-)
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