From b1d89867cdfc3312771aa93e28246ce1599778fd Mon Sep 17 00:00:00 2001 From: rbouckaert Date: Thu, 4 Aug 2022 11:45:57 +1200 Subject: [PATCH] move to beastclassic namespace --- .../app/beauti/BeautiDiscreteTraitProvider.java | 8 ++++---- .../app/beauti/BeautiLocationTraitProvider.java | 6 +++--- .../app/beauti/LocationInputEditor.java | 8 ++++---- .../app/beauti/TraitDialog.java | 2 +- .../app/beauti/TraitInputEditor.java | 6 +++--- .../AbstractMultivariateTraitLikelihood.java | 12 ++++++------ .../FullyConjugateMultivariateTraitLikelihood.java | 6 +++--- .../IntegratedMultivariateTraitLikelihood.java | 10 +++++----- .../continuous/MultivariateDiffusionModel.java | 6 +++--- .../SampledMultivariateTraitLikelihood.java | 2 +- src/{dr/math => beastclassic/dr}/GammaFunction.java | 2 +- .../dr/evolmodel}/continuous/MissingTraits.java | 4 ++-- .../distributions/MultivariateDistribution.java | 2 +- .../MultivariateNormalDistribution.java | 2 +- .../dr/math/distributions/WishartDistribution.java | 7 ++----- .../distributions/WishartSufficientStatistics.java | 2 +- src/{dr/math => beastclassic/dr}/util/ArcCos.java | 2 +- .../evolution/alignment/AlignmentFromTrait.java | 2 +- .../evolution/alignment/AlignmentFromTraitMap.java | 6 +++--- .../evolution/datatype/ContinuousDataType.java | 2 +- .../evolution/datatype/LocationDataType.java | 2 +- .../likelihood/AncestralSequenceLogger.java | 2 +- .../likelihood/AncestralStateTreeLikelihood.java | 6 +++--- .../evolution/likelihood/LeafTrait.java | 2 +- .../evolution/operators/BitFlipBSSVSOperator.java | 2 +- .../GMRFMultilocusSkyrideBlockUpdateOperator.java | 4 ++-- .../operators/GMRFSkyrideBlockUpdateOperator.java | 4 ++-- .../evolution/operators/GeneralIntegerOperator.java | 2 +- .../evolution/operators/PickIndicatorOperator.java | 2 +- .../operators/PrecisionMatrixGibbsOperator.java | 8 ++++---- .../operators/RegressionGibbsEffectOperator.java | 8 ++++---- .../operators/RegressionGibbsPrecisionOperator.java | 5 +++-- .../operators/RootTraitRandowWalkOperator.java | 4 ++-- .../evolution/operators/SphereRandomWalker.java | 2 +- .../evolution/operators/TraitGibbsOperator.java | 13 ++++++------- .../speciation/BirthDeathSerialSampling.java | 2 +- .../ContinuousSubstitutionModel.java | 4 ++-- .../evolution/substitutionmodel/FLU.java | 2 +- .../evolution/substitutionmodel/GLM.java | 2 +- .../substitutionmodel/GLMBasedSubstModel.java | 2 +- .../evolution/substitutionmodel/GlmModel.java | 2 +- .../evolution/substitutionmodel/LG.java | 2 +- .../evolution/substitutionmodel/LogLinear.java | 2 +- .../substitutionmodel/RobustEigenSystem.java | 2 +- .../SVSGeneralSubstitutionModel.java | 4 ++-- .../SVSGeneralSubstitutionModelLogger.java | 2 +- .../evolution/tree/RootTrait.java | 2 +- .../evolution/tree/TreeTrait.java | 2 +- .../evolution/tree/TreeTraitMap.java | 2 +- .../evolution/tree/TreeTraitProvider.java | 2 +- .../evolution/tree/TreeWithTraitLogger.java | 2 +- .../evolution/tree/coalescent/Expansion.java | 2 +- .../coalescent/GMRFMultilocusSkyrideLikelihood.java | 2 +- .../tree/coalescent/GMRFSkyrideLikelihood.java | 2 +- .../evolution/tree/coalescent/LogisticGrowth.java | 2 +- .../geo/GeoSpatialDistribution.java | 4 ++-- src/{beast => beastclassic}/geo/Polygon2D.java | 2 +- .../BayesianStochasticSearchVariableSelection.java | 2 +- .../distribution/GeneralizedLinearModel.java | 2 +- .../inference/distribution/LinearRegression.java | 2 +- .../inference/distribution/LogisticRegression.java | 2 +- .../math/distributions/CTMCScalePrior.java | 4 ++-- .../MultivariateNormalDistribution.java | 10 +++++----- .../math/distributions/WishartDistribution.java | 10 +++++----- .../phylogeography/RateIndicatorInitializer.java | 2 +- .../substitutionmodel/RobustEigenSystemTest.java | 2 +- .../math/distributions/WishartDisitrbutionTest.java | 8 ++++---- 67 files changed, 127 insertions(+), 130 deletions(-) rename src/{beast => beastclassic}/app/beauti/BeautiDiscreteTraitProvider.java (95%) rename src/{beast => beastclassic}/app/beauti/BeautiLocationTraitProvider.java (94%) rename src/{beast => beastclassic}/app/beauti/LocationInputEditor.java (98%) rename src/{beast => beastclassic}/app/beauti/TraitDialog.java (98%) rename src/{beast => beastclassic}/app/beauti/TraitInputEditor.java (99%) rename src/{beast => beastclassic}/continuous/AbstractMultivariateTraitLikelihood.java (99%) rename src/{beast => beastclassic}/continuous/FullyConjugateMultivariateTraitLikelihood.java (99%) rename src/{beast => beastclassic}/continuous/IntegratedMultivariateTraitLikelihood.java (99%) rename src/{beast => beastclassic}/continuous/MultivariateDiffusionModel.java (96%) rename src/{beast => beastclassic}/continuous/SampledMultivariateTraitLikelihood.java (99%) rename src/{dr/math => beastclassic/dr}/GammaFunction.java (99%) rename src/{dr/evomodel => beastclassic/dr/evolmodel}/continuous/MissingTraits.java (97%) rename src/{ => beastclassic}/dr/math/distributions/MultivariateDistribution.java (83%) rename src/{ => beastclassic}/dr/math/distributions/MultivariateNormalDistribution.java (99%) rename src/{ => beastclassic}/dr/math/distributions/WishartDistribution.java (99%) rename src/{ => beastclassic}/dr/math/distributions/WishartSufficientStatistics.java (94%) rename src/{dr/math => beastclassic/dr}/util/ArcCos.java (99%) rename src/{beast => beastclassic}/evolution/alignment/AlignmentFromTrait.java (98%) rename src/{beast => beastclassic}/evolution/alignment/AlignmentFromTraitMap.java (92%) rename src/{beast => beastclassic}/evolution/datatype/ContinuousDataType.java (97%) rename src/{beast => beastclassic}/evolution/datatype/LocationDataType.java (93%) rename src/{beast => beastclassic}/evolution/likelihood/AncestralSequenceLogger.java (99%) rename src/{beast => beastclassic}/evolution/likelihood/AncestralStateTreeLikelihood.java (99%) rename src/{beast => beastclassic}/evolution/likelihood/LeafTrait.java (93%) rename src/{beast => beastclassic}/evolution/operators/BitFlipBSSVSOperator.java (98%) rename src/{beast => beastclassic}/evolution/operators/GMRFMultilocusSkyrideBlockUpdateOperator.java (99%) rename src/{beast => beastclassic}/evolution/operators/GMRFSkyrideBlockUpdateOperator.java (99%) rename src/{beast => beastclassic}/evolution/operators/GeneralIntegerOperator.java (98%) rename src/{beast => beastclassic}/evolution/operators/PickIndicatorOperator.java (97%) rename src/{beast => beastclassic}/evolution/operators/PrecisionMatrixGibbsOperator.java (97%) rename src/{beast => beastclassic}/evolution/operators/RegressionGibbsEffectOperator.java (95%) rename src/{beast => beastclassic}/evolution/operators/RegressionGibbsPrecisionOperator.java (95%) rename src/{beast => beastclassic}/evolution/operators/RootTraitRandowWalkOperator.java (94%) rename src/{beast => beastclassic}/evolution/operators/SphereRandomWalker.java (99%) rename src/{beast => beastclassic}/evolution/operators/TraitGibbsOperator.java (96%) rename src/{beast => beastclassic}/evolution/speciation/BirthDeathSerialSampling.java (99%) rename src/{beast => beastclassic}/evolution/substitutionmodel/ContinuousSubstitutionModel.java (92%) rename src/{beast => beastclassic}/evolution/substitutionmodel/FLU.java (99%) rename src/{beast => beastclassic}/evolution/substitutionmodel/GLM.java (99%) rename src/{beast => beastclassic}/evolution/substitutionmodel/GLMBasedSubstModel.java (96%) rename src/{beast => beastclassic}/evolution/substitutionmodel/GlmModel.java (97%) rename src/{beast => beastclassic}/evolution/substitutionmodel/LG.java (99%) rename src/{beast => beastclassic}/evolution/substitutionmodel/LogLinear.java (98%) rename src/{beast => beastclassic}/evolution/substitutionmodel/RobustEigenSystem.java (97%) rename src/{beast => beastclassic}/evolution/substitutionmodel/SVSGeneralSubstitutionModel.java (98%) rename src/{beast => beastclassic}/evolution/substitutionmodel/SVSGeneralSubstitutionModelLogger.java (98%) rename src/{beast => beastclassic}/evolution/tree/RootTrait.java (97%) rename src/{beast => beastclassic}/evolution/tree/TreeTrait.java (99%) rename src/{beast => beastclassic}/evolution/tree/TreeTraitMap.java (99%) rename src/{beast => beastclassic}/evolution/tree/TreeTraitProvider.java (99%) rename src/{beast => beastclassic}/evolution/tree/TreeWithTraitLogger.java (99%) rename src/{beast => beastclassic}/evolution/tree/coalescent/Expansion.java (97%) rename src/{beast => beastclassic}/evolution/tree/coalescent/GMRFMultilocusSkyrideLikelihood.java (99%) rename src/{beast => beastclassic}/evolution/tree/coalescent/GMRFSkyrideLikelihood.java (99%) rename src/{beast => beastclassic}/evolution/tree/coalescent/LogisticGrowth.java (98%) rename src/{beast => beastclassic}/geo/GeoSpatialDistribution.java (96%) rename src/{beast => beastclassic}/geo/Polygon2D.java (99%) rename src/{beast => beastclassic}/inference/BayesianStochasticSearchVariableSelection.java (99%) rename src/{beast => beastclassic}/inference/distribution/GeneralizedLinearModel.java (99%) rename src/{beast => beastclassic}/inference/distribution/LinearRegression.java (98%) rename src/{beast => beastclassic}/inference/distribution/LogisticRegression.java (95%) rename src/{beast => beastclassic}/math/distributions/CTMCScalePrior.java (98%) rename src/{beast => beastclassic}/math/distributions/MultivariateNormalDistribution.java (91%) rename src/{beast => beastclassic}/math/distributions/WishartDistribution.java (87%) rename src/{beast => beastclassic}/phylogeography/RateIndicatorInitializer.java (98%) diff --git a/src/beast/app/beauti/BeautiDiscreteTraitProvider.java b/src/beastclassic/app/beauti/BeautiDiscreteTraitProvider.java similarity index 95% rename from src/beast/app/beauti/BeautiDiscreteTraitProvider.java rename to src/beastclassic/app/beauti/BeautiDiscreteTraitProvider.java index 0b41530..cf71290 100644 --- a/src/beast/app/beauti/BeautiDiscreteTraitProvider.java +++ b/src/beastclassic/app/beauti/BeautiDiscreteTraitProvider.java @@ -1,4 +1,4 @@ -package beast.app.beauti; +package beastclassic.app.beauti; import java.awt.Frame; import java.util.ArrayList; @@ -19,10 +19,10 @@ import beast.base.parser.PartitionContext; import beast.base.evolution.alignment.Alignment; import beast.base.evolution.datatype.UserDataType; -import beast.evolution.alignment.AlignmentFromTrait; -import beast.evolution.likelihood.AncestralStateTreeLikelihood; +import beastclassic.evolution.alignment.AlignmentFromTrait; +import beastclassic.evolution.likelihood.AncestralStateTreeLikelihood; +import beastclassic.evolution.substitutionmodel.SVSGeneralSubstitutionModel; import beast.base.evolution.sitemodel.SiteModel; -import beast.evolution.substitutionmodel.SVSGeneralSubstitutionModel; import beast.base.evolution.tree.Tree; import beast.base.inference.distribution.ParametricDistribution; import beast.base.inference.distribution.Poisson; diff --git a/src/beast/app/beauti/BeautiLocationTraitProvider.java b/src/beastclassic/app/beauti/BeautiLocationTraitProvider.java similarity index 94% rename from src/beast/app/beauti/BeautiLocationTraitProvider.java rename to src/beastclassic/app/beauti/BeautiLocationTraitProvider.java index 5656c07..065e667 100644 --- a/src/beast/app/beauti/BeautiLocationTraitProvider.java +++ b/src/beastclassic/app/beauti/BeautiLocationTraitProvider.java @@ -1,4 +1,4 @@ -package beast.app.beauti; +package beastclassic.app.beauti; import java.awt.Frame; import java.util.ArrayList; @@ -11,7 +11,7 @@ import beastfx.app.inputeditor.BeautiAlignmentProvider; import beastfx.app.inputeditor.BeautiDoc; import beast.base.parser.PartitionContext; -import beast.continuous.SampledMultivariateTraitLikelihood; +import beastclassic.continuous.SampledMultivariateTraitLikelihood; import beast.base.core.BEASTInterface; import beast.base.core.Description; import beast.base.inference.State; @@ -56,7 +56,7 @@ public List getAlignments(BeautiDoc doc) { @Override public int matches(Alignment alignment) { for (BEASTInterface output : alignment.getOutputs()) { - if (output instanceof beast.continuous.SampledMultivariateTraitLikelihood) { + if (output instanceof beastclassic.continuous.SampledMultivariateTraitLikelihood) { return 10; } } diff --git a/src/beast/app/beauti/LocationInputEditor.java b/src/beastclassic/app/beauti/LocationInputEditor.java similarity index 98% rename from src/beast/app/beauti/LocationInputEditor.java rename to src/beastclassic/app/beauti/LocationInputEditor.java index 166bcaa..5902cd6 100644 --- a/src/beast/app/beauti/LocationInputEditor.java +++ b/src/beastclassic/app/beauti/LocationInputEditor.java @@ -1,4 +1,4 @@ -package beast.app.beauti; +package beastclassic.app.beauti; import java.awt.Color; @@ -28,9 +28,9 @@ import beastfx.app.inputeditor.GuessPatternDialog; import beastfx.app.inputeditor.ListInputEditor; import beastfx.app.inputeditor.SmallLabel; -import beast.continuous.SampledMultivariateTraitLikelihood; -import beast.evolution.alignment.AlignmentFromTraitMap; -import beast.evolution.tree.TreeTraitMap; +import beastclassic.evolution.tree.TreeTraitMap; +import beastclassic.continuous.SampledMultivariateTraitLikelihood; +import beastclassic.evolution.alignment.AlignmentFromTraitMap; import beast.base.core.BEASTInterface; import beast.base.core.BEASTObject; import beast.base.core.Input; diff --git a/src/beast/app/beauti/TraitDialog.java b/src/beastclassic/app/beauti/TraitDialog.java similarity index 98% rename from src/beast/app/beauti/TraitDialog.java rename to src/beastclassic/app/beauti/TraitDialog.java index b57f840..b653446 100644 --- a/src/beast/app/beauti/TraitDialog.java +++ b/src/beastclassic/app/beauti/TraitDialog.java @@ -1,4 +1,4 @@ -package beast.app.beauti; +package beastclassic.app.beauti; import javax.swing.JDialog; diff --git a/src/beast/app/beauti/TraitInputEditor.java b/src/beastclassic/app/beauti/TraitInputEditor.java similarity index 99% rename from src/beast/app/beauti/TraitInputEditor.java rename to src/beastclassic/app/beauti/TraitInputEditor.java index 74ffab8..9a87416 100644 --- a/src/beast/app/beauti/TraitInputEditor.java +++ b/src/beastclassic/app/beauti/TraitInputEditor.java @@ -1,4 +1,4 @@ -package beast.app.beauti; +package beastclassic.app.beauti; import java.awt.Color; import java.awt.Component; @@ -36,8 +36,8 @@ import beast.base.evolution.alignment.Alignment; import beast.base.evolution.alignment.TaxonSet; import beast.base.evolution.datatype.UserDataType; -import beast.evolution.alignment.AlignmentFromTrait; -import beast.evolution.likelihood.AncestralStateTreeLikelihood; +import beastclassic.evolution.alignment.AlignmentFromTrait; +import beastclassic.evolution.likelihood.AncestralStateTreeLikelihood; import beast.base.evolution.tree.TraitSet; import beast.base.evolution.tree.Tree; import beast.base.evolution.tree.TreeInterface; diff --git a/src/beast/continuous/AbstractMultivariateTraitLikelihood.java b/src/beastclassic/continuous/AbstractMultivariateTraitLikelihood.java similarity index 99% rename from src/beast/continuous/AbstractMultivariateTraitLikelihood.java rename to src/beastclassic/continuous/AbstractMultivariateTraitLikelihood.java index 6683f74..0cb85f8 100644 --- a/src/beast/continuous/AbstractMultivariateTraitLikelihood.java +++ b/src/beastclassic/continuous/AbstractMultivariateTraitLikelihood.java @@ -1,4 +1,4 @@ -package beast.continuous; +package beastclassic.continuous; @@ -16,13 +16,13 @@ import beast.base.core.Input.Validate; import beast.base.inference.parameter.RealParameter; import beast.base.evolution.branchratemodel.BranchRateModel; -import beast.evolution.alignment.AlignmentFromTraitMap; -import beast.evolution.datatype.ContinuousDataType; import beast.base.evolution.likelihood.GenericTreeLikelihood; import beast.base.evolution.sitemodel.SiteModel; -import beast.evolution.substitutionmodel.ContinuousSubstitutionModel; -import beast.evolution.tree.TreeTrait; -import beast.evolution.tree.TreeTraitMap; +import beastclassic.evolution.tree.TreeTrait; +import beastclassic.evolution.tree.TreeTraitMap; +import beastclassic.evolution.alignment.AlignmentFromTraitMap; +import beastclassic.evolution.datatype.ContinuousDataType; +import beastclassic.evolution.substitutionmodel.ContinuousSubstitutionModel; import beast.base.evolution.tree.Node; import beast.base.evolution.tree.TreeInterface; diff --git a/src/beast/continuous/FullyConjugateMultivariateTraitLikelihood.java b/src/beastclassic/continuous/FullyConjugateMultivariateTraitLikelihood.java similarity index 99% rename from src/beast/continuous/FullyConjugateMultivariateTraitLikelihood.java rename to src/beastclassic/continuous/FullyConjugateMultivariateTraitLikelihood.java index 0caf151..0db7429 100644 --- a/src/beast/continuous/FullyConjugateMultivariateTraitLikelihood.java +++ b/src/beastclassic/continuous/FullyConjugateMultivariateTraitLikelihood.java @@ -23,15 +23,15 @@ * Boston, MA 02110-1301 USA */ -package beast.continuous; +package beastclassic.continuous; import beast.base.core.Description; -import dr.math.distributions.MultivariateNormalDistribution; -import dr.math.distributions.WishartSufficientStatistics; import java.util.List; import beast.base.inference.parameter.RealParameter; +import beastclassic.dr.math.distributions.MultivariateNormalDistribution; +import beastclassic.dr.math.distributions.WishartSufficientStatistics; import beast.base.evolution.branchratemodel.BranchRateModel; import beast.base.evolution.tree.Node; import beast.base.evolution.tree.TreeInterface; diff --git a/src/beast/continuous/IntegratedMultivariateTraitLikelihood.java b/src/beastclassic/continuous/IntegratedMultivariateTraitLikelihood.java similarity index 99% rename from src/beast/continuous/IntegratedMultivariateTraitLikelihood.java rename to src/beastclassic/continuous/IntegratedMultivariateTraitLikelihood.java index 1f5bba4..d5810ec 100644 --- a/src/beast/continuous/IntegratedMultivariateTraitLikelihood.java +++ b/src/beastclassic/continuous/IntegratedMultivariateTraitLikelihood.java @@ -23,21 +23,21 @@ * Boston, MA 02110-1301 USA */ -package beast.continuous; +package beastclassic.continuous; import java.util.Arrays; import java.util.List; import beast.base.core.Description; -import dr.evomodel.continuous.MissingTraits; -import dr.math.distributions.WishartSufficientStatistics; import beast.base.core.Input; import beast.base.inference.parameter.RealParameter; import beast.base.evolution.branchratemodel.BranchRateModel; import beast.base.evolution.tree.Node; import beast.base.evolution.tree.TreeInterface; import beast.base.math.matrixalgebra.SymmetricMatrix; +import beastclassic.dr.evolmodel.continuous.MissingTraits; +import beastclassic.dr.math.distributions.WishartSufficientStatistics; /** * A multivariate trait likelihood that analytically integrates out the unobserved trait values at all internal @@ -941,7 +941,7 @@ private void preOrderTraverseSample(/*MultivariateTraitTree*/ TreeInterface tree double[][] variance = computeMarginalRootMeanAndVariance(rootMean, treePrecision, treeVariance, rootPrecision); - double[] draw = dr.math.distributions.MultivariateNormalDistribution.nextMultivariateNormalVariance(rootMean, variance); + double[] draw = beastclassic.dr.math.distributions.MultivariateNormalDistribution.nextMultivariateNormalVariance(rootMean, variance); if (DEBUG_PREORDER) { Arrays.fill(draw, 1.0); @@ -1004,7 +1004,7 @@ private void preOrderTraverseSample(/*MultivariateTraitTree*/ TreeInterface tree var[i][j] = treeVariance[i][j] / totalPrecision; } } - double[] draw = dr.math.distributions.MultivariateNormalDistribution.nextMultivariateNormalVariance(mean, var); + double[] draw = beastclassic.dr.math.distributions.MultivariateNormalDistribution.nextMultivariateNormalVariance(mean, var); System.arraycopy(draw, 0, drawnStates, thisOffset, dimTrait); // if (DEBUG) { diff --git a/src/beast/continuous/MultivariateDiffusionModel.java b/src/beastclassic/continuous/MultivariateDiffusionModel.java similarity index 96% rename from src/beast/continuous/MultivariateDiffusionModel.java rename to src/beastclassic/continuous/MultivariateDiffusionModel.java index ba12ce6..eae5923 100644 --- a/src/beast/continuous/MultivariateDiffusionModel.java +++ b/src/beastclassic/continuous/MultivariateDiffusionModel.java @@ -1,12 +1,12 @@ -package beast.continuous; +package beastclassic.continuous; import beast.base.core.Description; import beast.base.core.Input; import beast.base.core.Input.Validate; import beast.base.inference.parameter.RealParameter; -import beast.evolution.substitutionmodel.*; +import beastclassic.dr.math.distributions.MultivariateNormalDistribution; +import beastclassic.evolution.substitutionmodel.ContinuousSubstitutionModel; import beast.base.evolution.tree.Tree; -import dr.math.distributions.MultivariateNormalDistribution; diff --git a/src/beast/continuous/SampledMultivariateTraitLikelihood.java b/src/beastclassic/continuous/SampledMultivariateTraitLikelihood.java similarity index 99% rename from src/beast/continuous/SampledMultivariateTraitLikelihood.java rename to src/beastclassic/continuous/SampledMultivariateTraitLikelihood.java index ea35f81..004f9cc 100644 --- a/src/beast/continuous/SampledMultivariateTraitLikelihood.java +++ b/src/beastclassic/continuous/SampledMultivariateTraitLikelihood.java @@ -1,4 +1,4 @@ -package beast.continuous; +package beastclassic.continuous; //import dr.evolution.tree.NodeRef; //import dr.evolution.tree.Tree; diff --git a/src/dr/math/GammaFunction.java b/src/beastclassic/dr/GammaFunction.java similarity index 99% rename from src/dr/math/GammaFunction.java rename to src/beastclassic/dr/GammaFunction.java index 878cc63..ec10574 100644 --- a/src/dr/math/GammaFunction.java +++ b/src/beastclassic/dr/GammaFunction.java @@ -23,7 +23,7 @@ * Boston, MA 02110-1301 USA */ -package dr.math; +package beastclassic.dr; import beast.base.core.Description; diff --git a/src/dr/evomodel/continuous/MissingTraits.java b/src/beastclassic/dr/evolmodel/continuous/MissingTraits.java similarity index 97% rename from src/dr/evomodel/continuous/MissingTraits.java rename to src/beastclassic/dr/evolmodel/continuous/MissingTraits.java index d1da0d5..280f50f 100644 --- a/src/dr/evomodel/continuous/MissingTraits.java +++ b/src/beastclassic/dr/evolmodel/continuous/MissingTraits.java @@ -23,15 +23,15 @@ * Boston, MA 02110-1301 USA */ -package dr.evomodel.continuous; +package beastclassic.dr.evolmodel.continuous; import java.util.Arrays; import java.util.List; import java.util.logging.Logger; -import beast.continuous.IntegratedMultivariateTraitLikelihood; import beast.base.evolution.tree.TreeInterface; +import beastclassic.continuous.IntegratedMultivariateTraitLikelihood; /** * @author Marc A. Suchard diff --git a/src/dr/math/distributions/MultivariateDistribution.java b/src/beastclassic/dr/math/distributions/MultivariateDistribution.java similarity index 83% rename from src/dr/math/distributions/MultivariateDistribution.java rename to src/beastclassic/dr/math/distributions/MultivariateDistribution.java index 81d43f9..16d3cdd 100644 --- a/src/dr/math/distributions/MultivariateDistribution.java +++ b/src/beastclassic/dr/math/distributions/MultivariateDistribution.java @@ -1,4 +1,4 @@ -package dr.math.distributions; +package beastclassic.dr.math.distributions; /** * @author Marc A. Suchard diff --git a/src/dr/math/distributions/MultivariateNormalDistribution.java b/src/beastclassic/dr/math/distributions/MultivariateNormalDistribution.java similarity index 99% rename from src/dr/math/distributions/MultivariateNormalDistribution.java rename to src/beastclassic/dr/math/distributions/MultivariateNormalDistribution.java index 488bb81..72cf421 100644 --- a/src/dr/math/distributions/MultivariateNormalDistribution.java +++ b/src/beastclassic/dr/math/distributions/MultivariateNormalDistribution.java @@ -1,4 +1,4 @@ -package dr.math.distributions; +package beastclassic.dr.math.distributions; import beast.base.core.Description; diff --git a/src/dr/math/distributions/WishartDistribution.java b/src/beastclassic/dr/math/distributions/WishartDistribution.java similarity index 99% rename from src/dr/math/distributions/WishartDistribution.java rename to src/beastclassic/dr/math/distributions/WishartDistribution.java index 55ddea0..a9ccde0 100644 --- a/src/dr/math/distributions/WishartDistribution.java +++ b/src/beastclassic/dr/math/distributions/WishartDistribution.java @@ -1,4 +1,4 @@ -package dr.math.distributions; +package beastclassic.dr.math.distributions; import org.apache.commons.math.distribution.GammaDistribution; @@ -9,10 +9,7 @@ import beast.base.math.matrixalgebra.IllegalDimension; import beast.base.math.matrixalgebra.Matrix; import beast.base.util.Randomizer; - - - -import dr.math.GammaFunction; +import beastclassic.dr.GammaFunction; /** * @author Marc Suchard diff --git a/src/dr/math/distributions/WishartSufficientStatistics.java b/src/beastclassic/dr/math/distributions/WishartSufficientStatistics.java similarity index 94% rename from src/dr/math/distributions/WishartSufficientStatistics.java rename to src/beastclassic/dr/math/distributions/WishartSufficientStatistics.java index 1b19e48..2173082 100644 --- a/src/dr/math/distributions/WishartSufficientStatistics.java +++ b/src/beastclassic/dr/math/distributions/WishartSufficientStatistics.java @@ -1,4 +1,4 @@ -package dr.math.distributions; +package beastclassic.dr.math.distributions; import java.util.Arrays; diff --git a/src/dr/math/util/ArcCos.java b/src/beastclassic/dr/util/ArcCos.java similarity index 99% rename from src/dr/math/util/ArcCos.java rename to src/beastclassic/dr/util/ArcCos.java index 5c2c65a..6f09289 100644 --- a/src/dr/math/util/ArcCos.java +++ b/src/beastclassic/dr/util/ArcCos.java @@ -1,4 +1,4 @@ -package dr.math.util; +package beastclassic.dr.util; import static java.lang.Math.sqrt; diff --git a/src/beast/evolution/alignment/AlignmentFromTrait.java b/src/beastclassic/evolution/alignment/AlignmentFromTrait.java similarity index 98% rename from src/beast/evolution/alignment/AlignmentFromTrait.java rename to src/beastclassic/evolution/alignment/AlignmentFromTrait.java index e68ba53..1f3b351 100644 --- a/src/beast/evolution/alignment/AlignmentFromTrait.java +++ b/src/beastclassic/evolution/alignment/AlignmentFromTrait.java @@ -1,4 +1,4 @@ -package beast.evolution.alignment; +package beastclassic.evolution.alignment; import java.util.ArrayList; import java.util.Arrays; diff --git a/src/beast/evolution/alignment/AlignmentFromTraitMap.java b/src/beastclassic/evolution/alignment/AlignmentFromTraitMap.java similarity index 92% rename from src/beast/evolution/alignment/AlignmentFromTraitMap.java rename to src/beastclassic/evolution/alignment/AlignmentFromTraitMap.java index 92bc91e..80976a7 100644 --- a/src/beast/evolution/alignment/AlignmentFromTraitMap.java +++ b/src/beastclassic/evolution/alignment/AlignmentFromTraitMap.java @@ -1,4 +1,4 @@ -package beast.evolution.alignment; +package beastclassic.evolution.alignment; import java.util.ArrayList; @@ -8,8 +8,8 @@ import beast.base.core.Input; import beast.base.core.Input.Validate; import beast.base.evolution.alignment.Alignment; -import beast.evolution.datatype.ContinuousDataType; -import beast.evolution.tree.TreeTraitMap; +import beastclassic.evolution.tree.TreeTraitMap; +import beastclassic.evolution.datatype.ContinuousDataType; diff --git a/src/beast/evolution/datatype/ContinuousDataType.java b/src/beastclassic/evolution/datatype/ContinuousDataType.java similarity index 97% rename from src/beast/evolution/datatype/ContinuousDataType.java rename to src/beastclassic/evolution/datatype/ContinuousDataType.java index cf1e6cd..675f3d9 100644 --- a/src/beast/evolution/datatype/ContinuousDataType.java +++ b/src/beastclassic/evolution/datatype/ContinuousDataType.java @@ -1,4 +1,4 @@ -package beast.evolution.datatype; +package beastclassic.evolution.datatype; import java.util.List; diff --git a/src/beast/evolution/datatype/LocationDataType.java b/src/beastclassic/evolution/datatype/LocationDataType.java similarity index 93% rename from src/beast/evolution/datatype/LocationDataType.java rename to src/beastclassic/evolution/datatype/LocationDataType.java index c72ebfc..fb5f0a2 100644 --- a/src/beast/evolution/datatype/LocationDataType.java +++ b/src/beastclassic/evolution/datatype/LocationDataType.java @@ -1,4 +1,4 @@ -package beast.evolution.datatype; +package beastclassic.evolution.datatype; import beast.base.core.Description; diff --git a/src/beast/evolution/likelihood/AncestralSequenceLogger.java b/src/beastclassic/evolution/likelihood/AncestralSequenceLogger.java similarity index 99% rename from src/beast/evolution/likelihood/AncestralSequenceLogger.java rename to src/beastclassic/evolution/likelihood/AncestralSequenceLogger.java index bfccf41..bd7cf10 100644 --- a/src/beast/evolution/likelihood/AncestralSequenceLogger.java +++ b/src/beastclassic/evolution/likelihood/AncestralSequenceLogger.java @@ -1,4 +1,4 @@ -package beast.evolution.likelihood; +package beastclassic.evolution.likelihood; import java.io.PrintStream; diff --git a/src/beast/evolution/likelihood/AncestralStateTreeLikelihood.java b/src/beastclassic/evolution/likelihood/AncestralStateTreeLikelihood.java similarity index 99% rename from src/beast/evolution/likelihood/AncestralStateTreeLikelihood.java rename to src/beastclassic/evolution/likelihood/AncestralStateTreeLikelihood.java index 1c2665a..aedbb78 100644 --- a/src/beast/evolution/likelihood/AncestralStateTreeLikelihood.java +++ b/src/beastclassic/evolution/likelihood/AncestralStateTreeLikelihood.java @@ -1,4 +1,4 @@ -package beast.evolution.likelihood; +package beastclassic.evolution.likelihood; @@ -23,8 +23,8 @@ import beast.base.evolution.tree.Tree; import beast.base.evolution.tree.TreeInterface; import beast.base.util.Randomizer; -import beast.evolution.tree.TreeTrait; -import beast.evolution.tree.TreeTraitProvider; +import beastclassic.evolution.tree.TreeTrait; +import beastclassic.evolution.tree.TreeTraitProvider; /** * @author Marc A. Suchard diff --git a/src/beast/evolution/likelihood/LeafTrait.java b/src/beastclassic/evolution/likelihood/LeafTrait.java similarity index 93% rename from src/beast/evolution/likelihood/LeafTrait.java rename to src/beastclassic/evolution/likelihood/LeafTrait.java index 68610bd..5ba2e9d 100644 --- a/src/beast/evolution/likelihood/LeafTrait.java +++ b/src/beastclassic/evolution/likelihood/LeafTrait.java @@ -1,4 +1,4 @@ -package beast.evolution.likelihood; +package beastclassic.evolution.likelihood; import beast.base.inference.CalculationNode; import beast.base.core.Description; diff --git a/src/beast/evolution/operators/BitFlipBSSVSOperator.java b/src/beastclassic/evolution/operators/BitFlipBSSVSOperator.java similarity index 98% rename from src/beast/evolution/operators/BitFlipBSSVSOperator.java rename to src/beastclassic/evolution/operators/BitFlipBSSVSOperator.java index d7f5629..3d92925 100644 --- a/src/beast/evolution/operators/BitFlipBSSVSOperator.java +++ b/src/beastclassic/evolution/operators/BitFlipBSSVSOperator.java @@ -1,4 +1,4 @@ -package beast.evolution.operators; +package beastclassic.evolution.operators; import beast.base.core.Description; import beast.base.core.Input; diff --git a/src/beast/evolution/operators/GMRFMultilocusSkyrideBlockUpdateOperator.java b/src/beastclassic/evolution/operators/GMRFMultilocusSkyrideBlockUpdateOperator.java similarity index 99% rename from src/beast/evolution/operators/GMRFMultilocusSkyrideBlockUpdateOperator.java rename to src/beastclassic/evolution/operators/GMRFMultilocusSkyrideBlockUpdateOperator.java index 24e41e0..0e0ba11 100644 --- a/src/beast/evolution/operators/GMRFMultilocusSkyrideBlockUpdateOperator.java +++ b/src/beastclassic/evolution/operators/GMRFMultilocusSkyrideBlockUpdateOperator.java @@ -23,7 +23,7 @@ * Boston, MA 02110-1301 USA */ -package beast.evolution.operators; +package beastclassic.evolution.operators; import no.uib.cipr.matrix.*; @@ -39,8 +39,8 @@ import beast.base.inference.Operator; import beast.base.inference.StateNode; import beast.base.inference.parameter.RealParameter; -import beast.evolution.tree.coalescent.GMRFMultilocusSkyrideLikelihood; import beast.base.util.Randomizer; +import beastclassic.evolution.tree.coalescent.GMRFMultilocusSkyrideLikelihood; /* A Metropolis-Hastings operator to update the log population sizes and precision parameter jointly under a Gaussian Markov random field prior * diff --git a/src/beast/evolution/operators/GMRFSkyrideBlockUpdateOperator.java b/src/beastclassic/evolution/operators/GMRFSkyrideBlockUpdateOperator.java similarity index 99% rename from src/beast/evolution/operators/GMRFSkyrideBlockUpdateOperator.java rename to src/beastclassic/evolution/operators/GMRFSkyrideBlockUpdateOperator.java index 3461fb1..2ff5730 100644 --- a/src/beast/evolution/operators/GMRFSkyrideBlockUpdateOperator.java +++ b/src/beastclassic/evolution/operators/GMRFSkyrideBlockUpdateOperator.java @@ -1,4 +1,4 @@ -package beast.evolution.operators; +package beastclassic.evolution.operators; import no.uib.cipr.matrix.*; @@ -14,8 +14,8 @@ import beast.base.inference.StateNode; import beast.base.core.Input.Validate; import beast.base.inference.parameter.RealParameter; -import beast.evolution.tree.coalescent.GMRFSkyrideLikelihood; import beast.base.util.Randomizer; +import beastclassic.evolution.tree.coalescent.GMRFSkyrideLikelihood; diff --git a/src/beast/evolution/operators/GeneralIntegerOperator.java b/src/beastclassic/evolution/operators/GeneralIntegerOperator.java similarity index 98% rename from src/beast/evolution/operators/GeneralIntegerOperator.java rename to src/beastclassic/evolution/operators/GeneralIntegerOperator.java index fd6f5df..2980e7a 100644 --- a/src/beast/evolution/operators/GeneralIntegerOperator.java +++ b/src/beastclassic/evolution/operators/GeneralIntegerOperator.java @@ -1,4 +1,4 @@ -package beast.evolution.operators; +package beastclassic.evolution.operators; import java.util.Arrays; diff --git a/src/beast/evolution/operators/PickIndicatorOperator.java b/src/beastclassic/evolution/operators/PickIndicatorOperator.java similarity index 97% rename from src/beast/evolution/operators/PickIndicatorOperator.java rename to src/beastclassic/evolution/operators/PickIndicatorOperator.java index 9d1c8b3..284a12a 100644 --- a/src/beast/evolution/operators/PickIndicatorOperator.java +++ b/src/beastclassic/evolution/operators/PickIndicatorOperator.java @@ -1,4 +1,4 @@ -package beast.evolution.operators; +package beastclassic.evolution.operators; import java.util.HashSet; diff --git a/src/beast/evolution/operators/PrecisionMatrixGibbsOperator.java b/src/beastclassic/evolution/operators/PrecisionMatrixGibbsOperator.java similarity index 97% rename from src/beast/evolution/operators/PrecisionMatrixGibbsOperator.java rename to src/beastclassic/evolution/operators/PrecisionMatrixGibbsOperator.java index 99cf9ac..a125578 100644 --- a/src/beast/evolution/operators/PrecisionMatrixGibbsOperator.java +++ b/src/beastclassic/evolution/operators/PrecisionMatrixGibbsOperator.java @@ -23,12 +23,13 @@ * Boston, MA 02110-1301 USA */ -package beast.evolution.operators; +package beastclassic.evolution.operators; -import beast.continuous.AbstractMultivariateTraitLikelihood; -import beast.evolution.tree.TreeTraitMap; +import beastclassic.evolution.tree.TreeTraitMap; +import beastclassic.continuous.AbstractMultivariateTraitLikelihood; +import beastclassic.math.distributions.WishartDistribution; import beast.base.core.Description; import beast.base.core.Input; import beast.base.inference.Operator; @@ -37,7 +38,6 @@ import beast.base.evolution.tree.Node; import beast.base.evolution.tree.Tree; import beast.base.evolution.tree.TreeInterface; -import beast.math.distributions.WishartDistribution; import beast.base.math.matrixalgebra.IllegalDimension; import beast.base.math.matrixalgebra.SymmetricMatrix; diff --git a/src/beast/evolution/operators/RegressionGibbsEffectOperator.java b/src/beastclassic/evolution/operators/RegressionGibbsEffectOperator.java similarity index 95% rename from src/beast/evolution/operators/RegressionGibbsEffectOperator.java rename to src/beastclassic/evolution/operators/RegressionGibbsEffectOperator.java index 65c28f6..61dcddb 100644 --- a/src/beast/evolution/operators/RegressionGibbsEffectOperator.java +++ b/src/beastclassic/evolution/operators/RegressionGibbsEffectOperator.java @@ -1,14 +1,14 @@ -package beast.evolution.operators; +package beastclassic.evolution.operators; import beast.base.core.Description; import beast.base.core.Input; import beast.base.inference.Operator; import beast.base.inference.parameter.RealParameter; -import beast.inference.distribution.LinearRegression; -import dr.math.distributions.MultivariateDistribution; -import dr.math.distributions.MultivariateNormalDistribution; import beast.base.math.matrixalgebra.SymmetricMatrix; +import beastclassic.dr.math.distributions.MultivariateDistribution; +import beastclassic.dr.math.distributions.MultivariateNormalDistribution; +import beastclassic.inference.distribution.LinearRegression; /** diff --git a/src/beast/evolution/operators/RegressionGibbsPrecisionOperator.java b/src/beastclassic/evolution/operators/RegressionGibbsPrecisionOperator.java similarity index 95% rename from src/beast/evolution/operators/RegressionGibbsPrecisionOperator.java rename to src/beastclassic/evolution/operators/RegressionGibbsPrecisionOperator.java index 6ad1c8e..2728083 100644 --- a/src/beast/evolution/operators/RegressionGibbsPrecisionOperator.java +++ b/src/beastclassic/evolution/operators/RegressionGibbsPrecisionOperator.java @@ -1,4 +1,4 @@ -package beast.evolution.operators; +package beastclassic.evolution.operators; @@ -8,7 +8,8 @@ import beast.base.inference.parameter.RealParameter; import beast.base.inference.distribution.Gamma; import beast.base.util.Randomizer; -import beast.inference.distribution.*; +import beastclassic.inference.distribution.*; +import beastclassic.inference.distribution.LinearRegression; /** diff --git a/src/beast/evolution/operators/RootTraitRandowWalkOperator.java b/src/beastclassic/evolution/operators/RootTraitRandowWalkOperator.java similarity index 94% rename from src/beast/evolution/operators/RootTraitRandowWalkOperator.java rename to src/beastclassic/evolution/operators/RootTraitRandowWalkOperator.java index 115664c..4d800e5 100644 --- a/src/beast/evolution/operators/RootTraitRandowWalkOperator.java +++ b/src/beastclassic/evolution/operators/RootTraitRandowWalkOperator.java @@ -1,4 +1,4 @@ -package beast.evolution.operators; +package beastclassic.evolution.operators; import beast.base.core.Description; import beast.base.core.Input; @@ -7,7 +7,7 @@ import beast.base.inference.operator.RealRandomWalkOperator; import beast.base.evolution.tree.Node; import beast.base.util.Randomizer; -import beast.evolution.tree.TreeTraitMap; +import beastclassic.evolution.tree.TreeTraitMap; @Description("Random walk opeartor root of a tree trait") public class RootTraitRandowWalkOperator extends RealRandomWalkOperator { diff --git a/src/beast/evolution/operators/SphereRandomWalker.java b/src/beastclassic/evolution/operators/SphereRandomWalker.java similarity index 99% rename from src/beast/evolution/operators/SphereRandomWalker.java rename to src/beastclassic/evolution/operators/SphereRandomWalker.java index 387389c..a1f93da 100644 --- a/src/beast/evolution/operators/SphereRandomWalker.java +++ b/src/beastclassic/evolution/operators/SphereRandomWalker.java @@ -1,4 +1,4 @@ -package beast.evolution.operators; +package beastclassic.evolution.operators; import java.text.DecimalFormat; diff --git a/src/beast/evolution/operators/TraitGibbsOperator.java b/src/beastclassic/evolution/operators/TraitGibbsOperator.java similarity index 96% rename from src/beast/evolution/operators/TraitGibbsOperator.java rename to src/beastclassic/evolution/operators/TraitGibbsOperator.java index 356d242..23d5ffd 100644 --- a/src/beast/evolution/operators/TraitGibbsOperator.java +++ b/src/beastclassic/evolution/operators/TraitGibbsOperator.java @@ -23,7 +23,7 @@ * Boston, MA 02110-1301 USA */ -package beast.evolution.operators; +package beastclassic.evolution.operators; //import dr.evomodel.continuous.AbstractMultivariateTraitLikelihood; //import dr.evomodel.continuous.SampledMultivariateTraitLikelihood; @@ -33,24 +33,23 @@ //import dr.inference.distribution.MultivariateDistributionLikelihood; import beast.base.core.Description; -import dr.math.distributions.MultivariateDistribution; -//import dr.math.distributions.MultivariateNormalDistribution; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; -import beast.continuous.SampledMultivariateTraitLikelihood; -import beast.evolution.tree.TreeTraitMap; +import beastclassic.evolution.tree.TreeTraitMap; import beast.base.core.Input; import beast.base.inference.Operator; import beast.base.core.Input.Validate; import beast.base.inference.parameter.RealParameter; import beast.base.evolution.tree.Node; import beast.base.evolution.tree.Tree; -import beast.geo.GeoSpatialDistribution; -import beast.math.distributions.MultivariateNormalDistribution; +import beastclassic.continuous.SampledMultivariateTraitLikelihood; +import beastclassic.dr.math.distributions.MultivariateDistribution; +import beastclassic.geo.GeoSpatialDistribution; +import beastclassic.math.distributions.MultivariateNormalDistribution; import beast.base.math.matrixalgebra.SymmetricMatrix; import beast.base.util.Randomizer; diff --git a/src/beast/evolution/speciation/BirthDeathSerialSampling.java b/src/beastclassic/evolution/speciation/BirthDeathSerialSampling.java similarity index 99% rename from src/beast/evolution/speciation/BirthDeathSerialSampling.java rename to src/beastclassic/evolution/speciation/BirthDeathSerialSampling.java index 590d3bc..a95d232 100644 --- a/src/beast/evolution/speciation/BirthDeathSerialSampling.java +++ b/src/beastclassic/evolution/speciation/BirthDeathSerialSampling.java @@ -1,4 +1,4 @@ -package beast.evolution.speciation; +package beastclassic.evolution.speciation; import java.util.Set; diff --git a/src/beast/evolution/substitutionmodel/ContinuousSubstitutionModel.java b/src/beastclassic/evolution/substitutionmodel/ContinuousSubstitutionModel.java similarity index 92% rename from src/beast/evolution/substitutionmodel/ContinuousSubstitutionModel.java rename to src/beastclassic/evolution/substitutionmodel/ContinuousSubstitutionModel.java index 4e241ee..dd8543f 100644 --- a/src/beast/evolution/substitutionmodel/ContinuousSubstitutionModel.java +++ b/src/beastclassic/evolution/substitutionmodel/ContinuousSubstitutionModel.java @@ -1,12 +1,12 @@ -package beast.evolution.substitutionmodel; +package beastclassic.evolution.substitutionmodel; import beast.base.core.Description; import beast.base.core.Input.Validate; -import beast.evolution.datatype.ContinuousDataType; import beast.base.evolution.datatype.DataType; import beast.base.evolution.substitutionmodel.EigenDecomposition; import beast.base.evolution.substitutionmodel.SubstitutionModel; import beast.base.evolution.tree.Node; +import beastclassic.evolution.datatype.ContinuousDataType; @Description("Substitution model that can deal with an alignment containing continuous data") abstract public class ContinuousSubstitutionModel extends SubstitutionModel.Base { diff --git a/src/beast/evolution/substitutionmodel/FLU.java b/src/beastclassic/evolution/substitutionmodel/FLU.java similarity index 99% rename from src/beast/evolution/substitutionmodel/FLU.java rename to src/beastclassic/evolution/substitutionmodel/FLU.java index cdd5c0a..41a03c6 100644 --- a/src/beast/evolution/substitutionmodel/FLU.java +++ b/src/beastclassic/evolution/substitutionmodel/FLU.java @@ -1,4 +1,4 @@ -package beast.evolution.substitutionmodel; +package beastclassic.evolution.substitutionmodel; import beast.base.core.Description; import beast.base.evolution.datatype.Aminoacid; diff --git a/src/beast/evolution/substitutionmodel/GLM.java b/src/beastclassic/evolution/substitutionmodel/GLM.java similarity index 99% rename from src/beast/evolution/substitutionmodel/GLM.java rename to src/beastclassic/evolution/substitutionmodel/GLM.java index 0cfa84f..21c2bb4 100644 --- a/src/beast/evolution/substitutionmodel/GLM.java +++ b/src/beastclassic/evolution/substitutionmodel/GLM.java @@ -1,4 +1,4 @@ -package beast.evolution.substitutionmodel; +package beastclassic.evolution.substitutionmodel; diff --git a/src/beast/evolution/substitutionmodel/GLMBasedSubstModel.java b/src/beastclassic/evolution/substitutionmodel/GLMBasedSubstModel.java similarity index 96% rename from src/beast/evolution/substitutionmodel/GLMBasedSubstModel.java rename to src/beastclassic/evolution/substitutionmodel/GLMBasedSubstModel.java index b561075..c68407b 100644 --- a/src/beast/evolution/substitutionmodel/GLMBasedSubstModel.java +++ b/src/beastclassic/evolution/substitutionmodel/GLMBasedSubstModel.java @@ -1,4 +1,4 @@ -package beast.evolution.substitutionmodel; +package beastclassic.evolution.substitutionmodel; import beast.base.core.Description; diff --git a/src/beast/evolution/substitutionmodel/GlmModel.java b/src/beastclassic/evolution/substitutionmodel/GlmModel.java similarity index 97% rename from src/beast/evolution/substitutionmodel/GlmModel.java rename to src/beastclassic/evolution/substitutionmodel/GlmModel.java index 1aa1dd7..42f6575 100644 --- a/src/beast/evolution/substitutionmodel/GlmModel.java +++ b/src/beastclassic/evolution/substitutionmodel/GlmModel.java @@ -1,4 +1,4 @@ -package beast.evolution.substitutionmodel; +package beastclassic.evolution.substitutionmodel; import java.util.ArrayList; import java.util.List; diff --git a/src/beast/evolution/substitutionmodel/LG.java b/src/beastclassic/evolution/substitutionmodel/LG.java similarity index 99% rename from src/beast/evolution/substitutionmodel/LG.java rename to src/beastclassic/evolution/substitutionmodel/LG.java index 1da18d9..7e55c6e 100644 --- a/src/beast/evolution/substitutionmodel/LG.java +++ b/src/beastclassic/evolution/substitutionmodel/LG.java @@ -23,7 +23,7 @@ * Boston, MA 02110-1301 USA */ -package beast.evolution.substitutionmodel; +package beastclassic.evolution.substitutionmodel; import beast.base.core.Citation; import beast.base.core.Description; diff --git a/src/beast/evolution/substitutionmodel/LogLinear.java b/src/beastclassic/evolution/substitutionmodel/LogLinear.java similarity index 98% rename from src/beast/evolution/substitutionmodel/LogLinear.java rename to src/beastclassic/evolution/substitutionmodel/LogLinear.java index 130fab9..ce96580 100644 --- a/src/beast/evolution/substitutionmodel/LogLinear.java +++ b/src/beastclassic/evolution/substitutionmodel/LogLinear.java @@ -1,4 +1,4 @@ -package beast.evolution.substitutionmodel; +package beastclassic.evolution.substitutionmodel; import java.io.PrintStream; diff --git a/src/beast/evolution/substitutionmodel/RobustEigenSystem.java b/src/beastclassic/evolution/substitutionmodel/RobustEigenSystem.java similarity index 97% rename from src/beast/evolution/substitutionmodel/RobustEigenSystem.java rename to src/beastclassic/evolution/substitutionmodel/RobustEigenSystem.java index fcf0f0c..8372223 100644 --- a/src/beast/evolution/substitutionmodel/RobustEigenSystem.java +++ b/src/beastclassic/evolution/substitutionmodel/RobustEigenSystem.java @@ -1,4 +1,4 @@ -package beast.evolution.substitutionmodel; +package beastclassic.evolution.substitutionmodel; import beast.base.evolution.substitutionmodel.EigenDecomposition; import beast.base.evolution.substitutionmodel.EigenSystem; diff --git a/src/beast/evolution/substitutionmodel/SVSGeneralSubstitutionModel.java b/src/beastclassic/evolution/substitutionmodel/SVSGeneralSubstitutionModel.java similarity index 98% rename from src/beast/evolution/substitutionmodel/SVSGeneralSubstitutionModel.java rename to src/beastclassic/evolution/substitutionmodel/SVSGeneralSubstitutionModel.java index d22e020..a5ed746 100644 --- a/src/beast/evolution/substitutionmodel/SVSGeneralSubstitutionModel.java +++ b/src/beastclassic/evolution/substitutionmodel/SVSGeneralSubstitutionModel.java @@ -1,4 +1,4 @@ -package beast.evolution.substitutionmodel; +package beastclassic.evolution.substitutionmodel; @@ -9,9 +9,9 @@ import beast.base.core.Input.Validate; import beast.base.inference.parameter.BooleanParameter; import beast.base.inference.parameter.Parameter; +import beastclassic.inference.BayesianStochasticSearchVariableSelection; import beast.base.core.Log; import beast.base.evolution.substitutionmodel.DefaultEigenSystem; -import beast.inference.BayesianStochasticSearchVariableSelection; import beastlabs.evolution.substitutionmodel.ComplexSubstitutionModel; diff --git a/src/beast/evolution/substitutionmodel/SVSGeneralSubstitutionModelLogger.java b/src/beastclassic/evolution/substitutionmodel/SVSGeneralSubstitutionModelLogger.java similarity index 98% rename from src/beast/evolution/substitutionmodel/SVSGeneralSubstitutionModelLogger.java rename to src/beastclassic/evolution/substitutionmodel/SVSGeneralSubstitutionModelLogger.java index 598fb22..db81369 100644 --- a/src/beast/evolution/substitutionmodel/SVSGeneralSubstitutionModelLogger.java +++ b/src/beastclassic/evolution/substitutionmodel/SVSGeneralSubstitutionModelLogger.java @@ -15,7 +15,7 @@ * along with this program. If not, see . */ -package beast.evolution.substitutionmodel; +package beastclassic.evolution.substitutionmodel; import beast.base.core.BEASTObject; import beast.base.core.Description; diff --git a/src/beast/evolution/tree/RootTrait.java b/src/beastclassic/evolution/tree/RootTrait.java similarity index 97% rename from src/beast/evolution/tree/RootTrait.java rename to src/beastclassic/evolution/tree/RootTrait.java index e575841..a8c374a 100644 --- a/src/beast/evolution/tree/RootTrait.java +++ b/src/beastclassic/evolution/tree/RootTrait.java @@ -1,4 +1,4 @@ -package beast.evolution.tree; +package beastclassic.evolution.tree; import java.io.PrintStream; diff --git a/src/beast/evolution/tree/TreeTrait.java b/src/beastclassic/evolution/tree/TreeTrait.java similarity index 99% rename from src/beast/evolution/tree/TreeTrait.java rename to src/beastclassic/evolution/tree/TreeTrait.java index 762ff06..57e6daf 100644 --- a/src/beast/evolution/tree/TreeTrait.java +++ b/src/beastclassic/evolution/tree/TreeTrait.java @@ -1,4 +1,4 @@ -package beast.evolution.tree; +package beastclassic.evolution.tree; diff --git a/src/beast/evolution/tree/TreeTraitMap.java b/src/beastclassic/evolution/tree/TreeTraitMap.java similarity index 99% rename from src/beast/evolution/tree/TreeTraitMap.java rename to src/beastclassic/evolution/tree/TreeTraitMap.java index 2d2ed12..cdd0d89 100644 --- a/src/beast/evolution/tree/TreeTraitMap.java +++ b/src/beastclassic/evolution/tree/TreeTraitMap.java @@ -1,4 +1,4 @@ -package beast.evolution.tree; +package beastclassic.evolution.tree; import java.util.List; diff --git a/src/beast/evolution/tree/TreeTraitProvider.java b/src/beastclassic/evolution/tree/TreeTraitProvider.java similarity index 99% rename from src/beast/evolution/tree/TreeTraitProvider.java rename to src/beastclassic/evolution/tree/TreeTraitProvider.java index 951bc03..032d335 100644 --- a/src/beast/evolution/tree/TreeTraitProvider.java +++ b/src/beastclassic/evolution/tree/TreeTraitProvider.java @@ -1,4 +1,4 @@ -package beast.evolution.tree; +package beastclassic.evolution.tree; import java.util.Collection; import java.util.HashMap; diff --git a/src/beast/evolution/tree/TreeWithTraitLogger.java b/src/beastclassic/evolution/tree/TreeWithTraitLogger.java similarity index 99% rename from src/beast/evolution/tree/TreeWithTraitLogger.java rename to src/beastclassic/evolution/tree/TreeWithTraitLogger.java index 05abcc5..32f5cea 100644 --- a/src/beast/evolution/tree/TreeWithTraitLogger.java +++ b/src/beastclassic/evolution/tree/TreeWithTraitLogger.java @@ -1,4 +1,4 @@ -package beast.evolution.tree; +package beastclassic.evolution.tree; import java.util.ArrayList; import java.util.List; diff --git a/src/beast/evolution/tree/coalescent/Expansion.java b/src/beastclassic/evolution/tree/coalescent/Expansion.java similarity index 97% rename from src/beast/evolution/tree/coalescent/Expansion.java rename to src/beastclassic/evolution/tree/coalescent/Expansion.java index 769c11b..d7b1f23 100644 --- a/src/beast/evolution/tree/coalescent/Expansion.java +++ b/src/beastclassic/evolution/tree/coalescent/Expansion.java @@ -1,4 +1,4 @@ -package beast.evolution.tree.coalescent; +package beastclassic.evolution.tree.coalescent; import java.util.ArrayList; diff --git a/src/beast/evolution/tree/coalescent/GMRFMultilocusSkyrideLikelihood.java b/src/beastclassic/evolution/tree/coalescent/GMRFMultilocusSkyrideLikelihood.java similarity index 99% rename from src/beast/evolution/tree/coalescent/GMRFMultilocusSkyrideLikelihood.java rename to src/beastclassic/evolution/tree/coalescent/GMRFMultilocusSkyrideLikelihood.java index edd5821..53feec7 100644 --- a/src/beast/evolution/tree/coalescent/GMRFMultilocusSkyrideLikelihood.java +++ b/src/beastclassic/evolution/tree/coalescent/GMRFMultilocusSkyrideLikelihood.java @@ -1,4 +1,4 @@ -package beast.evolution.tree.coalescent; +package beastclassic.evolution.tree.coalescent; import beast.base.core.Citation; import beast.base.core.Description; diff --git a/src/beast/evolution/tree/coalescent/GMRFSkyrideLikelihood.java b/src/beastclassic/evolution/tree/coalescent/GMRFSkyrideLikelihood.java similarity index 99% rename from src/beast/evolution/tree/coalescent/GMRFSkyrideLikelihood.java rename to src/beastclassic/evolution/tree/coalescent/GMRFSkyrideLikelihood.java index c3e4696..0a3e807 100644 --- a/src/beast/evolution/tree/coalescent/GMRFSkyrideLikelihood.java +++ b/src/beastclassic/evolution/tree/coalescent/GMRFSkyrideLikelihood.java @@ -23,7 +23,7 @@ * Boston, MA 02110-1301 USA */ -package beast.evolution.tree.coalescent; +package beastclassic.evolution.tree.coalescent; diff --git a/src/beast/evolution/tree/coalescent/LogisticGrowth.java b/src/beastclassic/evolution/tree/coalescent/LogisticGrowth.java similarity index 98% rename from src/beast/evolution/tree/coalescent/LogisticGrowth.java rename to src/beastclassic/evolution/tree/coalescent/LogisticGrowth.java index 1aea325..a324e74 100644 --- a/src/beast/evolution/tree/coalescent/LogisticGrowth.java +++ b/src/beastclassic/evolution/tree/coalescent/LogisticGrowth.java @@ -23,7 +23,7 @@ * Boston, MA 02110-1301 USA */ -package beast.evolution.tree.coalescent; +package beastclassic.evolution.tree.coalescent; import java.util.ArrayList; diff --git a/src/beast/geo/GeoSpatialDistribution.java b/src/beastclassic/geo/GeoSpatialDistribution.java similarity index 96% rename from src/beast/geo/GeoSpatialDistribution.java rename to src/beastclassic/geo/GeoSpatialDistribution.java index 4645679..15c7910 100644 --- a/src/beast/geo/GeoSpatialDistribution.java +++ b/src/beastclassic/geo/GeoSpatialDistribution.java @@ -1,4 +1,4 @@ -package beast.geo; +package beastclassic.geo; @@ -14,7 +14,7 @@ import beast.base.core.Input; import beast.base.core.Input.Validate; import beast.base.inference.CalculationNode; -import dr.math.distributions.MultivariateDistribution; +import beastclassic.dr.math.distributions.MultivariateDistribution; @Description("Distribution over a geographical area") diff --git a/src/beast/geo/Polygon2D.java b/src/beastclassic/geo/Polygon2D.java similarity index 99% rename from src/beast/geo/Polygon2D.java rename to src/beastclassic/geo/Polygon2D.java index d0a08ba..3bd6c2e 100644 --- a/src/beast/geo/Polygon2D.java +++ b/src/beastclassic/geo/Polygon2D.java @@ -1,4 +1,4 @@ -package beast.geo; +package beastclassic.geo; import java.awt.*; diff --git a/src/beast/inference/BayesianStochasticSearchVariableSelection.java b/src/beastclassic/inference/BayesianStochasticSearchVariableSelection.java similarity index 99% rename from src/beast/inference/BayesianStochasticSearchVariableSelection.java rename to src/beastclassic/inference/BayesianStochasticSearchVariableSelection.java index 8652d40..e689d56 100644 --- a/src/beast/inference/BayesianStochasticSearchVariableSelection.java +++ b/src/beastclassic/inference/BayesianStochasticSearchVariableSelection.java @@ -1,4 +1,4 @@ -package beast.inference; +package beastclassic.inference; import beast.base.inference.CalculationNode; import beast.base.core.Description; diff --git a/src/beast/inference/distribution/GeneralizedLinearModel.java b/src/beastclassic/inference/distribution/GeneralizedLinearModel.java similarity index 99% rename from src/beast/inference/distribution/GeneralizedLinearModel.java rename to src/beastclassic/inference/distribution/GeneralizedLinearModel.java index e92638b..f03e2be 100644 --- a/src/beast/inference/distribution/GeneralizedLinearModel.java +++ b/src/beastclassic/inference/distribution/GeneralizedLinearModel.java @@ -1,4 +1,4 @@ -package beast.inference.distribution; +package beastclassic.inference.distribution; diff --git a/src/beast/inference/distribution/LinearRegression.java b/src/beastclassic/inference/distribution/LinearRegression.java similarity index 98% rename from src/beast/inference/distribution/LinearRegression.java rename to src/beastclassic/inference/distribution/LinearRegression.java index ac9c2a9..6d6216c 100644 --- a/src/beast/inference/distribution/LinearRegression.java +++ b/src/beastclassic/inference/distribution/LinearRegression.java @@ -1,4 +1,4 @@ -package beast.inference.distribution; +package beastclassic.inference.distribution; import beast.base.core.Description; diff --git a/src/beast/inference/distribution/LogisticRegression.java b/src/beastclassic/inference/distribution/LogisticRegression.java similarity index 95% rename from src/beast/inference/distribution/LogisticRegression.java rename to src/beastclassic/inference/distribution/LogisticRegression.java index 6d82841..19678a4 100644 --- a/src/beast/inference/distribution/LogisticRegression.java +++ b/src/beastclassic/inference/distribution/LogisticRegression.java @@ -1,4 +1,4 @@ -package beast.inference.distribution; +package beastclassic.inference.distribution; import beast.base.core.Description; diff --git a/src/beast/math/distributions/CTMCScalePrior.java b/src/beastclassic/math/distributions/CTMCScalePrior.java similarity index 98% rename from src/beast/math/distributions/CTMCScalePrior.java rename to src/beastclassic/math/distributions/CTMCScalePrior.java index b841c8c..2758f4c 100644 --- a/src/beast/math/distributions/CTMCScalePrior.java +++ b/src/beastclassic/math/distributions/CTMCScalePrior.java @@ -23,7 +23,7 @@ * Boston, MA 02110-1301 USA */ -package beast.math.distributions; +package beastclassic.math.distributions; import java.util.List; @@ -33,10 +33,10 @@ import beast.base.core.Input; import beast.base.inference.State; import beast.base.inference.parameter.RealParameter; +import beastclassic.dr.GammaFunction; import beast.base.evolution.substitutionmodel.SubstitutionModel; import beast.base.evolution.tree.Tree; import beast.base.evolution.tree.TreeUtils; -import dr.math.GammaFunction; /** * @author Alexander V. Alekseyenko (alexander.alekseyenko@gmail.com) diff --git a/src/beast/math/distributions/MultivariateNormalDistribution.java b/src/beastclassic/math/distributions/MultivariateNormalDistribution.java similarity index 91% rename from src/beast/math/distributions/MultivariateNormalDistribution.java rename to src/beastclassic/math/distributions/MultivariateNormalDistribution.java index aa9aa23..0ca188f 100644 --- a/src/beast/math/distributions/MultivariateNormalDistribution.java +++ b/src/beastclassic/math/distributions/MultivariateNormalDistribution.java @@ -1,4 +1,4 @@ -package beast.math.distributions; +package beastclassic.math.distributions; import java.util.List; @@ -20,13 +20,13 @@ public class MultivariateNormalDistribution extends Distribution { public Input precision = new Input("precision", "description here"); public Input argInput = new Input("arg", "argument of distribution"); - dr.math.distributions.MultivariateNormalDistribution multivariatenormaldistribution; + beastclassic.dr.math.distributions.MultivariateNormalDistribution multivariatenormaldistribution; Function arg; @Override public void initAndValidate() { - multivariatenormaldistribution = new dr.math.distributions.MultivariateNormalDistribution( + multivariatenormaldistribution = new beastclassic.dr.math.distributions.MultivariateNormalDistribution( mean.get().getValues(), precision.get().getValues()); arg = argInput.get(); @@ -100,7 +100,7 @@ void nextScaledMultivariateNormal(double [] arg0, double arg1, double [] arg2) { // return multivariatenormaldistribution.getInverse(arg0); // } static public double [] nextMultivariateNormalPrecision(double [] arg0, double [][] arg1) { - return dr.math.distributions.MultivariateNormalDistribution.nextMultivariateNormalPrecision(arg0, arg1); + return beastclassic.dr.math.distributions.MultivariateNormalDistribution.nextMultivariateNormalPrecision(arg0, arg1); } double [] nextMultivariateNormalVariance(double [] arg0, double [][] arg1) { return multivariatenormaldistribution.nextMultivariateNormalVariance(arg0, arg1); @@ -116,7 +116,7 @@ void testRandomDraws() { } public static void main(String[] args) { try { - beast.math.distributions.MultivariateNormalDistribution m = new MultivariateNormalDistribution(); + beastclassic.math.distributions.MultivariateNormalDistribution m = new MultivariateNormalDistribution(); RealParameter mean = new RealParameter("0.0"); RealParameter precision = new RealParameter("1.0"); m.initByName("mean", mean, "precision", precision); diff --git a/src/beast/math/distributions/WishartDistribution.java b/src/beastclassic/math/distributions/WishartDistribution.java similarity index 87% rename from src/beast/math/distributions/WishartDistribution.java rename to src/beastclassic/math/distributions/WishartDistribution.java index 2e49e93..b60a4b6 100644 --- a/src/beast/math/distributions/WishartDistribution.java +++ b/src/beastclassic/math/distributions/WishartDistribution.java @@ -1,4 +1,4 @@ -package beast.math.distributions; +package beastclassic.math.distributions; import java.util.List; import java.util.Random; @@ -20,15 +20,15 @@ public class WishartDistribution extends Distribution { public Input scaleMatrix = new Input<>("scaleMatrix", "description here"); public Input argInput = new Input<>("arg", "argument of distribution"); - dr.math.distributions.WishartDistribution wishartdistribution; + beastclassic.dr.math.distributions.WishartDistribution wishartdistribution; Function arg; @Override public void initAndValidate() { if (scaleMatrix.get() != null) { - wishartdistribution = new dr.math.distributions.WishartDistribution(df.get(), scaleMatrix.get().getValues()); + wishartdistribution = new beastclassic.dr.math.distributions.WishartDistribution(df.get(), scaleMatrix.get().getValues()); } else { - wishartdistribution = new dr.math.distributions.WishartDistribution((int)(double) df.get()); + wishartdistribution = new beastclassic.dr.math.distributions.WishartDistribution((int)(double) df.get()); } arg = argInput.get(); } @@ -74,7 +74,7 @@ void testMe() { return wishartdistribution.nextWishart(); } public static double [][] nextWishart(double arg0, double [][] arg1) { - return dr.math.distributions.WishartDistribution.nextWishart(arg0, arg1); + return beastclassic.dr.math.distributions.WishartDistribution.nextWishart(arg0, arg1); } double logPdf(double [] arg0) { return wishartdistribution.logPdf(arg0); diff --git a/src/beast/phylogeography/RateIndicatorInitializer.java b/src/beastclassic/phylogeography/RateIndicatorInitializer.java similarity index 98% rename from src/beast/phylogeography/RateIndicatorInitializer.java rename to src/beastclassic/phylogeography/RateIndicatorInitializer.java index 32631e8..7c24c25 100644 --- a/src/beast/phylogeography/RateIndicatorInitializer.java +++ b/src/beastclassic/phylogeography/RateIndicatorInitializer.java @@ -1,4 +1,4 @@ -package beast.phylogeography; +package beastclassic.phylogeography; import java.util.List; diff --git a/src/test/beast/evolution/substitutionmodel/RobustEigenSystemTest.java b/src/test/beast/evolution/substitutionmodel/RobustEigenSystemTest.java index 903350a..7402bef 100644 --- a/src/test/beast/evolution/substitutionmodel/RobustEigenSystemTest.java +++ b/src/test/beast/evolution/substitutionmodel/RobustEigenSystemTest.java @@ -7,8 +7,8 @@ import beast.base.evolution.substitutionmodel.DefaultEigenSystem; import beast.base.evolution.substitutionmodel.EigenDecomposition; import beast.base.evolution.substitutionmodel.EigenSystem; -import beast.evolution.substitutionmodel.RobustEigenSystem; import beast.base.util.Randomizer; +import beastclassic.evolution.substitutionmodel.RobustEigenSystem; import junit.framework.TestCase; public class RobustEigenSystemTest extends TestCase { diff --git a/src/test/math/distributions/WishartDisitrbutionTest.java b/src/test/math/distributions/WishartDisitrbutionTest.java index 1144899..a3ced71 100644 --- a/src/test/math/distributions/WishartDisitrbutionTest.java +++ b/src/test/math/distributions/WishartDisitrbutionTest.java @@ -7,7 +7,7 @@ import org.junit.Test; import beast.base.inference.parameter.RealParameter; -import beast.math.distributions.WishartDistribution; +import beastclassic.math.distributions.WishartDistribution; @@ -56,7 +56,7 @@ public void testWishartDistribution() throws Exception { @Test public void testClassicWishartDistribution() { - dr.math.distributions.WishartDistribution wd = new dr.math.distributions.WishartDistribution(2, new Double[]{500.0}); + beastclassic.dr.math.distributions.WishartDistribution wd = new beastclassic.dr.math.distributions.WishartDistribution(2, new Double[]{500.0}); // The above is just an approximation GammaDistribution gd = new GammaDistributionImpl(1.0 / 1000.0, 1000.0); double[] x = new double[]{1.0}; @@ -65,12 +65,12 @@ public void testClassicWishartDistribution() { assertEquals(-6.915086640662835, gd.logDensity(x[0]), 1e-10); - wd = new dr.math.distributions.WishartDistribution(4, new Double[]{5.0}); + wd = new beastclassic.dr.math.distributions.WishartDistribution(4, new Double[]{5.0}); gd = new GammaDistributionImpl(2.0, 10.0); x = new double[]{1.0}; assertEquals(-4.7051701859880914, wd.logPdf(x), 1e-10); - wd = new dr.math.distributions.WishartDistribution(1); + wd = new beastclassic.dr.math.distributions.WishartDistribution(1); x = new double[]{0.1}; assertEquals(2.3025850929940455, wd.logPdf(x), 1e-10); x = new double[]{1.0};