[med-svn] [beast-mcmc] branch master updated (3652f17 -> 98d6828)
Andreas Tille
tille at debian.org
Fri Jan 29 15:22:02 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 3652f17 Upload to unstable
new 30b40fd Adapt d/watch to changed release names
new 492b6ec Rename new binary tracer to beast-tracer
new 8fc8789 Imported Upstream version 1.8.2
new 670424d Merge tag 'upstream/1.8.2'
new a5a6b1c Adapt patches
new 98d6828 Upload to unstable
The 6 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:
.classpath | 2 +-
.gitignore | 7 +
.idea/libraries/lib.xml | 10 +
.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 +
.project | 17 +
.travis.yml | 6 +
NOTIFY | 2 +-
README.md | 34 +
build.xml | 25 +-
build_pathogen.xml | 8 +-
build_tracer.xml | 6 +-
debian/bin/{tracer => beast-tracer} | 0
debian/changelog | 8 +
.../fix_classpath_in_build_tracer_xml.patch | 11 +-
debian/patches/fix_classpath_in_build_xml.patch | 20 +-
debian/watch | 2 +-
old_issue_list/all-issues.csv | 102 ++
old_issue_list/open-issues.csv | 81 ++
packaging_tools/mac/universalJavaApplicationStub | 308 ++++++
packaging_tools/windows/launch4j/.classpath | 17 +
packaging_tools/windows/launch4j/.gitignore | 2 +
packaging_tools/windows/launch4j/.project | 17 +
.../.settings/org.eclipse.core.resources.prefs | 2 +
.../.settings/org.eclipse.core.runtime.prefs | 2 +
.../launch4j/.settings/org.eclipse.jdt.core.prefs | 81 ++
packaging_tools/windows/launch4j/LICENSE.txt | 30 +
packaging_tools/windows/launch4j/build.xml | 73 ++
.../windows/launch4j/demo/ConsoleApp/.gitignore | 1 +
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.../src/net/sf/launch4j/example/ConsoleApp.java | 72 ++
packaging_tools/windows/launch4j/demo/LICENSE.txt | 30 +
.../windows/launch4j/demo/SimpleApp/.gitignore | 1 +
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.../src/net/sf/launch4j/example/SimpleApp.java | 122 ++
packaging_tools/windows/launch4j/demo/readme.txt | 3 +
packaging_tools/windows/launch4j/head/LICENSE.txt | 26 +
.../windows/launch4j/head_src/LICENSE.txt | 26 +
.../launch4j/head_src/consolehead/.gitignore | 2 +
.../launch4j/head_src/consolehead/Makefile.win | 33 +
.../launch4j/head_src/consolehead/consolehead.c | 97 ++
.../launch4j/head_src/consolehead/consolehead.dev | 108 ++
.../windows/launch4j/head_src/guihead/.gitignore | 2 +
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.../windows/launch4j/head_src/guihead/guihead.dev | 109 ++
.../windows/launch4j/head_src/guihead/guihead.h | 43 +
packaging_tools/windows/launch4j/head_src/head.c | 1167 ++++++++++++++++++++
packaging_tools/windows/launch4j/head_src/head.h | 136 +++
.../windows/launch4j/head_src/resource.h | 75 ++
packaging_tools/windows/launch4j/launch4j | 7 +
packaging_tools/windows/launch4j/launch4j.jfpr | Bin 0 -> 125 bytes
.../launch4j/lib/JGoodies.Forms.LICENSE.txt | 31 +
.../launch4j/lib/JGoodies.Looks.LICENSE.txt | 31 +
.../launch4j/lib/Nuvola.Icon.Theme.LICENSE.txt | 504 +++++++++
.../windows/launch4j/lib/XStream.LICENSE.txt | 27 +
.../windows/launch4j/lib/ant.LICENSE.txt | 201 ++++
.../windows/launch4j/lib/commons.LICENSE.txt | 50 +
.../windows/launch4j/lib/foxtrot.LICENSE.txt | 25 +
.../windows/launch4j/manifest/uac.exe.manifest | 12 +
packaging_tools/windows/launch4j/maven/.classpath | 24 +
packaging_tools/windows/launch4j/maven/.project | 23 +
.../maven/.settings/org.eclipse.m2e.core.prefs | 4 +
.../launch4j/maven/assembly/assemble-dist.xml | 14 +
.../launch4j/maven/assembly/assemble-linux.xml | 51 +
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.../windows/launch4j/maven/maven-readme.txt | 10 +
packaging_tools/windows/launch4j/maven/pom.xml | 518 +++++++++
packaging_tools/windows/launch4j/sign4j/README.txt | 18 +
packaging_tools/windows/launch4j/sign4j/sign4j.c | 259 +++++
packaging_tools/windows/launch4j/src/LICENSE.txt | 30 +
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.../windows/launch4j/src/launch4j.properties | 2 +
.../launch4j/src/net/sf/launch4j/Builder.java | 214 ++++
.../src/net/sf/launch4j/BuilderException.java | 52 +
.../src/net/sf/launch4j/ExecException.java | 66 ++
.../src/net/sf/launch4j/FileChooserFilter.java | 76 ++
.../net/sf/launch4j/KanjiEscapeOutputStream.java | 86 ++
.../windows/launch4j/src/net/sf/launch4j/Log.java | 105 ++
.../windows/launch4j/src/net/sf/launch4j/Main.java | 94 ++
.../launch4j/src/net/sf/launch4j/Messages.java | 78 ++
.../launch4j/src/net/sf/launch4j/RcBuilder.java | 408 +++++++
.../windows/launch4j/src/net/sf/launch4j/Util.java | 220 ++++
.../src/net/sf/launch4j/ant/AntClassPath.java | 63 ++
.../src/net/sf/launch4j/ant/AntConfig.java | 131 +++
.../launch4j/src/net/sf/launch4j/ant/AntJre.java | 69 ++
.../src/net/sf/launch4j/ant/Launch4jTask.java | 162 +++
.../launch4j/src/net/sf/launch4j/ant/Messages.java | 55 +
.../src/net/sf/launch4j/ant/StringWrapper.java | 69 ++
.../src/net/sf/launch4j/ant/messages.properties | 35 +
.../src/net/sf/launch4j/ant/messages_es.properties | 35 +
.../src/net/sf/launch4j/binding/Binding.java | 62 ++
.../net/sf/launch4j/binding/BindingException.java | 52 +
.../src/net/sf/launch4j/binding/Bindings.java | 333 ++++++
.../src/net/sf/launch4j/binding/IValidatable.java | 44 +
.../binding/InvariantViolationException.java | 67 ++
.../net/sf/launch4j/binding/JComboBoxBinding.java | 119 ++
.../src/net/sf/launch4j/binding/JListBinding.java | 121 ++
.../sf/launch4j/binding/JRadioButtonBinding.java | 146 +++
.../net/sf/launch4j/binding/JTextAreaBinding.java | 128 +++
.../sf/launch4j/binding/JTextComponentBinding.java | 108 ++
.../sf/launch4j/binding/JToggleButtonBinding.java | 108 ++
.../src/net/sf/launch4j/binding/Messages.java | 78 ++
.../sf/launch4j/binding/OptComponentBinding.java | 122 ++
.../sf/launch4j/binding/OptJTextAreaBinding.java | 146 +++
.../src/net/sf/launch4j/binding/Validator.java | 252 +++++
.../net/sf/launch4j/binding/messages.properties | 52 +
.../net/sf/launch4j/binding/messages_es.properties | 51 +
.../src/net/sf/launch4j/config/ClassPath.java | 92 ++
.../src/net/sf/launch4j/config/Config.java | 395 +++++++
.../net/sf/launch4j/config/ConfigPersister.java | 276 +++++
.../launch4j/config/ConfigPersisterException.java | 51 +
.../launch4j/src/net/sf/launch4j/config/Jre.java | 292 +++++
.../src/net/sf/launch4j/config/LdDefaults.java | 62 ++
.../src/net/sf/launch4j/config/Messages.java | 78 ++
.../launch4j/src/net/sf/launch4j/config/Msg.java | 111 ++
.../src/net/sf/launch4j/config/SingleInstance.java | 74 ++
.../src/net/sf/launch4j/config/Splash.java | 103 ++
.../src/net/sf/launch4j/config/VersionInfo.java | 168 +++
.../src/net/sf/launch4j/config/messages.properties | 96 ++
.../net/sf/launch4j/config/messages_es.properties | 75 ++
.../src/net/sf/launch4j/form/BasicForm.java | 284 +++++
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.../src/net/sf/launch4j/form/Messages.java | 55 +
.../src/net/sf/launch4j/form/MessagesForm.java | 183 +++
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.../src/net/sf/launch4j/form/SplashForm.jfrm | Bin 0 -> 7347 bytes
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.../net/sf/launch4j/form/messages_es.properties | 117 ++
.../launch4j/formimpl/AbstractAcceptListener.java | 75 ++
.../net/sf/launch4j/formimpl/BasicFormImpl.java | 101 ++
.../sf/launch4j/formimpl/BrowseActionListener.java | 79 ++
.../sf/launch4j/formimpl/ClassPathFormImpl.java | 222 ++++
.../net/sf/launch4j/formimpl/ConfigFormImpl.java | 100 ++
.../launch4j/formimpl/EnvironmentVarsFormImpl.java | 50 +
.../src/net/sf/launch4j/formimpl/FileChooser.java | 66 ++
.../src/net/sf/launch4j/formimpl/GlassPane.java | 67 ++
.../net/sf/launch4j/formimpl/HeaderFormImpl.java | 102 ++
.../src/net/sf/launch4j/formimpl/JreFormImpl.java | 175 +++
.../src/net/sf/launch4j/formimpl/MainFrame.java | 360 ++++++
.../src/net/sf/launch4j/formimpl/Messages.java | 55 +
.../net/sf/launch4j/formimpl/MessagesFormImpl.java | 58 +
.../launch4j/formimpl/SingleInstanceFormImpl.java | 54 +
.../net/sf/launch4j/formimpl/SplashFormImpl.java | 61 +
.../sf/launch4j/formimpl/VersionInfoFormImpl.java | 63 ++
.../net/sf/launch4j/formimpl/messages.properties | 80 ++
.../sf/launch4j/formimpl/messages_es.properties | 56 +
.../src/net/sf/launch4j/messages.properties | 45 +
.../src/net/sf/launch4j/messages_es.properties | 44 +
.../windows/launch4j/w32api/MinGW.LICENSE.txt | 25 +
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packaging_tools/windows/launch4j/w32api/libgcc.a | Bin 0 -> 53694 bytes
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packaging_tools/windows/launch4j/web/bullet.gif | Bin 0 -> 151 bytes
.../windows/launch4j/web/changelog.html | 434 ++++++++
packaging_tools/windows/launch4j/web/docs.html | 668 +++++++++++
packaging_tools/windows/launch4j/web/index.html | 122 ++
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packaging_tools/windows/launch4j/web/links.html | 60 +
packaging_tools/windows/launch4j/web/style.css | 166 +++
.../branchmodel/BranchAssignmentModel.java | 172 +++
.../beagle/evomodel/branchmodel/BranchModel.java | 2 +-
.../branchmodel/BranchSpecificBranchModel.java | 48 +-
.../evomodel/branchmodel/EpochBranchModel.java | 2 +-
.../branchmodel/ExternalInternalBranchModel.java | 2 +-
.../branchmodel/HomogeneousBranchModel.java | 2 +-
.../branchmodel/RandomBranchAssignmentModel.java | 156 +++
.../evomodel/branchmodel/RandomBranchModel.java | 29 +-
.../lineagespecific/BeagleBranchLikelihood.java | 539 +++++++++
.../BeagleBranchLikelihoodParser.java | 96 ++
.../lineagespecific/BranchLikelihood.java | 234 ++++
.../lineagespecific/BranchSpecificTrait.java | 73 ++
.../lineagespecific/BranchSpecificTraitParser.java | 26 +-
.../CountableRealizationsParameter.java | 4 +-
.../CountableRealizationsParameterParser.java | 4 +-
.../lineagespecific/DirichletProcessOperator.java | 228 ++--
.../DirichletProcessOperatorParser.java | 44 +-
.../lineagespecific/DirichletProcessPrior.java | 25 +
.../DirichletProcessPriorLogger.java | 25 +
.../DirichletProcessPriorLoggerParser.java | 25 +
.../DirichletProcessPriorParser.java | 25 +
.../LineageSpecificBranchModel.java | 31 +-
.../LineageSpecificBranchModelParser.java | 30 +-
.../lineagespecific/RatioParameter.java | 25 +
.../lineagespecific/RatioParameterParser.java | 25 +
.../newtreelikelihood/NewBeagleTreeLikelihood.java | 4 +-
.../newtreelikelihood/NewGammaSiteModel.java | 2 +-
.../evomodel/newtreelikelihood/SiteModel.java | 4 +-
.../operators/PatternWeightIncrementOperator.java | 4 +-
.../evomodel/operators/TipStateSwapOperator.java | 2 +-
.../evomodel/parsers/ALSTreeLikelihoodParser.java | 2 +-
.../AncestralStateTreeLikelihoodParser.java | 2 +-
.../BalancedBeagleTreeLikelihoodParser.java | 2 +-
.../evomodel/parsers/BeagleOperationParser.java | 2 +-
.../BeagleSubstitutionEpochModelParser.java | 2 +-
.../parsers/BeagleTreeLikelihoodParser.java | 10 +-
.../parsers/BinaryCovarionModelParser.java | 2 +-
.../parsers/BinarySubstitutionModelParser.java | 2 +-
.../parsers/BranchAssignmentModelParser.java | 97 ++
.../parsers/BranchSpecificBranchModelParser.java | 7 +-
.../CodonPartitionedRobustCountingParser.java | 2 +-
.../parsers/CompleteHistoryLoggerParser.java | 2 +-
.../parsers/ComplexSubstitutionModelParser.java | 2 +-
.../evomodel/parsers/CompoundLikelihoodParser.java | 2 +-
.../beagle/evomodel/parsers/DnDsLoggerParser.java | 2 +-
.../parsers/EmpiricalAminoAcidModelParser.java | 2 +-
.../parsers/EmpiricalCodonModelParser.java | 2 +-
.../evomodel/parsers/EpochBranchModelParser.java | 2 +-
.../parsers/ExternalInternalBranchModelParser.java | 89 ++
...ernalInternalBranchSubstitutionModelParser.java | 2 +-
.../evomodel/parsers/FrequencyModelParser.java | 2 +-
.../parsers/GLMSubstitutionModelParser.java | 2 +-
src/dr/app/beagle/evomodel/parsers/GTRParser.java | 2 +-
.../evomodel/parsers/GY94CodonModelParser.java | 2 +-
.../evomodel/parsers/GammaSiteModelParser.java | 2 +-
.../parsers/GeneralSubstitutionModelParser.java | 2 +-
src/dr/app/beagle/evomodel/parsers/HKYParser.java | 2 +-
.../evomodel/parsers/HistoryFilterParser.java | 2 +-
.../parsers/LewisMkSubstitutionModelParser.java | 2 +-
.../evomodel/parsers/MG94CodonModelParser.java | 2 +-
.../parsers/MarkovJumpsLikelihoodLoggerParser.java | 2 +-
.../parsers/MarkovJumpsTreeLikelihoodParser.java | 2 +-
.../MarkovModulatedGY94CodonModelParser.java | 2 +-
.../MarkovModulatedHiddenClassRewardParser.java | 2 +-
.../MarkovModulatedSubstitutionModelParser.java | 2 +-
.../evomodel/parsers/MutationDeathModelParser.java | 2 +-
.../OldAncestralStateTreeLikelihoodParser.java | 2 +-
.../OldMarkovJumpsTreeLikelihoodParser.java | 2 +-
.../evomodel/parsers/OldTreeLikelihoodParser.java | 4 +-
.../OptimizedBeagleTreeLikelihoodParser.java | 2 +-
.../evomodel/parsers/PCACodonModelParser.java | 2 +-
.../PatternWeightIncrementOperatorParser.java | 4 +-
.../parsers/RandomBranchAssignmentModelParser.java | 97 ++
.../evomodel/parsers/RandomBranchModelParser.java | 25 +
.../evomodel/parsers/StarTreeLikelihoodParser.java | 2 +-
.../parsers/StratifiedTraitLoggerParser.java | 2 +-
src/dr/app/beagle/evomodel/parsers/TN93Parser.java | 2 +-
.../parsers/TipStateSwapOperatorParser.java | 2 +-
.../sitemodel/BranchSubstitutionModel.java | 2 +-
.../sitemodel/EpochBranchSubstitutionModel.java | 2 +-
.../ExternalInternalBranchSubstitutionModel.java | 2 +-
.../evomodel/sitemodel/GammaSiteRateModel.java | 2 +-
.../HomogenousBranchSubstitutionModel.java | 2 +-
.../beagle/evomodel/sitemodel/SiteRateModel.java | 2 +-
.../evomodel/substmodel/AbstractCodonModel.java | 2 +-
.../evomodel/substmodel/AbstractCovarionModel.java | 2 +-
.../evomodel/substmodel/AbstractPCARateMatrix.java | 2 +-
.../evomodel/substmodel/BaseSubstitutionModel.java | 2 +-
.../evomodel/substmodel/BinaryCovarionModel.java | 2 +-
.../beagle/evomodel/substmodel/CodonLabeling.java | 2 +-
.../substmodel/CodonPartitionedRobustCounting.java | 2 +-
.../evomodel/substmodel/ColtEigenSystem.java | 2 +-
.../substmodel/ComplexColtEigenSystem.java | 2 +-
.../substmodel/ComplexSubstitutionModel.java | 2 +-
.../substmodel/CovarionFrequencyModel.java | 2 +-
.../evomodel/substmodel/DefaultEigenSystem.java | 2 +-
.../DependentProductChainSubstitutionModel.java | 2 +-
.../evomodel/substmodel/EigenDecomposition.java | 2 +-
.../beagle/evomodel/substmodel/EigenSystem.java | 2 +-
.../substmodel/EmpiricalAminoAcidModel.java | 2 +-
.../evomodel/substmodel/EmpiricalCodonModel.java | 2 +-
.../evomodel/substmodel/EmpiricalRateMatrix.java | 2 +-
.../substmodel/ExposeRateCategoriesWrapper.java | 2 +-
.../beagle/evomodel/substmodel/FrequencyModel.java | 2 +-
.../evomodel/substmodel/GLMSubstitutionModel.java | 2 +-
src/dr/app/beagle/evomodel/substmodel/GTR.java | 2 +-
.../beagle/evomodel/substmodel/GY94CodonModel.java | 2 +-
.../substmodel/GeneralSubstitutionModel.java | 2 +-
src/dr/app/beagle/evomodel/substmodel/HKY.java | 4 +-
.../beagle/evomodel/substmodel/MG94CodonModel.java | 2 +-
.../evomodel/substmodel/MG94HKYCodonModel.java | 4 +-
.../substmodel/MarkovJumpsSubstitutionModel.java | 2 +-
.../substmodel/MarkovModulatedFrequencyModel.java | 2 +-
.../substmodel/MarkovModulatedGY94CodonModel.java | 2 +-
.../MarkovModulatedSubstitutionModel.java | 2 +-
.../evomodel/substmodel/MutationDeathModel.java | 2 +-
.../beagle/evomodel/substmodel/PCACodonModel.java | 2 +-
.../evomodel/substmodel/PCARateMatrixMammalia.java | 2 +-
.../substmodel/ProductChainFrequencyModel.java | 2 +-
.../substmodel/ProductChainSubstitutionModel.java | 2 +-
.../substmodel/SVSComplexSubstitutionModel.java | 2 +-
.../substmodel/SVSGeneralSubstitutionModel.java | 2 +-
.../substmodel/StratifiedTraitOutputFormat.java | 2 +-
.../evomodel/substmodel/SubstitutionModel.java | 2 +-
.../evomodel/substmodel/SubstitutionProcess.java | 2 +-
src/dr/app/beagle/evomodel/substmodel/TN93.java | 4 +-
.../substmodel/UniformizedSubstitutionModel.java | 2 +-
.../treelikelihood/ALSBeagleTreeLikelihood.java | 2 +-
.../AbstractSinglePartitionTreeLikelihood.java | 25 +
.../treelikelihood/AbstractTreeLikelihood.java | 2 +-
.../AncestralStateBeagleTreeLikelihood.java | 2 +-
.../AncestralStateTraitProvider.java | 2 +-
.../treelikelihood/BeagleOperationReport.java | 2 +-
.../treelikelihood/BeagleTreeLikelihood.java | 2 +-
.../evomodel/treelikelihood/BufferIndexHelper.java | 2 +-
.../MarkovJumpsBeagleTreeLikelihood.java | 2 +-
.../treelikelihood/MarkovJumpsTraitProvider.java | 2 +-
.../MultiPartitionTreeLikelihood.java | 4 +-
.../OldAncestralStateBeagleTreeLikelihood.java | 2 +-
.../treelikelihood/OldBeagleTreeLikelihood.java | 4 +-
.../OldMarkovJumpsBeagleTreeLikelihood.java | 2 +-
.../treelikelihood/PartialsRescalingScheme.java | 2 +-
.../treelikelihood/SplitBySiteTraitLogger.java | 2 +-
.../treelikelihood/StarTreeLikelihood.java | 2 +-
.../treelikelihood/SubstitutionModelDelegate.java | 2 +-
.../evomodel/utilities/CompleteHistoryLogger.java | 2 +-
.../app/beagle/evomodel/utilities/DnDsLogger.java | 2 +-
.../beagle/evomodel/utilities/HistoryFilter.java | 2 +-
.../beagle/evomodel/utilities/TreeTraitLogger.java | 2 +-
.../MassivelyParallelMDSImpl.java | 32 +-
.../MultiDimensionalScalingCore.java | 8 +-
.../MultiDimensionalScalingCoreImpl.java | 10 +-
.../MultiDimensionalScalingCoreImpl2.java | 219 +++-
.../MultiDimensionalScalingLikelihood.java | 45 +-
.../NativeMDSSingleton.java | 12 +-
.../app/beagle/tools/BeagleSequenceSimulator.java | 2 +-
.../app/beagle/tools/CompleteHistorySimulator.java | 2 +-
src/dr/app/beagle/tools/Partition.java | 2 +-
.../app/beagle/tools/SiteLogLikelihoodLogger.java | 25 +
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.../branchratemodel/RelaxedDriftModel.java | 25 +
.../branchratemodel/ScaledTreeLengthRateModel.java | 10 +-
.../SericolaLatentStateBranchRateModel.java | 2 +-
.../branchratemodel/StrictClockBranchRates.java | 2 +-
.../branchratemodel/TipBranchRateModel.java | 2 +-
src/dr/evomodel/clock/ACLikelihood.java | 25 +
src/dr/evomodel/clock/RateEvolutionLikelihood.java | 10 +-
src/dr/evomodel/clock/UCLikelihood.java | 25 +
src/dr/evomodel/clock/UniversalClock.java | 2 +-
.../coalescent/AbstractCoalescentLikelihood.java | 2 +-
.../evomodel/coalescent/AsymptoticGrowthModel.java | 105 ++
src/dr/evomodel/coalescent/BMPriorLikelihood.java | 25 +
.../coalescent/BayesianSkylineLikelihood.java | 2 +-
.../BayesianSkylinePopSizeStatistic.java | 25 +
.../coalescent/CataclysmicDemographicModel.java | 10 +-
.../coalescent/CoalescentConstantLikelihood.java | 4 +-
.../coalescent/CoalescentEventsStatistic.java | 175 +--
.../coalescent/CoalescentIntervalProvider.java | 2 +-
.../coalescent/CoalescentIntervalStatistic.java | 2 +-
.../evomodel/coalescent/CoalescentLikelihood.java | 4 +-
.../evomodel/coalescent/CoalescentSimulator.java | 10 +-
.../CoalescentTreeIntervalStatistic.java | 2 +-
src/dr/evomodel/coalescent/ConstExpConstModel.java | 10 +-
.../coalescent/ConstantExponentialModel.java | 10 +-
.../evomodel/coalescent/ConstantLogisticModel.java | 10 +-
.../coalescent/ConstantPopulationModel.java | 10 +-
.../coalescent/CovariateGMRFSkylineLikelihood.java | 25 +
src/dr/evomodel/coalescent/DemographicModel.java | 2 +-
src/dr/evomodel/coalescent/EBSPAnalysis.java | 25 +
.../evomodel/coalescent/EmergingEpidemicModel.java | 12 +-
.../coalescent/EmpiricalPiecewiseModel.java | 10 +-
.../coalescent/ExpConstExpDemographicModel.java | 10 +-
src/dr/evomodel/coalescent/ExpansionModel.java | 10 +-
.../coalescent/ExponentialConstantModel.java | 12 +-
.../coalescent/ExponentialExponentialModel.java | 12 +-
.../coalescent/ExponentialGrowthModel.java | 10 +-
.../coalescent/ExponentialLogisticModel.java | 10 +-
.../coalescent/ExponentialProductLikelihood.java | 25 +
...ExponentialProductPosteriorMeansLikelihood.java | 45 +-
...ntialProductSufficientStatisticsLikelihood.java | 25 +
.../coalescent/ExponentialSawtoothModel.java | 10 +-
.../coalescent/ExponentialSkythingLikelihood.java | 4 +-
.../coalescent/GMRFBivariateCurveAnalysis.java | 25 +
.../evomodel/coalescent/GMRFDensityComponent.java | 25 +
.../coalescent/GMRFFixedGridLikelihood.java | 25 +
.../coalescent/GMRFIntervalHeightsStatistic.java | 4 +-
.../GMRFMultilocusSkyrideLikelihood.java | 7 +-
.../evomodel/coalescent/GMRFPopSizeStatistic.java | 25 +
.../evomodel/coalescent/GMRFSkyrideLikelihood.java | 2 +-
src/dr/evomodel/coalescent/GMRFTestLikelihood.java | 25 +
src/dr/evomodel/coalescent/GPSkytrackAnalysis.java | 25 +
.../coalescent/GammaProductLikelihood.java | 25 +
...aussianProcessMultilocusSkytrackLikelihood.java | 4 +-
.../GaussianProcessSkytrackLikelihood.java | 2 +-
.../evomodel/coalescent/LineageCountStatistic.java | 25 +
src/dr/evomodel/coalescent/LinearGrowthModel.java | 81 ++
.../evomodel/coalescent/LogisticGrowthModel.java | 10 +-
src/dr/evomodel/coalescent/MultiLociTreeSet.java | 25 +
.../OldAbstractCoalescentLikelihood.java | 4 +-
.../OrnsteinUhlenbeckPriorLikelihood.java | 25 +
.../evomodel/coalescent/PeakAndDeclineModel.java | 112 ++
.../coalescent/PiecewisePopulationModel.java | 10 +-
src/dr/evomodel/coalescent/PopSizeStatistic.java | 2 +-
.../evomodel/coalescent/PopulationSizeGraph.java | 25 +
.../evomodel/coalescent/PowerLawGrowthModel.java | 98 ++
.../evomodel/coalescent/ScaledPiecewiseModel.java | 10 +-
src/dr/evomodel/coalescent/SkylineLikelihood.java | 2 +-
.../coalescent/TwoEpochDemographicModel.java | 10 +-
.../evomodel/coalescent/VDdemographicFunction.java | 25 +
.../coalescent/VariableDemographicModel.java | 10 +-
.../coalescent/VariableSkylineLikelihood.java | 2 +-
.../operators/BayesianSkylineGibbsOperator.java | 25 +
.../GMRFMultilocusSkyrideBlockUpdateOperator.java | 25 +
.../operators/GMRFSkyrideBlockUpdateOperator.java | 25 +
.../GMRFSkyrideFixedEffectsGibbsOperator.java | 25 +
...GaussianProcessSkytrackBlockUpdateOperator.java | 25 +
.../GaussianProcessSkytrackTreeOperator.java | 25 +
.../operators/SampleNonActiveGibbsOperator.java | 25 +
.../coalescent/structure/ColourSamplerModel.java | 10 +-
.../structure/ConstantMigrationModel.java | 2 +-
.../coalescent/structure/MetaPopulationModel.java | 10 +-
.../coalescent/structure/MigrationModel.java | 2 +-
.../structure/StructuredCoalescentLikelihood.java | 10 +-
.../structure/TreeColouringOperator.java | 2 +-
.../AbstractMultivariateTraitLikelihood.java | 47 +-
.../BiasedMultivariateDiffusionModel.java | 25 +
.../continuous/BifractionalDiffusionModel.java | 25 +
.../BinaryLatentLiabilityLikelihood.java | 2 +-
.../BivariateDiscreteDiffusionModel.java | 10 +-
.../BivariateTraitBranchAttributeProvider.java | 25 +
.../BranchDirectionAttributeProvider.java | 25 +
.../BranchMagnitudeAttributeProvider.java | 25 +
.../continuous/CartogramDiffusionModel.java | 25 +
.../continuous/ContinuousDiffusionStatistic.java | 429 ++++---
.../evomodel/continuous/ContinuousLikelihood.java | 2 +-
...gableIntegratedMultivariateTraitLikelihood.java | 2 +-
src/dr/evomodel/continuous/DiffusionModel.java | 10 +-
.../DiffusionRateCovarianceStatistic.java | 2 +-
.../continuous/DiffusionRateStatistic.java | 2 +-
.../FullyConjugateMultivariateTraitLikelihood.java | 187 +++-
.../continuous/GaussianProcessFromTree.java | 50 +-
.../GibbsIndependentCoalescentOperator.java | 2 +-
.../continuous/GreatCircleDiffusionModel.java | 10 +-
.../continuous/IndependentCoalescentSampler.java | 2 +-
.../continuous/InhibitionAssayLikelihood.java | 25 +
.../IntegratedMultivariateTraitLikelihood.java | 289 ++++-
.../IntervalLatentLiabilityLikelihood.java | 2 +-
src/dr/evomodel/continuous/LatentTruncation.java | 2 +-
src/dr/evomodel/continuous/MapDiffusionModel.java | 25 +
src/dr/evomodel/continuous/MissingTraits.java | 4 +-
.../continuous/MixtureCartogramDiffusionModel.java | 25 +
.../MultinomialLatentLiabilityLikelihood.java | 2 +-
.../continuous/MultivariateDiffusionModel.java | 25 +
.../continuous/MultivariateTDiffusionModel.java | 25 +
.../continuous/MultivariateTraitUtils.java | 2 +-
...NonPhylogeneticMultivariateTraitLikelihood.java | 2 +-
.../OrderedLatentLiabilityLikelihood.java | 2 +-
src/dr/evomodel/continuous/RootTraitMLE.java | 2 +-
src/dr/evomodel/continuous/RootTraitStatistic.java | 25 +
.../SampledMultivariateTraitLikelihood.java | 2 +-
.../SemiConjugateMultivariateTraitLikelihood.java | 2 +-
src/dr/evomodel/continuous/SimulateTrait.java | 2 +-
.../continuous/SoftThresholdLikelihood.java | 25 +
.../StochasticDifferentialEquationModel.java | 25 +
src/dr/evomodel/continuous/TopographicalMap.java | 25 +
src/dr/evomodel/continuous/TraitLikelihood.java | 2 +-
.../TreeTraitNormalDistributionModel.java | 2 +-
src/dr/evomodel/continuous/TreeTraitSimulator.java | 25 +
.../continuous/TruncatedWorkingDistribution.java | 2 +-
.../continuous/VonMisesFisherDiffusionModel.java | 25 +
.../evomodel/continuous/plink/PlinkImporter.java | 25 +
src/dr/evomodel/epidemiology/DynamicalForce.java | 25 +
src/dr/evomodel/epidemiology/DynamicalSystem.java | 25 +
.../evomodel/epidemiology/DynamicalVariable.java | 25 +
src/dr/evomodel/epidemiology/LambertW.java | 47 +-
src/dr/evomodel/epidemiology/LogisticGrowthN0.java | 25 +
.../epidemiology/LogisticGrowthN0Model.java | 27 +-
.../epidemiology/LogisticGrowthN0ModelParser.java | 25 +
.../epidemiology/ODEDemographicFunction.java | 25 +
src/dr/evomodel/epidemiology/SIRModel.java | 25 +
src/dr/evomodel/epidemiology/SIRModelParser.java | 25 +
src/dr/evomodel/epidemiology/SIRepidemic.java | 25 +
src/dr/evomodel/epidemiology/SIRepidemicModel.java | 25 +
.../epidemiology/SIRepidemicModelParser.java | 25 +
.../epidemiology/casetocase/AbstractCase.java | 25 +
.../epidemiology/casetocase/AbstractOutbreak.java | 25 +
.../casetocase/BadPartitionException.java | 25 +
.../epidemiology/casetocase/BranchMapModel.java | 25 +
.../CaseToCaseTransmissionLikelihood.java | 25 +
.../casetocase/CaseToCaseTreeLikelihood.java | 111 +-
.../epidemiology/casetocase/CategoryOutbreak.java | 25 +
.../casetocase/PartitionedTreeLogger.java | 25 +
.../casetocase/PartitionedTreeLoggerParser.java | 25 +
.../casetocase/PartitionedTreeModel.java | 25 +
.../casetocase/PartitionedTreeModelParser.java | 4 +-
.../epidemiology/casetocase/SpatialKernel.java | 25 +
.../casetocase/WithinCaseCoalescent.java | 312 ++++--
.../operators/InfectionBranchGibbsOperator.java | 25 +
.../operators/InfectionBranchMovementOperator.java | 25 +
.../operators/TransmissionExchangeOperatorA.java | 25 +
.../operators/TransmissionExchangeOperatorB.java | 25 +
.../operators/TransmissionSubtreeSlideA.java | 25 +
.../operators/TransmissionSubtreeSlideB.java | 25 +
.../operators/TransmissionTreeOperator.java | 25 +
.../operators/TransmissionWilsonBaldingA.java | 25 +
.../operators/TransmissionWilsonBaldingB.java | 25 +
.../AbstractPeriodPriorDistribution.java | 25 +
.../casetocase/periodpriors/IndividualPrior.java | 25 +
...KnownVarianceNormalPeriodPriorDistribution.java | 25 +
.../NormalPeriodPriorDistribution.java | 25 +
.../OneOverStDevPeriodPriorDistribution.java | 25 +
src/dr/evomodel/ibd/AvgPosteriorIBDReporter.java | 25 +
src/dr/evomodel/ibd/HKYRates.java | 25 +
src/dr/evomodel/ibd/IBDReporter.java | 11 +-
src/dr/evomodel/indel/HomologyRecursion.java | 2 +-
src/dr/evomodel/indel/IndelModel.java | 2 +-
src/dr/evomodel/indel/IntMathVec.java | 2 +-
src/dr/evomodel/indel/IstvanOperator.java | 2 +-
src/dr/evomodel/indel/IstvansProposal.java | 2 +-
src/dr/evomodel/indel/NativeTreeLikelihood.java | 2 +-
src/dr/evomodel/indel/TKF91Likelihood.java | 2 +-
src/dr/evomodel/indel/TKF91Model.java | 10 +-
.../evomodel/lineage/LineageModelLikelihood.java | 25 +
src/dr/evomodel/lineage/LineageSitePatterns.java | 25 +
.../lineage/LineageSitePatternsParser.java | 4 +-
.../FloatGeneralLikelihoodCore.java | 4 +-
src/dr/evomodel/newtreelikelihood/GPUInfo.java | 25 +
.../newtreelikelihood/GPULikelihoodCore.java | 25 +
.../newtreelikelihood/GeneralLikelihoodCore.java | 4 +-
.../evomodel/newtreelikelihood/LikelihoodCore.java | 2 +-
.../newtreelikelihood/LikelihoodCoreFactory.java | 25 +
.../newtreelikelihood/NativeLikelihoodCore.java | 25 +
.../OTFPCGeneralLikelihoodCore.java | 4 +-
.../ThreadedGPULikelihoodCore.java | 25 +
.../evomodel/newtreelikelihood/TreeLikelihood.java | 10 +-
.../VectorTreeLikelihoodParser.java | 25 +
.../AbstractImportanceDistributionOperator.java | 10 +-
.../evomodel/operators/AbstractTreeOperator.java | 25 +
.../operators/AlloppChangeNumHybridizations.java | 25 +
.../evomodel/operators/AlloppHybPopSizesScale.java | 25 +
src/dr/evomodel/operators/AlloppMoveLegs.java | 25 +
.../evomodel/operators/AlloppNetworkNodeSlide.java | 25 +
.../operators/AlloppSequenceReassignment.java | 25 +
.../BitFlipInSubstitutionModelOperator.java | 4 +-
.../CCPImportanceDistributionOperator.java | 10 +-
src/dr/evomodel/operators/CategoryOperator.java | 2 +-
.../operators/ColouredExchangeOperator.java | 2 +-
src/dr/evomodel/operators/ColouredOperator.java | 2 +-
.../operators/ColouredSubtreeSlideOperator.java | 2 +-
.../operators/DiscretizedLocationOperator.java | 2 +-
.../EmpiricalTreeDistributionOperator.java | 25 +
src/dr/evomodel/operators/ExchangeOperator.java | 2 +-
src/dr/evomodel/operators/FNPR.java | 25 +
.../evomodel/operators/FixedColouredOperator.java | 2 +-
.../operators/FunkyPriorMixerOperator.java | 25 +
.../evomodel/operators/GibbsPruneAndRegraft.java | 25 +
src/dr/evomodel/operators/GibbsSubtreeSwap.java | 25 +
.../operators/ImportanceNarrowExchange.java | 25 +
.../operators/ImportancePruneAndRegraft.java | 10 +-
.../evomodel/operators/ImportanceSubtreeSwap.java | 10 +-
.../evomodel/operators/LatentLiabilityGibbs.java | 2 +-
src/dr/evomodel/operators/LinkageGroupSwap.java | 25 +
src/dr/evomodel/operators/MoveLinkageGroup.java | 25 +
src/dr/evomodel/operators/MulTreeNodeSlide.java | 25 +
.../operators/MulTreeSequenceReassignment.java | 25 +
src/dr/evomodel/operators/NNI.java | 25 +
.../operators/NodeHeightScaleOperator.java | 25 +
.../operators/OldLatentLiabilityGibbsOperator.java | 2 +-
src/dr/evomodel/operators/PopsIOTreeNodeSlide.java | 25 +
.../operators/PrecisionMatrixGibbsOperator.java | 39 +-
.../operators/RLCNarrowExchangeOperator.java | 4 +-
.../operators/RandomWalkOnMapOperator.java | 2 +-
.../evomodel/operators/RateExchangeOperator.java | 2 +-
src/dr/evomodel/operators/RateSampleOperator.java | 25 +
src/dr/evomodel/operators/RateScaleOperator.java | 25 +
.../operators/RateVarianceScaleOperator.java | 10 +-
src/dr/evomodel/operators/SubtreeJumpOperator.java | 181 ++-
.../evomodel/operators/SubtreeSlideOperator.java | 2 +-
.../evomodel/operators/TipStateSwapOperator.java | 25 +
.../evomodel/operators/TipTraitSwapOperator.java | 25 +
src/dr/evomodel/operators/TraitGibbsOperator.java | 2 +-
.../evomodel/operators/TraitRateGibbsOperator.java | 2 +-
src/dr/evomodel/operators/TreeBitMoveOperator.java | 25 +
.../operators/TreeBitRandomWalkOperator.java | 25 +
src/dr/evomodel/operators/TreeNodeSlide.java | 25 +
src/dr/evomodel/operators/TreeUniform.java | 4 +-
src/dr/evomodel/operators/WilsonBalding.java | 2 +-
src/dr/evomodel/simulator/Simulator.java | 2 +-
src/dr/evomodel/sitemodel/AlignmentScore.java | 2 +-
.../sitemodel/CategoryParameterStatistic.java | 2 +-
src/dr/evomodel/sitemodel/CategorySampleModel.java | 2 +-
src/dr/evomodel/sitemodel/CategorySiteModel.java | 2 +-
src/dr/evomodel/sitemodel/DirichletSiteModel.java | 3 +-
.../evomodel/sitemodel/DiscretizedLociRates.java | 25 +
src/dr/evomodel/sitemodel/GammaSiteBMA.java | 25 +
src/dr/evomodel/sitemodel/GammaSiteModel.java | 2 +-
src/dr/evomodel/sitemodel/PairDistance.java | 2 +-
.../sitemodel/SampleQuantileLociRates.java | 25 +
.../sitemodel/SampleStateAndCategoryModel.java | 2 +-
src/dr/evomodel/sitemodel/SampleStateModel.java | 10 +-
src/dr/evomodel/sitemodel/ScoreMatrix.java | 2 +-
src/dr/evomodel/sitemodel/SiteModel.java | 2 +-
src/dr/evomodel/sitemodel/SiteRateModel.java | 2 +-
.../evomodel/speciation/AlloppDiploidHistory.java | 25 +
src/dr/evomodel/speciation/AlloppLeggedTree.java | 25 +
src/dr/evomodel/speciation/AlloppMSCoalescent.java | 25 +
src/dr/evomodel/speciation/AlloppMulLabTree.java | 25 +
src/dr/evomodel/speciation/AlloppNetworkPrior.java | 25 +
.../speciation/AlloppNetworkPriorModel.java | 25 +
src/dr/evomodel/speciation/AlloppNode.java | 25 +
.../speciation/AlloppNumHybsStatistic.java | 25 +
.../evomodel/speciation/AlloppSpeciesBindings.java | 25 +
.../speciation/AlloppSpeciesNetworkModel.java | 25 +
src/dr/evomodel/speciation/BetaSplittingModel.java | 2 +-
.../speciation/BirthDeathCollapseModel.java | 25 +
.../BirthDeathCollapseNClustersStatistic.java | 25 +
.../speciation/BirthDeathGernhard08Model.java | 10 +-
.../speciation/BirthDeathSerialSamplingModel.java | 10 +-
.../speciation/BirthDeathSerialSkylineModel.java | 10 +-
.../evomodel/speciation/BranchingLikelihood.java | 10 +-
src/dr/evomodel/speciation/BranchingModel.java | 2 +-
.../speciation/CalibrationLineagesIterator.java | 25 +
src/dr/evomodel/speciation/CalibrationPoints.java | 25 +
.../speciation/MaskableSpeciationModel.java | 25 +
.../ModelAveragingResearch/MAIndexResearch.java | 25 +
.../ModelAveragingResearch/MAIndexResearchLog.java | 25 +
.../ModelAveragingIndexSpeciationLikelihood.java | 25 +
...elAveragingIndexSpeciationLikelihoodParser.java | 25 +
.../ModelAveragingSpeciationLikelihood.java | 25 +
src/dr/evomodel/speciation/MulMSCoalescent.java | 25 +
src/dr/evomodel/speciation/MulSpeciesBindings.java | 12 +-
.../evomodel/speciation/MulSpeciesTreeModel.java | 25 +
.../evomodel/speciation/MulSpeciesTreePrior.java | 25 +
.../speciation/MultiSpeciesCoalescent.java | 25 +
src/dr/evomodel/speciation/PopsIOMSCoalescent.java | 25 +
.../evomodel/speciation/PopsIOSpeciesBindings.java | 25 +
.../speciation/PopsIOSpeciesTreeModel.java | 25 +
.../speciation/PopsIOSpeciesTreePrior.java | 25 +
.../evomodel/speciation/RandomLocalYuleModel.java | 10 +-
.../evomodel/speciation/SpeciationLikelihood.java | 10 +-
src/dr/evomodel/speciation/SpeciationModel.java | 10 +-
src/dr/evomodel/speciation/SpeciesBindings.java | 10 +-
src/dr/evomodel/speciation/SpeciesTreeBMPrior.java | 25 +
src/dr/evomodel/speciation/SpeciesTreeModel.java | 25 +
.../speciation/SpeciesTreeSimplePrior.java | 25 +
.../speciation/TaxonRichnessBirthDeathModel.java | 25 +
.../speciation/UltrametricSpeciationModel.java | 10 +-
src/dr/evomodel/speciation/YuleModel.java | 10 +-
.../substmodel/AbstractAminoAcidModel.java | 2 +-
src/dr/evomodel/substmodel/AbstractCodonModel.java | 2 +-
.../substmodel/AbstractCovarionDNAModel.java | 25 +
.../evomodel/substmodel/AbstractCovarionModel.java | 25 +
.../substmodel/AbstractNucleotideModel.java | 2 +-
.../evomodel/substmodel/AbstractPCARateMatrix.java | 25 +
.../substmodel/AbstractSubstitutionModel.java | 10 +-
src/dr/evomodel/substmodel/AminoAcidModelType.java | 12 +-
.../substmodel/AsymmetricQuadraticModel.java | 25 +
.../evomodel/substmodel/BinaryCovarionModel.java | 2 +-
src/dr/evomodel/substmodel/Blosum62.java | 2 +-
src/dr/evomodel/substmodel/CPREV.java | 2 +-
.../substmodel/ComplexSubstitutionModel.java | 25 +
.../substmodel/CovarionFrequencyModel.java | 25 +
src/dr/evomodel/substmodel/CovarionGTR.java | 25 +
src/dr/evomodel/substmodel/CovarionHKY.java | 2 +-
src/dr/evomodel/substmodel/Dayhoff.java | 2 +-
.../substmodel/EmpiricalAminoAcidModel.java | 2 +-
.../evomodel/substmodel/EmpiricalCodonModel.java | 25 +
.../substmodel/EmpiricalCodonRateMatrix.java | 25 +
.../evomodel/substmodel/EmpiricalRateMatrix.java | 2 +-
src/dr/evomodel/substmodel/FLU.java | 25 +
src/dr/evomodel/substmodel/FrequencyModel.java | 2 +-
.../evomodel/substmodel/GLMSubstitutionModel.java | 25 +
src/dr/evomodel/substmodel/GTR.java | 2 +-
src/dr/evomodel/substmodel/GeneralF81Model.java | 25 +
.../substmodel/GeneralSubstitutionModel.java | 2 +-
src/dr/evomodel/substmodel/HKY.java | 2 +-
src/dr/evomodel/substmodel/JTT.java | 2 +-
src/dr/evomodel/substmodel/LG.java | 2 +-
src/dr/evomodel/substmodel/LinearBiasModel.java | 25 +
src/dr/evomodel/substmodel/MTREV.java | 2 +-
.../substmodel/MarginalVarianceStatistic.java | 25 +
.../evomodel/substmodel/MicrosatelliteModel.java | 25 +
src/dr/evomodel/substmodel/MsatBMA.java | 25 +
.../evomodel/substmodel/MultivariateOUModel.java | 25 +
src/dr/evomodel/substmodel/MutationDeathModel.java | 25 +
.../substmodel/NewMicrosatelliteModel.java | 25 +
src/dr/evomodel/substmodel/NtdBMA.java | 25 +
src/dr/evomodel/substmodel/NucModelType.java | 12 +-
src/dr/evomodel/substmodel/OnePhaseModel.java | 25 +
src/dr/evomodel/substmodel/PCACodonModel.java | 25 +
.../evomodel/substmodel/PCARateMatrixMammalia.java | 25 +
.../PositiveDefiniteSubstitutionModel.java | 25 +
src/dr/evomodel/substmodel/PseudoCodonModel.java | 2 +-
.../substmodel/SVSComplexSubstitutionModel.java | 25 +
.../substmodel/SVSGeneralSubstitutionModel.java | 25 +
.../substmodel/SubstitutionEpochModel.java | 10 +-
src/dr/evomodel/substmodel/SubstitutionModel.java | 2 +-
.../substmodel/SubstitutionModelUtils.java | 25 +
src/dr/evomodel/substmodel/TN93.java | 2 +-
src/dr/evomodel/substmodel/TwoPhaseModel.java | 25 +
.../evomodel/substmodel/TwoStateCovarionModel.java | 2 +-
src/dr/evomodel/substmodel/WAG.java | 2 +-
src/dr/evomodel/substmodel/YangCodonModel.java | 2 +-
.../HierarchicalTransmissionDemographicModel.java | 2 +-
.../transmission/TransmissionDemographicModel.java | 2 +-
.../transmission/TransmissionHistoryModel.java | 10 +-
.../transmission/TransmissionLikelihood.java | 2 +-
.../transmission/TransmissionSimulator.java | 2 +-
.../transmission/TransmissionStatistic.java | 2 +-
.../tree/AbstractCladeImportanceDistribution.java | 10 +-
.../evomodel/tree/AbstractTreeParameterModel.java | 2 +-
src/dr/evomodel/tree/AncestralTrait.java | 4 +-
src/dr/evomodel/tree/BackboneNodeFilter.java | 25 +
src/dr/evomodel/tree/CompatibilityStatistic.java | 4 +-
.../evomodel/tree/ConditionalCladeFrequency.java | 10 +-
src/dr/evomodel/tree/Convergence.java | 25 +
src/dr/evomodel/tree/ConvergenceListener.java | 25 +
src/dr/evomodel/tree/ConvergenceLogger.java | 25 +
.../tree/EmpiricalTreeDistributionModel.java | 39 +-
src/dr/evomodel/tree/ExternalLengthStatistic.java | 4 +-
src/dr/evomodel/tree/HiddenLinkageLogger.java | 25 +
src/dr/evomodel/tree/HiddenLinkageModel.java | 25 +
src/dr/evomodel/tree/HiddenLinkageTreeLogger.java | 25 +
src/dr/evomodel/tree/MRCATraitStatistic.java | 4 +-
.../tree/MicrosatelliteSamplerTreeModel.java | 25 +
src/dr/evomodel/tree/MonophylyStatistic.java | 2 +-
.../tree/MultivariateTreeParameterModel.java | 2 +-
src/dr/evomodel/tree/NewTreeParameterModel.java | 2 +-
src/dr/evomodel/tree/NodeHeightsStatistic.java | 4 +-
src/dr/evomodel/tree/NodeTraitLogger.java | 25 +
src/dr/evomodel/tree/ParsimonyStateStatistic.java | 2 +-
src/dr/evomodel/tree/ParsimonyStatistic.java | 2 +-
.../tree/ProgressiveScalarTreeTransform.java | 2 +-
src/dr/evomodel/tree/RateCovarianceStatistic.java | 2 +-
src/dr/evomodel/tree/RateStatistic.java | 2 +-
.../evomodel/tree/SingleScalarTreeTransform.java | 2 +-
.../tree/SlicedMultivariateTreeParameterModel.java | 2 +-
src/dr/evomodel/tree/SpeciesTreeStatistic.java | 2 +-
src/dr/evomodel/tree/StarTreeModel.java | 2 +-
src/dr/evomodel/tree/TMRCAStatistic.java | 2 +-
src/dr/evomodel/tree/TipHeightLikelihood.java | 2 +-
src/dr/evomodel/tree/TransformedTreeModel.java | 2 +-
src/dr/evomodel/tree/TreeHeightStatistic.java | 25 +
src/dr/evomodel/tree/TreeLengthStatistic.java | 4 +-
src/dr/evomodel/tree/TreeLogger.java | 2 +-
src/dr/evomodel/tree/TreeMetricStatistic.java | 2 +-
src/dr/evomodel/tree/TreeModel.java | 16 +-
src/dr/evomodel/tree/TreeParameterModel.java | 2 +-
src/dr/evomodel/tree/TreeShapeStatistic.java | 2 +-
src/dr/evomodel/tree/TreeSpaceLogger.java | 25 +
src/dr/evomodel/tree/TreeStatistic.java | 2 +-
src/dr/evomodel/tree/TreeSummary.java | 25 +
src/dr/evomodel/tree/TreeTraceAnalysis.java | 10 +-
src/dr/evomodel/tree/TreeTransform.java | 2 +-
src/dr/evomodel/tree/TrialTreeParameterModel.java | 2 +-
src/dr/evomodel/tree/UniformNodeHeightPrior.java | 10 +-
src/dr/evomodel/tree/WanderingTaxonLogger.java | 25 +
.../tree/WeightedMultiplicativeBinary.java | 10 +-
.../tree/randomlocalmodel/RLTVAnalyzer.java | 25 +
.../evomodel/tree/randomlocalmodel/RLTVLogger.java | 25 +
.../tree/randomlocalmodel/RLTVLoggerOnTree.java | 25 +
.../randomlocalmodel/RandomLocalTreeVariable.java | 25 +
.../treelikelihood/AbstractLikelihoodCore.java | 2 +-
.../treelikelihood/AbstractTreeLikelihood.java | 10 +-
.../treelikelihood/AdvancedTreeLikelihood.java | 2 +-
.../treelikelihood/AminoAcidLikelihoodCore.java | 2 +-
.../AncestralStateTreeLikelihood.java | 25 +
.../ArbitraryPrecisionLikelihoodCore.java | 2 +-
.../EpochTreeBranchSubstitutionModel.java | 25 +
.../treelikelihood/EpochTreeLikelihood.java | 25 +
.../treelikelihood/GeneralLikelihoodCore.java | 2 +-
.../treelikelihood/HiddenLinkageLikelihood.java | 25 +
.../treelikelihood/HypermutantErrorModel.java | 25 +
src/dr/evomodel/treelikelihood/LikelihoodCore.java | 2 +-
.../treelikelihood/LikelihoodPartialsProvider.java | 2 +-
.../treelikelihood/LikelihoodScalingProvider.java | 2 +-
.../MicrosatelliteSamplerTreeLikelihood.java | 25 +
.../NativeAminoAcidLikelihoodCore.java | 25 +
.../NativeCovarionLikelihoodCore.java | 25 +
.../NativeGeneralLikelihoodCore.java | 25 +
.../NativeNucleotideLikelihoodCore.java | 2 +-
.../NodePosteriorTreeLikelihood.java | 25 +
.../treelikelihood/NucleotideLikelihoodCore.java | 2 +-
.../PrecisionTestTreeLikelihood.java | 4 +-
.../PurifyingGammaTreeLikelihood.java | 10 +-
.../treelikelihood/PurifyingTreeLikelihood.java | 2 +-
.../treelikelihood/ScaleFactorsHelper.java | 2 +-
.../treelikelihood/SequenceErrorModel.java | 25 +
src/dr/evomodel/treelikelihood/TipStatesModel.java | 12 +-
.../TreeBranchSubstitutionModel.java | 10 +-
src/dr/evomodel/treelikelihood/TreeLikelihood.java | 2 +-
src/dr/evomodelxml/CSVExporterParser.java | 12 +-
.../ConditionalCladeFrequencyParser.java | 10 +-
.../EmpiricalTreeDistributionModelParser.java | 16 +-
.../EmpiricalTreeDistributionOperatorParser.java | 12 +-
src/dr/evomodelxml/MSSD/ALSSiteModelParser.java | 25 +
.../evomodelxml/MSSD/ALSTreeLikelihoodParser.java | 2 +-
.../MSSD/AnyTipObservationProcessParser.java | 25 +
src/dr/evomodelxml/MSSD/CTMCScalePriorParser.java | 2 +-
.../ExponentialBranchLengthTreePriorParser.java | 25 +
.../MSSD/SingleTipObservationProcessParser.java | 25 +
src/dr/evomodelxml/TreeTraceAnalysisParser.java | 2 +-
src/dr/evomodelxml/TreeWorkingPriorParsers.java | 31 +-
src/dr/evomodelxml/WanderingTaxonLoggerParser.java | 25 +
.../ArbitraryBranchRatesParser.java | 2 +-
.../AttributeBranchRateModelParser.java | 4 +-
.../branchratemodel/BranchCategoriesParser.java | 4 +-
.../CompoundBranchRateModelParser.java | 25 +
.../ContinuousBranchRatesParser.java | 25 +
.../ContinuousTraitBranchRateModelParser.java | 25 +
.../CountableMixtureBranchRatesParser.java | 2 +-
.../DiscreteTraitBranchRateModelParser.java | 25 +
.../DiscretizedBranchRatesParser.java | 2 +-
.../branchratemodel/FixedDriftModelParser.java | 25 +
.../LatentStateBranchRateModelParser.java | 2 +-
.../branchratemodel/LocalClockModelParser.java | 25 +
.../MixtureModelBranchRatesParser.java | 25 +
.../RandomDiscretizedBranchRatesParser.java | 25 +
.../RandomLocalClockModelParser.java | 25 +
.../RateEpochBranchRateModelParser.java | 25 +
.../branchratemodel/RelaxedDriftModelParser.java | 25 +
.../ScaledTreeLengthRateModelParser.java | 2 +-
.../StrictClockBranchRatesParser.java | 25 +
src/dr/evomodelxml/clock/ACLikelihoodParser.java | 25 +
src/dr/evomodelxml/clock/UCLikelihoodParser.java | 25 +
.../coalescent/AsymptoticGrowthModelParser.java | 92 ++
.../coalescent/BMPriorLikelihoodParser.java | 25 +
.../BayesianSkylineLikelihoodParser.java | 25 +
.../BayesianSkylinePopSizeStatisticParser.java | 25 +
.../CataclysmicDemographicModelParser.java | 25 +
.../CoalescentEventsStatisticParser.java | 24 +-
.../CoalescentIntervalStatisticParser.java | 2 +-
.../coalescent/CoalescentLikelihoodParser.java | 25 +
.../coalescent/CoalescentSimulatorParser.java | 25 +
.../CoalescentTreeIntervalStatisticParser.java | 2 +-
.../coalescent/ConstExpConstModelParser.java | 25 +
.../coalescent/ConstantExponentialModelParser.java | 25 +
.../coalescent/ConstantLogisticModelParser.java | 25 +
.../coalescent/ConstantPopulationModelParser.java | 25 +
.../evomodelxml/coalescent/EBSPAnalysisParser.java | 25 +
.../coalescent/EmergingEpidemicModelParser.java | 25 +
.../coalescent/EmpiricalPiecewiseModelParser.java | 25 +
.../ExpConstExpDemographicModelParser.java | 25 +
.../coalescent/ExpansionModelParser.java | 25 +
.../coalescent/ExponentialConstantModelParser.java | 25 +
.../ExponentialExponentialModelParser.java | 25 +
.../coalescent/ExponentialGrowthModelParser.java | 25 +
.../coalescent/ExponentialLogisticModelParser.java | 25 +
.../coalescent/ExponentialSawtoothModelParser.java | 25 +
.../GMRFBivariateCurveAnalysisParser.java | 25 +
.../GMRFIntervalHeightsStatisticParser.java | 25 +
.../coalescent/GMRFPopSizeStatisticParser.java | 25 +
.../coalescent/GMRFSkyrideLikelihoodParser.java | 2 +-
.../coalescent/GMRFTestLikelihoodParser.java | 25 +
.../coalescent/GPSkytrackAnalysisParser.java | 25 +
.../GaussianProcessSkytrackLikelihoodParser.java | 2 +-
.../coalescent/LineageCountStatisticParser.java | 25 +
.../coalescent/LinearGrowthModelParser.java | 80 ++
.../coalescent/LogisticGrowthModelParser.java | 25 +
.../coalescent/OldCoalescentSimulatorParser.java | 25 +
.../OrnsteinUhlenbeckPriorLikelihoodParser.java | 25 +
.../coalescent/PeakAndDeclineModelParser.java | 99 ++
.../coalescent/PiecewisePopulationModelParser.java | 25 +
.../coalescent/PopulationSizeGraphParser.java | 25 +
.../coalescent/PowerLawGrowthModelParser.java | 92 ++
.../coalescent/ScaledPiecewiseModelParser.java | 25 +
.../coalescent/TwoEpochDemographicModelParser.java | 25 +
.../coalescent/VariableDemographicModelParser.java | 25 +
.../VariableSkylineLikelihoodParser.java | 25 +
.../BayesianSkylineGibbsOperatorParser.java | 25 +
.../GMRFSkyrideBlockUpdateOperatorParser.java | 2 +-
...GMRFSkyrideFixedEffectsGibbsOperatorParser.java | 25 +
...anProcessSkytrackBlockUpdateOperatorParser.java | 25 +
.../GaussianProcessSkytrackTreeOperatorParser.java | 25 +
.../SampleNonActiveGibbsOperatorParser.java | 25 +
.../continuous/BuildCompoundSymmetricMatrix.java | 25 +
.../continuous/DataFromTreeTipsParser.java | 2 +-
.../continuous/GaussianProcessFromTreeParser.java | 25 +
.../continuous/LeafTraitExtractorParser.java | 2 +-
src/dr/evomodelxml/indel/IstvanOperatorParser.java | 25 +
.../evomodelxml/indel/TKF91LikelihoodParser.java | 25 +
src/dr/evomodelxml/indel/TKF91ModelParser.java | 25 +
.../AlloppChangeNumHybridizationsParser.java | 25 +
.../operators/AlloppHybPopSizesScaleParser.java | 25 +
.../operators/AlloppMoveLegsParser.java | 25 +
.../operators/AlloppNetworkNodeSlideParser.java | 25 +
.../AlloppSequenceReassignmentParser.java | 25 +
.../operators/ExchangeOperatorParser.java | 10 +-
src/dr/evomodelxml/operators/FNPRParser.java | 25 +
.../operators/FunkyPriorMixerOperatorParser.java | 25 +
.../operators/GibbsPruneAndRegraftParser.java | 25 +
.../operators/GibbsSubtreeSwapParser.java | 25 +
.../operators/ImportanceNarrowExchangeParser.java | 25 +
.../operators/ImportancePruneAndRegraftParser.java | 25 +
.../operators/ImportanceSubtreeSwapParser.java | 25 +
.../operators/MoveLinkageGroupParser.java | 25 +
.../operators/MulTreeNodeSlideParser.java | 25 +
.../MulTreeSequenceReassignmentParser.java | 25 +
src/dr/evomodelxml/operators/NNIParser.java | 25 +
.../operators/PopsIOTreeNodeSlideParser.java | 25 +
.../operators/RateExchangeOperatorParser.java | 25 +
.../operators/RateSampleOperatorParser.java | 25 +
.../operators/RateScaleOperatorParser.java | 25 +
.../operators/RateVarianceScaleOperatorParser.java | 25 +
.../operators/SubtreeJumpOperatorParser.java | 53 +-
.../operators/SubtreeSlideOperatorParser.java | 25 +
.../operators/TreeBitMoveOperatorParser.java | 25 +
.../operators/TreeBitRandomWalkOperatorParser.java | 25 +
.../evomodelxml/operators/TreeNodeSlideParser.java | 25 +
.../evomodelxml/operators/TreeUniformParser.java | 25 +
.../evomodelxml/operators/WilsonBaldingParser.java | 25 +
.../sitemodel/CategorySiteModelParser.java | 25 +
.../sitemodel/DiscretizedLociRatesParser.java | 25 +
.../evomodelxml/sitemodel/GammaSiteBMAParser.java | 25 +
.../sitemodel/GammaSiteModelParser.java | 25 +
.../sitemodel/SampleQuantileLociRatesParser.java | 25 +
.../SampleStateAndCategoryModelParser.java | 25 +
.../sitemodel/SampleStateModelParser.java | 25 +
.../speciation/AlloppMSCoalescentParser.java | 25 +
.../speciation/AlloppNetworkPriorModelParser.java | 25 +
.../speciation/AlloppNetworkPriorParser.java | 25 +
.../speciation/AlloppNumHybsStatisticParser.java | 25 +
.../AlloppSpeciesBindingsApSpInfoParser.java | 25 +
.../AlloppSpeciesBindingsIndividualParser.java | 25 +
.../speciation/AlloppSpeciesBindingsParser.java | 25 +
.../AlloppSpeciesNetworkModelParser.java | 25 +
.../speciation/BetaSplittingModelParser.java | 25 +
.../speciation/BirthDeathCollapseModelParser.java | 25 +
...BirthDeathCollapseNClustersStatisticParser.java | 25 +
.../BirthDeathEpidemiologyModelParser.java | 24 +-
.../speciation/BirthDeathModelParser.java | 10 +-
.../BirthDeathSerialSamplingModelParser.java | 10 +-
.../BirthDeathSerialSkylineModelParser.java | 10 +-
.../speciation/BranchingLikelihoodParser.java | 25 +
.../ModelAveragingSpeciationLikelihoodParser.java | 25 +
.../speciation/MulMSCoalescentParser.java | 25 +
.../speciation/MulSpeciesBindingsParser.java | 25 +
.../speciation/MulSpeciesTreeModelParser.java | 25 +
.../speciation/MulSpeciesTreePriorParser.java | 25 +
.../speciation/MultiSpeciesCoalescentParser.java | 25 +
.../speciation/PopsIOMSCoalescentParser.java | 25 +
.../speciation/PopsIOSpeciesBindingsParser.java | 25 +
.../PopsIOSpeciesBindingsSpInfoParser.java | 25 +
.../speciation/PopsIOSpeciesTreeModelParser.java | 25 +
.../speciation/PopsIOSpeciesTreePriorParser.java | 25 +
.../evomodelxml/speciation/RLTVLoggerParser.java | 25 +
.../speciation/RandomLocalYuleModelParser.java | 25 +
.../speciation/SpeciationLikelihoodParser.java | 25 +
.../speciation/SpeciesBindingsParser.java | 25 +
.../speciation/SpeciesBindingsSPinfoParser.java | 25 +
.../speciation/SpeciesTreeBMPriorParser.java | 25 +
.../speciation/SpeciesTreeModelParser.java | 25 +
.../speciation/SpeciesTreeSimplePriorParser.java | 25 +
.../TaxonRichnessBirthDeathModelParser.java | 25 +
src/dr/evomodelxml/speciation/YuleModelParser.java | 10 +-
.../substmodel/AsymQuadModelParser.java | 25 +
.../substmodel/BinaryCovarionModelParser.java | 2 +-
.../substmodel/BinarySubstitutionModelParser.java | 25 +
.../substmodel/ComplexSubstitutionModelParser.java | 25 +
.../evomodelxml/substmodel/CovarionGTRParser.java | 25 +
.../evomodelxml/substmodel/CovarionHKYParser.java | 25 +
.../substmodel/EmpiricalAminoAcidModelParser.java | 25 +
.../substmodel/EmpiricalCodonModelParser.java | 25 +
.../substmodel/FrequencyModelParser.java | 25 +
.../substmodel/GLMSubstitutionModelParser.java | 25 +
src/dr/evomodelxml/substmodel/GTRParser.java | 25 +
.../substmodel/GeneralF81ModelParser.java | 25 +
.../substmodel/GeneralSubstitutionModelParser.java | 25 +
src/dr/evomodelxml/substmodel/HKYParser.java | 25 +
.../substmodel/LewisMkSubstitutionModelParser.java | 25 +
.../substmodel/LinearBiasModelParser.java | 25 +
src/dr/evomodelxml/substmodel/MkModelParser.java | 10 +-
src/dr/evomodelxml/substmodel/MsatBMAParser.java | 25 +
.../substmodel/MultivariateOUModelParser.java | 25 +
.../substmodel/MutationDeathModelParser.java | 2 +-
.../substmodel/NewMicrosatelliteModelParser.java | 25 +
src/dr/evomodelxml/substmodel/NtdBMAParser.java | 25 +
.../substmodel/PCACodonModelParser.java | 25 +
.../PositiveDefiniteSubstitutionModelParser.java | 25 +
.../substmodel/SubstitutionEpochModelParser.java | 25 +
src/dr/evomodelxml/substmodel/TN93Parser.java | 25 +
.../substmodel/TwoPhaseModelParser.java | 25 +
.../substmodel/TwoStateCovarionModelParser.java | 25 +
.../substmodel/YangCodonModelParser.java | 25 +
src/dr/evomodelxml/tree/AncestralTraitParser.java | 25 +
.../tree/CompatibilityStatisticParser.java | 25 +
.../tree/ExternalLengthStatisticParser.java | 25 +
.../tree/HiddenLinkageLoggerParser.java | 25 +
.../evomodelxml/tree/HiddenLinkageModelParser.java | 25 +
.../tree/HiddenLinkageTreeLoggerParser.java | 25 +
.../evomodelxml/tree/MRCATraitStatisticParser.java | 25 +
.../tree/MicrosatelliteSamplerTreeModelParser.java | 25 +
.../evomodelxml/tree/MonophylyStatisticParser.java | 25 +
.../tree/NodeHeightsStatisticParser.java | 25 +
.../tree/ParsimonyStateStatisticParser.java | 25 +
.../evomodelxml/tree/ParsimonyStatisticParser.java | 25 +
.../evomodelxml/tree/RLTVLoggerOnTreeParser.java | 25 +
.../tree/RateCovarianceStatisticParser.java | 25 +
src/dr/evomodelxml/tree/RateStatisticParser.java | 25 +
.../tree/SpeciesTreeStatisticParser.java | 25 +
src/dr/evomodelxml/tree/StarTreeModelParser.java | 2 +-
src/dr/evomodelxml/tree/TMRCAStatisticParser.java | 25 +
.../tree/TipHeightLikelihoodParser.java | 25 +
.../tree/TransformedTreeModelParser.java | 2 +-
.../tree/TreeHeightStatisticParser.java | 25 +
.../tree/TreeLengthStatisticParser.java | 25 +
src/dr/evomodelxml/tree/TreeLoggerParser.java | 25 +
.../tree/TreeMetricStatisticParser.java | 25 +
src/dr/evomodelxml/tree/TreeModelParser.java | 10 +-
.../evomodelxml/tree/TreeShapeStatisticParser.java | 25 +
.../tree/UniformNodeHeightPriorParser.java | 25 +
.../AncestralStateTreeLikelihoodParser.java | 27 +-
.../HiddenLinkageLikelihoodParser.java | 25 +
.../MarkovJumpsTreeLikelihoodParser.java | 27 +-
.../MicrosatelliteSamplerTreeLikelihoodParser.java | 25 +
.../treelikelihood/SequenceErrorModelParser.java | 25 +
.../treelikelihood/TreeLikelihoodParser.java | 25 +
.../treelikelihood/TreeTraitParserUtilities.java | 30 +-
src/dr/evoxml/AlignmentParser.java | 2 +-
src/dr/evoxml/AscertainedSitePatternsParser.java | 25 +
src/dr/evoxml/AttributePatternsParser.java | 4 +-
.../evoxml/BifractionalDiffusionModelParser.java | 25 +
src/dr/evoxml/CompositeDataTypeParser.java | 4 +-
src/dr/evoxml/ConstantPatternsParser.java | 4 +-
src/dr/evoxml/ConvertAlignmentParser.java | 2 +-
src/dr/evoxml/DateParser.java | 10 +-
src/dr/evoxml/DistanceMatrixParser.java | 2 +-
src/dr/evoxml/GeneralDataTypeParser.java | 2 +-
src/dr/evoxml/HiddenNucleotideParser.java | 25 +
src/dr/evoxml/HypermutantAlignmentParser.java | 4 +-
src/dr/evoxml/KStateDataTypeParser.java | 10 +-
src/dr/evoxml/LineageCountThroughTimeParser.java | 10 +-
src/dr/evoxml/LinkageConstraintsParser.java | 25 +
src/dr/evoxml/LinkedGroupParser.java | 25 +
src/dr/evoxml/LocationParser.java | 4 +-
src/dr/evoxml/MaskedPatternsParser.java | 4 +-
src/dr/evoxml/MergePatternsParser.java | 2 +-
src/dr/evoxml/MetagenomeDataParser.java | 25 +
src/dr/evoxml/MicrosatelliteParser.java | 25 +
src/dr/evoxml/MicrosatellitePatternParser.java | 25 +
src/dr/evoxml/MicrosatelliteSimulatorParser.java | 25 +
src/dr/evoxml/MsatPatternStatisticParser.java | 25 +
src/dr/evoxml/MultiLociDistanceParser.java | 25 +
src/dr/evoxml/MutationDeathTypeParser.java | 25 +
src/dr/evoxml/NeighborJoiningParser.java | 2 +-
src/dr/evoxml/NewickParser.java | 73 +-
src/dr/evoxml/PatternSubSetParser.java | 4 +-
src/dr/evoxml/PearsonCorrelationParser.java | 25 +
src/dr/evoxml/PolarCoordinatesParser.java | 2 +-
src/dr/evoxml/RandomSubsetTaxaParser.java | 25 +
src/dr/evoxml/RandomTaxaSampleParser.java | 25 +
src/dr/evoxml/RescaledTreeParser.java | 2 +-
src/dr/evoxml/SequenceParser.java | 2 +-
src/dr/evoxml/SimpleNodeParser.java | 2 +-
src/dr/evoxml/SimpleTreeParser.java | 10 +-
src/dr/evoxml/SitePatternsParser.java | 2 +-
src/dr/evoxml/TaxaParser.java | 2 +-
src/dr/evoxml/TaxonParser.java | 10 +-
src/dr/evoxml/UPGMATreeParser.java | 2 +-
src/dr/evoxml/util/DataTypeUtils.java | 25 +
src/dr/evoxml/util/DateUnitsType.java | 12 +-
src/dr/evoxml/util/GraphMLUtils.java | 25 +
src/dr/evoxml/util/XMLUnits.java | 10 +-
src/dr/geo/BrownianBridge1D.java | 25 +
src/dr/geo/GTOPO30Browser.java | 10 +-
src/dr/geo/GTOPO30Panel.java | 10 +-
src/dr/geo/GTOPO30RandomWalk.java | 25 +
src/dr/geo/GTOPO30Tile.java | 25 +
src/dr/geo/GeoSpatialCollectionModel.java | 10 +-
src/dr/geo/GeoSpatialDistribution.java | 2 +-
src/dr/geo/GreatCircleDistances.java | 25 +
src/dr/geo/InhomogeneousRandomWalk.java | 25 +
src/dr/geo/IslandLattice.java | 25 +
src/dr/geo/KMLCoordinates.java | 25 +
src/dr/geo/KMLRenderer.java | 25 +
src/dr/geo/KMLViewer.java | 12 +-
src/dr/geo/KernelDensityEstimator2D.java | 25 +
src/dr/geo/Lattice.java | 25 +
src/dr/geo/Location.java | 25 +
src/dr/geo/MultiRegionGeoSpatialDistribution.java | 2 +-
src/dr/geo/MultivariateBrownianBridge.java | 10 +-
src/dr/geo/NewPolygon2D.java | 10 +-
src/dr/geo/NumericalSpaceTimeProbs2D.java | 10 +-
src/dr/geo/Polygon.java | 25 +
src/dr/geo/Polygon2D.java | 25 +
src/dr/geo/RateMatrix.java | 25 +
src/dr/geo/Reject.java | 25 +
src/dr/geo/SpaceTime.java | 10 +-
src/dr/geo/SpaceTimeRejector.java | 10 +-
src/dr/geo/SpaceTimeRejector1D.java | 25 +
src/dr/geo/SpaceTimeSimulator.java | 10 +-
src/dr/geo/ViewTransform.java | 25 +
src/dr/geo/VisualizeBrownianBridge2D.java | 10 +-
src/dr/geo/VisualizeKMLBrownianBridge.java | 10 +-
src/dr/geo/VisualizeKMLJointProb.java | 10 +-
src/dr/geo/VisualizeKMLNumericalProbs.java | 10 +-
src/dr/geo/VisualizeSpaceTimeSim2D.java | 10 +-
src/dr/geo/cartogram/CartogramMapping.java | 10 +-
src/dr/geo/color/ChannelColorScheme.java | 2 +-
src/dr/geo/color/ColorScheme.java | 2 +-
src/dr/geo/contouring/ContourAttrib.java | 25 +
src/dr/geo/contouring/ContourGenerator.java | 25 +
src/dr/geo/contouring/ContourMaker.java | 25 +
src/dr/geo/contouring/ContourMode.java | 25 +
src/dr/geo/contouring/ContourPath.java | 25 +
src/dr/geo/contouring/ContourWithR.java | 25 +
src/dr/geo/contouring/ContourWithSynder.java | 25 +
src/dr/geo/contouring/SnyderContour.java | 25 +
.../FisherBinghamKentDistribution.java | 25 +
.../geo/distributions/HyperSphereDistribution.java | 25 +
src/dr/geo/distributions/VonMisesDistribution.java | 25 +
.../distributions/VonMisesFisherDistribution.java | 25 +
src/dr/geo/math/Space.java | 25 +
src/dr/geo/math/SphericalPolarCoordinates.java | 2 +-
src/dr/geo/math/Vector3D.java | 2 +-
.../geo/operators/UniformGeoSpatialOperator.java | 2 +-
.../operators/UniformGeoSpatialOperatorParser.java | 2 +-
src/dr/geo/testGreatCircleDistances.xml | 25 +
src/dr/geo/testLocations.xml | 25 +
.../AbstractDistributionLikelihood.java | 2 +-
.../distribution/BetaDistributionModel.java | 2 +-
.../inference/distribution/BinomialLikelihood.java | 48 +-
.../distribution/CachedDistributionLikelihood.java | 25 +
.../distribution/ConditionalCladeProbability.java | 25 +
.../distribution/DirichletProcessLikelihood.java | 10 +-
.../distribution/DistributionLikelihood.java | 18 +-
.../EmpiricalDistributionLikelihood.java | 2 +-
.../distribution/ExponentialDistributionModel.java | 10 +-
.../distribution/ExponentialMarkovModel.java | 10 +-
.../distribution/GammaDistributionModel.java | 10 +-
.../distribution/GeneralizedLinearModel.java | 2 +-
.../distribution/HierarchicalGraphLikelihood.java | 25 +
.../InverseGammaDistributionModel.java | 12 +-
.../InverseGaussianDistributionModel.java | 25 +-
.../inference/distribution/LinearRegression.java | 25 +
.../distribution/LocationScaleJeffreysPrior.java | 2 +-
src/dr/inference/distribution/LogLinearModel.java | 25 +
.../distribution/LogNormalDistributionModel.java | 2 +-
.../inference/distribution/LogisticRegression.java | 25 +
.../distribution/MixedDistributionLikelihood.java | 25 +
.../ModelSpecificPseudoPriorLikelihood.java | 25 +
.../distribution/MomentDistributionModel.java | 203 ++++
.../MultivariateDistributionLikelihood.java | 2 +-
.../MultivariateNormalDistributionModel.java | 12 +-
.../distribution/NormalDistributionModel.java | 2 +-
.../distribution/ParametricDistributionModel.java | 2 +-
.../ParametricMultivariateDistributionModel.java | 2 +-
src/dr/inference/distribution/RandomWalkModel.java | 25 +
.../distribution/SkewNormalDistributionModel.java | 2 +-
.../distribution/SplineInterpolatedLikelihood.java | 10 +-
.../inference/distribution/TDistributionModel.java | 2 +-
.../TruncatedNormalDistributionModel.java | 25 +
.../TwoPartsDistributionLikelihood.java | 25 +
.../TwoPieceLocationScaleDistributionModel.java | 2 +-
.../distribution/UniformDistributionModel.java | 2 +-
.../WishartGammalDistributionModel.java | 2 +-
src/dr/inference/loggers/ArrayLogFormatter.java | 25 +
src/dr/inference/loggers/BooleanColumn.java | 25 +
src/dr/inference/loggers/Columns.java | 2 +-
src/dr/inference/loggers/LogColumn.java | 2 +-
src/dr/inference/loggers/LogFormatter.java | 2 +-
src/dr/inference/loggers/Loggable.java | 2 +-
src/dr/inference/loggers/Logger.java | 2 +-
src/dr/inference/loggers/MCLogger.java | 2 +-
src/dr/inference/loggers/MLLogger.java | 2 +-
src/dr/inference/loggers/MatrixEntryColumn.java | 25 +
src/dr/inference/loggers/NumberColumn.java | 2 +-
src/dr/inference/loggers/PercentColumn.java | 25 +
.../inference/loggers/TabDelimitedFormatter.java | 2 +-
src/dr/inference/markovchain/Acceptor.java | 2 +-
src/dr/inference/markovchain/MarkovChain.java | 15 +-
.../inference/markovchain/MarkovChainDelegate.java | 4 +-
.../inference/markovchain/MarkovChainListener.java | 2 +-
src/dr/inference/markovchain/Profiler.java | 2 +-
src/dr/inference/markovjumps/MarkovJumpsCore.java | 25 +
.../markovjumps/MarkovJumpsRegisterAcceptor.java | 25 +
src/dr/inference/markovjumps/MarkovJumpsType.java | 25 +
src/dr/inference/markovjumps/MarkovReward.java | 2 +-
.../markovjumps/SericolaSeriesMarkovReward.java | 2 +-
src/dr/inference/markovjumps/StateChange.java | 2 +-
src/dr/inference/markovjumps/StateHistory.java | 2 +-
.../inference/markovjumps/SubordinatedProcess.java | 25 +
.../markovjumps/TwoStateOccupancyMarkovReward.java | 360 +++++-
.../TwoStateSericolaSeriesMarkovReward.java | 2 +-
.../markovjumps/UniformizedStateHistory.java | 25 +
src/dr/inference/mcmc/DebugChainListener.java | 81 ++
src/dr/inference/mcmc/DebugUtils.java | 188 ++++
src/dr/inference/mcmc/FrequencyDistribution2D.java | 83 --
src/dr/inference/mcmc/MCMC.java | 162 +--
src/dr/inference/mcmc/MCMCCriterion.java | 2 +-
src/dr/inference/mcmc/MCMCOptions.java | 2 +-
.../mcmc/MarginalLikelihoodEstimator.java | 2 +-
src/dr/inference/mcmcmc/MCMCMC.java | 50 +-
src/dr/inference/mcmcmc/MCMCMCOptions.java | 2 +-
src/dr/inference/mcmcmc/MCMCMCRunner.java | 2 +-
src/dr/inference/ml/GreatDelugeCriterion.java | 2 +-
src/dr/inference/ml/HillClimbingCriterion.java | 2 +-
src/dr/inference/ml/MLOptimizer.java | 2 +-
src/dr/inference/model/AbstractModel.java | 10 +-
.../inference/model/AbstractModelLikelihood.java | 25 +
.../BayesianStochasticSearchVariableSelection.java | 25 +
.../model/BlockDiagonalMatrixParameter.java | 2 +-
.../model/BlockUpperTriangularMatrixParameter.java | 29 +-
src/dr/inference/model/BooleanLikelihood.java | 2 +-
src/dr/inference/model/BooleanStatistic.java | 2 +-
src/dr/inference/model/Bounds.java | 2 +-
src/dr/inference/model/CompoundLikelihood.java | 32 +-
.../inference/model/CompoundMatrixParameter.java | 100 ++
src/dr/inference/model/CompoundModel.java | 2 +-
src/dr/inference/model/CompoundParameter.java | 13 +-
.../inference/model/CompoundSymmetricMatrix.java | 25 +
src/dr/inference/model/ConstantLikelihood.java | 2 +-
.../inference/model/CopyParameterValuesParser.java | 94 ++
src/dr/inference/model/CorrelationStatistic.java | 25 +
src/dr/inference/model/CoulombPrior.java | 4 +-
src/dr/inference/model/DecomposedMatrix.java | 25 +
src/dr/inference/model/DefaultModel.java | 2 +-
src/dr/inference/model/DesignMatrix.java | 2 +-
src/dr/inference/model/DiagonalMatrix.java | 2 +-
.../inference/model/DifferenceMatrixParameter.java | 251 +++++
src/dr/inference/model/DifferenceParameter.java | 129 +++
src/dr/inference/model/DifferenceStatistic.java | 4 +-
src/dr/inference/model/DummyLikelihood.java | 2 +-
src/dr/inference/model/DuplicatedParameter.java | 25 +
.../model/EqualityConstrainedParameter.java | 2 +-
.../inference/model/EqualityConstraintModel.java | 2 +-
src/dr/inference/model/ExponentialStatistic.java | 2 +-
src/dr/inference/model/ExpressionStatistic.java | 2 +-
src/dr/inference/model/FiniteSetParameter.java | 10 +-
.../inference/model/IndianBuffetProcessPrior.java | 233 ++++
src/dr/inference/model/IntersectionBounds.java | 10 +-
src/dr/inference/model/JointParameter.java | 4 +-
src/dr/inference/model/LatentFactorModel.java | 2 +-
src/dr/inference/model/Likelihood.java | 2 +-
src/dr/inference/model/LikelihoodBenchmarker.java | 10 +-
src/dr/inference/model/LikelihoodProfile.java | 2 +-
src/dr/inference/model/LogarithmStatistic.java | 2 +-
src/dr/inference/model/LoggableStatistic.java | 10 +-
.../inference/model/MarkovRandomFieldMatrix.java | 62 +-
src/dr/inference/model/MaskedParameter.java | 29 +-
src/dr/inference/model/MatrixInverseStatistic.java | 25 +
src/dr/inference/model/MatrixMatrixProduct.java | 25 +
src/dr/inference/model/MatrixParameter.java | 2 +-
.../model/MatrixVectorProductParameter.java | 4 +-
src/dr/inference/model/MeanStatistic.java | 2 +-
src/dr/inference/model/MixtureModelLikelihood.java | 2 +-
src/dr/inference/model/Model.java | 2 +-
src/dr/inference/model/ModelListener.java | 2 +-
src/dr/inference/model/MonotonicStatistic.java | 25 +
src/dr/inference/model/NegativeStatistic.java | 2 +-
src/dr/inference/model/NewMatrixParameter.java | 25 +
src/dr/inference/model/NotBooleanStatistic.java | 2 +-
src/dr/inference/model/NotStatistic.java | 25 +
src/dr/inference/model/OneOnX3Prior.java | 25 +
src/dr/inference/model/OneOnXPrior.java | 2 +-
.../model/ParallelCompoundLikelihood.java | 25 +
src/dr/inference/model/ParallelLikelihood.java | 25 +
src/dr/inference/model/Parameter.java | 13 +-
src/dr/inference/model/ParameterChooser.java | 25 +
src/dr/inference/model/ParameterChooserParser.java | 25 +
src/dr/inference/model/ParameterIntegerParser.java | 4 +-
src/dr/inference/model/ParameterParser.java | 2 +-
src/dr/inference/model/PathLikelihood.java | 10 +-
src/dr/inference/model/PearsonCorrelation.java | 25 +
src/dr/inference/model/ProductParameter.java | 2 +-
src/dr/inference/model/ProductStatistic.java | 2 +-
src/dr/inference/model/RPNcalculatorStatistic.java | 4 +-
.../inference/model/RPNexpressionCalculator.java | 25 +
src/dr/inference/model/RatioStatistic.java | 4 +-
src/dr/inference/model/ReciprocalStatistic.java | 2 +-
src/dr/inference/model/SplineBasis.java | 25 +
src/dr/inference/model/Statistic.java | 2 +-
src/dr/inference/model/StatisticList.java | 2 +-
src/dr/inference/model/StatisticParser.java | 2 +-
src/dr/inference/model/SubStatistic.java | 10 +-
src/dr/inference/model/SumStatistic.java | 10 +-
src/dr/inference/model/TestStatistic.java | 2 +-
.../model/TestThreadedCompoundLikelihood.java | 2 +-
src/dr/inference/model/ThreadAwareLikelihood.java | 2 +-
.../model/ThreadedCompoundLikelihood.java | 4 +-
src/dr/inference/model/TransformedParameter.java | 6 +-
...nsposedBlockUpperTriangularMatrixParameter.java | 27 +-
.../inference/model/TransposedMatrixParameter.java | 2 +-
src/dr/inference/model/ValuesPool.java | 25 +
src/dr/inference/model/ValuesPoolParser.java | 25 +
src/dr/inference/model/Variable.java | 2 +-
src/dr/inference/model/VariableListener.java | 10 +-
src/dr/inference/model/VarianceStatistic.java | 2 +-
src/dr/inference/model/VectorSliceParameter.java | 50 +-
src/dr/inference/model/WeightedMixtureModel.java | 25 +
.../operators/AbstractCoercableOperator.java | 25 +
...daptableVarianceMultivariateNormalOperator.java | 2 +-
src/dr/inference/operators/BitFlipOperator.java | 9 +-
src/dr/inference/operators/BitMoveOperator.java | 25 +
src/dr/inference/operators/BitSwapOperator.java | 10 +-
.../inference/operators/CenteredScaleOperator.java | 2 +-
.../inference/operators/CoercableMCMCOperator.java | 2 +-
src/dr/inference/operators/CoercionMode.java | 25 +
.../operators/CombinedOperatorSchedule.java | 25 +
.../inference/operators/DeltaExchangeOperator.java | 10 +-
src/dr/inference/operators/DeltaMixOperator.java | 20 +-
.../operators/DirtyLikelihoodOperator.java | 25 +
.../operators/EllipticalSliceOperator.java | 144 ++-
.../inference/operators/FactorGibbsOperator.java | 2 +-
.../operators/FactorIndependenceOperator.java | 2 +-
src/dr/inference/operators/FactorOperator.java | 2 +-
src/dr/inference/operators/GeneralOperator.java | 25 +
.../operators/GenericIndependentSampler.java | 2 +-
.../operators/GibbsIndependentGammaOperator.java | 4 +-
.../GibbsIndependentJointNormalGammaOperator.java | 238 ++++
...GibbsIndependentNormalDistributionOperator.java | 2 +-
src/dr/inference/operators/GibbsOperator.java | 2 +-
.../operators/HierarchicalBitFlipOperator.java | 25 +
.../operators/IndependentGammaSampler.java | 2 +-
.../IndependentNormalDistributionSampler.java | 2 +-
src/dr/inference/operators/JointOperator.java | 25 +
src/dr/inference/operators/LNVarianceOperator.java | 2 +-
.../LatentFactorModelPrecisionGibbsOperator.java | 2 +-
.../inference/operators/LoadingsGibbsOperator.java | 2 +-
.../operators/LoadingsIndependenceOperator.java | 2 +-
.../inference/operators/LogRandomWalkOperator.java | 4 +-
...daptableVarianceMultivariateNormalOperator.java | 2 +-
src/dr/inference/operators/MCMCOperator.java | 2 +-
.../operators/MVOUCovarianceOperator.java | 25 +
.../operators/MicrosatUpDownOperator.java | 25 +
.../MicrosatelliteModelSelectOperator.java | 25 +
.../inference/operators/MsatBitFlipOperator.java | 25 +
...MsatFullAncestryImportanceSamplingOperator.java | 25 +
.../MsatSingleAncestralStateGibbsOperator.java | 25 +
.../MultipleRandomWalkIntegerOperator.java | 25 +
.../operators/MultivariateNormalGibbsOperator.java | 25 +
.../MultivariateNormalIndependenceSampler.java | 2 +-
.../operators/MultivariateNormalOperator.java | 2 +-
...daptableVarianceMultivariateNormalOperator.java | 2 +-
.../NormalGammaPrecisionGibbsOperator.java | 10 +-
.../operators/NormalNormalMeanGibbsOperator.java | 10 +-
.../operators/OperatorAnalysisPrinter.java | 25 +
.../operators/OperatorFailedException.java | 2 +-
src/dr/inference/operators/OperatorSchedule.java | 2 +-
src/dr/inference/operators/OperatorUtils.java | 2 +-
...andomWalkIntegerNodeHeightWeightedOperator.java | 25 +
.../operators/RandomWalkIntegerOperator.java | 25 +
.../RandomWalkIntegerSetSizeWeightedOperator.java | 25 +
src/dr/inference/operators/RandomWalkOperator.java | 2 +-
.../operators/RateBitExchangeOperator.java | 25 +
.../operators/RegressionGibbsEffectOperator.java | 25 +
.../RegressionGibbsPrecisionOperator.java | 25 +
.../RegressionMetropolizedIndicatorOperator.java | 25 +
src/dr/inference/operators/Scalable.java | 10 +-
src/dr/inference/operators/ScaleOperator.java | 10 +-
src/dr/inference/operators/SelectorOperator.java | 25 +
src/dr/inference/operators/SetOperator.java | 2 +-
src/dr/inference/operators/SimpleMCMCOperator.java | 2 +-
.../operators/SimpleMetropolizedGibbsOperator.java | 29 +-
src/dr/inference/operators/SimpleOperator.java | 25 +
.../operators/SimpleOperatorSchedule.java | 28 +-
src/dr/inference/operators/SliceInterval.java | 25 +
src/dr/inference/operators/SliceOperator.java | 25 +
src/dr/inference/operators/SwapOperator.java | 2 +-
.../operators/SwapParameterGibbsOperator.java | 48 +
.../inference/operators/SwapParameterOperator.java | 124 +++
src/dr/inference/operators/TeamOperator.java | 25 +
.../operators/TransformedRandomWalkOperator.java | 4 +-
src/dr/inference/operators/TwoPhaseOperator.java | 2 +-
.../operators/UniformIntegerOperator.java | 25 +
src/dr/inference/operators/UniformOperator.java | 2 +-
src/dr/inference/operators/UpDownOperator.java | 2 +-
.../operators/ValuesPoolSwapOperator.java | 25 +
src/dr/inference/parallel/MPILikelihoodRunner.java | 25 +
src/dr/inference/parallel/MPISerializable.java | 25 +
src/dr/inference/parallel/MPIServices.java | 10 +-
src/dr/inference/parallel/ServiceRequest.java | 25 +
src/dr/inference/prior/AbstractParameterPrior.java | 2 +-
src/dr/inference/prior/CompositePrior.java | 2 +-
src/dr/inference/prior/Prior.java | 10 +-
src/dr/inference/prior/UniformParameterPrior.java | 2 +-
.../inference/regression/RegressionJNIWrapper.java | 2 +-
.../regression/SelfControlledCaseSeries.java | 2 +-
src/dr/inference/trace/AbstractTraceList.java | 25 +
src/dr/inference/trace/ArrayTraceList.java | 27 +-
src/dr/inference/trace/CnCsPerSiteAnalysis.java | 31 +-
.../inference/trace/CnCsToDnDsPerSiteAnalysis.java | 8 +-
src/dr/inference/trace/DensityEstimate.java | 25 +
src/dr/inference/trace/DensityRectangle.java | 2 +-
src/dr/inference/trace/DnDsPerSiteAnalysis.java | 29 +-
src/dr/inference/trace/Filter.java | 25 +
src/dr/inference/trace/FilteredTraceList.java | 25 +
.../GeneralizedSteppingStoneSamplingAnalysis.java | 25 +
src/dr/inference/trace/KernelDensityEstimate.java | 25 +
src/dr/inference/trace/LogFileTraceExporter.java | 25 +
src/dr/inference/trace/LogFileTraces.java | 26 +-
.../trace/MarginalLikelihoodAnalysis.java | 16 +-
src/dr/inference/trace/OldDnDsPerSiteAnalysis.java | 29 +-
src/dr/inference/trace/PathSamplingAnalysis.java | 31 +-
.../trace/SteppingStoneSamplingAnalysis.java | 25 +
src/dr/inference/trace/Trace.java | 2 +-
src/dr/inference/trace/TraceAnalysis.java | 8 +-
src/dr/inference/trace/TraceCorrelation.java | 2 +-
src/dr/inference/trace/TraceCustomized.java | 4 +-
src/dr/inference/trace/TraceDistribution.java | 2 +-
src/dr/inference/trace/TraceException.java | 2 +-
src/dr/inference/trace/TraceFactory.java | 25 +
src/dr/inference/trace/TraceList.java | 4 +-
src/dr/inference/trace/TracesListener.java | 25 +
src/dr/inference/trace/TracesReader.java | 25 +
src/dr/inference/tutorial/Tutorial1.java | 10 +-
src/dr/inferencexml/MCMCParser.java | 2 +-
src/dr/inferencexml/MLOptimizerParser.java | 25 +
.../distribution/BetaDistributionModelParser.java | 2 +-
.../distribution/BinomialLikelihoodParser.java | 35 +-
.../CachedDistributionLikelihoodParser.java | 25 +
.../DirichletProcessLikelihoodParser.java | 12 +-
.../distribution/DistributionLikelihoodParser.java | 10 +-
.../distribution/DistributionModelParser.java | 10 +-
.../EmpiricalDistributionLikelihoodParser.java | 2 +-
.../ExponentialDistributionModelParser.java | 25 +
.../distribution/ExponentialMarkovModelParser.java | 10 +-
.../distribution/GammaDistributionModelParser.java | 25 +
.../distribution/GeneralizedLinearModelParser.java | 25 +
.../HierarchicalGraphLikelihoodParser.java | 25 +
.../InverseGammaDistributionModelParser.java | 25 +
.../InverseGaussianDistributionModelParser.java | 25 +
.../LocationScaleJeffreysPriorParser.java | 2 +-
.../LogNormalDistributionModelParser.java | 25 +
.../MixedDistributionLikelihoodParser.java | 25 +
.../ModelSpecificPseudoPriorLikelihoodParser.java | 25 +
.../MomentDistributionModelParser.java | 95 ++
.../MultivariateNormalDistributionModelParser.java | 2 +-
.../NormalDistributionModelParser.java | 25 +
.../OnePGammaDistributionModelParser.java | 25 +
src/dr/inferencexml/distribution/PriorParsers.java | 2 +-
.../distribution/RandomWalkModelParser.java | 25 +
.../ScaledBetaDistributionModelParser.java | 4 +-
.../SkewNormalDistributionModelParser.java | 2 +-
.../distribution/TDistributionModelParser.java | 2 +-
.../TruncatedNormalDistributionModelParser.java | 25 +
.../TwoPartsDistributionLikelihoodParser.java | 25 +
...oPieceLocationScaleDistributionModelParser.java | 2 +-
.../UniformDistributionModelParser.java | 25 +
.../WishartGammaDistributionModelParser.java | 2 +-
.../distribution/WorkingPriorParsers.java | 287 ++++-
src/dr/inferencexml/loggers/ColumnsParser.java | 25 +
src/dr/inferencexml/loggers/LoggerParser.java | 13 +-
src/dr/inferencexml/loggers/MLLoggerParser.java | 25 +
.../BlockUpperTriangularMatrixParameterParser.java | 25 +
.../model/BooleanLikelihoodParser.java | 25 +
.../model/CompoundLikelihoodParser.java | 13 +-
.../model/CompoundParameterParser.java | 25 +
.../model/CompoundSymmetricMatrixParser.java | 25 +
src/dr/inferencexml/model/CoulombPriorParser.java | 25 +
src/dr/inferencexml/model/DefaultModelParser.java | 25 +
.../inferencexml/model/DiagonalMatrixParser.java | 25 +
.../model/DifferenceMatrixParameterParser.java | 81 ++
.../model/DifferenceParameterParser.java | 80 ++
.../model/DifferenceStatisticParser.java | 25 +
.../inferencexml/model/DummyLikelihoodParser.java | 25 +
.../model/DuplicatedParameterParser.java | 25 +
.../model/ExponentialStatisticParser.java | 25 +
.../model/ExpressionStatisticParser.java | 25 +
.../model/IndianBuffetProcessPriorParser.java | 96 ++
.../inferencexml/model/JointParameterParser.java | 25 +
.../model/LatentFactorModelParser.java | 2 +-
.../model/LikelihoodBenchmarkerParser.java | 10 +-
.../model/LogarithmStatisticParser.java | 25 +
.../model/MarkovRandomFieldMatrixParser.java | 25 +-
.../model/MaskedMatrixParameterParser.java | 125 +++
.../inferencexml/model/MaskedParameterParser.java | 25 +
.../model/MatrixMatrixProductParser.java | 25 +
.../model/MatrixVectorProductParameterParser.java | 2 +-
src/dr/inferencexml/model/MeanStatisticParser.java | 25 +
.../model/NegativeStatisticParser.java | 25 +
.../model/NotBooleanStatisticParser.java | 2 +-
src/dr/inferencexml/model/NotStatisticParser.java | 25 +
src/dr/inferencexml/model/OneOnX3PriorParser.java | 25 +
src/dr/inferencexml/model/OneOnXPriorParser.java | 25 +
.../inferencexml/model/ProductParameterParser.java | 2 +-
.../inferencexml/model/ProductStatisticParser.java | 25 +
.../model/RPNcalculatorStatisticParser.java | 25 +
.../inferencexml/model/RatioStatisticParser.java | 25 +
.../model/ReciprocalStatisticParser.java | 25 +
src/dr/inferencexml/model/SubStatisticParser.java | 25 +
src/dr/inferencexml/model/SumStatisticParser.java | 25 +
src/dr/inferencexml/model/TestStatisticParser.java | 25 +
.../model/ThreadedCompoundLikelihoodParser.java | 25 +
.../model/TransformedParameterParser.java | 2 +-
.../model/VarianceStatisticParser.java | 25 +
.../operators/ApplyOperatorOnceParser.java | 2 +-
.../operators/BitFlipOperatorParser.java | 25 +
.../operators/BitMoveOperatorParser.java | 25 +
.../operators/BitSwapOperatorParser.java | 25 +
.../operators/CenteredScaleOperatorParser.java | 25 +
.../operators/DeltaExchangeOperatorParser.java | 25 +
.../operators/DeltaMixOperatorParser.java | 25 +
.../operators/DirtyLikelihoodOperatorParser.java | 25 +
.../operators/EllipticalSliceOperatorParser.java | 26 +-
.../operators/FactorGibbsOperatorParser.java | 2 +-
.../FactorIndependenceOperatorParser.java | 2 +-
.../operators/FactorOperatorParser.java | 2 +-
.../HierarchicalBitFlipOperatorParser.java | 25 +
.../operators/JointOperatorParser.java | 25 +
...entFactorModelPrecisionGibbsOperatorParser.java | 2 +-
.../operators/LoadingsGibbsOperatorParser.java | 2 +-
.../LoadingsIndependenceOperatorParser.java | 2 +-
.../operators/LogRandomWalkOperatorParser.java | 25 +
.../operators/MVOUCovarianceOperatorParser.java | 25 +
.../operators/MicrosatUpDownOperatorParser.java | 25 +
.../MicrosatelliteModelSelectOperatorParser.java | 25 +
.../operators/MsatBitFlipOperatorParser.java | 25 +
...llAncestryImportanceSamplingOperatorParser.java | 25 +
...satSingleAncestralStateGibbsOperatorParser.java | 25 +
.../MultipleRandomWalkIntegerOperatorParser.java | 25 +
.../MultivariateNormalGibbsOperatorParser.java | 25 +
...alkIntegerNodeHeightWeightedOperatorParser.java | 25 +
.../operators/RandomWalkIntegerOperatorParser.java | 25 +
...omWalkIntegerSetSizeWeightedOperatorParser.java | 25 +
.../operators/RandomWalkOperatorParser.java | 25 +
.../operators/ScaleOperatorParser.java | 25 +
.../operators/SelectorOperatorParser.java | 25 +
.../inferencexml/operators/SetOperatorParser.java | 25 +
.../operators/SimpleOperatorScheduleParser.java | 25 +
.../inferencexml/operators/SwapOperatorParser.java | 25 +
.../operators/SwapParameterOperatorParser.java | 89 ++
.../inferencexml/operators/TeamOperatorParser.java | 25 +
.../TransformedRandomWalkOperatorParser.java | 25 +
.../operators/TwoPhaseOperatorParser.java | 2 +-
.../operators/UniformIntegerOperatorParser.java | 25 +
.../operators/UniformOperatorParser.java | 25 +
.../operators/UpDownOperatorParser.java | 25 +
.../operators/ValuesPoolSwapOperatorParser.java | 25 +
src/dr/inferencexml/trace/AICMAnalysisParser.java | 31 +-
.../trace/ArithmeticMeanAnalysisParser.java | 31 +-
.../trace/HarmonicMeanAnalysisParser.java | 33 +-
.../trace/LogFileTraceExporterParser.java | 25 +
.../trace/MarginalLikelihoodAnalysisParser.java | 31 +-
src/dr/inferencexml/trace/TraceAnalysisParser.java | 10 +-
src/dr/math/BFloat.java | 2 +-
src/dr/math/BigDecimalUtils.java | 25 +
src/dr/math/Binomial.java | 2 +-
src/dr/math/BoundsCheckedFunction.java | 2 +-
src/dr/math/ComplexArray.java | 25 +
src/dr/math/CompoundFunction.java | 2 +-
src/dr/math/ConjugateDirectionSearch.java | 2 +-
src/dr/math/ConjugateGradientSearch.java | 2 +-
src/dr/math/DifferentialEvolution.java | 2 +-
src/dr/math/EmpiricalBayesPoissonSmoother.java | 2 +-
src/dr/math/ErrorFunction.java | 2 +-
src/dr/math/FastFourierTransform.java | 25 +
src/dr/math/GammaFunction.java | 2 +-
.../math/GeneralisedGaussLaguerreQuadrature.java | 25 +
src/dr/math/IntegrableUnivariateFunction.java | 25 +
src/dr/math/Integral.java | 2 +-
src/dr/math/KroneckerOperation.java | 25 +
src/dr/math/LineFunction.java | 2 +-
src/dr/math/LogTricks.java | 25 +
src/dr/math/MFWithGradient.java | 2 +-
src/dr/math/MachineAccuracy.java | 2 +-
src/dr/math/MathUtils.java | 2 +-
src/dr/math/MersenneTwisterFast.java | 2 +-
src/dr/math/MinimiserMonitor.java | 2 +-
src/dr/math/MittagLefflerFunction.java | 25 +
src/dr/math/ModifiedBesselFirstKind.java | 25 +
src/dr/math/MonteCarloIntegral.java | 2 +-
src/dr/math/MultivariateFunction.java | 2 +-
src/dr/math/MultivariateIntegral.java | 4 +-
src/dr/math/MultivariateMinimum.java | 2 +-
src/dr/math/MultivariateMonteCarloIntegral.java | 4 +-
src/dr/math/NumericalDerivative.java | 2 +-
src/dr/math/Poisson.java | 2 +-
src/dr/math/Polynomial.java | 25 +
src/dr/math/Procrustes.java | 25 +
src/dr/math/RiemannApproximation.java | 2 +-
src/dr/math/SparseMatrixExponential.java | 25 +
src/dr/math/UnivariateFunction.java | 2 +-
src/dr/math/UnivariateMinimum.java | 2 +-
src/dr/math/distributions/BetaDistribution.java | 25 +
src/dr/math/distributions/BetaKDEDistribution.java | 25 +
.../BifractionalDiffusionDensity.java | 25 +
.../math/distributions/ChiSquareDistribution.java | 2 +-
.../math/distributions/DirichletDistribution.java | 25 +
.../distributions/DiscreteUniformDistribution.java | 25 +
src/dr/math/distributions/Distribution.java | 2 +-
.../distributions/ExponentialDistribution.java | 2 +-
src/dr/math/distributions/GammaDistribution.java | 43 +-
.../math/distributions/GammaKDEDistribution.java | 49 +
.../GaussianProcessRandomGenerator.java | 5 +-
.../GeneralizedIntegerGammaDistribution.java | 182 +++
src/dr/math/distributions/HalfTDistribution.java | 2 +-
.../distributions/InverseGammaDistribution.java | 4 +-
.../distributions/InverseGaussianDistribution.java | 2 +-
.../distributions/InverseWishartDistribution.java | 2 +-
.../KernelDensityEstimatorDistribution.java | 25 +
src/dr/math/distributions/LaplaceDistribution.java | 25 +
.../math/distributions/LogNormalDistribution.java | 2 +-
.../LogTransformedNormalKDEDistribution.java | 256 ++++-
.../LogitTransformedNormalKDEDistribution.java | 461 ++++++++
.../distributions/MultivariateDistribution.java | 25 +
.../MultivariateGammaDistribution.java | 25 +
.../distributions/MultivariateKDEDistribution.java | 61 +-
.../MultivariateNormalDistribution.java | 7 +-
.../MultivariatePolyaDistributionLikelihood.java | 25 +
.../NegativeBinomialDistribution.java | 25 +
src/dr/math/distributions/NormalDistribution.java | 2 +-
.../distributions/NormalGammaDistribution.java | 25 +
.../math/distributions/NormalKDEDistribution.java | 50 +
.../distributions/OffsetPositiveDistribution.java | 25 +
src/dr/math/distributions/PoissonDistribution.java | 25 +
src/dr/math/distributions/RandomGenerator.java | 2 +-
.../distributions/ReflectedNormalDistribution.java | 4 +-
src/dr/math/distributions/TDistribution.java | 25 +
.../math/distributions/TruncatedDistribution.java | 25 +
.../distributions/TruncatedNormalDistribution.java | 25 +
src/dr/math/distributions/UniformDistribution.java | 2 +-
src/dr/math/distributions/WishartDistribution.java | 2 +-
src/dr/math/distributions/WishartStatistics.java | 2 +-
.../distributions/WishartSufficientStatistics.java | 25 +
src/dr/math/functionEval/DrMath.java | 2 +-
src/dr/math/functionEval/FunctionDerivative.java | 2 +-
src/dr/math/functionEval/GammaFunction.java | 2 +-
src/dr/math/functionEval/PolynomialFunction.java | 2 +-
.../ConjugateWishartStatisticsProvider.java | 4 +-
.../math/interfaces/CurveMouseClickListener.java | 2 +-
src/dr/math/interfaces/ManyVariableFunction.java | 2 +-
src/dr/math/interfaces/OneVariableFunction.java | 2 +-
.../ParametrizedOneVariableFunction.java | 2 +-
src/dr/math/interfaces/PointSeries.java | 2 +-
src/dr/math/interfaces/PointSeriesWithErrors.java | 2 +-
src/dr/math/iterations/BisectionZeroFinder.java | 2 +-
src/dr/math/iterations/FunctionalIterator.java | 2 +-
src/dr/math/iterations/IterativeProcess.java | 2 +-
src/dr/math/iterations/NewtonZeroFinder.java | 2 +-
.../math/matrixAlgebra/CholeskyDecomposition.java | 25 +
src/dr/math/matrixAlgebra/IllegalDimension.java | 2 +-
.../math/matrixAlgebra/JacobiTransformation.java | 2 +-
src/dr/math/matrixAlgebra/LUPDecomposition.java | 2 +-
.../matrixAlgebra/LargestEigenvalueFinder.java | 2 +-
src/dr/math/matrixAlgebra/LinearEquations.java | 2 +-
src/dr/math/matrixAlgebra/Matrix.java | 2 +-
.../math/matrixAlgebra/NonSymmetricComponents.java | 2 +-
.../matrixAlgebra/RobustEigenDecomposition.java | 34 +-
.../RobustSingularValueDecomposition.java | 29 +-
src/dr/math/matrixAlgebra/SymmetricMatrix.java | 2 +-
src/dr/math/matrixAlgebra/Vector.java | 2 +-
src/dr/matrix/ConcreteMatrix.java | 2 +-
src/dr/matrix/Matrix.java | 2 +-
src/dr/matrix/MutableMatrix.java | 2 +-
src/dr/stats/DiscreteStatistics.java | 2 +-
src/dr/stats/Regression.java | 10 +-
src/dr/stats/Variate.java | 10 +-
src/dr/util/AlloppMisc.java | 25 +
src/dr/util/Assert.java | 2 +-
src/dr/util/Attributable.java | 2 +-
src/dr/util/Attribute.java | 2 +-
src/dr/util/Author.java | 25 +
src/dr/util/Citable.java | 25 +
src/dr/util/Citation.java | 25 +
src/dr/util/CollectionHash.java | 2 +-
src/dr/util/CommonCitations.java | 2 +-
src/dr/util/ComparableDouble.java | 2 +-
src/dr/util/DataTable.java | 25 +
src/dr/util/ErrorLogHandler.java | 2 +-
src/dr/util/FileHelpers.java | 10 +-
src/dr/util/FrequencyDistribution.java | 2 +-
src/dr/util/FrequencySet.java | 2 +-
src/dr/util/HTMLOutput.java | 2 +-
src/dr/util/HeapSort.java | 10 +-
src/dr/util/Identifiable.java | 10 +-
src/dr/util/MergeSort.java | 22 +-
src/dr/util/MessageLogHandler.java | 2 +-
src/dr/util/NumberFormatter.java | 2 +-
src/dr/util/Permutator.java | 2 +-
src/dr/util/Property.java | 2 +-
src/dr/util/TIFFWriter.java | 2 +-
src/dr/util/TabularData.java | 25 +
src/dr/util/TaskListener.java | 25 +
src/dr/util/Timer.java | 2 +-
src/dr/util/Transform.java | 2 +-
src/dr/util/Version.java | 2 +-
src/dr/util/XHTMLable.java | 2 +-
src/dr/xml/AbstractXMLObjectParser.java | 2 +-
src/dr/xml/AndRule.java | 4 +-
src/dr/xml/AttributeParser.java | 2 +-
src/dr/xml/AttributeRule.java | 2 +-
src/dr/xml/AttributesParser.java | 2 +-
src/dr/xml/ClassComparator.java | 2 +-
src/dr/xml/ContentRule.java | 2 +-
src/dr/xml/ElementRule.java | 2 +-
src/dr/xml/ObjectNotFoundException.java | 2 +-
src/dr/xml/ObjectStore.java | 2 +-
src/dr/xml/OrRule.java | 2 +-
src/dr/xml/PropertyParser.java | 2 +-
src/dr/xml/Reference.java | 2 +-
src/dr/xml/Report.java | 10 +-
src/dr/xml/Reportable.java | 25 +
src/dr/xml/Spawnable.java | 10 +-
src/dr/xml/StringAttributeRule.java | 10 +-
src/dr/xml/UserInput.java | 2 +-
src/dr/xml/WikiDocumentationHandler.java | 4 +-
src/dr/xml/XHTMLReport.java | 2 +-
src/dr/xml/XMLDocumentationHandler.java | 10 +-
src/dr/xml/XMLModelCombiner.java | 25 +
src/dr/xml/XMLModelFile.java | 25 +
src/dr/xml/XMLModelIdentifiable.java | 25 +
src/dr/xml/XMLObject.java | 2 +-
src/dr/xml/XMLObjectParser.java | 2 +-
src/dr/xml/XMLParseException.java | 2 +-
src/dr/xml/XMLParser.java | 2 +-
src/dr/xml/XMLSyntaxRule.java | 2 +-
src/dr/xml/XORRule.java | 2 +-
src/test/dr/math/GeneralizedIntegerGammaTest.java | 134 +++
2532 files changed, 56915 insertions(+), 5048 deletions(-)
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delete mode 100644 src/dr/inference/mcmc/FrequencyDistribution2D.java
create mode 100644 src/dr/inference/model/CompoundMatrixParameter.java
create mode 100644 src/dr/inference/model/CopyParameterValuesParser.java
create mode 100644 src/dr/inference/model/DifferenceMatrixParameter.java
create mode 100644 src/dr/inference/model/DifferenceParameter.java
create mode 100644 src/dr/inference/model/IndianBuffetProcessPrior.java
create mode 100644 src/dr/inference/operators/GibbsIndependentJointNormalGammaOperator.java
create mode 100644 src/dr/inference/operators/SwapParameterGibbsOperator.java
create mode 100644 src/dr/inference/operators/SwapParameterOperator.java
create mode 100644 src/dr/inferencexml/distribution/MomentDistributionModelParser.java
create mode 100644 src/dr/inferencexml/model/DifferenceMatrixParameterParser.java
create mode 100644 src/dr/inferencexml/model/DifferenceParameterParser.java
create mode 100644 src/dr/inferencexml/model/IndianBuffetProcessPriorParser.java
create mode 100644 src/dr/inferencexml/model/MaskedMatrixParameterParser.java
create mode 100644 src/dr/inferencexml/operators/SwapParameterOperatorParser.java
create mode 100644 src/dr/math/distributions/GeneralizedIntegerGammaDistribution.java
create mode 100644 src/dr/math/distributions/LogitTransformedNormalKDEDistribution.java
create mode 100644 src/test/dr/math/GeneralizedIntegerGammaTest.java
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