API Reference

• tyche
  • evolution
    • tree
      • MetadataTree
        • MetadataTree
          • tipMetaData
          • processTraits
          • getTipMetaData
          • getTipMetaDataNames
      • GermlineRootTree
        • GermlineRootTree
          • germlineNum
          • nodeType
          • GRTCompatibleOperatorsSuggestions
          • initAndValidate
          • findGermline
          • getGermlineNum
          • lookForRandomTree
          • isIncompatibleOperator
          • lookAtOperators
          • newNode
      • GRTNode
        • GRTNode
          • germline
          • EPSILON
          • addGermline
          • isGermline
          • hasGermline
          • setHeight
          • setSuperHeight
          • setNormalDirt
          • assignTo
          • assignFrom
          • setHeight
          • setHeightDA
          • getMinimumHeight
          • adjustRootAndGermline
          • makeNewFromNode
          • getHeight
          • getDate
          • addChild
          • removeChild
          • copy
          • scale
    • likelihood
      • AncestralTypeLikelihood
        • AncestralTypeLikelihood
          • STATES_KEY
          • tagInput
          • useJava
          • nodeTypesInput
          • nodeTypes
          • qMatrix
          • patternCount
          • stateCount
          • tipStates
          • treeTraits
          • dataType
          • tag
          • jointLogLikelihood
          • storedJointLogLikelihood
          • initAndValidate
          • requiresRecalculation
          • calculateLogP
          • traverseTypeTree
          • store
          • restore
          • getTransitionMatrix
          • getDataType
          • getStatesForNode
          • getTreeTraits
          • getTreeTrait
          • getFormattedState
    • branchratemodel
      • TycheExpectedOccupancyClockModel
        • TycheExpectedOccupancyClockModel
          • isExpectedOccupancy
          • getBranchRate
      • AbstractTycheTypeLinkedClockModel
        • AbstractTycheTypeLinkedClockModel
          • typeLinkedRatesInput
          • nodeTypesInput
          • typeSwitchClockRateInput
          • svsInput
          • branchRatesInput
          • occupanciesInput
          • typeSwitchClockRate
          • svs
          • qMatrix
          • typeLinkedRates
          • branchRates
          • occupancies
          • nodeTypes
          • muParameter
          • initAndValidate
          • getTypeLinkedRate
          • getOccupancy
          • getBranchRate
          • getRateForBranch
          • isExpectedOccupancy
          • requiresRecalculation
      • TycheMixedSwitchClockModel
        • TycheMixedSwitchClockModel
          • isExpectedOccupancy
          • getBranchRate
      • TycheInstantSwitchClockModel
        • TycheInstantSwitchClockModel
          • getBranchRate
    • operator
      • SubtreeTypeSwitchOperator
        • SubtreeTypeSwitchOperator
          • setTraverseMode
          • setTypeSwitchMode
          • setGenerationsLimit
          • getGenerationsForProposal
      • LeafConsciousTypeTreeOperator
        • LeafConsciousTypeTreeOperator
          • nodeTypesInput
          • traitNameInput
          • nodeTypes
          • lowerInt
          • upperInt
          • germlineNum
          • traitName
          • isAmbiguous
          • isGermlineRoot
          • LeafConsciousTypeTreeOperator
          • LeafConsciousTypeTreeOperator
          • getAmbiguousTips
          • initAndValidate
          • proposal
      • GRTBactrianScaleOperator
        • GRTBactrianScaleOperator
          • doGRTProposal
          • proposal
      • MultiNodeTypeSwitchOperator
        • MultiNodeTypeSwitchOperator
          • numberOfTypes
          • mode
          • typeSwitchMode
          • generationLimit
          • homogenousValue
          • currentOriginTypes
          • isHomogenous
          • currentProposalType
          • MultiNodeTypeSwitchOperator
          • MultiNodeTypeSwitchOperator
          • initAndValidate
          • proposal
          • setTraverseMode
          • setTypeSwitchMode
          • setGenerationsLimit
          • getGenerationsForProposal
          • setNodes
          • getHastingsRatio
          • getProposalDistribution
          • getRelatedNodeTypeProposalValue
          • updateIsHomogenous
          • setRelatedNodeType
          • setSubtree
          • setUptree
      • GRTCompatibleOperator
        • GRTCompatibleOperator
        • possible
          • doGRTProposal
      • GRTExchange
        • GRTExchange
          • doGRTProposal
          • proposal
      • GRTSubtreeSlide
        • GRTSubtreeSlide
          • isGermline
          • doGRTProposal
          • proposal
          • getDelta
          • intersectingEdges
      • GRTScaleOperator
        • GRTScaleOperator
          • doGRTProposal
          • proposal
      • GRTWilsonBalding
        • GRTWilsonBalding
          • doGRTProposal
          • proposal
      • CombinedRootOperator
        • CombinedRootOperator
          • CombinedRootOperator
          • CombinedRootOperator
          • initAndValidate
          • getNewHeight
          • getRandomType
          • adjustRoot
          • proposal
    • substitutionmodel
      • TycheSVSGeneralSubstitutionModel
        • TycheSVSGeneralSubstitutionModel
          • storedRateMatrix
          • rateIndicator
          • initAndValidate
          • getTransitionProbabilities
          • store
          • restore
  • inference
    • distribution
      • ElementwisePrior
        • ElementwisePrior
          • parameterInput
          • distsInput
          • parameter
          • dists
          • initAndValidate
          • calculateLogP
          • getParameterName
          • getArguments
          • getConditions
          • sample