Index

A

addChild() (tyche.evolution.tree.GRTNode method) addGermline() (tyche.evolution.tree.GRTNode method) adjustRoot() (tyche.evolution.operator.CombinedRootOperator method)

adjustRootAndGermline() (tyche.evolution.tree.GRTNode method) assignFrom() (tyche.evolution.tree.GRTNode method) assignTo() (tyche.evolution.tree.GRTNode method)

B

branchRates (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute)

branchRatesInput (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute)

C

calculateLogP() (tyche.evolution.likelihood.AncestralTypeLikelihood method) (tyche.inference.distribution.ElementwisePrior method) CombinedRootOperator() (tyche.evolution.operator.CombinedRootOperator method), [1]

copy() (tyche.evolution.tree.GRTNode method) currentOriginTypes (tyche.evolution.operator.MultiNodeTypeSwitchOperator attribute) currentProposalType (tyche.evolution.operator.MultiNodeTypeSwitchOperator attribute)

D

dataType (tyche.evolution.likelihood.AncestralTypeLikelihood attribute) dists (tyche.inference.distribution.ElementwisePrior attribute) distsInput (tyche.inference.distribution.ElementwisePrior attribute) doGRTProposal() (possible method) (tyche.evolution.operator.GRTBactrianScaleOperator method) (tyche.evolution.operator.GRTExchange method) (tyche.evolution.operator.GRTScaleOperator method) (tyche.evolution.operator.GRTSubtreeSlide method) (tyche.evolution.operator.GRTWilsonBalding method)

E

EPSILON (tyche.evolution.tree.GRTNode attribute)

F

findGermline() (tyche.evolution.tree.GermlineRootTree method)

G

generationLimit (tyche.evolution.operator.MultiNodeTypeSwitchOperator attribute) germline (tyche.evolution.tree.GRTNode attribute) germlineNum (tyche.evolution.operator.LeafConsciousTypeTreeOperator attribute) (tyche.evolution.tree.GermlineRootTree attribute) getAmbiguousTips() (tyche.evolution.operator.LeafConsciousTypeTreeOperator method) getArguments() (tyche.inference.distribution.ElementwisePrior method) getBranchRate() (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel method) (tyche.evolution.branchratemodel.TycheExpectedOccupancyClockModel method) (tyche.evolution.branchratemodel.TycheInstantSwitchClockModel method) (tyche.evolution.branchratemodel.TycheMixedSwitchClockModel method) getConditions() (tyche.inference.distribution.ElementwisePrior method) getDataType() (tyche.evolution.likelihood.AncestralTypeLikelihood method) getDate() (tyche.evolution.tree.GRTNode method) getDelta() (tyche.evolution.operator.GRTSubtreeSlide method) getFormattedState() (tyche.evolution.likelihood.AncestralTypeLikelihood method) getGenerationsForProposal() (tyche.evolution.operator.MultiNodeTypeSwitchOperator method) (tyche.evolution.operator.SubtreeTypeSwitchOperator method) getGermlineNum() (tyche.evolution.tree.GermlineRootTree method)

getHastingsRatio() (tyche.evolution.operator.MultiNodeTypeSwitchOperator method) getHeight() (tyche.evolution.tree.GRTNode method) getMinimumHeight() (tyche.evolution.tree.GRTNode method) getNewHeight() (tyche.evolution.operator.CombinedRootOperator method) getOccupancy() (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel method) getParameterName() (tyche.inference.distribution.ElementwisePrior method) getProposalDistribution() (tyche.evolution.operator.MultiNodeTypeSwitchOperator method) getRandomType() (tyche.evolution.operator.CombinedRootOperator method) getRateForBranch() (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel method) getRelatedNodeTypeProposalValue() (tyche.evolution.operator.MultiNodeTypeSwitchOperator method) getStatesForNode() (tyche.evolution.likelihood.AncestralTypeLikelihood method) getTipMetaData() (tyche.evolution.tree.MetadataTree method) getTipMetaDataNames() (tyche.evolution.tree.MetadataTree method) getTransitionMatrix() (tyche.evolution.likelihood.AncestralTypeLikelihood method) getTransitionProbabilities() (tyche.evolution.substitutionmodel.TycheSVSGeneralSubstitutionModel method) getTreeTrait() (tyche.evolution.likelihood.AncestralTypeLikelihood method) getTreeTraits() (tyche.evolution.likelihood.AncestralTypeLikelihood method) getTypeLinkedRate() (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel method) GRTCompatibleOperatorsSuggestions (tyche.evolution.tree.GermlineRootTree attribute)

H

hasGermline() (tyche.evolution.tree.GRTNode method)

homogenousValue (tyche.evolution.operator.MultiNodeTypeSwitchOperator attribute)

I

initAndValidate() (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel method) (tyche.evolution.likelihood.AncestralTypeLikelihood method) (tyche.evolution.operator.CombinedRootOperator method) (tyche.evolution.operator.LeafConsciousTypeTreeOperator method) (tyche.evolution.operator.MultiNodeTypeSwitchOperator method) (tyche.evolution.substitutionmodel.TycheSVSGeneralSubstitutionModel method) (tyche.evolution.tree.GermlineRootTree method) (tyche.inference.distribution.ElementwisePrior method) intersectingEdges() (tyche.evolution.operator.GRTSubtreeSlide method)

isAmbiguous (tyche.evolution.operator.LeafConsciousTypeTreeOperator attribute) isExpectedOccupancy() (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel method) (tyche.evolution.branchratemodel.TycheExpectedOccupancyClockModel method) (tyche.evolution.branchratemodel.TycheMixedSwitchClockModel method) isGermline() (tyche.evolution.operator.GRTSubtreeSlide method) (tyche.evolution.tree.GRTNode method) isGermlineRoot (tyche.evolution.operator.LeafConsciousTypeTreeOperator attribute) isHomogenous (tyche.evolution.operator.MultiNodeTypeSwitchOperator attribute) isIncompatibleOperator() (tyche.evolution.tree.GermlineRootTree method)

J

jointLogLikelihood (tyche.evolution.likelihood.AncestralTypeLikelihood attribute)

L

LeafConsciousTypeTreeOperator() (tyche.evolution.operator.LeafConsciousTypeTreeOperator method), [1] lookAtOperators() (tyche.evolution.tree.GermlineRootTree method)

lookForRandomTree() (tyche.evolution.tree.GermlineRootTree method) lowerInt (tyche.evolution.operator.LeafConsciousTypeTreeOperator attribute)

M

makeNewFromNode() (tyche.evolution.tree.GRTNode method) mode (tyche.evolution.operator.MultiNodeTypeSwitchOperator attribute)

MultiNodeTypeSwitchOperator() (tyche.evolution.operator.MultiNodeTypeSwitchOperator method), [1] muParameter (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute)

N

newNode() (tyche.evolution.tree.GermlineRootTree method) nodeType (tyche.evolution.tree.GermlineRootTree attribute) nodeTypes (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute) (tyche.evolution.likelihood.AncestralTypeLikelihood attribute) (tyche.evolution.operator.LeafConsciousTypeTreeOperator attribute)

nodeTypesInput (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute) (tyche.evolution.likelihood.AncestralTypeLikelihood attribute) (tyche.evolution.operator.LeafConsciousTypeTreeOperator attribute) numberOfTypes (tyche.evolution.operator.MultiNodeTypeSwitchOperator attribute)

O

occupancies (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute)

occupanciesInput (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute)

P

parameter (tyche.inference.distribution.ElementwisePrior attribute) parameterInput (tyche.inference.distribution.ElementwisePrior attribute) patternCount (tyche.evolution.likelihood.AncestralTypeLikelihood attribute) possible (built-in class) processTraits() (tyche.evolution.tree.MetadataTree method) proposal() (tyche.evolution.operator.CombinedRootOperator method) (tyche.evolution.operator.GRTBactrianScaleOperator method) (tyche.evolution.operator.GRTExchange method) (tyche.evolution.operator.GRTScaleOperator method) (tyche.evolution.operator.GRTSubtreeSlide method) (tyche.evolution.operator.GRTWilsonBalding method) (tyche.evolution.operator.LeafConsciousTypeTreeOperator method) (tyche.evolution.operator.MultiNodeTypeSwitchOperator method)

Q

qMatrix (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute) (tyche.evolution.likelihood.AncestralTypeLikelihood attribute)

R

rateIndicator (tyche.evolution.substitutionmodel.TycheSVSGeneralSubstitutionModel attribute) removeChild() (tyche.evolution.tree.GRTNode method) requiresRecalculation() (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel method) (tyche.evolution.likelihood.AncestralTypeLikelihood method)

restore() (tyche.evolution.likelihood.AncestralTypeLikelihood method) (tyche.evolution.substitutionmodel.TycheSVSGeneralSubstitutionModel method)

S

sample() (tyche.inference.distribution.ElementwisePrior method) scale() (tyche.evolution.tree.GRTNode method) setGenerationsLimit() (tyche.evolution.operator.MultiNodeTypeSwitchOperator method) (tyche.evolution.operator.SubtreeTypeSwitchOperator method) setHeight() (tyche.evolution.tree.GRTNode method), [1] setHeightDA() (tyche.evolution.tree.GRTNode method) setNodes() (tyche.evolution.operator.MultiNodeTypeSwitchOperator method) setNormalDirt() (tyche.evolution.tree.GRTNode method) setRelatedNodeType() (tyche.evolution.operator.MultiNodeTypeSwitchOperator method) setSubtree() (tyche.evolution.operator.MultiNodeTypeSwitchOperator method) setSuperHeight() (tyche.evolution.tree.GRTNode method) setTraverseMode() (tyche.evolution.operator.MultiNodeTypeSwitchOperator method) (tyche.evolution.operator.SubtreeTypeSwitchOperator method)

setTypeSwitchMode() (tyche.evolution.operator.MultiNodeTypeSwitchOperator method) (tyche.evolution.operator.SubtreeTypeSwitchOperator method) setUptree() (tyche.evolution.operator.MultiNodeTypeSwitchOperator method) stateCount (tyche.evolution.likelihood.AncestralTypeLikelihood attribute) STATES_KEY (tyche.evolution.likelihood.AncestralTypeLikelihood attribute) store() (tyche.evolution.likelihood.AncestralTypeLikelihood method) (tyche.evolution.substitutionmodel.TycheSVSGeneralSubstitutionModel method) storedJointLogLikelihood (tyche.evolution.likelihood.AncestralTypeLikelihood attribute) storedRateMatrix (tyche.evolution.substitutionmodel.TycheSVSGeneralSubstitutionModel attribute) svs (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute) svsInput (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute)

T

tag (tyche.evolution.likelihood.AncestralTypeLikelihood attribute) tagInput (tyche.evolution.likelihood.AncestralTypeLikelihood attribute) tipMetaData (tyche.evolution.tree.MetadataTree attribute) tipStates (tyche.evolution.likelihood.AncestralTypeLikelihood attribute) traitName (tyche.evolution.operator.LeafConsciousTypeTreeOperator attribute) traitNameInput (tyche.evolution.operator.LeafConsciousTypeTreeOperator attribute) traverseTypeTree() (tyche.evolution.likelihood.AncestralTypeLikelihood method) treeTraits (tyche.evolution.likelihood.AncestralTypeLikelihood attribute) tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel (built-in class) tyche.evolution.branchratemodel.TycheExpectedOccupancyClockModel (built-in class) tyche.evolution.branchratemodel.TycheInstantSwitchClockModel (built-in class) tyche.evolution.branchratemodel.TycheMixedSwitchClockModel (built-in class) tyche.evolution.likelihood.AncestralTypeLikelihood (built-in class) tyche.evolution.operator.CombinedRootOperator (built-in class) tyche.evolution.operator.GRTBactrianScaleOperator (built-in class) tyche.evolution.operator.GRTCompatibleOperator (built-in class)

tyche.evolution.operator.GRTExchange (built-in class) tyche.evolution.operator.GRTScaleOperator (built-in class) tyche.evolution.operator.GRTSubtreeSlide (built-in class) tyche.evolution.operator.GRTWilsonBalding (built-in class) tyche.evolution.operator.LeafConsciousTypeTreeOperator (built-in class) tyche.evolution.operator.MultiNodeTypeSwitchOperator (built-in class) tyche.evolution.operator.SubtreeTypeSwitchOperator (built-in class) tyche.evolution.substitutionmodel.TycheSVSGeneralSubstitutionModel (built-in class) tyche.evolution.tree.GermlineRootTree (built-in class) tyche.evolution.tree.GRTNode (built-in class) tyche.evolution.tree.MetadataTree (built-in class) tyche.inference.distribution.ElementwisePrior (built-in class) typeLinkedRates (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute) typeLinkedRatesInput (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute) typeSwitchClockRate (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute) typeSwitchClockRateInput (tyche.evolution.branchratemodel.AbstractTycheTypeLinkedClockModel attribute) typeSwitchMode (tyche.evolution.operator.MultiNodeTypeSwitchOperator attribute)

U

updateIsHomogenous() (tyche.evolution.operator.MultiNodeTypeSwitchOperator method)

upperInt (tyche.evolution.operator.LeafConsciousTypeTreeOperator attribute) useJava (tyche.evolution.likelihood.AncestralTypeLikelihood attribute)