Rev Language Reference
TimeTree - Tree datatype
The Tree datatype stores information to describe the shared ancestryof a taxon set. Information includes taxon labels, topology, nodecount, and branch lengths. Tree objects also possess several usefulmethods to traverse and manipulate the Tree's value.
Methods
- addFossil(Taxon fossil, Taxon[] clade)
- branchLength(Natural node)
- calculateEDR()
- calculateMNTD(AbstractHomologousDiscreteCharacterData characters, Natural stateIndex, Natural site, Bool zScore, Bool useBranchLengths, Natural randomizations)
- calculateMPD(AbstractHomologousDiscreteCharacterData characters, Natural stateIndex, Natural site, Bool zScore, Bool useBranchLengths, Natural randomizations)
- child(Natural node, Natural index)
- collapseNegativeBranches(RealPos length)
- colless()
- containsClade(Clade clade)
- dropFossils()
- dropTip(String node)
- fitchScore(AbstractHomologousDiscreteCharacterData characters)
- gammaStatistic()
- getClade(Taxon[] clade)
- getDescendantTaxa(Natural node)
- getFossils()
- getIndices()
- getInverseES()
- getPSSP(AbstractHomologousDiscreteCharacterData characters, Natural stateIndex)
- getRootIndex()
- hasSameTopology(Tree tree)
- isBinary()
- isContainedInClade(Natural node, Clade clade)
- isInternal(Natural node)
- isRoot(Natural node)
- makeBifurcating(Bool fossils_only, Clade clade)
- meanInverseES(AbstractHomologousDiscreteCharacterData characters, Natural stateIndex)
- names()
- nnodes()
- nodeAge(Natural node)
- nodeName(Natural node)
- ntips()
- numSampledAncestors()
- offset(RealPos factor)
- parent(Natural node)
- removeDuplicateTaxa()
- renumberNodes(Tree referenceTree)
- reroot(Clade clade, Bool makeBifurcating)
- rescale(RealPos factor)
- rootAge()
- setBranchLength(Natural index, RealPos value)
- setNegativeConstraint(Bool flag)
- setTaxonName(String current, String new)
- taxa()
- tipIndex(String name)
- treeLength()
- unroot()
See Also
Distributions
- dnBirthDeath
- dnBirthDeathBurstProcess
- dnBirthDeathSamplingTreatment
- dnCBDSP
- dnCDBDP
- dnCoalescent
- dnCoalescentDemography
- dnCoalescentSkyline
- dnCompleteBirthDeath
- dnConstrainedNodeAge
- dnConstrainedNodeOrder
- dnConstrainedTopology
- dnDiversityDependentYule
- dnDuplicationLoss
- dnEpisodicBirthDeath
- dnFossilizedBirthDeath
- dnFossilizedBirthDeathSpecies
- dnGeneralizedLineageHeterogeneousBirthDeathProcess
- dnHBDP
- dnHeterochronousCoalescent
- dnHeterochronousCoalescentSkyline
- dnMultiSpeciesCoalescent
- dnMultiSpeciesCoalescentInverseGamma
- dnMultiSpeciesCoalescentUniformPrior
- dnMultispeciesCoalescentMigration
- dnOutgroupBirthDeath
- dnPhylodynamicBirthDeathProcess
- dnPiecewiseOccurrenceBirthDeath
- dnSBBDP
- dnTimeVaryingStateDependentSpeciationExtinction
- dnUltrametricTree
- dnUniformSerialSampledTimeTree
- dnUniformTimeTree
- dnWeightedConstrainedNodeOrder
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