Package index

Enumeration

Count quartets within trees

AllQuartets()

List all quartets

CompareQuartets()

Compare quartet states by explicit enumeration

CompareQuartetsMulti()

Compare one tree's quartets against others'

ResolvedQuartets() ResolvedTriplets()

Count resolved quartets

Comparison

Compare trees and quartet states

CompareQuartets()

Compare quartet states by explicit enumeration

CompareQuartetsMulti()

Compare one tree's quartets against others'

CompareSplits() CompareBipartitions()

Compare status of splits

PairwiseQuartets()

Pairwise quartet distances

QuartetState() QuartetStates()

Quartet State(s)

SharedQuartetStatus() QuartetStatus() ManyToManyQuartetAgreement() TwoListQuartetAgreement() SingleTreeQuartetAgreement()

Status of quartets

SplitStatus() SharedSplitStatus()

Matching partitions

SimilarityMetrics() DoNotConflict() ExplicitlyAgree() StrictJointAssertions() SemiStrictJointAssertions() SymmetricDifference() RawSymmetricDifference() RobinsonFoulds() MarczewskiSteinhaus() SteelPenny() QuartetDivergence() SimilarityToReference()

Tree similarity measures

Visualization

Plot and display quartet statuses and differences

PlotQuartet()

Plot quartet on tree topologies

QuartetPoints() SplitPoints() BipartitionPoints()

Plot tree differences on ternary plots

SymmetricDifferenceLineEnds() SymmetricDifferenceLines()

Plot contours of equal symmetric difference on a ternary plot

VisualizeQuartets()

Visualize quartet difference on trees, by split

Datasets

Example datasets for use with Quartet

sq_trees

Eighteen example trees

TQDist wrappers

Direct access to TQDist functions

QuartetDistance() QuartetAgreement() PairsQuartetDistance() OneToManyQuartetAgreement() AllPairsQuartetDistance() AllPairsQuartetAgreement() TripletDistance() PairsTripletDistance() AllPairsTripletDistance()

Direct entry points to "tqDist" functions

TQDist() TQAE()

Wrapper for tqDist