Package index

All functions

AllQuartets()

List all quartets

CompareQuartets()

Compare quartet states by explicit enumeration

CompareQuartetsMulti()

Compare one tree's quartets against others'

CompareSplits() CompareBipartitions()

Compare status of splits

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

Direct entry points to "tqDist" functions

PlotQuartet()

Plot quartet on tree topologies

QuartetPoints() SplitPoints() BipartitionPoints()

Plot tree differences on ternary plots

QuartetState() QuartetStates()

Quartet State(s)

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

Status of quartets

ResolvedQuartets() ResolvedTriplets()

Count resolved quartets

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

Tree similarity measures

SplitStatus() SharedSplitStatus()

Matching partitions

SymmetricDifferenceLineEnds() SymmetricDifferenceLines()

Plot contours of equal symmetric difference on a ternary plot

TQDist() TQAE()

Wrapper for tqDist

VisualizeQuartets()

Visualize quartet difference on trees, by split

sq_trees

Eighteen example trees