QuartetState: Quartet State(s)

In Quartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures

Quartet State(s)

Description

Report the status of the specified quartet(s) in given trees or lists of splits \insertCiteEstabrook1985Quartet.

Usage

QuartetState(tips, bips, splits = bips, asRaw = FALSE)

QuartetStates(splits, asRaw = FALSE)

## S3 method for class 'Splits'
QuartetStates(splits, asRaw = FALSE)

## S3 method for class 'list'
QuartetStates(splits, asRaw = FALSE)

## S3 method for class 'multiPhylo'
QuartetStates(splits, asRaw = FALSE)

Arguments

tips	A four-element array listing a quartet of leaves, either by their number (if class numeric) or their name (if class character).
bips	Deprecated; included for compatibility with v1.0.2 and below.
splits	An object, such as a tree of class phylo, that can be induced to a Splits object using as.Splits.
asRaw	Logical specifying whether return format should be raw, which uses less memory and can be processed faster than integer type. Default is currently set to FALSE for backwards compatibility; suggest overriding to TRUE.

Details

One of the three possible four-leaf trees will be consistent with any set of splits generated from a fully resolved tree. If the leaves are numbered 1 to 4, this tree can be identified by naming the leaf most closely related to leaf 4. If a set of splits is generated from a tree that contains polytomies, it is possible that all three four-leaf trees are consistent with the set of splits.

Value

QuartetState() returns 0 if the relationships of the four leaves are not constrained by the provided splits, or the index of the closest relative to tips[4], otherwise.

QuartetStates() returns a raw vector listing the status of each quartet of leaves (in the order listed by AllQuartets()) in turn, or if multiple trees are provided, a matrix in which each row corresponds to such a vector.

Author(s)

Martin R. Smith ([e-mail])

References

\insertAllCited

See Also

Compare quartet states between trees (slowly) using CompareQuartets() and CompareQuartetsMulti().

Other element-by-element comparisons: CompareQuartets(), CompareQuartetsMulti(), CompareSplits(), PairSharedQuartetStatus(), SharedQuartetStatus(), SplitStatus()

Examples

trees <- list(TreeTools::BalancedTree(6),
              TreeTools::PectinateTree(6))

trees[[3]] <- TreeTools::CollapseNode(trees[[2]], 9:10)

QuartetState(c(1, 3, 4, 6), trees[[2]])  
QuartetState(1:4, trees[[1]]) == QuartetState(1:4, trees[[2]])
QuartetState(c(1, 3, 4, 6), trees[[3]])  

QuartetStates(trees[[2]])
QuartetStates(trees[[3]])

CompareQuartets(QuartetStates(trees[[2]]), QuartetStates(trees[[3]]))
CompareQuartetsMulti(trees[[1]], trees[2:3])

Quartet documentation built on Nov. 1, 2024, 1:07 a.m.