Quartet State(s)

Report the status of the specified quartet(s) in given trees or lists of splits (Estabrook et al. 1985) .

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.

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.

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.

References

Estabrook GF, McMorris FR, Meacham CA (1985). “Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units.” Systematic Zoology, 34(2), 193–200. doi:10.2307/2413326 .

See also

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

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

Author

Martin R. Smith (martin.smith@durham.ac.uk)

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]])  
#> [1] 3
QuartetState(1:4, trees[[1]]) == QuartetState(1:4, trees[[2]])
#> [1] TRUE
QuartetState(c(1, 3, 4, 6), trees[[3]])  
#> [1] 0

QuartetStates(trees[[2]])
#>  [1] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
QuartetStates(trees[[3]])
#>  [1] 0 0 0 0 0 3 0 0 3 3 0 0 3 3 3

CompareQuartets(QuartetStates(trees[[2]]), QuartetStates(trees[[3]]))
#>  N  Q  s  d r1 r2  u 
#> 30 15  6  0  9  0  0 
CompareQuartetsMulti(trees[[1]], trees[2:3])
#>      N      Q  s_all  s_any  d_all  d_any r1_all r1_any r2_all r2_any  u_all 
#>     45     15      3     12      3      3      0      9      0      0      0 
#>  u_any x_only 
#>      0      3