List all quartets

Lists all choices of four taxa from a tree.

A more computationally efficient alternative to combn.

AllQuartets(nTips)

# S3 method for numeric
AllQuartets(nTips)

# S3 method for phylo
AllQuartets(nTips)

Arguments

nTips

Integer, specifying the number of tips in a tree; or a tree, whose tips will be counted.

Value

AllQuartets() returns a matrix with four rows and choose(n_tips, 4) columns, with each column corresponding to a unique selection of four different integers less than or equal to nTips.

See also

States of quartets in given trees: QuartetStates()

Other quartet counting functions: CompareQuartets(), CompareQuartetsMulti(), ResolvedQuartets()

Author

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

Examples

AllQuartets(5)
#>      [,1] [,2] [,3] [,4] [,5]
#> [1,]    1    1    1    1    2
#> [2,]    2    2    2    3    3
#> [3,]    3    3    4    4    4
#> [4,]    4    5    5    5    5
 
combn(5, 4) # Provides the same information, but for large 
#>      [,1] [,2] [,3] [,4] [,5]
#> [1,]    1    1    1    1    2
#> [2,]    2    2    2    3    3
#> [3,]    3    3    4    4    4
#> [4,]    4    5    5    5    5
            # values of n_tips is significantly slower.