calcDstTrp: Calculate the triplet distance between two trees

In treeman: Phylogenetic Tree Manipulation Class and Methods

Description

Returns the triplet distance between two trees.

Usage

calcDstTrp(tree_1, tree_2, nrmlsd = FALSE, parallel = FALSE, progress = "none")

Arguments

tree_1	TreeMan object
tree_2	TreeMan object
nrmlsd	Boolean, should returned value be between 0 and 1? Default, FALSE.
parallel	logical, make parallel?
progress	name of the progress bar to use, see create_progress_bar

Details

The triplet distance is calculated as the sum of different outgroups among every triplet of tips between the two trees. Normalisation is performed by dividing the resulting number by the total number of triplets shared between the two trees. The triplet distance is calculated only for shared tips between the two trees. Parallelizable.

References

Critchlow DE, Pearl DK, Qian C. (1996) The Triples Distance for rooted bifurcating phylogenetic trees. Systematic Biology, 45, 323-34.

See Also

calcDstBLD, calcDstRF https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

library(treeman)
tree_1 <- randTree(10)
tree_2 <- randTree(10)
calcDstTrp(tree_1, tree_2)

Example output

[1] 87

treeman documentation built on July 8, 2020, 7:28 p.m.