rnni {rrnni}

Calculate RNNI distance

Description

Calculate Ranked Nearest Neighbour Interchange (RNNI) distance.

Usage

rnni(x, y, normalize = FALSE)

Arguments

x

a tree of class "rankedPhylo"

y

a tree of class "rankedPhylo"

normalize

normalize the distance to the maximum distance of diameter (n-1)(n-2)/2 where n is the number of tips/leaves.

Details

The RNNI distance is the shortest distance between two trees in the RNNI space, which is defined by rank and NNI moves. This space is defined only for ranked trees. Non-ranked ultrametric trees can be coerced to ranked trees with as_ranked or rankedPhylo functions.

The distance can be normalized to the maximum possible distance, the diameter of the tree-space. The diameter is defined as (n-1)(n-2)/2, where n is the number of tips/leaves.

The used algorithm implements the TREEPATH algorithm described in Collienne (2021).

Value

an integer RNNI distance between x and y

References

Collienne, L. (2021). Spaces of Phylogenetic Time Trees. University of Otago.