R: Calculate various imbalance statistics for a tree.

tree_imbalance {castor} | R Documentation

## Calculate various imbalance statistics for a tree.

### Description

Given a rooted phylogenetic tree, calculate various "imbalance" statistics of the tree, such as Colless' Index or Sackin's Index.

### Usage

    tree_imbalance(tree, type)

### Arguments

`tree` | A rooted tree of class "phylo".
`type` | Character, specifying the statistic to be calculated. Must be one of "Colless" (Shao 1990), "Colless_normalized" (Colless normalized by the maximum possible value in the case of a bifurcating tree) or "Sackin" (Sackin 1972).

### Details

The tree may include multifurcations and monofurcations. Note that the Colless Index is traditionally only defined for bifurcating trees. For non-bifurcating trees this function calculates a generalization of the index, by summing over all children pairs at each node.

### Value

Numeric, the requested imbalance statistic of the tree.

### Author(s)

Stilianos Louca

### References

M. J. Sackin (1972). "Good" and "Bad" Phenograms. Systematic Biology. 21:225-226.

K.T. Shao, R. R. Sokal (1990). Tree Balance. Systematic Biology. 39:266-276.

### Examples

    # generate a random tree
    Ntips = 100
    tree = generate_random_tree(list(birth_rate_intercept=1),Ntips)$tree

    # calculate Colless statistic
    colless_index = tree_imbalance(tree, type="Colless")

[Package castor version 1.6.7 Index]