tci {TotalCopheneticIndex}

Total Cophenetic Index

Description

Calculate the Total Cophenetic Index for any tree. Now simply a wrapper for TreeTools::TotalCopheneticIndex().

Usage

tci(tree)

Arguments

tree

a tree of class phylo.

Details

The Total Cophenetic Index is a measure of tree balance - i.e. whether a (phylogenetic) tree comprises symmetric pairs of nodes, or has a pectinate 'caterpillar' shape. The index has a greater resolution power than Sackin's and Colless' indices, and can be applied to trees that are not perfectly resolved. Full details are provided by Mir et al. (2013).

Value

Returns the Total Cophenetic Index, a measure of the balance of the tree.

Author(s)

Martin R. Smith

References

A. Mir, F. Rossello, L. A. Rotger, A new balance index for phylogenetic trees. Math. Biosci. 241, 125-136 (2013).

See Also

The 'CollessLike' package (https://github.com/LuciaRotger/CollessLike) provides an alternative implementation of this index, and its predecessors. See its function cophen.index.

The range of possible values for a tree with n tips, and the values expected under simple models of evolution, is provided by tci.context(tree)

Examples

  tree12 <- ape::read.tree(text='(1, (2, (3, (4, 5))));')  #Fig. 4, tree 12
  tci(tree12) # 10
  tree8  <- ape::read.tree(text='((1, 2, 3, 4), 5);')      #Fig. 4, tree 8
  tci(tree8)  # 6