tci.context: Contextualize Total Cophenetic Index value
In TotalCopheneticIndex: Quantify the Balance of Phylogenetic Trees

Description Usage Arguments Details Value Author(s) References See Also Examples

Calculate the range of values that the Total Cophenetic Index can take, and expected values under the Yule and Uniform models of evolution. Now simply a wrapper for TreeTools::TCIContext().

1 2	tci.context(tree) tci.context.n(n)

`tree`	a tree of class `phylo`;
`n`	integer specifying the number of tips in a tree.

For a tree with n tips, the Total Cophenetic Index can take values of 0 to choose(nTips, 3) The minimum value is higher for a perfectly resolved (i.e. dichotomous) tree (see Lemma 14) Formulae to calculate the expected values under the Yule and Uniform models of evolution are given in Theorems 17 and 23.

A data frame detailing the maximum and minimum value obtainable for the Total Cophenetic Index for dichotomous trees with the number of tips of the given tree, and the expected value under the Yule and Uniform models. The variance of the expected value is given under the Yule model, but cannot be obtained by calculation for the Uniform model.

Martin R. Smith

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

tci, the Total Cophenetic Index for a given tree

  tree12 <- ape::read.tree(text='(1, (2, (3, (4, 5))));')  #Fig. 4, tree 12
  tci(tree12)
  tci.context(tree12)
  tci.context.n(5) # For any tree with 5 tips