tci.context {TotalCopheneticIndex} | R Documentation |
Contextualize Total Cophenetic Index value
Description
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()
.
Usage
tci.context(tree)
tci.context.n(n)
Arguments
tree |
a tree of class |
n |
integer specifying the number of tips in a tree. |
Details
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.
Value
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.
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
tci
, the Total Cophenetic Index for a given tree
Examples
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