Description Usage Arguments Value Author(s) References Examples
This function calculates the total cophenetic index TCI(T) of a given rooted tree T. The tree must not necessarily be binary. TCI(T) is defined as
TCI(T)=∑_{1<=i<j<=n} depth(lca(i,j)) =∑_{u in V'_in(T)} binom(n_u,2)
in which depth(lca(i,j)) denotes the depth of the last
common ancestor of the two leaves i and j and V'_in(T)
denotes the set of all inner vertices exept the root and n_u denotes the
number of descendant leaves of u. The second formula is useful for efficient
computation of TCI(T). The total cophenetic index is an imbalance index.
For n=1 the function returns TCI(T)=0.
1 | totCophI(tree)
|
tree |
A rooted tree in phylo format. |
totCophI
returns the total cophenetic index of the given tree.
Sophie Kersting
A. Mir, F. Rosselló, and L. Rotger. A new balance index for phylogenetic trees. Mathematical Bio-sciences, 241(1):125-136, 2013. doi: 10.1016/j.mbs.2012.10.005.
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