Description Usage Arguments Value Author(s) References Examples
This function calculates the stairs1 value st1(T) for a given rooted binary tree T. It is a modified version of the Rogers J index and is defined as the fraction of inner vertices whose balance value is unequal to zero, more precisely
st1(T)=1/(n-1)*∑ (1-I(n_ua=n_ub)) over all u in V_in(T)
in which V_in(T) denotes the set of all inner vertices
of T, and in which n_ua
and n_ub denote the number of leaves in the two pending subtrees that are
rooted at the direct descendants of u. The stairs1 value is an imbalance index.
Special cases: For n=1, the function returns st1(T)=0 and a warning.
A rooted binary tree in phylo format.
stairs1 returns the stairs1 value of the given tree.
M. M. Norström, M. C. Prosperi, R. R. Gray, A. C. Karlsson, and M. Salemi. PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences. Evolutionary Bioinformatics, 8:EBO.S9738, 2012. ISSN 1176-9343, 1176-9343. doi:10.4137/EBO.S9738.
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