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.
1 | stairs1(tree)
|
tree |
A rooted binary tree in phylo format. |
stairs1
returns the stairs1 value of the given tree.
Sophie Kersting
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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