Description Usage Arguments Value Author(s) References Examples
This function calculates the B2 index B2(T) for a given rooted tree T. The tree must not necessarily be binary. B2(T) is defined as
B2(T)=-∑_{x in V_L(T)} p_x * log(p_x)
in which V_L(T) denotes the leaf set of T, and in which
p_x= ∏_{v in anc(x)} 1/|child(v)|
denotes
the probability of reaching leaf x when starting at the root and assuming
equiprobable branching at each vertex v in anc(x) with anc(x)
denoting the set of ancestors of x excluding
x. child(v) denotes the set of children of the inner vertex v.
The B2 index is a balance index.
For n=1 the function returns B2(T)=0 and a warning.
1 | B2I(tree, logbase = 2)
|
tree |
A rooted tree in phylo format. |
logbase |
The base that shall be used for the logarithm. For binary trees it is common to use base 2. |
B2I
returns the B2 index of the given tree.
Sophie Kersting, Luise Kuehn
K.-T. Shao and R. R. Sokal. Tree Balance. Systematic Zoology, 39(3):266, 1990.
doi: 10.2307/2992186.
P.-M. Agapow and A. Purvis. Power of Eight Tree Shape Statistics to Detect Nonrandom
Diversification: A Comparison by Simulation of Two Models of Cladogenesis. Systematic Biology,
51(6):866-872, 2002.doi: 10.1080/10635150290102564.
URL https://doi.org/10.1080/10635150290102564.
M. Hayati, B. Shadgar, and L. Chindelevitch. A new resolution function to evaluate tree shape
statistics. PLOS ONE, 14(11):e0224197, 2019. doi: 10.1371/journal.pone.0224197.
URL https://doi.org/10.1371/journal.pone.0224197.
M. Kirkpatrick and M. Slatkin. Searching for evolutionary patterns in the shape of a phylogenetic tree. Evolution, 47(4):1171-1181, 1993. doi: 10.1111/j.1558-5646.1993.tb02144.x.
1 2 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.