expected.pd: Expected PD and Edge Abundance Distribution of a phylogeny
Description
Calculates the expected phylogenetic diversity (Faith's PD) under binomial sampling with a fixed probability of each tip being sampled, and the Edge-length Abundance Distribution of a phylogeny.
Usage
expected.pd(phy)
ead(phy)
Arguments
phy
phylo object
Value
nExpected Number of tips sampled
expected.pdExpected PD for a given n
num.childrenNumber of tips descended from an edge
edge.lengthTotal phylogenetic edge length for a given number of tips descended from an edge
Details
The function expected.pd calculates the expected phylogenetic diversity (Faith's PD - total branch length) for all subsets of a phylogeny, based on an analytic solution for expected PD.
The function ead calculates the edge abundance distribution (EAD), the length of edges with different numbers of descendant tips.
References
O'Dwyer, Kembel, and Green. 2012. Phylogenetic diversity theory sheds light on the structure of microbial communities.