rank.abund.pd: Cumulative PD across rank abundance distribution

In NGSwenson/lefse_0.5: Phylogenetic and Functional Analyses for Ecology

Description

Quantifies Faiths PD index beginning with the 2 most common species in a community and recalculating as increasingly rare species are added.

Usage

rank.abund.pd(my.sample, my.phylo)

Arguments

my.sample	A community data matrix
my.phylo	A community phylogeny

Value

rank.abund.pd The PD value first for the 2 most common species and then for the 3 most common until the rarest species is added.

Author(s)

Nathan G. Swenson

References

Mi, X., N.G. Swenson, R. Valencia, W.J. Kress, D.L. Erickson, A. Perez-Castaneda, H. Ren, S.H. Su, N. Gunatilleke, S. Gunatilleke, Z. Hao, W. Ye, M. Cao, H.S. Suresh, H.S. Dattaraja, R. Sukumar, and K. Ma. 2012. The contribution of rare species to community phylogenetic diversity across a global network of forest plots. The American Naturalist 180:E17-E30.

Examples

data(lefse.phylo)
data(lefse.sample)
rank.abund.pd(lefse.sample,lefse.phylo)

NGSwenson/lefse_0.5 documentation built on May 7, 2019, 6:01 p.m.