Jost Diversity Measures for Community Data
Description
This package computes diversity for community data sets
using the methods outlined by Jost (2006, 2007). While there
are differing opinions on the ideal way to calculate diversity
(e.g. Magurran 2004), this method offers the advantage of
providing diversity numbers equivalents, independent alpha and
beta diversities, and the ability to incorporate 'order' (q) as
a continuous measure of the importance of rare species in the
metrics. The functions provided in this package largely
correspond with the equations offered by Jost in the cited
papers. The package computes alpha diversities, beta
diversities, gamma diversities, and similarity indices.
Confidence intervals for diversity measures are calculated
using a bootstrap method described by Chao et al. (2008). For
datasets with many samples (sites, plots), sim.table creates
tables of all pairwise comparisons possible, and for grouped
samples sim.groups calculates pairwise combinations of within-
and between-group comparisons.