I am trying to calculate species richness, evenness (using Hurlbert's PIE), and
diversity (using Shannons) for plant community data. However, my sampling units
(eg, forest patches) vary greatly in size, and thus so does the sampling
intensity. Therefore, I am trying to use rarefaction to better account for the
different abundances within forest patches. I know the VEGAN package can
calculate species richness using rarefaction, but I know that it does not
calculate evenness, and from what I can tell it does not calculate Shannons in
a way that uses the corrected values of richness. So my question is, is there
an R package that can do all of this?
To clarify, I am wanting to use PIE for evenness based on the suggestion by
Nicholas Gotelli in his book "Null Models in Ecology", and I want to use
Shannons for diversity based on suggestions from my graduate advisor. However,
if there are better options I would be open to exploring these if they are
backed by recent literature. Thanks!
Richard Sample
PhD Candidate
Department of Forestry and Natural Resources
Purdue University
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