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
R functions for calculating species evenness (via Hurlburt's PIE) and species diversity (Shannon's) using rarefaction
2 messages · Richard D Sample, Florencia Grattarola
Hi Richard, Have you heard of the package iNEXT? https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.12613 You can estimate Hill numbers (species richness, Shannon and Simpson diversity) using individual-based abundance data or sampling-unit-based incidence data, and it enables you to standardise by sampling coverage. Here's a good introduction to the idea: https://esajournals.onlinelibrary.wiley.com/doi/full/10.1890/13-0133.1 Hope it helps. Cheers, Flo El lun, 26 jul 2021 a las 17:10, Richard D Sample (<rsample at purdue.edu>) escribi?:
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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*Florencia Grattarola* Faculty of Environmental Sciences Czech University of Life Sciences Prague Web-site: flograttarola.com Twitter: @flograttarola <https://twitter.com/flograttarola> E-mail: grattarola at fzp.czu.cz [[alternative HTML version deleted]]