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 (<rsam...@purdue.edu>) escribió: > 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 > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > -- *Florencia Grattarola* Faculty of Environmental Sciences Czech University of Life Sciences Prague Web-site: flograttarola.com Twitter: @flograttarola <https://twitter.com/flograttarola> E-mail: grattar...@fzp.czu.cz [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
