Taxonomic diversity through Hill Numbers
Calculate taxonomic diversity for each site (alpha diversity).
hill_taxa(comm, q = 0, MARGIN = 1, base = exp(1))
comm |
A data frame of vegetation data. Sites as rows, species as columns. |
q |
Hill number, |
MARGIN |
default is 1, if sites are columns, set |
base |
default is |
A named vector, diversity values for each site in the comm.
Chao, Anne, Chun-Huo Chiu, and Lou Jost. Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures Through Hill Numbers. Annual Review of Ecology, Evolution, and Systematics 45, no. 1 (2014): 297–324. <doi:10.1146/annurev-ecolsys-120213-091540>.
Jost, Lou. Entropy and diversity. Oikos 113, no. 2 (2006): 363-375. <doi:10.1111/j.2006.0030-1299.14714.x>.
dummy = FD::dummy hill_taxa(comm = dummy$abun, q = 0) # same as: vegan::specnumber(dummy$abun) hill_taxa(comm = dummy$abun, q = 1) # same as: exp(vegan::diversity(x = dummy$abun, index = 'shannon')) hill_taxa(comm = dummy$abun, q = 2) # same as: vegan::diversity(x = dummy$abun, index = 'invsimpson') hill_taxa(comm = dummy$abun, q = 0.999)
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