hill_taxa: Taxonomic diversity through Hill Numbers

In hillR: Diversity Through Hill Numbers

Taxonomic diversity through Hill Numbers

Description

Calculate taxonomic diversity for each site (alpha diversity).

Usage

hill_taxa(comm, q = 0, MARGIN = 1, base = exp(1))

Arguments

comm	A data frame of vegetation data. Sites as rows, species as columns.
q	Hill number, q = 0 (default) to get species richness, q = 1 to get shannon entropy, q = 2 will give inverse Simpson.
MARGIN	default is 1, if sites are columns, set MARGIN to 2.
base	default is exp(1), the base of log.

Value

A named vector, diversity values for each site in the comm.

References

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>.

Examples

dummy = FD::dummy
hill_taxa(comm = dummy$abun, q = 0)
# same as: vegan::specnumber(dummy$abun)
hill_taxa(comm = dummy$abun, q = 0.999)
hill_taxa(comm = dummy$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')

hillR documentation built on Aug. 20, 2023, 1:08 a.m.