Computes scarcity from a relative abundance matrix of species. Scarcity is close to 1 when a species is rare in a community and close to 0 when it is abundant. It requires a site-species matrix with relative abundances. See Details section for the formula. The sites-species matrix should have sites in rows and species in columns, similar to vegan package defaults.




a site-species matrix, with species in rows and sites in columns, containing relative abundances values


a similar matrix to pres_matrix with scarcity values in lieu

of relative abundances.


The scarcity of species is computed as follow: $$ S_i = \exp{-N \log{2} A_i}, $$ with \(S_i\) the scarcity of species \(i\), \(N\) the total number of species in the community and \(A_i\) the relative abundance of species \(i\) in the community. Scarcity is thus a measure of the local rarity in terms of abundances. If \(S_i\) is close to 1 the species has a very low abundances while if it's close to 0, it is quite abundant in the community.

See also

vignette("rarity_indices", package = "funrar") for details on the scarcity metric; distinctiveness(), restrictedness(), uniqueness()


data("aravo", package = "ade4")
# Site-species matrix
mat = as.matrix(aravo$spe)
mat = make_relative(mat)

si = scarcity(pres_matrix = mat)
si[1:5, 1:5]
#>      Agro.rupe Alop.alpi Anth.nipp Heli.sede Aven.vers
#> AR07        NA        NA        NA        NA        NA
#> AR71        NA        NA        NA        NA        NA
#> AR26  0.231951        NA 0.6144201        NA 0.6144201
#> AR54        NA        NA        NA 0.3379268        NA
#> AR60        NA        NA        NA        NA        NA