scarcity: Scarcity on site-species matrix

Description

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.

Usage

scarcity(pres_matrix)

Value

a similar matrix to pres_matrix with scarcity values in lieu

of relative abundances.

Arguments

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

Details

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.

Examples

Run this code

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]