scarcity | R Documentation |
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.
scarcity(pres_matrix)
pres_matrix |
a site-species matrix, with species in rows and sites in columns, containing relative abundances values |
The scarcity of species is computed as follow:
S_i = exp^(-N*ln2*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.
a similar matrix to pres_matrix
with scarcity values in lieu
of relative abundances.
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]
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