restrictedness: Geographical Restrictedness on site-species matrix

Description Usage Arguments Details Value Examples

View source: R/restrictedness.R

Description

Computes geographical restrictedness from a site-species matrix. Geographical restrictedness is an index related to the extent of a species in a given dataset, it is close to 1 when the species is present in only a single site of the dataset (restricted) and close to 0 when the species is present at all sites. It estimates the geographical extent of a species in a dataset. See Details section to have details on the formula used for the computation. The sites-species matrix should have sites in rows and species in columns, similar to vegan package defaults.

Usage

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restrictedness(pres_matrix, relative = FALSE)

Arguments

pres_matrix

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

relative

a logical (default = FALSE), indicating if restrictedness should be computed relative to restrictedness from a species occupying a single site

Details

Geographical Restrictedness aims to measure the regional extent of a species in funrar it is computed the simplest way possible: a ratio of the number of sites where a species is present over the total number of sites in the dataset. We take this ratio off 1 to have a index between 0 and 1 that represents how restricted a species is:

R_i = 1 - (N_i/N_tot),

where R_i is the geographical restrictedness value, N_i the total number of sites where species i occur and N_tot the total number of sites in the dataset. When relative = TRUE, restrictedness is computed relatively to the restrictedness of a species present in a single site:

R_i = R_i / R_one

R_i = (1 - K_i/K_tot)(1 - 1/K_tot)

R_i = (K_tot - K_i)(K_tot - 1)

Other approaches can be used to measure the geographical extent (convex hulls, occupancy models, etc.) but for the sake of simplicity only the counting method is implemented in funrar.

Value

A stacked data.frame containing species' names and their restrictedness value in the Ri column, similar to what uniqueness() returns.

Examples

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

funrar documentation built on April 20, 2020, 5:05 p.m.