uniqueness: Functional Uniqueness for site-species matrix matrix

In Rekyt/outlieR: Functional Rarity Indices Computation

Functional Uniqueness for site-species matrix matrix

Description

Computes the functional uniqueness from a site-species matrix with the provided functional distance matrix. Functional Uniqueness represents how "isolated" is a species in the global species pool, it is the functional distance to the nearest neighbor of the species of interest (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

uniqueness(pres_matrix, dist_matrix)

Arguments

pres_matrix	a site-species matrix (presence-absence or relative abundances), with sites in rows and species in columns
dist_matrix	a species functional distance matrix

Details

Functional Uniqueness U_i is computed as follow:

U_i = \min(d_{ij}) \forall j, j \neq i,

with U_i the functional uniqueness of species i, and d_ij the functional distance between species i and species j

Value

A data.frame with functional uniqueness values per species, with one column with provided species column name and the Ui column with functional uniqueness values.

See Also

distinctiveness(), restrictedness(), scarcity()

Examples

data("aravo", package = "ade4")

# Site-species matrix
mat = as.matrix(aravo$spe)
colnames(mat) = as.character(colnames(mat))

# Example of trait table
tra = aravo$traits[, c("Height", "SLA", "N_mass")]
# Distance matrix
dist_mat = compute_dist_matrix(tra)

ui = uniqueness(mat, dist_mat)
head(ui)

# Computing uniqueness for each community
com_ui = apply(mat, 1,
                function(x, dist_m) {
                    smaller_com = x[x > 0 & !is.na(x)]
                    uniqueness(t(as.matrix(smaller_com)), dist_m)
                }, dist_m = dist_mat)

Rekyt/outlieR documentation built on April 12, 2024, 3:25 p.m.