Functional Uniqueness for site-species matrix matrix

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.

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

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.

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 $j$

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)
#> Only numeric traits provided, consider using euclidean distance.

ui = uniqueness(mat, dist_mat)
head(ui)
#>     species         Ui
#> 1 Agro.rupe 0.03635369
#> 2 Alop.alpi 0.03715692
#> 3 Anth.nipp 0.09414051
#> 4 Heli.sede 0.02270997
#> 5 Aven.vers 0.05675178
#> 6 Care.rosa 0.15922932

# 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)
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix
#> Distance matrix bigger than site-species matrix
#> Taking subset of distance matrix

Functional Uniqueness for site-species matrix matrix

Arguments

Value

Details

See also

Examples