Learn R Programming

funrar (version 1.5.0)

distinctiveness_range: Alternative Truncated Functional Distinctiveness

Description

Computes functional distinctiveness from a site-species matrix (containing presence-absence or relative abundances) of species with provided functional distance matrix considering only species within a given range in the functional space. The sites-species matrix should have sites in rows and species in columns, similar to vegan package defaults.

Usage

distinctiveness_range(pres_matrix, dist_matrix, given_range, relative = FALSE)

Value

a similar matrix from provided pres_matrix with Distinctiveness values in lieu of presences or relative abundances, species absent from communities will have an NA value (see Note section)

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

given_range

a numeric indicating the dissimilarity range at which the the influence of other species is not considered anymore

relative

a logical indicating if distinctiveness should be scaled relatively to the community (scaled by max functional distance among the species of the targeted community)

Details

The Functional Distinctiveness of a species is the average functional distance from a species to all the other in the given community. It is computed as such: $$ D_i(T) = 1 ~~ if ~~ T < min(d_{ij}), \\ D_i(T) = \left( \frac{ \sum\limits_{j = 1 ~, j \neq i ~, d_{ij} \leq T}^S d_{ij} \times Ab_j }{ \sum\limits_{ j = 1 ~, j \neq i ~, d_{ij} \leq T}^S Ab_j } \right) \times \left(1 - \frac{ \sum\limits_{ j = 1 ~, j \neq i ~, d_{ij} \leq T}^S Ab_j }{ N } \right) ~~ if ~~ T \geq min(d_{ij}), $$ with \(D_i\) the functional distinctiveness of species \(i\), \(N\) the total number of species in the community and \(d_{ij}\) the functional distance between species \(i\) and species \(j\). \(T\) is the chosen maximal range considered. When presence-absence are used \(Ab_j = 1/N\) and the term \( \left(1 - \frac{ \sum\limits_{ j = 1 ~, j \neq i ~, d_{ij} \leq T}^S Ab_j }{ N } \right)\) is replaced by 1. IMPORTANT NOTE: in order to get functional rarity indices between 0 and 1, the distance metric has to be scaled between 0 and 1.

Examples

Run this code
data("aravo", package = "ade4")
# Site-species matrix
mat = as.matrix(aravo$spe)

# Compute relative abundances
mat = make_relative(mat)

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

di = distinctiveness_range(pres_matrix = mat, dist_matrix = dist_mat, 0.2)
di[1:5, 1:5]

Run the code above in your browser using DataLab