uniqueness: Functional Uniqueness and Functional Redundancy of Biological Communities

Description

Hypothetical communities C1-C9 composed of nine species S1-S9 with varying abundances divided into three groups of three species each displayed with different shades (S1-S3, S4-S6 and S7-S9). All species within the same group are functionally identical to each other, while two species belonging to different groups are always maximally dissimilar.

Usage

uniqueness(comm, dis, tol = 1e-08, abundance = TRUE)

Arguments

comm

a matrix or a data frame containing the abundance or incidence (0/1) of species in communities (or plots). Columns are species and communities are rows.

dis

an object of class dist containing the functional distances among species

tol

a tolerance threshold (a value between -tol and tol is considered as null)

abundance

a logical. If TRUE, abundance data are used when available; if FALSE, incidence (0/1) data are used.

Value

The function uniqueness returns a list of three data frames:

kbar: this first data frame gives values for Ricotta et al. coefficient \(\bar{K}_i\)'s per species (rows) and community (columns).

V: this second data frame gives values for Ricotta et al. coefficient \(V_i\)'s per species (rows) and community (columns).

red: this third data set gives values for Ricotta et al. coefficients N (species richness), Q (quadratic diversity), D (Simpson diversity), and U (uniqueness) per community; in this third data frame, coefficients are columns and communities are rows, the coefficients are thus calculated per community only.

References

Ricotta, C, de Bello, F, Moretti, M, Caccianiga, M, Cerabolini, BE, Pavoine, S (2016). Measuring the functional redundancy of biological communities: A quantitative guide. Methods in Ecology and Evolution, 7, 1386--1395.

Examples

Run this code

# NOT RUN {
data(RDMCCP16)
uniqueness(RDMCCP16$ab, as.dist(RDMCCP16$dis))
# }