The function Uniqueness calculates community-level functional uniqueness and redundancy.
uniqueness(comm, dis, tol = 1e-08, abundance = TRUE)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.
an object of class dist containing the functional distances among species. Values in dis must be bounded between 0 and 1. If they are not bounded, the function divides all values in dis by the highest observed value in dis.
a tolerance threshold (a value between -tol and tol is considered as null).
a logical. If TRUE, abundance data are used when available; if FALSE, incidence (0/1) data are used.
The function uniqueness returns a list of three data frames:
kbar: this first data frame gives values for Ricotta et al. (2016) coefficient \(\bar{K}_i\)'s per species (rows) and community (columns).
V: this second data frame gives values for Ricotta et al. (2016) coefficient \(V_i\)'s per species (rows) and community (columns).
red: this third data set gives values, per community, for Ricotta et al. (2016) coefficients N (species richness), Q (quadratic diversity), D (Simpson diversity), U=Q/D (uniqueness), R=1-U (redundancy), and Pavoine and Ricotta (2019) Ustar=(1-D)/(1-Q) (uniqueness) and Rstar=1-Ustar (redundancy); in this third data frame, coefficients are columns and communities are rows, the coefficients are thus calculated per community only.
Ricotta, C., de Bello, F., Moretti, M., Caccianiga, M., Cerabolini, B.E., Pavoine, S. (2016). Measuring the functional redundancy of biological communities: A quantitative guide. Methods in Ecology and Evolution, 7, 1386--1395.
Pavoine, S., Ricotta, C. (2019). A simple translation from indices of species diversity to indices of phylogenetic diversity. Ecological Indicators, 101, 552--561.
# NOT RUN {
data(RDMCCP16)
uniqueness(RDMCCP16$ab, as.dist(RDMCCP16$dis))
# }
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