The function Uniqueness calculates community-level functional uniqueness and redundancy.
uniqueness(comm, dis, tol = 1e-08, abundance = TRUE)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.
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.
Sandrine Pavoine sandrine.pavoine@mnhn.fr
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.
QE, treeUniqueness
data(RDMCCP16)
uniqueness(RDMCCP16$ab, as.dist(RDMCCP16$dis))
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