Rarefy (version 1.1.1)

rarexpected_fun: Functional Diversity Rarefaction Curves

Description

The function calculates functional diversity rarefaction curves using the method proposed by Ricotta et al. (2010).

Usage

rarexpected_fun(comm,dist_f)

Value

A vector containing the values of the expected functional diversity for every sampling dimension is returned.

Arguments

comm

a community data frame or matrix with N plots as rows, S species as columns. Only presence/absence (1/0) of species in plots are allowed as entries.

dist_f

an object of class dist containing the pairwise functional distances among species. The distance matrix should be squared Euclidean or simply Euclidean.

Author

Giovanni Bacaro

Elisa Thouverai

Details

The expected occupancy frequencies for species at an increasingly larger cumulative number of plots N are used for the calculation of Rao's quadratic entropy to obtain an expected functional diversity between species in the N random plots. The expected occupancy frequency is the probability for every species in the community to find that species in the N random plots.

References

Botta-Dukat, Z. (2005) Rao's quadratic entropy as a measure of functional diversity based on multiple traits. Journal of Vegetation Science, 16, 533--540.

Rao, C.R. (1982) Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology, 21, 24--43.

Ricotta, C., Burrascano, S., Blasi, C. (2010) Incorporating functional dissimilarities into sample-based rarefaction curves: from taxon resampling to functional resampling. Journal of Vegetation Science, 21, 280--286.

See Also

ser_functional

Examples

require(ade4)
require(vegan)
data(duneFVG)
data(duneFVG.tr8)
tr8_N<-duneFVG.tr8$traits.tot[,c(1,3,4)]
tr8_D<-data.frame(duneFVG.tr8$traits.tot[,2])
tr8_Q<-duneFVG.tr8$traits.tot[,5:15]
tr8dist<-dist.ktab(ktab.list.df(list(tr8_N,tr8_D,tr8_Q)),type=c('N','D','Q'))
tr8dist<-cailliez(tr8dist) 
d<-decostand(duneFVG$total, method='pa')
rare<-rarexpected_fun(d,tr8dist)
plot(rare, ylab="Rao QE", xlab="Number of plots", type="l")