kernel.sad: Species-abundance distribution (SAD) using kernel density...

In BAT: Biodiversity Assessment Tools

Species-abundance distribution (SAD) using kernel density hypervolumes.

Description

Fits the SAD to community abundance data based on n-dimensional hypervolumes.

Usage

kernel.sad(comm, octaves = TRUE, scale = FALSE, raref = 0, runs = 100)

Arguments

comm	A 'Hypervolume' or 'HypervolumeList' object necessarily built using function kernel.build.
octaves	a boolean indicating whether octaves should be calculated.
scale	scale y-axis to sum 1.
raref	An integer specifying the number of individuals for rarefaction (individual based). If raref < 1 no rarefaction is made. If raref = 1 rarefaction is made by the minimum abundance among all sites. If raref > 1 rarefaction is made by the abundance indicated. If not specified, default is 0.
runs	Number of resampling runs for rarefaction. If not specified, default is 100.

Details

The Species Abundance Distribution describes the commonness and rarity in ecological systems. It was recently expanded to accomodate phylegenetic and functional differences between species (Matthews et al., subm.). Classes defined as n = 1, 2-3, 4-7, 8-15, .... Rarefaction allows comparison of sites with different total abundances.

Value

A vector or matrix with the different values per class per community.

References

Matthews et al. (subm.) Phylogenetic and functional dimensions of the species abundance distribution.

Examples

## Not run: 
comm = rbind(c(1,3,0,5,3), c(3,2,5,1,0))
colnames(comm) = c("SpA", "SpB", "SpC", "SpD", "SpE")
rownames(comm) = c("Site 1", "Site 2")

trait = data.frame(body = c(1,2,3,4,4), beak = c(1,5,4,1,2))
rownames(trait) = colnames(comm)

hv = kernel.build(comm, trait)
kernel.sad(hv, scale = TRUE)
kernel.sad(hv, octaves = FALSE)
kernel.sad(hv, raref = TRUE)

## End(Not run)

BAT documentation built on May 29, 2024, 7:35 a.m.