sad {BAT}

Species-abundance distribution (SAD).

Description

Fits the SAD to community abundance data, also using trees and with possible rarefaction.

Usage

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

Arguments

comm

Either a vector with the abundance per species, or a sites x species matrix.

tree

A phylo or hclust object (used only for PD or FD) or alternatively a species x traits matrix or data.frame to build a functional tree.

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

comm1 <- c(20,1,3,100,30)
comm2 <- c(1,2,12,0,45)
comm <- rbind(comm1, comm2)
tree <- hclust(dist(c(1:5), method="euclidean"), method="average")
sad(comm1)
sad(comm)
sad(comm, octaves = FALSE)
sad(comm, tree, scale = TRUE)
sad(comm, raref = 1)