SADbin: Species-abundance distribution (SAD) bins

In ordiconsensus: Consensus of canonical ordinations through the canonical redundancy analysis

Description

This function constructs bins for a species-abundance distribution. It was designed so that every variation of binnings can easily be constructed.

Usage

SADbin(data, method = c("log", "modlog", "modhalflog"), base = 2)

Arguments

data	A vector of species abundance for the whole study area.
method	A character string defining which binning method to use.
base	The log base to use to perform the binning.

Details

All value in data are expected to be count data. An error message will be sent if the value in data are not integers.

The different method of binning are defined as such :

log (using a base = 2) : Bin 1 = 1, Bin 2 = 2, Bin 3 = 3-4, Bin 4 = 5-8, ...

modlog (using a base = 2) : Bin 1 = 1, Bin 2 = 2-3, Bin 3 = 4-7, Bin 4 = 8-15,...

modhalflog (using a base = 2) : Bin 1 = half the number of species with 1 individuals, Bin 2 = half the number of species with 1 individuals and half of the number of species with 2 individuals, Bin 3 = half of the number of species with 2 individuals, all species with 3 individuals and half of the number of species with 4 individuals; and so on.

Value

bin	A vector defining the number of species in each bin
sp.bin	A matrix with the species in rows and the bins in columns. This matrix describe which species is in which bin

Author(s)

F. Guillaume Blanchet

References

Gray, J.S., A. Bjorgesaeter, and K. I. Ugland. 2006. On plotting species abundance distributions. Journal of Animal Ecology 75:752–756.

Examples

data(mite)
SADmite<-SADbin(colSums(mite))
barplot(SADmite$bin,names.arg=paste("Bin",1:length(SADmite$bin)),las=2)

ordiconsensus documentation built on May 2, 2019, 4:38 p.m.