pcnm: Function to compute classical PCNM(Principal Coordinates of...

Description Usage Arguments Value Author(s) References See Also Examples

Description

This function computed classical PCNM by the principal coordinate analysis of a truncated distance matrix.

Usage

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pcnm(matdist, thresh = give.thresh(as.dist(matdist)))

Arguments

matdist

A distance matrix.

thresh

A threshold value.

Value

A list of two elements:

values

Eigenvalues obtained by the principal coordinates analysis.

vectors

Eigenvectors obtained by the principal coordinates analysis. They have been normalized to unit norm.

Author(s)

Stephane Dray

References

Borcard D. and Legendre P. (2002) All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices. Ecological Modelling 153, 51–68.

See Also

give.thresh

Examples

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data(oribatid)
pcnm1 <- pcnm(dist(oribatid$xy))
par(mfrow=c(1,3))
s.value(oribatid$xy,pcnm1$vectors[,1],cleg=0, sub="PCNM 1",csub=3)
s.value(oribatid$xy,pcnm1$vectors[,2],cleg=0, sub="PCNM 2",csub=3)
s.value(oribatid$xy,pcnm1$vectors[,3],cleg=0, sub="PCNM 3",csub=3)

spacemakeR documentation built on May 31, 2017, 2:24 a.m.