pcnm: Function to compute classical PCNM(Principal Coordinates of...
In spacemakeR: Spatial modelling

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

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

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

`matdist`	A distance matrix.
`thresh`	A threshold 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.

Stephane Dray

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.

give.thresh

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)