[R-sig-eco] Which R package for Second-Stage nMDS ?

[Pierre THIRIET]

Thanks a lot dear Philip. I will try this.

all the best

Pierre


Le 22/03/2019 à 17:07, Dixon, Philip M [STAT] a écrit :
> Pierre,
>
> I don't know a function that does this, but it is extremely easy to code.
>
> Dist objects are vectors containing the 1st stage pairwise dissimilarities.   Call those dist1, dist2, dist3, ...  So alldist <- cbind(dist1=dist1, dist2=dist2, ...) will assemble the matrix of dissimilarities with useful column names.  stage2 <- as.dist(1-cor(alldist)) will compute the matrix of correlations, convert from similarity (the correlation) to distance (1-correlation) and convert to a distance object.  Then just run your favorite MDS on stage2.
>
> Note: sometimes folks prefer sqrt(1-cor) as the "correlation distance", instead of 1-cor.  I don't know which Clarke prefers.
>
> Best,
> Philip Dixon
>
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