[R-sig-eco] Dissimilarity ranking

[Dave Roberts]

Burak,

     I think your question is simpler than the suggestions of NMDS.  One 
approach, let's say you dissimilarity matrix is called demodis

 > demodis2 <- as.matrix(demodis)   # make a full matrix copy
 > is.na(diag(demodis2)) <- TRUE    # ignore the dissimilarity of a
                                    # plot to itself
 > apply(as.matrix(demodis),1,mean) # calcualte the mean dissimilarity
                                    # of every plot to the others


This is all done as part of function disana() in package labdsv along 
with some other simple dissimilarity analyses.

Dave Roberts



On 11/23/2010 01:09 PM, Pekin, Burak K wrote:
> Hello, I want to rank the dissimilarity of sites based on their species composition. For example, I would like to be able to say that site A is less similar in composition to the other sites than site B is similar to the other sites. I could do a cluster analysis and look at which sites are less closely clustered.
>
> It would be even better if I could come up with a quantitative scale rather than a relative ranking that would give a value for each site based on its relative dissimilarity to the rest of the sites. So site A might receive a 90 out of 100, whereas site B and C might receive a 60 and a 50 indicating the rank as well as 'relative quantity' of dissimilarity for each site.
>
> Thanks,
> Burak
>
> --------------------------
>
> Burak K. Pekin, PhD
> Postdoctoral Research Associate
> Purdue University
>
>
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