Problem in NMDS

Hi,

I am stuck in one problem when doing nonmetric multidimensional
scaling. I use the function 'metaMDS' in the package 'vegan' to work
on the presence/absence community data. The problem is when two
samples are identical (dissimilarity = 0), metaMDS cannot work with
zero dissimilarity.

I don't want to delete the duplicates as they are true samples from
different locations.

But they *must* be located in the exact same space in the nMDS
solution/plot, so what is the point in having them both in the analysis?
Just adjust the labelling when drawing the nMDS plot so that the single
point gets two labels (which you'll need to do by hand).

The other option is to look at argument 'zerodist' and its description
for details on another way to work round this "problem" --- see ?metaMDS
for details.

I don't recommend the workaround offered with 'zerodist' but you may
have a different opinion on this matter.

HTH

G

Thanks in advance.

Bingzhang Chen

      ___________________________________________________________ 
  ????????????????? 
http://card.mail.cn.yahoo.com/

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%