Tracy,

It doesn't make sense to include empty sites (without any species) in an
ordination of the communities. Just remove these empty lines from your
species dataset before perfoming NMDS.

Best regards,

François

-------------------------------------------------------------------------------
Prof. François Gillet
Community ecology and dynamic modelling
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Université de Franche-Comté - CNRS
UMR 6249 Chrono-environnement
UFR Sciences et Techniques
16, Route de Gray
F-25030 Besançon cedex
France
http://chrono-environnement.univ-fcomte.fr/
http://chrono-environnement.univ-fcomte.fr/spip.php?article530
Phone: +33 (0)3 81 66 62 81
Location: La Bouloie, Bât. Propédeutique, *-114L*
-------------------------------------------------------------------------------


"Numerical Ecology with R", by D. Borcard, F. Gillet and P. Legendre
http://www.springer.com/978-1-4419-7975-9
-------------------------------------------------------------------------------


2012/1/25 Pinney, Tracy A <Tracy_Pinney@baylor.edu>

> Hello,
>
>   I am trying to use metaMDS (or isoMDS) for a community data set with 10
> species.  However, I have several sites with no species present (empty
> rows), and this seems to present a problem in the dissimilarity matrix in
> the form of missing values.  Does anyone have suggestions on how to deal
> with this?  Is it appropriate to create a dummy variable in the original
> community matrix?  If so, what is the best way to do this?  Thanks for any
> help.
>
>
>
> Tracy Pinney
>
>
>
> PhD candidate
>
> Department of Biology
>
> Baylor University
>
> One Bear Place 97388-7388
>
> Waco, TX  76798-7388
>
>
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