[R-sig-eco] Problems with vegdist in Vegan

[tyler]

Manuel Spínola <mspinola at una.ac.cr>
writes:

> I am runnig a NMDS in Vegan (version 1.13.2, Windows) and I get the
> following message with the function vegdist:
>
>> aves.dis <- vegdist(avesp.esp, dist="jaccard")
> Warning messages:
> 1: In vegdist(avesp.esp, dist = "jaccard") :
>  you have empty rows: their dissimilarities may be meaningless in method bray
>
> 2: In vegdist(avesp.esp, dist = "jaccard") : missing values in results
>
> I have sites (point counts) without species, is it a problem?

The problem is that the Jaccard coefficient is undefined for empty
plots. You'll have to sort out for yourself how to deal with the problem
in your study, according to the biology of the system involved. 

If you're interested primarily in the relationships between communities
present at different sites, then the simplest thing is probably to drop
the empty rows and run the analysis without them. If you need to include
the empty plots, you'll have to use a distance measure that
appropriately quantifies their relationship to each other and the other
non-empty plots. This would only really make sense if you have reason to
believe that all the empty plots are empty for the same reason.

HTH,

Tyler

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