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

[Gavin Simpson]

I don't understand your data? Dissimilarities are computed with
vegdist() in vegan on an n x m matrix of n samples and m variables. The
m variables could be species or any other set of descriptor variables.

Is your data like this? Or did you mean that your data are n samples
with a single column of numbers representing the count of a single thing
at each of the n samples? If so, are some counts zero? This doesn't
sound like a community matrix as I describe above to me.

I think the error message is reasonably clear; You have some samples
(rows) with no positive values in them (i.e. some all-zero counts for a
given sample (row)). In such cases, the Jaccard distance is not defined
- the warning is coming from the Bray-Curtis routine [as these two
dissimilarities are equivalent] and hence the ambiguity there ("...may
be..."), as the connoisseur may know what they are doing and know what
to do with such results. 

The second message is a consequence of the first; as the Jaccard is not
defined for empty rows, you get NA values for those comparisons
concerning this/those sample(s).

So I think yes, it is a problem and you need to consider how to proceed.
Perhaps taking a look at rowSums(yourData) might indicate which samples
are causing the problem.

HTH

G

On Thu, 2008-11-27 at 16:40 -0600, Manuel Spínola wrote:
> Dear list members,
> 
> 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?
> Thank you very much in advance.
> Best,
> 
> Manuel Spínola
>