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 > _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology