Thanks for the fast response! My data is actually just the percentages of the substances found in the cuticular layer of the flies. The quantitative and qualitative composition of this layer differs in gender, locality and so on. My 70 „species“ are the chemical compounds we identified and my 48 „sites“ are the individuals (location and gender are encrypted in the individuals' recognition code). Therefore, I have the percentages of one chemical compound over all tested individuals in one row (as numeric data). You could say that these are the abundances of the species (the compounds) at the different sites (individuals). So my data is quite similar to community structure. I have done this before and it worked just fine. I used:
metaMDS(data, distance=“bray“, k=2, trymax=10000, autotransform=F) As I mentioned before, this time the stress is very low (around 9.5 * 10^-5) and R gives me that warning message. Though I have always had data in the same structure, I've never been in this situation. The NMDS just stops after the first run, because of the low stress. But there are obviously some differences in my data – I can see them with my eye. If I discard the 'distance=”bray”', nothing changes. May it be possible that these are simply just to little to be recognised correctly? How could I change that? If I add 'maxit=10', I get quite what I assumed. Two completely separated clusters with cloudlike appearance (stress around 0.02). The clusters are the two sexes and in each cluster, the localities group together. But I'm not quite sure, if I may set a maxit-level that low – or if I just create some false relations with that. I also recognised , that the stress gets lower, the higher I set 'maxit' and the lower I set 'trymax'. What could be going wrong? I really have no clue … Thanks for your help! Regards, Fabian -- View this message in context: http://r.789695.n4.nabble.com/Problem-with-metaMDS-in-vegan-tp4685022p4685043.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@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.
