[R] Problem with metaMDS in vegan

[David Carlson]

A reproducible example would help. Look at the example in metaMDS using the dune data set. It consists of 20 observations (sites) with 30 species observed (columns). You indicate that your compounds (species) are the rows and your sites are the columns. So perhaps you are analyzing the distances between compounds not between sites? Have you tried analyzing t(data)?

David C

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf Of Fabian B
Sent: Monday, February 10, 2014 9:58 AM
To: r-help at r-project.org
Subject: Re: [R] Problem with metaMDS in vegan

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






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