[R] Problem with metaMDS in vegan

David Carlson dcarlson at tamu.edu
Mon Feb 10 16:07:53 CET 2014

Without more information, it is hard to say. You did not tell us much about the data beyond the dimensions, but it looks like you have several different kinds of measurements including location and gender (probably categorical) and cuticular profiles (presumably numeric). Without the commands you used, we can only guess what you are doing, but the snippet you provided suggests that you dumped different data types into metaMDS and used the Bray distance coefficient. The Bray coefficient is designed for analyzing community structure by comparing the counts of different species between samples. It does not appear that this is what you are trying to do. 

David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352

-----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 5:27 AM
To: r-help at r-project.org
Subject: [R] Problem with metaMDS in vegan


I am relatively new to vegan and need some help with metaMDS. My R is
Version 3.0.2. I am analysing cuticular profiles of flys from different
locations an different gender. My data is in a 48 x 70 matrix. It is about
percentages and so, there are a lot of 0s included. If I run metaMDS, it
just gives me: 

Warning message:
In metaMDS(data1, distance = "bray", k = 2, trymax = 100, autotransform = F)
  Stress is (nearly) zero - you may have insufficient data

no matter, what I change. The error is always around 9.241406e-05, which
seems to be far to low for my data. By inspecting the data sheet, I clearly
see that there must be two clusters – but there are still some differences
in these (meaning: Not all female flies show the same pattern than the
others and there are slight differences in the locations …) - so I expect to
see two clusters for the sexes and in these, an accumulation of the
different locations. 
But metaMDS just gives me 2 points (with ordiplot), where the 24 males and
the 24 females are completely stacked. That's just some kind of worthless
for me.
So is there any chance to get some nice clusters? I tried to limit the
number of iterationswith maxit, but had to go down to 10 to reach a suitable
result. And I don't think, I may limit the number of iterations that much.
What could possibly be the problem?

It would be great if somebody could help me.



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