[R] Problem with metaMDS in vegan
fabian.boetzl at freenet.de
Mon Feb 10 12:26:54 CET 2014
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:
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
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
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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