[R] Problem with metaMDS in vegan

Fabian B 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: 

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.



View this message in context: http://r.789695.n4.nabble.com/Problem-with-metaMDS-in-vegan-tp4685022.html
Sent from the R help mailing list archive at Nabble.com.

More information about the R-help mailing list