问题
I have a species abundance dataset with quite a few zeros in it and even when I set trymax = 1000
for metaMDS()
the program is unable to find a stable solution for the stress. I have already tried combining data (collapsing multiple years together to reduce the number of zeros) and I can't do any more. I was just wondering if anyone knows - is it scientifically valid to pick what R gives me at the end (the lowest of the 1000 solutions) or should I not be using NMDS because it cannot find a stable spot? There seems to be very little information about this on the internet.
回答1:
One explanation for this is that you are trying to use too few dimensions for the mapping. I presume you are using the default k = 2
? If so, try k = 3
and compare the stress from the best solution you got from the 1000 tries for the k = 2
solution.
I would be a little concerned to take one solution out of 1000 just because it had the best/lowest stress.
You could also try 1000 more random starts and see if it converges if you run more iterations. When you saved the output from metaMDS()
, you can supply that object to another call to metaMDS()
via the previous.best
argument. It will then do trymax
further random starts but compare any lower-stress solutions with the previous best and converge if it finds one similar to it, rather than have to find two similar low-stress solutions in the 1000 starts.
来源:https://stackoverflow.com/questions/14434794/no-stable-solution-using-metamds-in-vegan