Greetings everyone,

I am running MDS on a very large dataset (12 x 25071 - 12 model runs with 25071 output values each), and also on a very much reduced version of the dataset (randomly select 1000 of the 25071 output values). I would like to look at similarities/dissimilarities between the 12 model runs. When I use metaMDS on the full dataset, I get a warning message:

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

I don't think I have insufficient data, with 12 x 25071 data points, and when I reduce the dataset to only 1000 values per model run (so only 12 x 1000) I don't get this warning (though the final stress is now only just below 0.2 - my desired value).

Is this warning because I have insufficient data? Or is it because of the nature of a large dataset?

I can supply a dataset in .txt format by email, if that would be helpful.

Thanks for your help,

Raeanne

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