[R-sig-eco] Follow-up to Vegan metaMDS: unusual first run stress values with large data set

[Ewan Isherwood]

Hi r-sig-ecology!

This is mostly a message for Jari Oksanen or another Vegan developer that
may be working specifically with metaMDS, but I'm opening up to anyone that
has any interest in this. First of all, you can see my original post here:
http://r-sig-ecology.471788.n2.nabble.com/Vegan-metaMDS-unusual-first-run-stress-values-with-large-data-set-td7577720.html

Basically, I'm having the same issues with the metaMDS engine as above (R
3.2.5, Vegan 2.3-5). This time my dataset is larger at 9239 sites x 85
species.

I've tried adjusting the sfgrmin value up to an absurd 1e-10,000,000
(decreasing this value to -7 resolved the issue last time)

I've tried upping the sratmax to about 0.99 recurring with 77 9's (I don't
think this should have an effect since it's concerned with the iterations
stopping when the stress ratio between two iterations goes above the
inputted value)

I've tried using the Jaccard and Bray methods (I don't think this should
have an effect)

I've trialled 3-6 dimensions randomly (this has in the past affected the
result, but that might be because of other factors)

I have always used the noshare = TRUE option otherwise it ejects some of
the sampling points with rare species to astronomical values on one or more
axes

I've tried iterations of this about 20-30 times but it still won't ever
give me a best solution that isn't the first run. Here is the basic code:

metaMDS(PSU.sp, k= x, distance = "jaccard", sfgrmin = x, sratmax = x,
noshare = TRUE)

I'm happy to privately share the raw dataset with Jari Oksanen if he's
interested in this phenomenon, but I would have to seek permission for
anyone else since I do not own it. In the meantime I will investigate other
methods to analyse this data, which shouldn't be an issue. Since my dataset
is unusually large for this method, this is probably more for curiosity's
sake for the Vegan developers.

Thanks for your help,

Ewan Isherwood

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