[R-sig-eco] metaMDS result

[Jari Oksanen]

On 02/02/2012, at 19:43 PM, Gian Maria Niccolò Benucci wrote:

> Hi Members,
> 
> I tried to use a metaMDS to explore my two fungal communities data.
> That's the result:
> 
> Call:
> metaMDS(comm = species.data_log, distance = "bray", k = 2, trymax =
> 200,      autotransform = F)
> 
> global Multidimensional Scaling using monoMDS
> 
> Data:     species.data_log
> Distance: bray
> 
> Dimensions: 2
> Stress:     0.0369308
> Stress type 1, weak ties
> Two convergent solutions found after 13 tries
> Scaling: centring, PC rotation, halfchange scaling
> Species: expanded scores based on Œspecies.data_log‚
> 
> species matrix was log10() trasformed before NMDS (otherwise I got really
> similar result with sqrt() trasfromed data)
> 
> I wonder if the stress is too low according to dune examples and maybe
> there is something not working in my data or code...
> 
> thanks you for helping,
> 

Not many people are worried for a low stress. NB, the stress is taken directly from the NMDS engine, and the current monoMDS() uses different stress scaling than the older isoMDS() engine: 0.037 of monoMDS corresponds to 3.7 of isoMDS. This is a low stress, but not directly alarming. Perhaps your data are easy and really two-dimensional (e.g., have some few strongly dominant taxa).

Looking at the stressplot() graphs may help in seeing if there is something strange.

Cheers, Jari Oksanen
--
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksanen at oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa