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 [email protected], Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa _______________________________________________ R-sig-ecology mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
