An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-sig-ecology/attachments/20120202/994f8de7/attachment.pl>
metaMDS result
5 messages · Jari Oksanen, Federico Tomasetto, Gian Maria Niccolò Benucci
On 02/02/2012, at 19:43 PM, Gian Maria Niccol? 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 ?species.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
An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-sig-ecology/attachments/20120202/6e224486/attachment.pl>
An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-sig-ecology/attachments/20120203/c8982f88/attachment.pl>
An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-sig-ecology/attachments/20120203/b0929a11/attachment.pl>