On Mon, 2012-02-20 at 16:28 +0100, Gian Maria Niccolò Benucci wrote: > Hi r-sig-ecology Members, > > I would please you to examine the differences I found in metaMDS() and > nmds() outputs and possibly draw some conclusions. As I wrote in past > emails I have 24 samples of ectomycorrhizal fungi grouped into two > different communities (12 natural and 12 cultivated). > > here is the code: > > > metaMDS(data_matrix2, distance="bray", k=2, autotransform=F) -> metaMDS > > metaMDS > > Call: > metaMDS(comm = data_matrix2, distance = "bray", k = 2, autotransform = F) > > global Multidimensional Scaling using monoMDS > > Data: data_matrix2 > Distance: bray > > Dimensions: 2 > *Stress: 0.04536661 * > Stress type 1, weak ties > No convergent solutions - best solution after 20 tries
Perhaps you could try running metaMDS with random starts until it does find convergent solutions?! Why expect metaMDS() to do better in 20 tries than nmds() with 100 random tries? add `trymax = 100` and `halfchange = FALSE` to try to make the two functions more comparable. HTH G > Scaling: centring, PC rotation, halfchange scaling > Species: expanded scores based on data_matrix2 > > > nmds <- nmds(dist_bray, mindim = 2, maxdim = 2, nits = 100) > Using random start configuration > Using random start configuration > ... > > nmds_min > X1 X2 > 1 -0.66226262 0.16392824 > 2 -0.68844987 -0.20891993 > 3 -0.47717515 0.55323693 > 4 -0.67213392 -0.09195847 > 5 0.03305172 0.41844232 > 6 0.31992006 0.53887910 > 7 -0.61944875 0.34411146 > 8 0.07013849 0.65723057 > 9 0.53053436 0.37444633 > 10 0.26704705 0.39849341 > 11 -0.20981416 0.70391983 > 12 -0.61620355 -0.43568743 > 13 0.14219660 -0.69571194 > 14 0.42365981 -0.43308767 > 15 0.15840330 -0.12872863 > 16 -0.00492407 -0.06889680 > 17 -0.20513513 -0.58052156 > 18 0.46546214 0.12019775 > 19 0.36753709 -0.25048256 > 20 -0.09446486 -0.61943616 > 21 0.15010553 -0.31995009 > 22 0.41540872 -0.29507200 > 23 0.42573367 -0.12321584 > 24 0.48081354 -0.02121688 > > min(nmds$stress) > [*1] 0.2787161* > > nmds$r2[which.min(nmds$stress)] > [1] 0.6338372 > > Is it possible I got so different stress values?? > > Thanks for replying, > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
