I would say that it *is* important, in general. However, you don't say if you retried running `monoMDS` on the Hellinger transformed data (without the Bray-Curtis metric - you should use Euclidean with Hellinger transformation)? If you didn't try rerunning with out Bray-Curtis and see if it converges. Otherwise, try many more iterations and get vegan to start monoMDS from the best solution from the first set of runs.
See `?metaMDS for details. G On Mon, 2013-04-22 at 08:26 +0000, Aurélie Boissezon wrote: > Hello everybody! > I didn't imagine that my questions will lead to such a debate among > researchers :) . It helps me to get ready for future reviewers' comments. ;) > Just a question still opened about NMDS (Gavin?): > Is it important to reach a convergent solution? since the "best" solution > ordinate species always in similar way? Because as I said even with stricter > criteria the analysis don't reach a convergent solution. > > Best regards, > > Aurélie > > ----------------------------------------------------------------------- > Aurélie Rey-Boissezon > Ph-D Student > University of Geneva > Section of Earth and Environmental Sciences - Institute F.-A. Forel > Aquatic Ecology Group > Uni Rondeau > Site de Battelle - Bâtiment D > 7, route de Drize - 1227 Carouge > Geneva > Switzerland > Tel. 0041 (0) 22379 04 88 > > aurelie.boisse...@unige.ch > http://leba.unige.ch/team/aboissezon.html > ________________________________ > De : fgill...@gmail.com [fgill...@gmail.com] de la part de François Gillet > [francois.gil...@univ-fcomte.fr] > Date d'envoi : samedi 20 avril 2013 10:59 > À : Gavin Simpson > Cc: Aurélie Boissezon; r-sig-ecology@r-project.org > Objet : Re: [R-sig-eco] RE : CCA vs NMDS and ordisurf > > > 2013/4/19 Gavin Simpson > <gavin.simp...@ucl.ac.uk<mailto:gavin.simp...@ucl.ac.uk>> > I really don't see why this has to be an either/or situation. > > I fully agree: direct and indirect gradient analyses are complementary! Sorry > for not having stressed that in my short answers... > > François > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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