[R-sig-eco] RE : CCA vs NMDS and ordisurf

[Gavin Simpson]

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.Boissezon at unige.ch
> http://leba.unige.ch/team/aboissezon.html
> ________________________________
> De : fgillet3 at gmail.com [fgillet3 at gmail.com] de la part de François Gillet [francois.gillet at univ-fcomte.fr]
> Date d'envoi : samedi 20 avril 2013 10:59
> À : Gavin Simpson
> Cc: Aurélie Boissezon; r-sig-ecology at r-project.org
> Objet : Re: [R-sig-eco] RE : CCA vs NMDS and ordisurf
> 
> 
> 2013/4/19 Gavin Simpson <gavin.simpson at ucl.ac.uk<mailto:gavin.simpson at 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
> 

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