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

[Jari Oksanen]

I also suggest (like I have suggested before) that you run metaMDS with argument plot = TRUE. The convergence criteria in metaMDS are pretty stringent, but with plot argument you can see how different the solutions are. Two most typical non-convergence cases are that 

(1) most points are stable, but there are a some outliers that don't find their place in this universe, and

(2) your data need more dimensions and you should increase 'k'.

Then you should also check the stressplot( ). If the fit line shoots right up at the maximum observed dissimilarity, you may need to turn on 'noshare' argument in metaMDS to trigger step across dissimilarities. We claim that this rarely necessary with the monoMDS engine we use currently, but sometimes it is needed.

Without hands on your data it is difficult to guess more.

Cheers, Jari Oksanen


Sent from my iPad

On 22.4.2013, at 22.31, "Gavin Simpson" <gavin.simpson at ucl.ac.uk> wrote:

> 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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