Dear Federico,

Instead of TWINSPAN, which is an odd method, I would suggest you use the
multipatt() function in package indicspecies to get indicator species for
each combination of site clusters (with permutation tests). However, you'll
have to add "manually" species to the dendrogram of the sites.
Another solution is to apply a classification tree with mvpart (or rpart)
using species as "explanatory" variables and the result of a partition of
sites as response. Here, you'll get a tree constrained by discriminating
species.

Hoping it will help.

Best regards,

François


-------------------------------------------------------------------------------
Prof. François Gillet
Community ecology and dynamic modelling
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Université de Franche-Comté - CNRS
UMR 6249 Chrono-environnement
UFR Sciences et Techniques
16, Route de Gray
F-25030 Besançon cedex
France
http://chrono-environnement.univ-fcomte.fr/
http://chrono-environnement.univ-fcomte.fr/spip.php?article530
Phone: +33 (0)3 81 66 62 81
Location: La Bouloie, Bât. Propédeutique, *-114L*
-------------------------------------------------------------------------------
Ecole Polytechnique Fédérale de Lausanne
EPFL - ENAC - IIE – ECOS
Ecological Systems Laboratory
Station 2 - Ecublens
CH-1015 Lausanne
Switzerland
-------------------------------------------------------------------------------

*Now available!*


"Numerical Ecology with R", by D. Borcard, F. Gillet and P. Legendre
http://www.springer.com/978-1-4419-7975-9
-------------------------------------------------------------------------------




2011/11/10 federicotomasetto <federicotomasetto@hotmail.it>

> Dear list,
>
> I am facing a problem when I overlay classification in ordination. I use
> ordihull function (vegan package) and it gives me a rough idea of clusters
> in the plant community that I am looking at.
>
> Is there any functions in vegan package or in different packages that does
> what TWINSPAN does when you look at the dendrogram of the cluster analysis
> of the samples
> (
> http://www.pisces-conservation.com/caphelp/index.html?non_metricmultidimens
> ionalsc.html)?
>
> Many thanks
>
> Federico Tomasetto
> PhD Student
>
>
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> R-sig-ecology@r-project.org
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>

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