[R-sig-eco] R: Simper in Vegan package

[Ludovico Frate]

Hi, simper Analysis is not always appropriate since much of the differences arise from within site variability rather than between site variability!  Have a look to the package mvabund by Warton!
Regards,
Ludovico

Inviata dal mio Windows Phone
________________________________
Da: JC Arronte [via r-sig-ecology]<mailto:ml-node+s471788n7579718h73 at n2.nabble.com>
Inviato: ‎14/‎03/‎2016 22:28
A: Ludovico Frate<mailto:ludovicofrate at hotmail.it>
Oggetto: Simper in Vegan package























Hi all,




I�m still new to R
and trying to learn how to use the library vegan. I�m carrying out a cluster
analysis on marine fish species distribution and I want to determine the
contribution of each species to the similarity of the cluster groups. I have read
that it can be done with the function �simper�. The problem arises when I want
to look, not only, at dissimilarities between groups but also at species
contribution to similarity within a group.


If I�m not wrong, simper function from the vegan package
computes discriminating compounds, rather then compounds that make a pair
unique.


Is there any way of obtaining information on the
contributions of the most important species to the average similarity within
each assemblage as it can get in PRIMER-E package?. And the average similarity
of each assemblage?.
I get the average dissimilarity using lapply(simper_clusterpeces,
FUN=function(x){x$overall}).


This is the first time I work with vegan and simper function,
thus any assistance would help.


Thanks in advance,


Juan Carlos



















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