R: Simper in Vegan package

Hi,

Thanks for the advice Ludovico.
I?ll look in deep to the package mvabund.
Regards,
Juan Carlos
From: r-sig-ecology-request at r-project.org
Subject: R-sig-ecology Digest, Vol 96, Issue 6
To: r-sig-ecology at r-project.org
Date: Tue, 15 Mar 2016 12:00:04 +0100

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Today's Topics:

   1. Simper in Vegan package (JC Arronte)
   2. R: Simper in Vegan package (Ludovico Frate)

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Message: 1
Date: Mon, 14 Mar 2016 22:26:34 +0100
From: JC Arronte <j_arronte at hotmail.com>
To: "r-sig-ecology at r-project.org" <r-sig-ecology at r-project.org>
Subject: [R-sig-eco] Simper in Vegan package
Message-ID: <DUB131-W2918C0565FEDB8DFAC72138B880 at phx.gbl>
Content-Type: text/plain; charset="UTF-8"

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

	[[alternative HTML version deleted]]

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Message: 2
Date: Mon, 14 Mar 2016 15:47:17 -0700 (MST)
From: Ludovico Frate <ludovicofrate at hotmail.it>
To: r-sig-ecology at r-project.org
Subject: [R-sig-eco] R: Simper in Vegan package
Message-ID: <DUB410-EAS14068DB561E9C3EB338C19AD6880 at phx.gbl>
Content-Type: text/plain; charset="UTF-8"

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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