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

[JC Arronte]

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:
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>    1. Simper in Vegan package (JC Arronte)
>    2. R: Simper in Vegan package (Ludovico Frate)
> 
> 
> ----------------------------------------------------------------------
> 
> 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"
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> Hi all,
> 
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> 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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> ------------------------------
> 
> 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
> 
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> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 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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