Thank you Olmo.

I found one example in the vegan manual.
 metaMDS (x, k=2, distfun  =  betadiver,  distance  =  "sim",trymax=100)

Elaine



On Sun, Jul 21, 2013 at 6:55 PM, Olmo <ulmusnigra@yahoo.es> wrote:

> Hi Elaine,
>
> There is some information in desingdist which can be of use, cause it
> allows you to define new similarity index, there is a warning about
> the resources used, it is not very efficient:
>
> http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/designdist.html
>
> I hope it helps a bit.
>
> Olmo.
>
> El Sun, 21 Jul 2013 07:46:42 +0800
> Elaine Kuo <elaine.kuo.tw@gmail.com> escribió:
> > Hello
> >
> > I am trying to perform NMDS using metaMDS (vegan).
> > However, in the argument of "distance," there is no option for Simpson
> > Dissimilarity Index.
> >
> > Please kindly whether it is necessary to set up the distance argument
> > if the distance matrix is produced based on the Simpson Dissimilarity
> > Index already.
> > If necessary, please kindly advise how to set up the distance
> > argement.
> >
> > Thank you.
> >
> > The code to produce the matrix is as followed:
> > # Compute the Simpson distance matrices for the dataset (3 hr using
> > 4GB) library(betapart)
> >   dist.sim<-beta.pair(dataR, index.family="sor")
> >   class(dist.sim)
> >
> >   betasim.sim<-dist.sim[["beta.sim"]]
> >   class(betasim.sim)
> >
> > Elaine
> >
> >       [[alternative HTML version deleted]]
> >
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>
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