[R-sig-eco] Simpson dissimilarity in metaMDS (vegan)

[Olmo]

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 at 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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