Hello Jari,

Thank you for the response.
Betasim.sim is in dist class and a matrix of Simpson Dissimilarity Index.
You are right. There is NaN in the upper triangle of the matrix.
Please kindly advise
1. If Nan can be ignored for performing metaMDS or any other items need to
be paid attention for Nan
2. for metaMDS (x, k=2, distfun  =  betadiver,  distance  =
 "sim",trymax=100),
   can x be a matrix of dissimilarity index instead of that of community
data?
   In the vegan manual, it says x can be a matrix of either community data
or dissimilarity index.
   However, in the example, x is always community data.
   If  x can be a matrix of dissimilarity index, please kindly advise how
to set disfun and distance.

Thank you very much
If any data are in need, I will send them to you off-list.

Elaine



On Sun, Jul 21, 2013 at 2:27 PM, Jari Oksanen <jari.oksanen@oulu.fi> wrote:

>
> On 21/07/2013, at 03:02 AM, Elaine Kuo wrote:
>
> > Hello
> >
> > I am trying to run MetaMDS but got the following error based on the code.
> > Please kindly indicate the error source and thank you.
> >
> > Elaine
> >
> > Code
> > # 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)
> >
> > # NMDS
> >  library(vegan)
> >  nms <- metaMDS(betasim.sim,trymax=100,zerodist="add",autotransform
> > =FALSE,k=2)
> >
> > Error
> > Error in if (any(autotransform, noshare > 0, wascores) && any(comm < 0))
> {
> > :
> >  missing value where TRUE/FALSE needed
>
> Elaine,
>
> I cannot reproduce this, and there is no information in the message to
> know what happens.
>
> Do you have missing values in betasim.sim? Are betasim.sim really
> dissimilarities?
>
> BTW, vegan has Simpson dissimilarity: use betadiver(x, "sim").
>
> Cheers, Jari Oksanen

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