Hi Yong,

first, I would change rows by lines, more specific, put species as rows and sites as lines. 

Then, use "vegdist" function, it will give to you a similarity matrix between sites. For this, you will have to load "vegan package" (probably is already instaled in your R). You can also configure wich similarity (or dissimilarity) index you want changing some parameters. (type "help(vegdist)" in your R)

For instance, last time I used a absence/presence with Bray Curtis (to build a similarity cluster between sites), I used this following parameters

"YOUR OBJECT NAME"<-vegdist("YOUR MATRIX",method="bray",binary=TRUE)

I think Bray Curtis is the right choice for your data. You can also build clusters using HCLUST function, for this, load CLUSTER package.

Cheers, hope I helped you,

Rafael (Brazil)


Rafael Vieira Nunes
Biólogo, CRBIo 70735/04-D
Universidade Federal do Mato Grosso - UFMT
http://lattes.cnpq.br/5048661854935501
http://www-museum.unl.edu/research/entomology/workers/RNunes.htm





      
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