Dear R-gurus

I have a data.frame with abundance data for species and sites which looks like:
mydf<-data.frame(
 sp1=sample(0:10,5,replace=T),
 sp2=sample(0:20,5,replace=T),
 sp3=sample(0:4,5,replace=T),
 sp4=sample(0:2,5,replace=T))
rownames(mydf)<-paste("sites",1:5,sep="")

I would like make an ordination analysis of these data and my worries is about the "zeros" (absence of species) into the matrix. Up to I read (Gotelli - A primir of ecological statistics, 2004), when I have abundance data I can´t compute Euclidian Distances because the zeros have the meaning of absence of the species and not as zero counting. Gotelli suggests one make "principal coordinates analysis". I would like to here from you what you think about and what is the best packages and functions to I compute my distance matrices and do my ordination analysis. Can I considere zero as NA on my data.frame? Is there a good PDF book available about Multivariate Analysis for abundance data available on the web?

Kind regards

Miltinho
Brazil

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