R-sig-ecology Digest, Vol 71, Issue 3

Gian,
Your question,

"how can I extract the names of the species (and even their
abundances) that are common and the species that are not common between the
different samples in my dataset?"
is a common question in ecological literature about what are called "Indicator Species". These are species with occurrence usually in only one of several habitat types and high abundance in that habitat.
You can use that term as a search term to find out more, but I'd refer you to Jon Bakker's compilation in R of a function to provide what he calls Indicator Values.
See:
Bakker, J.D. 2008. Increasing the utility of Indicator Species Analysis. Journal of Applied
Ecology 45:1829-1835.
and
Dufr?ne, M. & Legendre, P. (1997) Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecological Monographs 67:345-366.
Mike Marsh

Now my

question is, how can I extract the names of the species (and even their
abundances) that are common and the species that are not common between the
different samples in my dataset?