Personally I use the decostand function in the vegan package, with
method="pa".

Example:
library(vegan)
data(dune)
dunePresAbs = decostand(x=dune, method="pa")

#End run

What this does is:
x <- ifelse(x > 0, 1, 0)

where x is each square.

Regards,
Adrian Rasmussen

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