outer() generally works by expanding out the lists like
Y <- rep(y,length(x)) X <- rep(x,each=length(y)) # or maybe it's vice versa, never mind... FUN(X,Y,extras)
and then adds dims and dimnames. If FUN vectorizes, this is the efficient way, but it does not in your case and the rep()s are probably not cheap when lists are involved.
you might try this sort of stuff:
myfunc2 <- function(i,j)
mapply(function(i,j)
phylo.overlap(assemblages[[i]],assemblages[[j]],parrot.cm),
i,j)
ind <- seq(along=assemblages)
outer(ind,ind,myfunc2)
That now runs at about the same speed as the loops (although the loops still just have the edge).
Many thanks for the suggestions.
David
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