Manuel & readers,
I didn't comment on the use of stepacross with Euclidean distances
earlier, but I do it now: I don't think it makes sense. This is a user
choice, and technically it now works in the R-Forge version of vegan,
but I do think that no user should do this (but what am I to stop
them?). The problem is that the distances among points with nothing in
common are not necessarily longest Euclidean distances. You may have
very short Euclidean distances between two sites with no shared
species if the total abundances in these two sites are low. So the
stepacross finds the distances across low abundance sites instead of
really intermediate sites. I do think that you should use stepacross
only with the usual closed indices with upper limit = 1. If you want
to use them with open indices (no upper limit, variable values for
pairs with nothing in common), you should be prepared to research the
adequacy of your choice.
Setting noshare=0 will turn off automatic stepacross in metaMDS. I
recommend this be used with Euclidean, Manhattan and other open
distances, although this is not enforced: the choice is yours.
Cheers, Jari Oksanen