[R] question about capscale (vegan)

[Sarah Goslee]

Nice catch, Gavin - I missed that part of the original post. The
nucleic distances need to be included as the left-hand-side of
the formula, not as the "distance" argument.

"comm" is still optional, though, but it's not a good idea to omit
it if there's any way you can provide the original data. From the
help:
          "If this
          is not supplied, the ``species scores'' are the axes of
          initial metric scaling ('cmdscale') and may be confusing."

I don't know if it's true in this case, but there are applications
where there is no data matrix - the distances themselves are the
original data. I don't know offhand of any other constrained ordination
functions in R that will easily accomodate a precalculated distance
matrix, but I expect there are some somewhere.

My usual approach is to use metric or nonmetric multidimensional
scaling plus vector fitting, but the assumptions behind that are
different than those underlying a constrained ordination.

Sarah

-- 
Sarah Goslee
http://www.functionaldiversity.org