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 ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.