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Multinomial logist regression

Hi Steve,
I am not sure if I am on the right track here but you might check out
Frank Harrell rms package. It sounds as if the Proportional Odds model
may work for you. There is a paper by Guisan and Harrell that may be
of interest. Also Franks Regression Modeling Strategies book has some
nice examples for plotting such models. I am not sure how often these
methods are used in ecology though.

Guisan, A., and F. E. Harrell. 2000. Ordinal response regression
models in ecology. JOURNAL OF VEGETATION SCIENCE 11:617-626.

Hope this helps,
Michael