NMDS axes scores

Conny--

Note that Jari's surface fitting is using ordination scores on the
right-hand predictor size of the formula, with some z as the response.

If you need something about species composition as your _response_ variable
in a linear model (e.g., with time, disturbance type, and treatment as
predictors, and perhaps site as a random effect), why not use each stand's
dissimilarity/distance from your reference forest sites?  The trend line
would be compositional distance or dissim v. time, with
color/symbols/whatever for different treatments.  That would have the
advantage of being easily & directly interpretable.  [The use-case where
that would fail is >>100% turnover so lots of 0 similarities to the
reference forests, so step-across or nmds might help put those large
distances in order.]  You might be able to set up the equivalent to your
GLM in adonis to get permutation significance tests.

I hope that this helps, or at least gives you a different way to think
about your problem, or else is so stupid that Jari gets annoyed and blasts
it with a valid solution.

Tom 2

 ------
Tom Philippi
Quantitative Ecologist & Data Therapist
National Park Service

Thanks a lot for all the helpful responses and info.

But I?m actually still not sure how to use both NMDS axes as a response
(y) in a regression model - is this even possible??

My overall goal is to model species compositional change over time in a
restoration project (is the system getting more similar to the reference
forest). I would like to create a trend line here in a graph, rather than
just using an ordination plot.

I thought about using the fitted values returned by ordisurf(), but as I
understood it (please correct me if I?m wrong) it will use my restoration
time again as a response and my axes scores as predictors.

 So the z values will represent fitted age values rather than my sample
scores (?) ? so it would make no sense to plot it against my restoration
time?

I?m sorry if this is getting a bit confusing.

Cheers,
Conny

_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology