[R-sig-eco] NMDS axes scores

[Philippi, Tom]

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


On Sun, Jan 17, 2016 at 8:04 PM, Conny <constanze_keye at hotmail.com> wrote:

> 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
>
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