That sounds like a job for path analysis or for structural equation
modeling, depending on the level of sophistication desired and the
hypotheses to be tested.

There are plenty of good resources for both, in and out of R.

Sarah

On Wednesday, March 6, 2013, Jay Kerns wrote:

> Hello,
>
> I'm posting to this list because I believe it's the best place to
> go.  My question is R related only inasmuch as all the work I've
> done so far has been with R and I expect any answers I get from
> here will lead me to more R work.
>
> I'm consulting with an ecologist and an engineer on a project
> related to a reservoir nearby.  They've collected data on diatoms
> in the reservoir via core samples; they have sections of data over
> the past 100yrs.  They are looking at the community structure
> plus other environmental factors over the same time period.
>
> We've done a ton of work already and there's no point trying to
> hash all of that out here.  Short story: we did an NMDS, it fits
> OK (stress 0.17), there are obvious clusters in the ordination
> which correspond to a-priori clusters from ecological
> considerations (and which match an independent cluster analysis),
> we're really quite pleased overall.  We checked for relationships
> with =envfit=, most environmental variables are *highly*
> significant, yet there are a couple which aren't significant at
> all.  Here comes my question:
>
> The ecologist pointed out to me that our environmental variables
> don't have equal status (ecologically speaking); some variables
> lead to others.  For instance, there are so-called ultimate
> factors (population, percentage farmland) which contribute to
> intermediate factors (suspended solids, total phosphorous) which
> in turn contribute to direct factors (AREA, pH,...) which then in
> turn contribute to diatom structure.
>
> We have measured data on all the above and several more.  The
> model we are fitting with =envfit= is symmetric in those n
> environmental variables, but the ecology of the situation isn't
> symmetric, it's a directed top-down kind of relationship.  He
> asked me, "How can we quantify that?  How can we demonstrate
> that?  Can we quantify/demonstrate that?"  I don't know.
>
> There are ecologists on this list: what am I looking for, here?
> What methods do ecologists use to answer this (or related)
> question(s)?  Feel free to direct me to papers, literature,
> textbooks, whatever.  I'm trying to help answer this question
> and (this not being my subject specialty) I'm at a bit of a loss.
>
> If there are relevant R packages/vignettes/manuals you can point
> me to, that'd be cool too.
>
> Thanks for reading all the way down to here.
>
> Jay
>
> P.S. If it hadn't been for the archives of this list containing
> lengthy and poignant answers to *several* questions I've had
> already then I couldn't even have made it this far.  Thank you!
>
>
>
>

-- 
Sarah Goslee
http://www.stringpage.com
http://www.sarahgoslee.com
http://www.functionaldiversity.org

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