[R-sig-eco] quantifying directed dependence of environmental factors

[Gavin Simpson]

On Thu, 2013-03-07 at 10:59 -0800, Philippi, Tom wrote:
> Jay--
> 
> I'm not sure how one would combine SEM / graphical models with
> compositional dissimilarity as a response.  You might be able to fit a
> series of models in adonis() or capscale(), comparing just direct factors
> to direct + intermediate, etc..  I don't have any good ideas on how you
> might test more complex causal structures.
> 
> Given that you are dealing with diatoms across space (with environmental
> measurements) and down time (in cores, often without environmental
> measures), there may be an alternate approach possible based on calibration
> approaches to inferred environments (e.g., WACAL) or modern analogs.  I
> would look at packages bio.infer, paltran, fossil, and analogue, and search
> to see if anyone has pushed them in the direction you want to go.

I would probably caution against this, not least as calibration in the
sense employed by those R packages is not designed to look for directed
dependence and makes some pretty stringent assumptions about the
environment and species compositions through time to allow inference to
be made.

For example, Steve Juggins' has recently published a paper on
calibration which shows the problem of secondary gradients inducing
responses that show up as trends in the primary gradient (variable) one
is trying to reconstruct, even when in a simulation exercise the
variable to be reconstructed was held constant in the simulated core
samples!

See: http://dx.doi.org/10.1016/j.quascirev.2012.12.014

Gavin

> Tom
> 
> 
> 
> On Thu, Mar 7, 2013 at 6:50 AM, Jay Kerns <gjkernsysu at gmail.com> wrote:
> 
> > Dear Sarah,
> >
> > On Thu, Mar 7, 2013 at 9:32 AM, Sarah Goslee <sarah.goslee at gmail.com>
> > wrote:
> > > 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.
> > >
> >
> > *Yes!*  I said almost the exact same thing (I didn't say anything
> > about Path Analysis because I don't know much about it), but I had it
> > in my mind that SEM was targeted more to sociological things and
> > didn't know if/that it was common in ecological contexts.  Anyway,
> > it's nice to hear that word coming from somebody else.
> >
> > > There are plenty of good resources for both, in and out of R.
> >
> > Indeed.  I have some work to do.  Thank you.
> >
> > --
> > Jay
> >
> >
> >
> > > Sarah
> > >
> > >
> > > On Wednesday, March 6, 2013, Jay Kerns wrote:
> > >>
> > >> Hello,
> > >>
> >
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> >
> 
> 
>