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 <gjkerns...@gmail.com> wrote: > > > Dear Sarah, > > > > On Thu, Mar 7, 2013 at 9:32 AM, Sarah Goslee <sarah.gos...@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, > > >> > > > > _______________________________________________ > > R-sig-ecology mailing list > > R-sig-ecology@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > > > > > _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
