[R-sig-eco] Liner vs. Poisson vs. Mixed effect models

[Canning-Clode, Joao]

Hi all,

First of all thanks to all for helping me with my previous post on negative binomial.
As I mentioned I got a paper back for revision requesting alternative analysis, and I am seeking advice from the forum. I really appreciate any help you could provide.

My major question was to explore the local-regional richness relationship in fouling assemblages at a global scale. I have deployed PVC sampling plates in the water at 8 different regions, and sampled the benthic communities 4 times (after 2, 4, 6 and 8 months).

Therefore, my experimental design included 8 regions, each having one estimate for regional taxonomic richness (RTR), one estimate for regional functional richness(RFR) (both estimated with a jackknife estimator), 8 measures of open space (OS) on panels, 8 measures of local functional richness (LFR)and 8 measures of local taxonomic richness (LTR).

One of my objectives is to examine how these variables affect local taxonomical richness (LTR) and a suggestion to try a linear mixed effects models where RTR, RFR and OS are fixed effects; LFR is a random effect nested within region.  I square-root transformed LTR, used the lme function and set my model as

LTR.LME <- lme(LTR~RTR+RFR+OS+LFR, random=~1|LFR/region)

A question I have - is it okay to have the random effect LFR in the left (fixed-effects) equation?  I wish to estimate the coefficients to examine the effects of LFR; maybe I should treat this as a fixed effect instead?

A second question is that I have repeated measures (over four time periods).  Is it possible to set up the above equation in a repeated fashion say using a auto-regressive 1 structure?

Thank you in advance for any help,
Joao

João Canning Clode, PhD
Postdoctoral Fellow
Marine Invasions Research Lab
Smithsonian Environmental Research Center
647 Contees Wharf Road
Edgewater, MD 21037

Email: canning-clodej at si.edu
Web: www.canning-clode.com
Tel: 443-482-2354