Binomial GLMM or GAMM with random intercept and temporal correlation

Jay Ver Hoef developed a package:

glmmLDTS

that I think deals explicitly with all your issues (binomial, random
effects, temporal autocorrelation...but not GAMM).

see his page and two papers (Note, it only seems to run on < R.3.0):

https://sites.google.com/site/jayverhoef/

*Ver Hoef, J.M.*, London, J.M., and Boveng, P.L.  2010.  Fast computing of
some generalized linear mixed pseudo-models with temporal
autocorrelation. *Computational
Statistics **25*(1)*: *39 - 55*. * DOI: 10.1007/s00180-009-0160-1

London, J.M., *Ver Hoef, J.M.*, Jeffries, S.J., Lance, M.M., and Boveng,
P.L. 2012. Haul-out behavior of harbor seals (Phoca vitulina) in Hood
Canal, Washington.  *PLoS ONE **7*(6):e38180.
doi:10.1371/journal.pone.0038180


Ben Becker, Ph.D.
Science Coordinator and Marine Ecologist
Pacific Coast Science and Learning Center
Point Reyes National Seashore
www.sfnps.org/pcslc

Thanks for the responses.  I am going to try modelling the binomial data
with
a covariate representing the previous value and see if that's sufficient.

I haven't used INLA, I have some experience with JAGs but not sure where to
start with modelling temporal structures there.  I need to model both
regularly space and regularly spaces correlation.

For the gaussian data I have, I am using lme.  Is it ok to select temporal
correlation strucutres based on AIC between REML models.  I am trying a
number of correlation structures (e.g. corSpher, corExp, corAR1).

Thanks

Sam



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