[R-sig-ME] over-dispersed Poisson with lmer -- a trick, with a catch?
Ben Bolker
bolker at ufl.edu
Thu Jul 16 18:09:24 CEST 2009
David Atkins wrote:
[snip]
> ### create new var with unique value for each obs/row
> > snap.df$over <- 1:nrow(snap.df)
>
> ### include as separate random-effect in model
> > rapi.glmer2.1 <- glmer(rapisum ~ asex*time + (time|ID) + (1|over),
> + data = snap.df, verbose = TRUE,
> + family = poisson)
> Error in mer_finalize(ans) : q = 5252 > n = 3616
>
> So, we already have a random intercept and slope for time [ie,
> (time|ID)]. With 818 participants the random-effects specify 818
> intercepts plus 818 slopes, and now with an observation level
> random-effect [ie, (1|over)] with 3616 observations... we get 5252
> estimates. lmer() doesn't like it.
>
> I know there's been a bit of chatter about this error before, and I
> believe Doug mentioned that it was to avoid people radically
> over-parameterizing/over-fitting their data via random-effects. Though,
> I believe there is some room for debate (ie, the model above does not
> fit 5252 unique parameters).
>
> Anyhow, I would be curious for any input on:
>
> 1. Does this seem like a sensible approach to account for
> over-dispersion? (caveat: I don't have Rabe-Hesketh's book, so just
> going on recounting from colleague)
I think so. It's done in other places (for example, it's exactly
equivalent to what MCMCglmm does), and in Elston et al 2001 (they use a
PQL estimation procedure in Genstat). (Although "everybody does it"
doesn't *mean* it's correct ...)
> 2. If so, I wonder if we might be able to coax Doug to change the error
> to an argument in the model (that defaults to the error msg but could be
> over-ridden)?
Good luck with that ...
If you can conveniently build from source, you can just comment out
line 1068 (search for "> n =") in lmer.c ...
cheers
Ben
Elston, D.A., Moss, R., Boulinier, T., Arrowsmith, C. & Lambin, X.
(2001) Analysis of aggregation, a worked example: numbers of ticks on
red grouse chicks. Parasitology, 122, 563-569.
--
Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bolker at ufl.edu / www.zoology.ufl.edu/bolker
GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
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