[R] lmer and glmmPQL

Cox, Stephen stephen.cox at ttu.edu
Tue Dec 6 00:03:16 CET 2005

I have been looking into both of these approaches to conducting a GLMM,
and want to make sure I understand model specification in each.  In
particular - after looking at Bates' Rnews article and searching through
the help archives, I am unclear on the specification of nested factors
in lmer.  Do the following statements specify the same mode within each

m1 = glmmPQL(RICH ~ ZONE, family = poisson, data, random = ~ YEAR | SITE
m2 = lmer(RICH ~ ZONE +(YEAR|SITE)+ (YEAR|QUADRAT), family = poisson,

As a follow up - what would be the most appropriate model formula (using
glmmPQL syntax) to specify both a nested facor and repeated
observations?  Specifically, I am dealing with experimental data with
three factors.  ZONE is a fixed effect.  Three sites (SITE) are nested
within each ZONE.  Multiple quadrats within each SITE are measured
across multiple years.  I want to represent the nesting of SITE within
ZONE and allow for repeated observations within each QUADRAT over time
(the YEAR | QUADRAT random effect).  -- I am assuming that glmmPQL is
the best option at this point because of recent discussion on Rhelp
about issues associated with the Matrix package used in lmer (i.e., the
anova results do not seem to match parameter tests).

Any information would be very much appreciated!



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