[R-sig-ME] fitting method in glmer and var for the cond. modes

[vito muggeo]

dear all,
I 've just installed the last version of lme4.
Thanks to prof Bates for his excellent work.

I have an issue and a question.

1)issue:
I tried to fit binomial GLMM, everything works but it appears that the 
method="PQL" is not implemented..Namely the following two calls yield
exactly the same results
glmer(formula,family=binomial,data=d,method="Laplace")
glmer(formula,family=binomial,data=d,method="PQL")

The summary method on the relevant fits prints in each case (correctly?) 
``Generalized linear mixed model fit by the Laplace approximation''

The estimates are very similar to those coming from MASS::glmmPQL(). For 
instance the est. st.dev for the interc is 0.1613318 (via glmmPQL()) vs. 
0.16119 (via glmer()+laplace). Since the response is binary, I expected 
the estimates to be somewhat different..


2)question:
I am interested in obtaining the variances of the predictions (i.e. the 
variances of conditional modes \tilde{b}_i) from a simple LMM (fitted 
via lme or lmer)

As far as I remember correctly, there was the `bVar' slot in the early 
versions of lmer..Am I right?

Also, how I can extract the same quantities from a "lme" fits?



many thanks,
vito


-- 
====================================
Vito M.R. Muggeo
Dip.to Sc Statist e Matem `Vianelli'
Università di Palermo
viale delle Scienze, edificio 13
90128 Palermo - ITALY
tel: 091 6626240
fax: 091 485726/485612