[R-sig-ME] lmer, poisson family and mcmcsamp

Christopher David Desjardins desja004 at umn.edu
Mon Feb 16 17:06:06 CET 2009

Regarding mcmcsamp() see https://mailman.stat.ethz.ch/pipermail/r-sig-mixed-models/2008q4/001660.html 

...  In particular mcmcsamp is not currently working in that branch.   
My goal is to get mcmcsamp stable and to get all the other parts  
working in this branch then release it for testing and finally release  
lme4-1.0.  The subtext in that message is that only the models I  
describe above will be fit by the lme4-1.0 package.

On Feb 16, 2009, at 9:59 AM, Amelie LESCROEL wrote:

> Dear all,
> Could someone explain to me why summary(lmer.object) is giving z  
> values and Pr(>|z|) when the lmer.object was fitted with  
> family=poisson? I used to fit linear mixed models with  
> family=gaussian and link="identity" or link="log", then used  
> mcmcsamp() and HPDinterval() for computing "confidence" intervals  
> and considered that a fixed effect was significant when the 95% HPD  
> interval did not include zero. Now, with family=poisson, when I use  
> mcmcsamp(), I get the following:
> > set.seed(101); mcmcfm1 <- mcmcsamp(fm1, n=10000)
> Error in .local(object, n, verbose, ...) : Update not yet written
> but I get z values and Pr(>|z|). Why is it so? Can we "trust" this  
> probability for judging of the fixed effects significance? Would the  
> mcmcsamp method be available soon for families other than gaussian?
> Thanks in advance,
> Amélie
> PS: When will lme4_1.0 be released? Many thanks to Douglas Bates for  
> developing lme4 in interaction with users, and for sharing it.  
> Please don't give up on making it available in R. lme4 is a  
> wonderful tool which is helping me understanding penguin's foraging  
> behaviour (and advanced stats!) as it is helping others in plant  
> ecology or human psychology.
> > sessionInfo()
> R version 2.7.2 (2008-08-25)
> i386-pc-mingw32
> locale:
> LC_COLLATE=French_France.1252;LC_CTYPE=French_France. 
> 1252;LC_MONETARY=French_France. 
> 1252;LC_NUMERIC=C;LC_TIME=French_France.1252
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] lme4_0.999375-28   Matrix_0.999375-17 lattice_0.17-17     
> gdata_2.4.2
> loaded via a namespace (and not attached):
> [1] grid_2.7.2   gtools_2.5.0 tools_2.7.2
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Christopher David Desjardins
Ph.D. Student
Quantitative Methods in Education
Department of Educational Psychology
University of  Minnesota

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