R questions

Dear friends, 

in this web page http://cran.r-project.org/src/contrib/Views/Psychometrics.html, I read: A multilevel Rasch model can be estimated using the package lme4 with functions for mixed-effects models with crossed or partially crossed random effects. How can this be done? Is there an example to read?

Also, why are the random effects (BLUPS  usinf the ranef fucnction) and the fixed effects estimates the same most pf the time?

Thanks

jason

Dr. Iasonas Lamprianou
Department of Education
The University of Manchester
Oxford Road, Manchester M13 9PL, UK
Tel. 0044 161 275 3485
iasonas.lamprianou at manchester.ac.uk

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Today's Topics:

   1. simulate() fails for poisson lmer fits (William Valdar)
   2. Re: simulate() fails for poisson lmer fits (William Valdar)

----------------------------------------------------------------------

Message: 1
Date: Wed, 1 Aug 2007 18:49:58 +0100 (BST)
From: William Valdar <valdar at well.ox.ac.uk>
Subject: [R-sig-ME] simulate() fails for poisson lmer fits
To: R-SIG-Mixed-Models <r-sig-mixed-models at r-project.org>
Message-ID: <Pine.LNX.4.64.0708011822100.8824 at zeon.well.ox.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

Hello,

I wish to simulate() from a fitted Poisson GLMM. Both lmer() and lmer2() 
from lme4 (version info at the bottom) fail, apparently due to bugs. 
Here's a test case:

counts <- data.frame(
         count  = c(8, 3, 0, 3, 0, 9, 0, 11, 4, 7, 0, 0, 0, 4, 3, 6, 3,
                 15, 11, 9),
         batch = c(3.1, 3.1, 3.1, 3.3, 3.3, 3.3, 3.2, 3.12, 3.8, 3.11,
                 3.4, 3.4, 3.4, 3.4, 3.5, 3.5, 3.5, 3.5, 3.6, 3.6),
         weight = c(324.4, 372.5, 352.7, 379.6, 388.1, 431, 448.4, 377.3,
                 376.5, 358.4, 356, 351.4, 350.8, 332.1, 334.5, 392, 370.5,
                 409.7, 375, 318.5))

fit <- lmer(count ~ weight + (1|batch),  family=poisson, data=counts)
# Error: inherits(object, "lmer") is not TRUE

fit <- lmer2(count ~ weight + (1|batch),  family=poisson, data=counts)
simulate(fit)
# CHOLMOD error: X and/or Y have wrong dimensions
# Error in crossprod(object at ZXyt, c(unlist(lapply(seq_along(re), 
# function(k) (t(cholL[[k]]) %*%  :
#        Cholmod error 'X and/or Y have wrong dimensions' at 
# file:../MatrixOps/cholmod_sdmult.c, line 90

Is there a quick fix for either of these two? Otherwise, is there an 
alternative (I've checked objects produced by nlme, glmmPQL, GLMMGibbs 
with no luck)? I am using lme4 0.99875-6 version R 2.5.1 on Windows XP.

Many thanks,

Will

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Dr William Valdar               ++44 (0)1865 287 589
Wellcome Trust Centre           valdar at well.ox.ac.uk
for Human Genetics, Oxford      www.well.ox.ac.uk/~valdar

------------------------------

Message: 2
Date: Thu, 2 Aug 2007 00:23:07 +0100 (BST)
From: William Valdar <valdar at well.ox.ac.uk>
Subject: Re: [R-sig-ME] simulate() fails for poisson lmer fits
To: R-SIG-Mixed-Models <r-sig-mixed-models at r-project.org>
Message-ID: <Pine.LNX.4.64.0708020021210.7087 at zeon.well.ox.ac.uk>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

I missed out a line in the code below. The line that throws the error is 
not the fitting but the subsequent simulation, ie:

fit <- lmer(count ~ weight + (1|batch),  family=poisson, data=counts)
simulate(fit)
# Error: inherits(object, "lmer") is not TRUE