simulate() fails for poisson lmer fits
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
On Wed, 1 Aug 2007, William Valdar wrote:
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
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 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