I've got a problem with "mcmcsamp" used with glmer objects
produced
with "lmer" from the lme4 package.
When calling mcmcsamp, I get the error
Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed
This does not occur with all models, but I can't find anything wrong
with the dataset.
If the error is in my data, can someone tell me what I am looking for?
(Can I print the source code of the mcmcsamp method for glmer objects?
I'd like to know what "y" stands for.)
Many thanks for your advice!
==
> sessionInfo()
R version 2.6.1 (2007-11-26)
i686-pc-linux-gnu
locale:
LC_CTYPE
=
en_GB
.UTF
-8
;LC_NUMERIC
=
C
;LC_TIME
=
en_GB
.UTF
-8
;LC_COLLATE
=
en_GB
.UTF
-8
;LC_MONETARY
=
en_GB
.UTF
-8
;LC_MESSAGES
=
en_GB
.UTF
-8
;LC_PAPER
=
en_GB
.UTF
-8
;LC_NAME
=
C
;LC_ADDRESS
=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] languageR_0.4 coda_0.13-1 lme4_0.99875-9
Matrix_0.999375-4
[5] zipfR_0.6-0 lattice_0.17-2
loaded via a namespace (and not attached):
[1] grid_2.6.1 rcompgen_0.1-17
> emnlp.m1 <- lmer(primed ~ (role * derivation)/(log(dist.time) *
log(rule.freq)) + (1 + log(dist.time) | target.utt), family=binomial,
data=data.utts )
> summary(emnlp.m1)
Error: cannot allocate vector of size 120.3 Mb
> emnlp.m1
Generalized linear mixed model fit using Laplace
Formula: primed ~ (role * derivation)/(log(dist.time) *
log(rule.freq)) + (1 + log(dist.time) | target.utt)
Data: data.utts
Family: binomial(logit link)
AIC BIC logLik deviance
1145907 1146131 -572935 1145869
...
Pr(>|z|)
...
rolei:derivationI:log(dist.time) < 2e-16 ***
roler:derivationI:log(dist.time) < 2e-16 ***
rolei:derivationN:log(dist.time) < 2e-16 ***
roler:derivationN:log(dist.time) 0.000187 ***
...
> class(emnlp.m1)
[1] "glmer"
attr(,"package")
[1] "lme4"
> mc <- mcmcsamp(emnlp.m1)
> summary(mc)
Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed
Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed
Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed
Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed
Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed
...
2. Quantiles for each variable:
Mean SD Naive SE
(
rolei:derivationI:log(dist.time) -2.19615 NA NA
roler:derivationI:log(dist.time) -1.36876 NA NA
...
2.5%
25% 50%
rolei:derivationI:log(dist.time) -2.19615 -2.19615
-2.19615
roler:derivationI:log(dist.time) -1.36876 -1.36876
-1.36876
> traceback()
11: asMethod(object)
10: as(object, superClass)
9: validityMethod(as(object, superClass))
8: identical(x, TRUE)
7: anyStrings(validityMethod(as(object, superClass)))
6: validObject(.Object)
5: initialize(value, ...)
4: initialize(value, ...)
3: new(if (is(object, "glmer")) "summary.glmer" else {
if (is(object, "lmer"))
"summary.lmer"
else "summary.mer"
}, object, isG = glz, methTitle = methTitle, logLik = llik, ngrps
= sapply(object at flist,
function(x) length(levels(x))), sigma = .Call(mer_sigma,
object, REML), coefs = coefs, vcov = vcov, REmat = REmat,
AICtab = AICframe)
2: summary(emnlp.m1)
1: summary(emnlp.m1)
--
David Reitter
ICCS/HCRC, Informatics, University of Edinburgh
http://www.david-reitter.com
