using hglm to fit a gamma GLMM with nested randomeffects?
On Wed, 18 May 2011, Benjamin Caldwell wrote:
Apologies for continuing to ask about this but . . in my quest to fit a gamma GLMM model to my data (see partial copy of thread below), I'm exploring using hglm today. The question of the day has to do with the errors I'm currently getting from the hglm package. Can hglm handle a model with nested random effects?
I would say so, but not using the formula interface ie you would have to specify the Z matrix.
test.gamma<-hglm(fixed=post.f.crwn.length~lg.shigo.av+dbh+leaf.area+ bark.thick.bh+ht.any, random=~1|site/transect/plot, family=Gamma(link=log), data=rws30.BL) Error in `contrasts<-`(`*tmp*`, value = "contr.treatment") : contrasts can be applied only to factors with 2 or more levels In addition: Warning messages: 1: In Ops.factor(site, transect) : / not meaningful for factors 2: In Ops.factor(site/transect, plot) : / not meaningful for factors
This is coming from model.matrix.default AIUI, which does not understand
the "/" operator. But anyway,
#
# mother is nested in community
#
library(mlmRev)
data(guImmun)
hglm(fixed= immun=="Y" ~ kid2p + mom25p + ord, random=~ 1|mom + 1|comm,
data=guImmun, family=binomial())
Error in hglm.formula(fixed = immun == "Y" ~ kid2p + mom25p + ord, random
= ~1 | :
Currently only one random term is supported.
If I just fit ~1|mom, it runs an awfully long time
test.gamma<-hglm(fixed=post.f.crwn.length~lg.shigo.av+dbh+leaf.area+
bark.thick.bh+ht.any, random=~1|site, family=Gamma(link=log), data=rws30.BL) Error in hglm.default(X = X, y = Y, Z = z, family = family, rand.family = rand.family, : Length of X and Z differ.
This should work. Is there missing data [not being handled correctly]? Maybe try data=subset(rws30.BL, complete.cases(post.f.crwn ... Just 2c, David Duffy. PS Another alternative, which will definitely work, is to use BUGS.
| David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph: INT+61+7+3362-0217 fax: -0101 / * | Epidemiology Unit, Queensland Institute of Medical Research \_,-._/ | 300 Herston Rd, Brisbane, Queensland 4029, Australia GPG 4D0B994A v