[R-sig-ME] starting values in glmmadmb and / or covariance specification in glmer

paul debes paul.debes at utu.fi
Tue Aug 18 13:50:46 CEST 2015

Dear list members,

Does anybody know either how to use starting values for the variance  
components using glmmadmb (glmmADMB package) or how I can specify a common  
covariance across different variances for the random statement with glmer  
(NOT with lmer that seems to work differently)?

Sorry for asking two different questions, but an answer to only one would  
already help me.

Presently, I keep running out of memory (8GB) when trying to fit a set of  
binary GLMMs with binomial error distribution using glmmadmb that I cannot  
specify in glmer (which doesn't have any memory problems). Maybe  
specifying starting values in glmmadmb would help?

I can fit all of a set of models with PQL (asreml-r package), but only  
some with Laplace approximation (what I want) using glmer (lme4 package).  
Hence, it is possible to fit the models generally. But I have no clue how  
to specify a certain covariance structure in glmer (common covariance +  
diagonal, equal variance).

I tried the following models with both glmer and glmmadmb; both work fine:

a) ~ 1 + Fixed.Effects + (1|Group) + (1|Fixed.Effect:Group) # simplest  
model; common covariance (fitted by the Group term that is crossed with  
Fixed.Effect) & common variance between / for all levels of Fixed.Effect  
by Group

b) ~ 1 + Fixed.Effects + (0+Fixed.Effect|Group) # maximal model; different  
covariance & different variance between / for all levels of Fixed.Effect  
by Group levels

However, an intermediate model specification results in different  
covariance structures in glmmadmb (where I run out of memory; I tested its  
correct behaviour with a subset of data) vs. glmer:

c) ~ 1 + Fixed.Effects + (1|Group) + (0+Fixed.Effect|Group) # I try to  
fit: a common covariance among levels of Fixed.Effect by Group, different  
Group variances for each level of Fixed.Effect

The asreml-r syntax for the model I try to specify in c) is:

fixed = ~ 1 + Fixed.Effects,
random = ~ Group + idh(Fixed.Effects):Group

or alternatively (I'm not particularly interested in the amount of  
variance for the crossed Group term, just in inferences about fixed  

random = ~ corh(Fixed.Effects):Group

For c), glmmadmb and I understand each other - no covariances are fit  
among Fixed.Effect by Group levels in addition to that implied by the  
Group random term - whereas proper glmer syntax must be different as it  
fits BOTH individual-pair covariances (printed as correlations with  
'summary') AND the random term variance (I'm far away from wanting to fit  

How do I specify model c) appropriately in glmer or how do I specify  
starting values in glmmadmb (to get rid of my memory-limitation problem  
instead of learning new glmer syntax)?

Many thanks in advance,

Paul Debes
DFG Research Fellow
University of Turku
Department of Biology
Itäinen Pitkäkatu 4
20520 Turku

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