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Covariance matrices in GLMER

Voeten, C.C. 
Dear Diana,

1. No, both lmer and glmer by default use unstructured covariance matrices, although they can be massaged into using diagonal, see afex::lmer_alt. Those are the only two options.
2a. Support for other covariance matrices is available in MASS::glmmPQL (which I would not recommend; it inherits all the limitations of nlme::lme and uses PQL) and in glmmTMB::glmmTMB. Depending on what exactly you need to do, glmmTMB is probably what you're looking for.
2b. For glmer and glmmTMB, the ranef function will probably give you what you need.

Best,
Cesko

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Kornbrot, Diana Covariance matrices in GLMER Oct 30 Voeten, C.C. Covariance matrices in GLMER Oct 30