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correlated samples

Dear all, I?m a basic user of mixed models but there are things that I?ve
found hard to understand. On of these is how the model solves the
correlations among samples taken in the same site or levels of other kind
of grouping variable.

I?ve consulted Bolker (2015) in G. Fox et al Ed., Zuur et al 2009 and part
of Pinheiro and Bates (2000). But still don?t understand the way that GLMM
include the correlation effect in the predictions of the model.

I really appreciate any comment and/or bibliographic reference that help me
understand this.

Thanks in advanced,
Joaqu?n.