Because subject and item are crossed, the (2,1) block of
A is dense, as is the (2,1) block of
L. The (2,2) block of
A is diagonal because, like the (1,1) block, it is generated from a scalar random effects term. However, the (2,2) block of
L ends up being dense as a result of "fill-in" in the sparse Cholesky factorization. All the blocks associated with the fixed-effects or the response are stored as dense matrices but their dimensions are (relatively) small.