Routines that create identity-by-descent (ibd) coefficients often output their results as a list of values (i, j, x[i,j]), with unlisted values of the x matrix assumed to be zero. This routine recasts such a list into bdsmatrix form.
Sparse block diagonal matrices are used in the the large parameter matrices that can arise in random-effects coxph and survReg models. This routine creates such a matrix. Methods for these matrices allow them to be manipulated much like an ordinary matrix, but the total memory use can be much smaller.
This function solves the equation Ax=b for x, given b and the generalized Cholesky decompostion of A. If only the first argument is given, then a G-inverse of A is returned.
Generalized cholesky decomposition of a bdsmatrix object, A= LDL' where A is symmetric, L is lower triangular with 1 on the diagonal, and D is diagonal.
This function is used by coxme. When a random effect is expressed as a sum of variance terms (matrices), it is important that all of them have the same row/column order and the same block structure. This does so, while retaining as much sparsity in the result as possible.
providing 
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