lmer model representation

Description

A representation of a linear mixed-effects model using a blocked, sparse, symmetric, column-oriented matrix and dense matrices.

Objects from the Class

Objects can be created by calls of the form new("lmer", ...) or, more commonly, via the lmer function.

Slots

flist:

The list of (possibly permuted) grouping factors for the random effects.

perm:

A list of permutation vectors applied to the grouping factors.

Parent:

The extended parent array for the diagonal elements of L.

bVar:

A list of the diagonal inner blocks (upper triangles only) of the positive-definite matrices on the diagonal of the inverse of Z'Z+W.

L:

The blocked sparse representation of the unit lower triangular matrix in the LDL' factorization of Z'Z+W.

ZZpO:

Object of class "list" ~~

Omega:

A list of numeric matrices providing the components of symmetric, positive-definite matrix Omega. Only the upper triangle of each component is used and stored.

D:

A list of the diagonal factors (upper triangle) in the LDL' decomposition of Z'Z+W.

REML:

A "logical" indicator of whether the REML criterion is being used to determine parameter estimates.

RXX:

A matrix which is the (augmented) RXX component or the corresponding component from the inverse of Z'Z+W

RZX:

A matrix which is the (augmented) RZX component or the corresponding component from the inverse of Z'Z+W

ZtZ:

The blocks in the blocked sparse symmetric representation of the original Z'Z matrix

XtX:

The original X'X matrix

ZtX:

The original Z'X matrix

cnames:

Column names of the model matrices.

devComp:

Numeric vector of length 4 giving the components used to calculate the deviance. This slot's contents are current if status$factored is TRUE.

deviance:

Numeric vector of length 2 containing the deviance corresponding to the maximum likelihood (ML) and REML criteria. This slot's contents are current if status$factored is TRUE.

nc:

Integer vector of the number of columns in (augmented) model matrices and the number of observations in the model frame.

Gp:

Integer vector of 0-based row numbers of the ZtX and RZX matrices where new groups begin.

groups of rows in

Methods

coef

signature(object = "lmer"): Extract the parameters that determine the Omega matrices. The optional logical argument unconstr determines the constrained or unconstrained parameterization.

coef<-

signature(object = "lmer", value = "numeric"): Assign the parameters that determine the Omega matrices. The optional logical argument unconstr determines the constrained or unconstrained parameterization.

coerce

signature(from = "lmer", to = "dtTMatrix"): Ensure that the lmer object has been factored but not inverted and extract the unit lower triangular matrix L from the LDL decomposition of crossprod(Z)+Omega.

coerce

signature(from = "lmer", to = "dsTMatrix"): Ensure that the lmer object has been factored but not inverted and extract the symmetric matrix crossprod(Z)+Omega.

solve

signature(a = "lmer", b = "missing"): Invert the decomposed matrices.