lmer-class {lme4}R Documentation

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
status:
Logical vector of length 2 indicating if the object has been factored and if the factorization has been inverted.
call:
A copy of the matched call to the function that created the object.

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.

[Package lme4 version 0.95-5 Index]