lmer-class {lme4}R Documentation

Mixed model representations

Description

The mer class is mixed-effects representation using a blocked, sparse, symmetric, column-oriented matrix and dense matrices. The lmer class extends mer to represent a fitted linear mixed-effects model. The glmer class extends lmer to represent a fitted generalized linear mixed-effects model. The summary.lmer class represents summaries of these objects.

Objects from the Class

Objects can be created by calls of the form new("lmer", ...) or, more commonly, via the lmer function or by applying the summary generic to a glmer or lmer object.

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.
useScale:
logical indicator of the use of the scale factor when calculating variance-covariance objects. Only present in the summary.lmer class.
showCorrelation:
Logical indicator of whether to display the correlation of the fixed-effects estimates when showing the object. Only present in the summary.lmer class.

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 0.95-8 Index]