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]