[Lme4-commits] r1686 - in pkg: lme4/R lme4/man lme4.0/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Mar 22 04:18:02 CET 2012
Author: bbolker
Date: 2012-03-22 04:18:02 +0100 (Thu, 22 Mar 2012)
New Revision: 1686
Modified:
pkg/lme4.0/R/lmer.R
pkg/lme4/R/lmer.R
pkg/lme4/man/getME.Rd
Log:
added "A" and "flist" to getME()
Modified: pkg/lme4/R/lmer.R
===================================================================
--- pkg/lme4/R/lmer.R 2012-03-20 13:18:30 UTC (rev 1685)
+++ pkg/lme4/R/lmer.R 2012-03-22 03:18:02 UTC (rev 1686)
@@ -1307,9 +1307,6 @@
##' @S3method terms merMod
terms.merMod <- function(x, fixed.only=TRUE, ...) {
if (fixed.only) {
- ## do need to drop LHS (e.g. binomial example)
- ## mm <- model.frame(formula(x,fixed.only=TRUE)[-2],data=model.frame(x))
- ## terms(mm)
terms.formula(formula(x,fixed.only=TRUE))
} else attr(x at frame,"terms")
}
@@ -1479,9 +1476,14 @@
##' \item{Lambdat}{transpose of the relative covariance factor of the random effects.}
##' \item{Lind}{index vector for inserting elements of \eqn{\theta}{theta} into the
##' nonzeros of \eqn{\Lambda}{Lambda}}
+##' \item{A}{Scaled sparse model matrix (class
+##' \code{"\link[Matrix:dgCMatrix-class]{dgCMatrix}"}) for
+##' the unit, orthogonal random effects, \eqn{U},
+##' equal to \code{getME(.,"Zt") \%*\% getME(.,"Lambdat")}}
##' \item{RX}{Cholesky factor for the fixed-effects parameters}
##' \item{RZX}{cross-term in the full Cholesky factor}
-##' \item{beta}{fixed-effects parameter estimates (same as the result of \code{\link{fixef}})}
+##' \item{flist}{a list of the grouping variables (factors) involved in the random effect terms}
+##' \item{beta}{fixed-effects parameter estimates (identical to the result of \code{\link{fixef}}, but without names)}
##' \item{theta}{random-effects parameter estimates: these are parameterized as the relative Cholesky factors of each random effect term}
##' \item{n_rtrms}{number of random-effects terms}
##' \item{is_REML}{same as the result of \code{\link{isREML}}}
@@ -1515,8 +1517,9 @@
getME <- function(object,
name = c("X", "Z","Zt", "u",
"Gp",
- "L", "Lambda", "Lambdat", "Lind",
+ "L", "Lambda", "Lambdat", "Lind", "A",
"RX", "RZX",
+ "flist",
"beta", "theta",
"REML", "n_rtrms", "is_REML", "devcomp",
"offset", "lower"))
@@ -1538,6 +1541,7 @@
"L"= PR$ L(),
"Lambda"= t(PR$ Lambdat),
"Lambdat"= PR$ Lambdat,
+ "A" = PR$Lambdat %*% PR$Zt,
"Lind" = PR$ Lind,
"RX" = PR $ RX(), ## FIXME - add the column names and row names, either in the C++ or the R method
"RZX" = PR $ RZX, ## FIXME - add column names
Modified: pkg/lme4/man/getME.Rd
===================================================================
--- pkg/lme4/man/getME.Rd 2012-03-20 13:18:30 UTC (rev 1685)
+++ pkg/lme4/man/getME.Rd 2012-03-22 03:18:02 UTC (rev 1686)
@@ -5,7 +5,7 @@
\title{Extract or Get Generalize Components from a Fitted Mixed Effects Model}
\usage{
getME(object,
- name = c("X", "Z", "Zt", "u", "Gp", "L", "Lambda", "Lambdat", "Lind", "RX", "RZX", "beta", "theta", "REML", "n_rtrms", "is_REML", "devcomp", "offset", "lower"))
+ name = c("X", "Z", "Zt", "u", "Gp", "L", "Lambda", "Lambdat", "Lind", "A", "RX", "RZX", "flist", "beta", "theta", "REML", "n_rtrms", "is_REML", "devcomp", "offset", "lower"))
}
\arguments{
\item{object}{a fitted mixed-effects model of class
@@ -28,10 +28,17 @@
covariance factor of the random effects.}
\item{Lind}{index vector for inserting elements of
\eqn{\theta}{theta} into the nonzeros of
- \eqn{\Lambda}{Lambda}} \item{RX}{Cholesky factor for the
- fixed-effects parameters} \item{RZX}{cross-term in the
- full Cholesky factor} \item{beta}{fixed-effects parameter
- estimates (same as the result of \code{\link{fixef}})}
+ \eqn{\Lambda}{Lambda}} \item{A}{Scaled sparse model
+ matrix (class
+ \code{"\link[Matrix:dgCMatrix-class]{dgCMatrix}"}) for
+ the unit, orthogonal random effects, \eqn{U}, equal to
+ \code{getME(.,"Zt") \%*\% getME(.,"Lambdat")}}
+ \item{RX}{Cholesky factor for the fixed-effects
+ parameters} \item{RZX}{cross-term in the full Cholesky
+ factor} \item{flist}{a list of the grouping variables
+ (factors) involved in the random effect terms}
+ \item{beta}{fixed-effects parameter estimates (identical
+ to the result of \code{\link{fixef}}, but without names)}
\item{theta}{random-effects parameter estimates: these
are parameterized as the relative Cholesky factors of
each random effect term} \item{n_rtrms}{number of
@@ -40,7 +47,8 @@
of a named numeric vector, \dQuote{cmp}, and a named
integer vector, \dQuote{dims}, describing the fitted
model} \item{offset}{model offset} \item{lower}{lower
- bounds on model parameters} ## FIXME: theta only? }}
+ bounds on model parameters (random effects parameters
+ only)} }}
}
\value{
Unspecified, as very much depending on the
Modified: pkg/lme4.0/R/lmer.R
===================================================================
--- pkg/lme4.0/R/lmer.R 2012-03-20 13:18:30 UTC (rev 1685)
+++ pkg/lme4.0/R/lmer.R 2012-03-22 03:18:02 UTC (rev 1686)
@@ -2360,7 +2360,8 @@
getME <- function(object,
name = c("X", "Z","Zt", "u",
"Gp",
- "L", "Lambda", "Lambdat",
+ "L", "Lambda", "Lambdat", "A",
+ "flist",
"RX", "RZX",
"beta", "theta",
"REML", "n_rtrms", "is_REML"))
@@ -2380,9 +2381,10 @@
"beta" = unname(object at fixef),
"n_rtrms" = object at dims[["nt"]], ## = #{random-effect terms in the formula}
"is_REML" = as.logical(object at dims[["REML"]]),
-
- "Lambda"=, ## from object at L ??
- "Lambdat"=,
+ "Lambda"={warning("Lambda is not available in lme4.0"); NA}, ## FIXME??
+ "Lambdat"={warning("Lambdat is not available in lme4.0"); NA},
+ "A"=object at A,
+ "flist"=object at flist,
"theta"= {
mnames <- function(z) {
v <- colnames(z)
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