[Lme4-commits] r1622 - in pkg: . lme4.0 lme4.0/R lme4.0/inst/doc lme4.0/src lme4.0/tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Feb 27 12:14:50 CET 2012
Author: mmaechler
Date: 2012-02-27 12:14:49 +0100 (Mon, 27 Feb 2012)
New Revision: 1622
Added:
pkg/lme4.0/
Removed:
pkg/lme4/
Modified:
pkg/lme4.0/DESCRIPTION
pkg/lme4.0/R/lmer.R
pkg/lme4.0/inst/doc/Implementation.Rnw
pkg/lme4.0/inst/doc/PLSvGLS.Rnw
pkg/lme4.0/inst/doc/Theory.Rnw
pkg/lme4.0/src/Makevars
pkg/lme4.0/src/init.c
pkg/lme4.0/tests/Gamma.R
pkg/lme4.0/tests/drop.R
pkg/lme4.0/tests/extras.R
pkg/lme4.0/tests/lmer-1.R
pkg/lme4.0/tests/lmer-1.Rout.save
pkg/lme4.0/tests/lmer-conv.R
pkg/lme4.0/tests/lmer.R
pkg/lme4.0/tests/nlmer-conv.R
pkg/lme4.0/tests/nlmer.R
pkg/lme4.0/tests/nlmer.Rout.save
pkg/lme4.0/tests/simulate.R
Log:
rename lme4 to lme4.0 -- and fix the many (more than I expected) small issues
Modified: pkg/lme4.0/DESCRIPTION
===================================================================
--- pkg/lme4/DESCRIPTION 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/DESCRIPTION 2012-02-27 11:14:49 UTC (rev 1622)
@@ -1,17 +1,18 @@
-Package: lme4
-Version: 0.999375-42
-Date: 2011-10-02
+Package: lme4.0
+Version: 0.9999-0
+Date: 2011-12-31
Title: Linear mixed-effects models using S4 classes
+Description: Fit linear and generalized linear mixed-effects models.
+ This is the implementation of lme4 available on CRAN and developed up to 2011.
+ It has been renamed to lme4.0, and is now deprecated in favor of the new lme4 package.
Author: Douglas Bates <bates at stat.wisc.edu>,
Martin Maechler <maechler at R-project.org> and
Ben Bolker <bbolker at gmail.com>
Maintainer: <lme4-authors at R-forge.wu-wien.ac.at>
-Description: Fit linear and generalized linear mixed-effects models.
-Depends: methods, R(>= 2.11.1), Matrix(>= 0.9996875-1), lattice
+Depends: methods, R(>= 2.11.1), Matrix(>= 1.0-1), lattice
LinkingTo: Matrix, stats
Imports: graphics, nlme, stats4, stats
Suggests: mlmRev, MEMSS, coda, MASS, sfsmisc, MatrixModels
-LazyLoad: yes
LazyData: yes
License: GPL (>=2)
URL: http://lme4.r-forge.r-project.org/
Modified: pkg/lme4.0/R/lmer.R
===================================================================
--- pkg/lme4/R/lmer.R 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/R/lmer.R 2012-02-27 11:14:49 UTC (rev 1622)
@@ -765,12 +765,11 @@
contrasts, vnms)
mf <- fr$mf
env <- new.env()
- lapply(names(mf), function(nm) assign(nm, env = env, mf[[nm]]))
+ lapply(names(mf), function(nm) assign(nm, envir = env, mf[[nm]]))
n <- nrow(mf)
lapply(pnames,
- function(nm) assign(nm, env = env, rep(start$fixef[[nm]],
+ function(nm) assign(nm, envir = env, rep(start$fixef[[nm]],
length.out = n)))
-
n <- nrow(mf)
mf <- mf[rep(seq_len(n), s), ]
row.names(mf) <- NULL
@@ -922,7 +921,7 @@
lterm <- lapply(plist(reinds(object at Gp), cn),
function(el) {
cni <- el[[2]]
- matrix(rr[ el[[1]] ], nc = length(cni),
+ matrix(rr[ el[[1]] ], ncol = length(cni),
dimnames = list(NULL, cni))
})
wt <- whichterms(object)
@@ -1309,10 +1308,10 @@
etasim.fix <- etasim.fix+offset
}
etasim.reff <- as(t(object at A) %*% # UNSCALED random-effects contribution
- matrix(rnorm(nsim * dims["q"]), nc = nsim),
+ matrix(rnorm(nsim * dims["q"]), ncol = nsim),
"matrix")
if (length(object at V) == 0 && length(object at muEta) == 0) {
- etasim.resid <- matrix(rnorm(nsim * n), nc = nsim) ## UNSCALED residual
+ etasim.resid <- matrix(rnorm(nsim * n), ncol = nsim) ## UNSCALED residual
etasim <- etasim.fix + sigma*(etasim.reff+etasim.resid)
val <- etasim
}
@@ -1560,7 +1559,7 @@
p <- ncol(corF)
if (p > 1) {
rn <- rownames(so at coefs)
- rns <- abbreviate(rn, minlen=11)
+ rns <- abbreviate(rn, minlength=11)
cat("\nCorrelation of Fixed Effects:\n")
if (is.logical(symbolic.cor) && symbolic.cor) {
corf <- as(corF, "matrix")
@@ -1570,8 +1569,8 @@
}
else {
corf <- matrix(format(round(corF at x, 3), nsmall = 3),
- nc = p,
- dimnames = list(rns, abbreviate(rn, minlen=6)))
+ ncol = p, dimnames = list(rns,
+ abbreviate(rn, minlength=6)))
corf[!lower.tri(corf)] <- ""
print(corf[-1, -p, drop=FALSE], quote = FALSE)
}
@@ -2068,7 +2067,7 @@
## template <- FUN(x)
## if (!is.numeric(template))
## stop("simulestimate currently only handles functions that return numeric vectors")
-## ans <- matrix(template, nr = nsim, nc = length(template), byrow = TRUE)
+## ans <- matrix(template, nr = nsim, ncol = length(template), byrow = TRUE)
## colnames(ans) <- names(template)
## for (i in 1:nsim) {
## x at wrkres <- x at y <- lpred[,i]
Modified: pkg/lme4.0/inst/doc/Implementation.Rnw
===================================================================
--- pkg/lme4/inst/doc/Implementation.Rnw 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/inst/doc/Implementation.Rnw 2012-02-27 11:14:49 UTC (rev 1622)
@@ -11,11 +11,11 @@
{formatcom={\vspace{-2.5ex}},fontfamily=courier,fontseries=b,%
fontsize=\scriptsize}
%%\VignetteIndexEntry{Implementation Details}
-%%\VignetteDepends{lme4, MEMSS, mlmRev}
+%%\VignetteDepends{lme4.0, MEMSS, mlmRev}
%%
\newcommand{\trans}{\ensuremath{^\mathsf{T}}}
\newcommand{\invtrans}{\ensuremath{^\mathsf{-T}}}
-\title{Linear mixed model implementation in lme4}
+\title{Linear mixed model implementation in lme4.0}
\author{Douglas Bates\\Department of Statistics\\%
University of Wisconsin -- Madison}
\begin{document}
@@ -37,7 +37,7 @@
lattice.theme = function() canonical.theme("pdf", color = FALSE))
library(lattice)
library(Matrix)
-library(lme4)
+library(lme4.0)
data("Rail", package = "MEMSS")
data("ScotsSec", package = "mlmRev")
@
@@ -298,13 +298,13 @@
nms <- names(dev)
vals <- matrix(0, nrow = length(sg), ncol = nc, dimnames = list(NULL, nms))
for (i in seq(along = sg)) {
- .Call("mer_ST_setPars", mm, sg[i], PACKAGE = "lme4")
- .Call("mer_update_L", mm, PACKAGE = "lme4")
- res <- try(.Call("mer_update_RX", mm, PACKAGE = "lme4"), silent = TRUE)
+ .Call(lme4.0:::mer_ST_setPars, mm, sg[i])
+ .Call(lme4.0:::mer_update_L, mm)
+ res <- try(.Call(lme4.0:::mer_update_RX, mm), silent = TRUE)
if (inherits(res, "try-error")) {
vals[i,] <- NA
} else {
- .Call("mer_update_ranef", mm, PACKAGE = "lme4")
+ .Call(lme4.0:::mer_update_ranef, mm)
vals[i,] <- mm at deviance
}
}
@@ -358,13 +358,13 @@
vals <- matrix(0, nrow = length(sg), ncol = length(dev),
dimnames = list(NULL, names(dev)))
for (i in seq_along(sg)) {
- .Call("mer_ST_setPars", mm, sg[i], PACKAGE = "lme4")
- .Call("mer_update_L", mm, PACKAGE = "lme4")
- res <- try(.Call("mer_update_RX", mm, PACKAGE = "lme4"), silent = TRUE)
+ .Call(lme4.0:::mer_ST_setPars, mm, sg[i])
+ .Call(lme4.0:::mer_update_L, mm)
+ res <- try(.Call(lme4.0:::mer_update_RX, mm), silent = TRUE)
if (inherits(res, "try-error")) {
vals[i,] <- NA
} else {
- .Call("mer_update_ranef", mm, PACKAGE = "lme4")
+ .Call(lme4.0:::mer_update_ranef, mm)
vals[i,] <- mm at deviance
}
}
Modified: pkg/lme4.0/inst/doc/PLSvGLS.Rnw
===================================================================
--- pkg/lme4/inst/doc/PLSvGLS.Rnw 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/inst/doc/PLSvGLS.Rnw 2012-02-27 11:14:49 UTC (rev 1622)
@@ -10,7 +10,7 @@
{formatcom={\vspace{-1ex}},fontfamily=courier,fontseries=b,%
fontsize=\footnotesize}
%%\VignetteIndexEntry{PLS vs GLS for LMMs}
-%%\VignetteDepends{lme4}
+%%\VignetteDepends{lme4.0}
\title{Penalized least squares versus generalized least squares
representations of linear mixed models}
\author{Douglas Bates\\Department of Statistics\\%
@@ -24,13 +24,13 @@
\newcommand{\trans}{\ensuremath{^\prime}}
<<preliminaries,echo=FALSE,results=hide>>=
options(width=65,digits=5)
-#library(lme4)
+#library(lme4.0)
@
\maketitle
\begin{abstract}
- The methods in the \code{lme4} package for \code{R} for fitting
+ The methods in the \code{lme4.0} package for \code{R} for fitting
linear mixed models are based on sparse matrix methods, especially
the Cholesky decomposition of sparse positive-semidefinite matrices,
in a penalized least squares representation of the conditional model
@@ -268,7 +268,7 @@
\end{bmatrix} .
\end{equation}
-In the \code{lme4} package the \code{"mer"} class is the
+In the \code{lme4.0} package the \code{"mer"} class is the
representation of a mixed-effects model. Several slots in this class
are matrices corresponding directly to the matrices in the preceding
equations. The \code{A} slot contains the sparse matrix $\bm
Modified: pkg/lme4.0/inst/doc/Theory.Rnw
===================================================================
--- pkg/lme4/inst/doc/Theory.Rnw 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/inst/doc/Theory.Rnw 2012-02-27 11:14:49 UTC (rev 1622)
@@ -9,7 +9,7 @@
{formatcom={\vspace{-1ex}},fontfamily=courier,fontseries=b,%
fontsize=\footnotesize}
%%\VignetteIndexEntry{Computational Methods}
-%%\VignetteDepends{lme4}
+%%\VignetteDepends{lme4.0}
\title{Computational methods for mixed models}
\author{Douglas Bates\\Department of Statistics\\%
University of Wisconsin -- Madison}
@@ -25,11 +25,11 @@
\newcommand{\bc}[1]{\ensuremath{\bm{\mathcal{#1}}}}
<<preliminaries,echo=FALSE,results=hide>>=
options(width=65,digits=5)
-#library(lme4)
+#library(lme4.0)
@
\maketitle
\begin{abstract}
- The \package{lme4} package provides R functions to fit and analyze
+ The \package{lme4.0} package provides R functions to fit and analyze
several different types of mixed-effects models, including linear
mixed models, generalized linear mixed models and nonlinear mixed
models. In this vignette we describe the formulation of these
@@ -41,7 +41,7 @@
\section{Introduction}
\label{sec:intro}
-The \package{lme4} package provides \code{R} functions to fit and analyze
+The \package{lme4.0} package provides \code{R} functions to fit and analyze
linear mixed models, generalized linear mixed models and nonlinear
mixed models. These models are called \emph{mixed-effects models} or,
more simply, \emph{mixed models} because they incorporate both
@@ -56,7 +56,7 @@
models.
We begin by describing common properties of these mixed models and the
-general computational approach used in the \package{lme4} package. The
+general computational approach used in the \package{lme4.0} package. The
estimates of the parameters in a mixed model are determined as the
values that optimize an objective function --- either the likelihood
of the parameters given the observed data, for maximum likelihood
@@ -94,7 +94,7 @@
% models, can be evaluated exactly.
In the next section we describe the general form of the mixed models
-that can be represented in the \package{lme4} package and the
+that can be represented in the \package{lme4.0} package and the
computational approach embodied in the package. In the following
section we describe a particular form of mixed model,
called a linear mixed model, and the computational details for those
@@ -1197,7 +1197,7 @@
Z$ and use it to form $\bm\Lambda\trans(\bm\theta)\bm Z\trans\bm
Z\bm\Lambda(\theta)$ at each evaluation.
-In the \package{lme4} package we store $\bm Z\trans$ and use it to
+In the \package{lme4.0} package we store $\bm Z\trans$ and use it to
form $\bm\Lambda\trans(\bm\theta)\bm Z\trans$ from which $\bm L_{\bm
Z}$ is evaluated. There are two reasons for this choice. First,
the calculations for the more general forms of mixed models cannot be
@@ -1223,7 +1223,7 @@
\end{equation}
Again we have the choice of calculating and storing $\bm Z\trans\bm X$
or storing $\bm X$ and using it to reevaluate $\bm Z\trans\bm X$. In
-the \package{lme4} package we store $\bm X$, because the calculations
+the \package{lme4.0} package we store $\bm X$, because the calculations
for the more general models cannot be expressed in terms of $\bm Z\trans\bm X$.
Finally $\bm L_{\bm X}$ is evaluated as the (dense) solution to
Modified: pkg/lme4.0/src/Makevars
===================================================================
--- pkg/lme4/src/Makevars 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/src/Makevars 2012-02-27 11:14:49 UTC (rev 1622)
@@ -1 +1,7 @@
+# Dear Emacs, treat me as -*- Makefile -*-
PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+
+## default 'lme4.0.so' does not work in Namespace registration for R <= 2.14.x
+all: lme4.so
+lme4.so: $(OBJECTS)
+ $(SHLIB_LINK) -o $@ $(OBJECTS) $(ALL_LIBS)
Modified: pkg/lme4.0/src/init.c
===================================================================
--- pkg/lme4/src/init.c 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/src/init.c 2012-02-27 11:14:49 UTC (rev 1622)
@@ -125,6 +125,6 @@
/** Finalizer for lme4 called upon unloading the package.
*
*/
-void R_unload_lme4(DllInfo *dll){
+void R_unload_lme4(DllInfo *dll) {
M_cholmod_finish(&c);
}
Modified: pkg/lme4.0/tests/Gamma.R
===================================================================
--- pkg/lme4/tests/Gamma.R 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/tests/Gamma.R 2012-02-27 11:14:49 UTC (rev 1622)
@@ -39,7 +39,7 @@
dL$y <- rgamma(nrow(d),scale=dL$mu/2,shape=2)
############
-library(lme4)
+library(lme4.0)
gm0 <- glm(y~x, data=d, family=Gamma)
gm1 <- glm(y~x+block-1, data=d, family=Gamma)
Modified: pkg/lme4.0/tests/drop.R
===================================================================
--- pkg/lme4/tests/drop.R 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/tests/drop.R 2012-02-27 11:14:49 UTC (rev 1622)
@@ -1,4 +1,4 @@
-library(lme4)
+library(lme4.0)
fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
Modified: pkg/lme4.0/tests/extras.R
===================================================================
--- pkg/lme4/tests/extras.R 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/tests/extras.R 2012-02-27 11:14:49 UTC (rev 1622)
@@ -1,8 +1,9 @@
-## library(lme4)
-## This example takes too long
-## if (isTRUE(try(data(star, package = 'mlmRev')) == 'star')) {
-## fm1 <- lme4:::carryOver(math ~ gr+sx*eth+cltype+(yrs|id)+(1|tch)+(yrs|sch),
-## star, yrs ~ tch/id,
-## control = list(msV = 1, nit = 0, grad = 0))
-## print(fm1, corr = FALSE)
-## }
+if(FALSE) {## This example takes too long
+ library(lme4.0)
+ if (isTRUE(try(data(star, package = 'mlmRev')) == 'star')) {
+ fm1 <- lme4.0:::carryOver(math ~ gr+sx*eth+cltype+(yrs|id)+(1|tch)+(yrs|sch),
+ star, yrs ~ tch/id,
+ control = list(msV = 1, nit = 0, grad = 0))
+ print(fm1, corr = FALSE)
+ }
+}
Modified: pkg/lme4.0/tests/lmer-1.R
===================================================================
--- pkg/lme4/tests/lmer-1.R 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/tests/lmer-1.R 2012-02-27 11:14:49 UTC (rev 1622)
@@ -1,5 +1,5 @@
### suppressPackageStartupMessages(...) as we have an *.Rout.save to Rdiff against
-stopifnot(suppressPackageStartupMessages(require(lme4)))
+stopifnot(suppressPackageStartupMessages(require(lme4.0)))
options(show.signif.stars = FALSE)
(fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
Modified: pkg/lme4.0/tests/lmer-1.Rout.save
===================================================================
--- pkg/lme4/tests/lmer-1.Rout.save 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/tests/lmer-1.Rout.save 2012-02-27 11:14:49 UTC (rev 1622)
@@ -1,6 +1,6 @@
-R version 2.13.0 RC (2011-04-07 r55350)
-Copyright (C) 2011 The R Foundation for Statistical Computing
+R version 2.14.2 RC (2012-02-26 r58499)
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -17,7 +17,7 @@
Type 'q()' to quit R.
> ### suppressPackageStartupMessages(...) as we have an *.Rout.save to Rdiff against
-> stopifnot(suppressPackageStartupMessages(require(lme4)))
+> stopifnot(suppressPackageStartupMessages(require(lme4.0)))
> options(show.signif.stars = FALSE)
>
> (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
@@ -283,7 +283,7 @@
Attaching package: 'coda'
-The following object(s) are masked from 'package:lme4':
+The following object(s) are masked from 'package:lme4.0':
HPDinterval
@@ -635,5 +635,5 @@
> if(.unsafe.BLAS) rm(identical)
>
> cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
-Time elapsed: 6.933 0.147 7.379 0 0
+Time elapsed: 6.081 0.176 7.526 0 0.008
>
Modified: pkg/lme4.0/tests/lmer-conv.R
===================================================================
--- pkg/lme4/tests/lmer-conv.R 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/tests/lmer-conv.R 2012-02-27 11:14:49 UTC (rev 1622)
@@ -1,14 +1,14 @@
### lmer() convergence testing / monitoring / ...
## ------------------
### The output of tests here are *not* 'diff'ed (<==> no *.Rout.save file)
-library(lme4)
+library(lme4.0)
## Platform - and other such info -- so we find it in old saved outputs
SysI <- Sys.info()
structure(Sys.info()[c(4,5,1:3)], class="simple.list")
sessionInfo()
## and for even more details:
c(Matrix = packageDescription("Matrix")$Built,
- lme4 = packageDescription("lme4")$Built)
+ lme4.0 = packageDescription("lme4.0")$Built)
if(SysI[["sysname"]] == "Linux" && require("sfsmisc")) local({
nn <- names(.Sc <- sfsmisc::Sys.cpuinfo())
nn <- names(.Sc <- .Sc[nn != "flags"])
Modified: pkg/lme4.0/tests/lmer.R
===================================================================
--- pkg/lme4/tests/lmer.R 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/tests/lmer.R 2012-02-27 11:14:49 UTC (rev 1622)
@@ -1,4 +1,4 @@
-require(lme4)
+require(lme4.0)
source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
## Check that quasi families throw an error
Modified: pkg/lme4.0/tests/nlmer-conv.R
===================================================================
--- pkg/lme4/tests/nlmer-conv.R 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/tests/nlmer-conv.R 2012-02-27 11:14:49 UTC (rev 1622)
@@ -1,7 +1,7 @@
### nlmer() convergence testing / monitoring / ...
## -------------------
### The output of tests here are *not* 'diff'ed (<==> no *.Rout.save file)
-library(lme4)
+library(lme4.0)
## 'Theoph' Data modeling
Modified: pkg/lme4.0/tests/nlmer.R
===================================================================
--- pkg/lme4/tests/nlmer.R 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/tests/nlmer.R 2012-02-27 11:14:49 UTC (rev 1622)
@@ -1,5 +1,5 @@
### suppressPackageStartupMessages(...) as we have an *.Rout.save to Rdiff against
-stopifnot(suppressPackageStartupMessages(require(lme4)))
+stopifnot(suppressPackageStartupMessages(require(lme4.0)))
## TODO: nicer version of this is in system.file("test-tools.R", package = "Matrix")
showProc.time <- function() { ## CPU elapsed __since last called__
Modified: pkg/lme4.0/tests/nlmer.Rout.save
===================================================================
--- pkg/lme4/tests/nlmer.Rout.save 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/tests/nlmer.Rout.save 2012-02-27 11:14:49 UTC (rev 1622)
@@ -1,6 +1,6 @@
-R version 2.13.0 Patched (2011-04-20 r55568)
-Copyright (C) 2011 The R Foundation for Statistical Computing
+R version 2.14.2 RC (2012-02-26 r58499)
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -17,8 +17,9 @@
Type 'q()' to quit R.
> ### suppressPackageStartupMessages(...) as we have an *.Rout.save to Rdiff against
-> stopifnot(suppressPackageStartupMessages(require(lme4)))
+> stopifnot(suppressPackageStartupMessages(require(lme4.0)))
>
+> ## TODO: nicer version of this is in system.file("test-tools.R", package = "Matrix")
> showProc.time <- function() { ## CPU elapsed __since last called__
+ .ot <- .pc
+ .pc <<- proc.time()
@@ -58,7 +59,7 @@
lKa -0.264
lCl 0.671 -0.141
> showProc.time() # ~ 5.7s {dual-opteron 2814, on 64b, no optim.}
-Time elapsed: 9.708 0.028 9.849
+Time elapsed: 7.571 0.06 7.807
>
> (nm3 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
+ (lKe|Subject) + (lKa|Subject) + (lCl|Subject),
@@ -87,7 +88,7 @@
lKa -0.264
lCl 0.671 -0.133
> showProc.time() # ~ 3.2s
-Time elapsed: 7.003 0.015 7.054
+Time elapsed: 5.408 0.044 5.572
>
> ## dropping lKe from random effects:
> (nm4 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
@@ -116,7 +117,7 @@
lKa -0.264
lCl 0.671 -0.141
> showProc.time()
-Time elapsed: 3.735 0.001 3.75
+Time elapsed: 2.925 0.013 2.985
>
> (nm5 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~
+ (lKa|Subject) + (lCl|Subject),
@@ -144,7 +145,7 @@
lKa -0.264
lCl 0.671 -0.133
> showProc.time()
-Time elapsed: 3.225 0.007 3.251
+Time elapsed: 2.514 0 2.55
>
> e3 <- expand(nm3)
> stopifnot(identical(sapply(e3, class),
@@ -170,5 +171,5 @@
+ )
>
> showProc.time()
-Time elapsed: 0.04 0 0.04
+Time elapsed: 0.037 0 0.037
>
Modified: pkg/lme4.0/tests/simulate.R
===================================================================
--- pkg/lme4/tests/simulate.R 2012-02-23 22:06:24 UTC (rev 1615)
+++ pkg/lme4.0/tests/simulate.R 2012-02-27 11:14:49 UTC (rev 1622)
@@ -1,4 +1,4 @@
-require(lme4)
+require(lme4.0)
source(system.file("test-tools.R", package = "Matrix"))# identical3(),
##' Simple Parametric bootstrap Deviance between two models
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