[Lme4-commits] r1661 - in pkg/lme4Eigen: . R inst/doc man src tests vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Mar 15 22:05:29 CET 2012 

Author: dmbates
Date: 2012-03-15 22:05:29 +0100 (Thu, 15 Mar 2012)
New Revision: 1661

Modified:
   pkg/lme4Eigen/DESCRIPTION
   pkg/lme4Eigen/NAMESPACE
   pkg/lme4Eigen/R/AllClass.R
   pkg/lme4Eigen/R/lmer.R
   pkg/lme4Eigen/do-roxy
   pkg/lme4Eigen/inst/doc/Doxyfile
   pkg/lme4Eigen/inst/doc/Doxyfile.bak
   pkg/lme4Eigen/inst/doc/profiling.txt
   pkg/lme4Eigen/man/Dyestuff.Rd
   pkg/lme4Eigen/src/external.cpp
   pkg/lme4Eigen/src/glmFamily.cpp
   pkg/lme4Eigen/src/mcmcsamp.cpp
   pkg/lme4Eigen/src/mcmcsamp.h
   pkg/lme4Eigen/src/optimizer.cpp
   pkg/lme4Eigen/src/optimizer.h
   pkg/lme4Eigen/src/predModule.cpp
   pkg/lme4Eigen/src/predModule.h
   pkg/lme4Eigen/src/respModule.cpp
   pkg/lme4Eigen/src/respModule.h
   pkg/lme4Eigen/tests/drop.R
   pkg/lme4Eigen/tests/elston.R
   pkg/lme4Eigen/tests/extras.R
   pkg/lme4Eigen/tests/getME.R
   pkg/lme4Eigen/tests/glmer-1.R
   pkg/lme4Eigen/tests/lmer-1.R
   pkg/lme4Eigen/tests/lmer-1.Rout.save
   pkg/lme4Eigen/tests/lmer-conv.R
   pkg/lme4Eigen/tests/lmer.R
   pkg/lme4Eigen/tests/lmer2_ex.R
   pkg/lme4Eigen/tests/nadrop.R
   pkg/lme4Eigen/tests/nbinom.R
   pkg/lme4Eigen/tests/nlmer-conv.R
   pkg/lme4Eigen/tests/nlmer.R
   pkg/lme4Eigen/tests/nlmer.Rout.save
   pkg/lme4Eigen/tests/optimizer.R
   pkg/lme4Eigen/tests/predict.R
   pkg/lme4Eigen/tests/profile.R
   pkg/lme4Eigen/tests/refit.R
   pkg/lme4Eigen/tests/simulate.R
   pkg/lme4Eigen/tests/test-all.R
   pkg/lme4Eigen/tests/throw.R
   pkg/lme4Eigen/tests/varcorr.R
   pkg/lme4Eigen/tests/vcov-etc.R
   pkg/lme4Eigen/vignettes/PLSvGLS.Rnw
   pkg/lme4Eigen/vignettes/Theory.Rnw
Log:
Individual file changes for renaming lme4Eigen to lme4


Modified: pkg/lme4Eigen/DESCRIPTION
===================================================================
--- pkg/lme4Eigen/DESCRIPTION	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/DESCRIPTION	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-Package: lme4Eigen
+Package: lme4
 Version: 0.9996875-15
 Date: $Date$
 Revision: $Revision$

Modified: pkg/lme4Eigen/NAMESPACE
===================================================================
--- pkg/lme4Eigen/NAMESPACE	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/NAMESPACE	2012-03-15 21:05:29 UTC (rev 1661)
@@ -143,4 +143,4 @@
 S3method(vcov,summary.mer)
 S3method(weights,merMod)
 S3method(xyplot,thpr)
-useDynLib(lme4Eigen,.registration=TRUE)
+useDynLib(lme4,.registration=TRUE)

Modified: pkg/lme4Eigen/R/AllClass.R
===================================================================
--- pkg/lme4Eigen/R/AllClass.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/R/AllClass.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,5 +1,5 @@
 ### Class definitions for the package
-##' @useDynLib lme4Eigen .registration=TRUE
+##' @useDynLib lme4 .registration=TRUE
 NULL
 
 ##' Class "lmList" of 'lm' Objects on Common Model

Modified: pkg/lme4Eigen/R/lmer.R
===================================================================
--- pkg/lme4Eigen/R/lmer.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/R/lmer.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -711,7 +711,7 @@
     rho <- list2env(list(resp=x at resp$copy(),
                            pp=x at pp$copy(),
                            beta0=x at beta,
-                           u0=x at u), parent=as.environment("package:lme4Eigen"))
+                           u0=x at u), parent=as.environment("package:lme4"))
     mkdevfun(rho, getME(x, "devcomp")$dims["nAGQ"])
 }
 
@@ -1636,7 +1636,7 @@
     if (is.null(cnms <- x at cnms))
 	stop("VarCorr methods require reTrms, not just reModule")
     if(missing(sigma)) # "bug": fails via default 'sigma=sigma(x)'
-	sigma <- lme4Eigen::sigma(x)  ## FIXME: do we need lme4Eigen:: ?
+	sigma <- lme4::sigma(x)  ## FIXME: do we need lme4:: ?
     nc <- sapply(cnms, length)	  # no. of columns per term
     m <- mkVarCorr(sigma, cnms=cnms, nc=nc, theta = x at theta,
 	      nms = {fl <- x at flist; names(fl)[attr(fl, "assign")]})

Modified: pkg/lme4Eigen/do-roxy
===================================================================
--- pkg/lme4Eigen/do-roxy	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/do-roxy	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,6 +1,6 @@
 #! /usr/bin/env Rscript
 #
-pkg <- "lme4Eigen"
+pkg <- "lme4"
 pDIR <- switch((U <- Sys.getenv("USER")),
                "maechler" = "~/R/Pkgs",
                "bates"    = "~/sloc",
@@ -20,7 +20,7 @@
   roxygenize(pkgPATH)## <-- also recreates *.Rd files
 }
 owd <- setwd(pkgPATH)
-## FIX  NAMESPACE entry : useDynLib(lme4Eigen,".registration=TRUE")
+## FIX  NAMESPACE entry : useDynLib(lme4,".registration=TRUE")
 ll <- readLines("NAMESPACE")
 i <- grep("useDynLib", ll)
 ll[i] <- gsub('"', '', ll[i])#"

Modified: pkg/lme4Eigen/inst/doc/Doxyfile
===================================================================
--- pkg/lme4Eigen/inst/doc/Doxyfile	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/inst/doc/Doxyfile	2012-03-15 21:05:29 UTC (rev 1661)
@@ -25,7 +25,7 @@
 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded
 # by quotes) that should identify the project.
 
-PROJECT_NAME           = lme4Eigen
+PROJECT_NAME           = lme4
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number.
 # This could be handy for archiving the generated documentation or

Modified: pkg/lme4Eigen/inst/doc/Doxyfile.bak
===================================================================
--- pkg/lme4Eigen/inst/doc/Doxyfile.bak	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/inst/doc/Doxyfile.bak	2012-03-15 21:05:29 UTC (rev 1661)
@@ -25,7 +25,7 @@
 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded
 # by quotes) that should identify the project.
 
-PROJECT_NAME           = lme4Eigen
+PROJECT_NAME           = lme4
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number.
 # This could be handy for archiving the generated documentation or

Modified: pkg/lme4Eigen/inst/doc/profiling.txt
===================================================================
--- pkg/lme4Eigen/inst/doc/profiling.txt	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/inst/doc/profiling.txt	2012-03-15 21:05:29 UTC (rev 1661)
@@ -40,7 +40,7 @@
 at the risk of some redundancy (once you have done the work needed to
 calculate the profiled deviance for theta and sigma you could just as
 easily profile out sigma).  The (unexported) R function devfun in
-lme4Eigen takes a fitted model and returns a function with attributes that
+lme4 takes a fitted model and returns a function with attributes that
 evaluates the profiled deviance for the composite parameter (theta,
 log(sigma)).  However, I don't think even that is enough because it
 does not give profiles of the variances and covariances of the random

Modified: pkg/lme4Eigen/man/Dyestuff.Rd
===================================================================
--- pkg/lme4Eigen/man/Dyestuff.Rd	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/man/Dyestuff.Rd	2012-03-15 21:05:29 UTC (rev 1661)
@@ -74,7 +74,7 @@
  pkgI("Rcpp")
  pkgI("RcppEigen")
  pkgI("minqa")
- pkgI("lme4Eigen")
+ pkgI("lme4")
 }
 str(Dyestuff)
 dotplot(reorder(Batch, Yield) ~ Yield, Dyestuff,

Modified: pkg/lme4Eigen/src/external.cpp
===================================================================
--- pkg/lme4Eigen/src/external.cpp	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/src/external.cpp	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-// external.cpp: externally .Call'able functions in lme4Eigen
+// external.cpp: externally .Call'able functions in lme4
 //
 // Copyright (C)       2011-2012 Douglas Bates, Martin Maechler and Ben Bolker
 //
@@ -33,11 +33,11 @@
 
     using       glm::glmFamily;
 
-    using lme4Eigen::glmResp;
-    using lme4Eigen::lmResp;
-    using lme4Eigen::lmerResp;
-    using lme4Eigen::merPredD;
-    using lme4Eigen::nlsResp;
+    using lme4::glmResp;
+    using lme4::lmResp;
+    using lme4::lmerResp;
+    using lme4::merPredD;
+    using lme4::nlsResp;
 
     using optimizer::Golden;
     using optimizer::Nelder_Mead;
@@ -961,14 +961,14 @@
     {NULL, NULL, 0}
 };
 
-/** Initializer for lme4Eigen, called upon loading the package.
+/** Initializer for lme4, called upon loading the package.
  *
  *  Register routines that can be called directly from R.
  *  Initialize CHOLMOD and require the LL' form of the factorization.
  *  Install the symbols to be used by functions in the package.
  */
 extern "C"
-void R_init_lme4Eigen(DllInfo *dll)
+void R_init_lme4(DllInfo *dll)
 {
     R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
     R_useDynamicSymbols(dll, (Rboolean)FALSE);

Modified: pkg/lme4Eigen/src/glmFamily.cpp
===================================================================
--- pkg/lme4Eigen/src/glmFamily.cpp	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/src/glmFamily.cpp	2012-03-15 21:05:29 UTC (rev 1661)
@@ -3,7 +3,7 @@
 //
 // Copyright (C) 2011-2012 Douglas Bates, Martin Maechler and Ben Bolker
 //
-// This file is part of lme4Eigen.
+// This file is part of lme4.
 
 #include "glmFamily.h"
 #include <Rmath.h>

Modified: pkg/lme4Eigen/src/mcmcsamp.cpp
===================================================================
--- pkg/lme4Eigen/src/mcmcsamp.cpp	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/src/mcmcsamp.cpp	2012-03-15 21:05:29 UTC (rev 1661)
@@ -3,22 +3,22 @@
 //
 // Copyright (C) 2011-2012 Douglas Bates, Martin Maechler and Ben Bolker
 //
-// This file is part of lme4Eigen.
+// This file is part of lme4.
 
 #include "mcmcsamp.h"
 
 namespace lme4 {
     using Rcpp::as;
 
-    static inline double pwrss(lme4Eigen::merPredD *pred, lme4Eigen::lmResp *resp) {
+    static inline double pwrss(lme4::merPredD *pred, lme4::lmResp *resp) {
 	return pred->sqrL(1.) + resp->wrss();
     }
 
-    static inline double sigmaML(lme4Eigen::merPredD *pred, lme4Eigen::lmResp *resp) {
+    static inline double sigmaML(lme4::merPredD *pred, lme4::lmResp *resp) {
 	return std::sqrt(pwrss(pred, resp)/double(resp->y().size()));
     }
 
-    mcmcsamp::mcmcsamp(lme4Eigen::merPredD *pred, lme4Eigen::lmResp *resp,
+    mcmcsamp::mcmcsamp(lme4::merPredD *pred, lme4::lmResp *resp,
 		       SEXP dev, SEXP fixef, SEXP sigma, SEXP ranef)
 	: d_dev(  as<MVec>(dev)),
 	  d_fixef(as<MMat>(fixef)),

Modified: pkg/lme4Eigen/src/mcmcsamp.h
===================================================================
--- pkg/lme4Eigen/src/mcmcsamp.h	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/src/mcmcsamp.h	2012-03-15 21:05:29 UTC (rev 1661)
@@ -23,15 +23,15 @@
 	typedef Eigen::MatrixXd  Mat;
 	typedef Eigen::Map<Mat> MMat;
     protected:
-	// lme4Eigen::merPredD *d_pred;
-	// lme4Eigen::lmResp   *d_resp;
+	// lme4::merPredD *d_pred;
+	// lme4::lmResp   *d_resp;
 	MVec                    d_dev;
 	MMat                    d_fixef;
 	MVec                    d_sigma;
         MMat                    d_ranef;
     public:
 				// all the work is done in the constructor
-	mcmcsamp(lme4Eigen::merPredD *pred, lme4Eigen::lmResp *resp,
+	mcmcsamp(lme4::merPredD *pred, lme4::lmResp *resp,
 		 SEXP dev, SEXP fixef, SEXP sigma, SEXP ranef);
     };
 }

Modified: pkg/lme4Eigen/src/optimizer.cpp
===================================================================
--- pkg/lme4Eigen/src/optimizer.cpp	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/src/optimizer.cpp	2012-03-15 21:05:29 UTC (rev 1661)
@@ -8,7 +8,7 @@
 // Original implementation Copyright (C) 2007-2011 Massachusetts Institute of Technology
 // Modifications Copyright (C) 2011 Douglas Bates, Martin Maechler and Ben Bolker
 //
-// This file is part of lme4Eigen.
+// This file is part of lme4.
 
 #include "optimizer.h"
 

Modified: pkg/lme4Eigen/src/optimizer.h
===================================================================
--- pkg/lme4Eigen/src/optimizer.h	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/src/optimizer.h	2012-03-15 21:05:29 UTC (rev 1661)
@@ -4,7 +4,7 @@
 //
 // Copyright (C)       2011 Douglas Bates, Martin Maechler and Ben Bolker
 //
-// This file is part of lme4Eigen.
+// This file is part of lme4.
 
 #ifndef LME4_NELDER_MEAD_H
 #define LME4_NELDER_MEAD_H

Modified: pkg/lme4Eigen/src/predModule.cpp
===================================================================
--- pkg/lme4Eigen/src/predModule.cpp	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/src/predModule.cpp	2012-03-15 21:05:29 UTC (rev 1661)
@@ -3,11 +3,11 @@
 //
 // Copyright (C) 2011-2012 Douglas Bates, Martin Maechler and Ben Bolker
 //
-// This file is part of lme4Eigen.
+// This file is part of lme4.
 
 #include "predModule.h"
 
-namespace lme4Eigen {
+namespace lme4 {
     using    Rcpp::as;
 
     using     std::invalid_argument;

Modified: pkg/lme4Eigen/src/predModule.h
===================================================================
--- pkg/lme4Eigen/src/predModule.h	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/src/predModule.h	2012-03-15 21:05:29 UTC (rev 1661)
@@ -11,7 +11,7 @@
 
 #include <RcppEigen.h>
 
-namespace lme4Eigen {
+namespace lme4 {
 
     using Eigen::LLT;
     using Eigen::MatrixXd;

Modified: pkg/lme4Eigen/src/respModule.cpp
===================================================================
--- pkg/lme4Eigen/src/respModule.cpp	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/src/respModule.cpp	2012-03-15 21:05:29 UTC (rev 1661)
@@ -7,7 +7,7 @@
 #include "respModule.h"
 #include <cmath>
 
-namespace lme4Eigen {
+namespace lme4 {
     using Eigen::ArrayXd;
     using Eigen::VectorXd;
 

Modified: pkg/lme4Eigen/src/respModule.h
===================================================================
--- pkg/lme4Eigen/src/respModule.h	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/src/respModule.h	2012-03-15 21:05:29 UTC (rev 1661)
@@ -11,7 +11,7 @@
 
 #include "glmFamily.h"
 
-namespace lme4Eigen {
+namespace lme4 {
     typedef Eigen::Map<Eigen::VectorXd> MVec;
 
     using Rcpp::CharacterVector;

Modified: pkg/lme4Eigen/tests/drop.R
===================================================================
--- pkg/lme4Eigen/tests/drop.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/drop.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-library(lme4Eigen)
+library(lme4)
 fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
 
 ## slightly weird model but plausible --- not that

Modified: pkg/lme4Eigen/tests/elston.R
===================================================================
--- pkg/lme4Eigen/tests/elston.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/elston.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -22,7 +22,7 @@
 
 ## save("grouseticks","grouseticks_agg",file="grouseticks.rda")
 
-library(lme4Eigen)
+library(lme4)
 data(grouseticks)
 do.plots <- FALSE
 form <- TICKS~YEAR+HEIGHT+(1|BROOD)+(1|INDEX)+(1|LOCATION)

Modified: pkg/lme4Eigen/tests/extras.R
===================================================================
--- pkg/lme4Eigen/tests/extras.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/extras.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-## library(lme4Eigen)
+## 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),

Modified: pkg/lme4Eigen/tests/getME.R
===================================================================
--- pkg/lme4Eigen/tests/getME.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/getME.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-library(lme4Eigen)
+library(lme4)
 #### tests of getME()
 
 ###  are names correct? --------------

Modified: pkg/lme4Eigen/tests/glmer-1.R
===================================================================
--- pkg/lme4Eigen/tests/glmer-1.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/glmer-1.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,5 +1,5 @@
 ## generalized linear mixed model
-stopifnot(suppressPackageStartupMessages(require(lme4Eigen)))
+stopifnot(suppressPackageStartupMessages(require(lme4)))
 options(show.signif.stars = FALSE)
 source(system.file("test-tools.R", package = "Matrix"))# identical3(), showProc.time, etc
 
@@ -44,7 +44,7 @@
                     ##  these values are those of "old-lme4":
 		    ## c(-1.39853504914, -0.992334711,
 		    ##   -1.12867541477, -1.58037390498),
-                    ## lme4Eigen[r 1636], 64-bit ubuntu 11.10:
+                    ## lme4[r 1636], 64-bit ubuntu 11.10:
                     c(-1.3788385, -1.0589543,
                       -1.1936382, -1.6306271),
 		    tol = 1.e-3,
@@ -64,7 +64,7 @@
         structure(contr.sdif(3),
                   dimnames = list(NULL, c("diag", "encourage")))
     print(fm5 <- glmer(y ~ trt + wk2 + (1|ID), bacteria, binomial))
-    ## again *fails* (lme4Eigen[r 1636], 64-bit ubuntu 11.10)
+    ## again *fails* (lme4[r 1636], 64-bit ubuntu 11.10)
     ## used to fail with nlminb() : stuck at theta=1
 
     showProc.time() #

Modified: pkg/lme4Eigen/tests/lmer-1.R
===================================================================
--- pkg/lme4Eigen/tests/lmer-1.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/lmer-1.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,5 +1,5 @@
 ### suppressPackageStartupMessages(...)  as we have an *.Rout.save to Rdiff against
-stopifnot(suppressPackageStartupMessages(require(lme4Eigen)))
+stopifnot(suppressPackageStartupMessages(require(lme4)))
 options(show.signif.stars = FALSE)
 
 source(system.file("test-tools.R", package = "Matrix"))# identical3() etc

Modified: pkg/lme4Eigen/tests/lmer-1.Rout.save
===================================================================
--- pkg/lme4Eigen/tests/lmer-1.Rout.save	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/lmer-1.Rout.save	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,5 +1,5 @@
 
-R version 2.14.2 RC (2012-02-28 r58516)
+R version 2.15.0 alpha (2012-03-15 r58752)
 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(lme4Eigen)))
+> stopifnot(suppressPackageStartupMessages(require(lme4)))
 > options(show.signif.stars = FALSE)
 > 
 > source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
@@ -168,7 +168,7 @@
 + 			  c(1,3), dimnames = list("(Intercept)",
 + 				  c("Estimate", "Std. Error", "t value")))))
 > showProc.time() #
-Time elapsed:  0.812 0.012 0.825 
+Time elapsed:  0.804 0.008 0.811 
 > 
 > ### {from ../man/lmer.Rd } --- compare lmer & lmer1 ---------------
 > (fmX1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
@@ -229,7 +229,7 @@
 > #fmX2s <- lmer2(Reaction ~ Days + (Days|Subject), sleepstudy, sparseX=TRUE)
 > 
 > showProc.time() #
-Time elapsed:  0.332 0 0.333 
+Time elapsed:  0.352 0 0.352 
 > 
 > for(nm in c("coef", "fixef", "ranef", "sigma",
 + 	     "model.matrix", "model.frame" , "terms")) {
@@ -352,7 +352,7 @@
 
 > 
 > showProc.time() #
-Time elapsed:  0.552 0 0.555 
+Time elapsed:  0.484 0.004 0.49 
 > 
 > ## Invalid factor specification -- used to seg.fault:
 > set.seed(1)
@@ -477,7 +477,7 @@
 +             )
 > 
 > showProc.time() #
-Time elapsed:  0.26 0 0.261 
+Time elapsed:  0.296 0 0.297 
 > 
 > ## Wrong formula gave a seg.fault at times:
 > set.seed(2)# !
@@ -497,7 +497,7 @@
 In Ops.factor(ff, x1) : + not meaningful for factors
 > 
 > showProc.time() #
-Time elapsed:  1.244 0 1.249 
+Time elapsed:  1.396 0 1.399 
 > 
 > ## Reordering of grouping factors should not change the internal structure
 > #Pm1  <- lmer1(strength ~ (1|batch) + (1|sample), Pastes, doFit = FALSE)
@@ -512,3 +512,6 @@
 > #		 S4_2list(P2.2)))
 > 
 > 
+> proc.time()
+   user  system elapsed 
+  6.520   0.068   6.551 

Modified: pkg/lme4Eigen/tests/lmer-conv.R
===================================================================
--- pkg/lme4Eigen/tests/lmer-conv.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/lmer-conv.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,7 +1,7 @@
 ### lmer() convergence testing / monitoring / ...
 ##  ------------------
 ### The output of tests here are *not* 'diff'ed  (<==> no *.Rout.save file)
-library(lme4Eigen)
+library(lme4)
 
 ## convergence on boundary warnings
 load(system.file("external/test3comp.rda", package = "Matrix"))

Modified: pkg/lme4Eigen/tests/lmer.R
===================================================================
--- pkg/lme4Eigen/tests/lmer.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/lmer.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-require(lme4Eigen)
+require(lme4)
 source(system.file("test-tools.R", package = "Matrix"))# identical3() etc
 
 ## Check that quasi families throw an error

Modified: pkg/lme4Eigen/tests/lmer2_ex.R
===================================================================
--- pkg/lme4Eigen/tests/lmer2_ex.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/lmer2_ex.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-stopifnot(suppressPackageStartupMessages(require(lme4Eigen)))
+stopifnot(suppressPackageStartupMessages(require(lme4)))
 
 ## Using simple generated data -- fully balanced here, unbalanced later
 set.seed(1)

Modified: pkg/lme4Eigen/tests/nadrop.R
===================================================================
--- pkg/lme4Eigen/tests/nadrop.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/nadrop.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-library(lme4Eigen)
+library(lme4)
 d <- data.frame(x=runif(100),f=factor(rep(1:10,10)))
 set.seed(101)
 u <- rnorm(10)

Modified: pkg/lme4Eigen/tests/nbinom.R
===================================================================
--- pkg/lme4Eigen/tests/nbinom.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/nbinom.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,7 +1,7 @@
-library(lme4Eigen)
+library(lme4)
 
-getNBdisp <- lme4Eigen:::getNBdisp
-refitNB   <- lme4Eigen:::refitNB
+getNBdisp <- lme4:::getNBdisp
+refitNB   <- lme4:::refitNB
 
 simfun <- function(sd.u=1,NBtheta=0.5,
                     nblock=25,

Modified: pkg/lme4Eigen/tests/nlmer-conv.R
===================================================================
--- pkg/lme4Eigen/tests/nlmer-conv.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/nlmer-conv.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,7 +1,7 @@
 ### nlmer() convergence testing / monitoring / ...
 ##  -------------------
 ### The output of tests here are *not* 'diff'ed  (<==> no *.Rout.save file)
-library(lme4Eigen)
+library(lme4)
 
 ## 'Theoph' Data modeling
 

Modified: pkg/lme4Eigen/tests/nlmer.R
===================================================================
--- pkg/lme4Eigen/tests/nlmer.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/nlmer.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-library(lme4Eigen)
+library(lme4)
 
 allEQ <- function(x,y, tolerance = 4e-4, ...)
     all.equal.numeric(x,y, tolerance=tolerance, ...)

Modified: pkg/lme4Eigen/tests/nlmer.Rout.save
===================================================================
--- pkg/lme4Eigen/tests/nlmer.Rout.save	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/nlmer.Rout.save	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,5 +1,5 @@
 
-R version 2.14.2 RC (2012-02-28 r58516)
+R version 2.15.0 alpha (2012-03-15 r58752)
 Copyright (C) 2012 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
 Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -58,7 +58,7 @@
 +                          (lKe+lKa+lCl|Subject), 
 +                          Theoph, start = Th.start, tolPwrss=1e-8))
    user  system elapsed 
-  6.136   0.004   6.166 
+  7.248   0.004   7.260 
 > print(nm2, corr=FALSE)
 Nonlinear mixed model fit by maximum likelihood ['nlmerMod']
 Formula: conc ~ SSfol(Dose, Time, lKe, lKa, lCl) ~ (lKe + lKa + lCl |      Subject) 
@@ -85,7 +85,7 @@
 +                          (lKe|Subject) + (lKa|Subject) + (lCl|Subject),
 +                          Theoph, start = Th.start))
    user  system elapsed 
-   3.16    0.00    3.17 
+  3.536   0.000   3.543 
 > print(nm3, corr=FALSE)
 Nonlinear mixed model fit by maximum likelihood ['nlmerMod']
 Formula: conc ~ SSfol(Dose, Time, lKe, lKa, lCl) ~ (lKe | Subject) + (lKa |      Subject) + (lCl | Subject) 
@@ -112,7 +112,7 @@
 > system.time(nm4 <- nlmer(conc ~ SSfol(Dose, Time,lKe, lKa, lCl) ~ (lKa+lCl|Subject),
 +                          Theoph, start = Th.start, tolPwrss=1e-8))
    user  system elapsed 
-  1.848   0.000   1.856 
+  1.981   0.008   1.991 
 > print(nm4, corr=FALSE)
 Nonlinear mixed model fit by maximum likelihood ['nlmerMod']
 Formula: conc ~ SSfol(Dose, Time, lKe, lKa, lCl) ~ (lKa + lCl | Subject) 
@@ -139,7 +139,7 @@
 +                          Theoph,
 +                          start = Th.start, tolPwrss=1e-8))
    user  system elapsed 
-  1.189   0.004   1.197 
+  1.144   0.004   1.150 
 > print(nm5, corr=FALSE)
 Nonlinear mixed model fit by maximum likelihood ['nlmerMod']
 Formula: conc ~ SSfol(Dose, Time, lKe, lKa, lCl) ~ (lKa | Subject) + (lCl |      Subject) 
@@ -191,3 +191,6 @@
 lka  0.47106    0.19864    2.37
 lCl -3.21992    0.07995  -40.28
 > 
+> proc.time()
+   user  system elapsed 
+ 24.349   0.104  24.436 

Modified: pkg/lme4Eigen/tests/optimizer.R
===================================================================
--- pkg/lme4Eigen/tests/optimizer.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/optimizer.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-library(lme4Eigen)
+library(lme4)
 ## should be able to run any example with any bounds-constrained optimizer ...
 
 ## these are the only ones we know of

Modified: pkg/lme4Eigen/tests/predict.R
===================================================================
--- pkg/lme4Eigen/tests/predict.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/predict.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-library(lme4Eigen)
+library(lme4)
 gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
              data = cbpp, family = binomial)
 

Modified: pkg/lme4Eigen/tests/profile.R
===================================================================
--- pkg/lme4Eigen/tests/profile.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/profile.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-library(lme4Eigen)
+library(lme4)
 
 fm01ML <- lmer(Yield ~ 1|Batch, Dyestuff, REML = FALSE)
 
@@ -8,7 +8,7 @@
 
 (confint(tpr) -> CIpr)
 print(xyplot(tpr))
-##  comparing against lme4a reference values -- but lme4Eigen returns sigma
+##  comparing against lme4a reference values -- but lme4 returns sigma
 ## rather than log(sigma)
 stopifnot(dim(CIpr) == c(3,2),
           all.equal(unname(CIpr[".sigma",]),exp(c(3.64362, 4.21446)), tol=1e-6),

Modified: pkg/lme4Eigen/tests/refit.R
===================================================================
--- pkg/lme4Eigen/tests/refit.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/refit.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-library(lme4Eigen)
+library(lme4)
 
 ## testing refit
 ## for each type of model, should be able to

Modified: pkg/lme4Eigen/tests/simulate.R
===================================================================
--- pkg/lme4Eigen/tests/simulate.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/simulate.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-library(lme4Eigen)
+library(lme4)
 
 ## binomial (2-column and prob/weights)
 gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),

Modified: pkg/lme4Eigen/tests/test-all.R
===================================================================
--- pkg/lme4Eigen/tests/test-all.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/test-all.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,5 +1,5 @@
 if(require("testthat", quietly = TRUE)) {
-    pkg   <- "lme4Eigen"
+    pkg   <- "lme4"
     require(pkg, character.only=TRUE, quietly=TRUE)
     test_package(pkg)
 } else {

Modified: pkg/lme4Eigen/tests/throw.R
===================================================================
--- pkg/lme4Eigen/tests/throw.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/throw.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-library(lme4Eigen)
+library(lme4)
 set.seed(101)
 d <- expand.grid(block=LETTERS[1:26],rep=1:100)
 d$x <- runif(nrow(d))

Modified: pkg/lme4Eigen/tests/varcorr.R
===================================================================
--- pkg/lme4Eigen/tests/varcorr.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/varcorr.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-library(lme4Eigen)
+library(lme4)
 data(Orthodont, package="nlme")
 fm1 <- lmer(distance ~ age + (age|Subject), data = Orthodont)
 VarCorr(fm1)
@@ -15,8 +15,8 @@
 VarCorr(gm2)
 
 if (FALSE) {
-  ## testing lme4/lme4Eigen incompatibility
+  ## testing lme4/lme4 incompatibility
 ##  library(lme4)
   VarCorr(fm1)
-  lme4Eigen:::VarCorr.merMod(fm1) ## OK
+  lme4:::VarCorr.merMod(fm1) ## OK
 }

Modified: pkg/lme4Eigen/tests/vcov-etc.R
===================================================================
--- pkg/lme4Eigen/tests/vcov-etc.R	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/tests/vcov-etc.R	2012-03-15 21:05:29 UTC (rev 1661)
@@ -1,4 +1,4 @@
-stopifnot(require(lme4Eigen))
+stopifnot(require(lme4))
 ## "MEMSS" is just 'Suggest' -- must still work, when it's missing:
 if(data(ergoStool, package="MEMSS") != "ergoStool") {
     cat("'ergoStool' data from package 'MEMSS' is not available --> skipping test\n")

Modified: pkg/lme4Eigen/vignettes/PLSvGLS.Rnw
===================================================================
--- pkg/lme4Eigen/vignettes/PLSvGLS.Rnw	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/vignettes/PLSvGLS.Rnw	2012-03-15 21:05:29 UTC (rev 1661)
@@ -10,7 +10,7 @@
 {formatcom={\vspace{-1ex}},fontfamily=courier,fontseries=b,%
   fontsize=\footnotesize}
 %%\VignetteIndexEntry{PLS vs GLS for LMMs}
-%%\VignetteDepends{lme4Eigen}
+%%\VignetteDepends{lme4}
 \title{Penalized least squares versus generalized least squares
   representations of linear mixed models}
 \author{Douglas Bates\\Department of Statistics\\%

Modified: pkg/lme4Eigen/vignettes/Theory.Rnw
===================================================================
--- pkg/lme4Eigen/vignettes/Theory.Rnw	2012-03-15 20:43:03 UTC (rev 1660)
+++ pkg/lme4Eigen/vignettes/Theory.Rnw	2012-03-15 21:05:29 UTC (rev 1661)
@@ -9,7 +9,7 @@
 {formatcom={\vspace{-1ex}},fontfamily=courier,fontseries=b,%
   fontsize=\footnotesize}
 %%\VignetteIndexEntry{Computational Methods}
-%%\VignetteDepends{lme4Eigen}
+%%\VignetteDepends{lme4}
 \title{Computational methods for mixed models}
 \author{Douglas Bates\\Department of Statistics\\%
   University of Wisconsin -- Madison}

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