[Lme4-commits] r1514 - in branches/roxygen: . R

[noreply at r-forge.r-project.org]

Author: dmbates
Date: 2012-01-25 00:30:08 +0100 (Wed, 25 Jan 2012)
New Revision: 1514

Modified:
   branches/roxygen/DESCRIPTION
   branches/roxygen/R/lme4Eigen-package.R
   branches/roxygen/R/lmer.R
Log:
Update version and dependencies.  Use Matrix::image instead of image for sparse matrices.  Remove export of image.


Modified: branches/roxygen/DESCRIPTION
===================================================================
--- branches/roxygen/DESCRIPTION	2012-01-24 22:09:33 UTC (rev 1513)
+++ branches/roxygen/DESCRIPTION	2012-01-24 23:30:08 UTC (rev 1514)
@@ -1,20 +1,47 @@
 Package: lme4Eigen
-Version: 0.9996875-7
-Date: 2011-12-28
+Version: 0.9996875-8
+Date: 2012-01-24
 Title: Linear mixed-effects models using Eigen and S4
 Author: Douglas Bates <bates at stat.wisc.edu>,
-        Martin Maechler <maechler at R-project.org> and
-	Ben Bolker <bbolker at gmail.com>
+    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.
- The models and their components are represented using S4 classes and
- methods.  The core computational algorithms are implemented using the
- Eigen C++ library for numerical linear algebra and RcppEigen "glue".
-Depends: methods, R(>= 2.14.0), Matrix(>= 1.0), lattice, stats, minqa(>= 1.1.15)
+    The models and their components are represented using S4 classes and
+    methods.  The core computational algorithms are implemented using the
+    Eigen C++ library for numerical linear algebra and RcppEigen "glue".
+Depends:
+    lattice,
+    methods,
+    R(>= 2.14.0),
+    stats,
+    minqa(>= 1.1.15)
 LinkingTo: Rcpp, RcppEigen
-Imports: graphics, grid, nlme, splines, MatrixModels(>= 0.2.0)
-Suggests: mlmRev, MEMSS, boot, MASS, RUnit
+Imports:
+    Matrix(>= 1.0),
+    graphics,
+    grid,
+    nlme,
+    splines
+Suggests:
+    mlmRev,
+    MEMSS,
+    boot,
+    MASS,
+    RUnit
 LazyLoad: yes
 LazyData: yes
 License: GPL (>=2)
 URL: http://lme4.r-forge.r-project.org/
+Collate:
+    'AllClass.R'
+    'AllGeneric.R'
+    'GHrule.R'
+    'jml.R'
+    'lme4Eigen-package.R'
+    'lmer.R'
+    'lmList.R'
+    'mlirt.R'
+    'profile.R'
+    'sparsegrid.R'
+    'utilities.R'

Modified: branches/roxygen/R/lme4Eigen-package.R
===================================================================
--- branches/roxygen/R/lme4Eigen-package.R	2012-01-24 22:09:33 UTC (rev 1513)
+++ branches/roxygen/R/lme4Eigen-package.R	2012-01-24 23:30:08 UTC (rev 1514)
@@ -321,7 +321,7 @@
 ##' (fm5 <- lmer(strength ~ (1|batch) + (1|cask), Pastes))
 ##' 
 ##' L <- getME(fm1, "L")
-##' image(L, sub = "Structure of random effects interaction in pastes model")
+##' Matrix::image(L, sub = "Structure of random effects interaction in pastes model")
 ##' 
 NULL
 
@@ -369,8 +369,8 @@
 ##' (fm1 <- lmer(diameter ~ (1|plate) + (1|sample), Penicillin))
 ##' 
 ##' L <- getME(fm1, "L")
-##' image(L, main = "L",
-##'       sub = "Penicillin: Structure of random effects interaction")
+##' Matrix::image(L, main = "L",
+##'               sub = "Penicillin: Structure of random effects interaction")
 ##' 
 NULL
 

Modified: branches/roxygen/R/lmer.R
===================================================================
--- branches/roxygen/R/lmer.R	2012-01-24 22:09:33 UTC (rev 1513)
+++ branches/roxygen/R/lmer.R	2012-01-24 23:30:08 UTC (rev 1514)
@@ -786,7 +786,7 @@
 ##' \item{cnms}{a list of column names of the random effects according to
 ##'     the grouping factors}
 ##' @importFrom Matrix sparseMatrix rBind drop0
-##' @importMethodsFrom Matrix coerce image
+##' @importMethodsFrom Matrix coerce
 ##' @export
 mkReTrms <- function(bars, fr) {
     if (!length(bars))