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Revision 1300 - (download) (annotate)
Mon Jun 12 10:52:01 2006 UTC (14 years, 8 months ago) by bates
File size: 30185 byte(s)
2006-06-12  Douglas Bates  <>

	* R/lmer.R (mcmcsamp method): Corrected arrangments of names on
	the output from mcmcsamp.

2006-06-10  Douglas Bates  <>

	* R/lmer.R (simulestimate): added C code for calculating the trace
	of the hat matrix.

2006-06-09  Martin Maechler  <>

	* R/diagMatrix.R (setAs): define coercion methods to sparse matrix

2006-06-08  Martin Maechler  <>

	* R/dgTMatrix.R (colSums): etc. All four of
	colSums(), rowSums(), colMeans(), rowMeans() now should work for
	all "Matrices".

2006-06-01  Douglas Bates  <>

	* R/lmer.R ( Add a reference line at zero and a
	background grid to the qqmath plot of ranef.lmer.

2006-05-30  Douglas Bates  <>

	* R/lmer.R (expandSlash): Functions (non-exported) to allow nested
	grouping factors to be specified in the formula as (1|foo/bar).

2006-05-27  Douglas Bates  <>

	* R/lmer.R (findbars and others): Change check of is.numeric to
	!is.language to resolve the bug reported by Jacob Wegelin.

	* src/pedigree.c (pedigree_inbreeding): Initial implementation of
	code to evaluate inbreeding coefficients without calculating T,
	based on code in Sargolzaei and Iwaisaki's paper.

2006-05-27  Douglas Bates  <>

	* R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
	generic and mer methods for isNested and denomDF. This denomDF was
	an attempt to emulate that in lme but I don't think that makes
	sense.  Use the trace of the hat matrix instead.

2006-05-17  Martin Maechler  <>

	* R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
	the C code depending on a slot structure that's no longer valid.
	* src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)

2006-05-17  Douglas Bates  <>

	*  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
	of lowerTriMatrix generic and methods to tril (also upper to triu)
	and added a general band extractor.

2006-05-16  Douglas Bates  <>

	* R/pedigree.R (pedigree): Replace sire and dam values outside the
	allowable range with NAs. Added a corresponding check in the
	validity check for the pedigree class.

	* R/[CT]sparse.R ([t]crossprod): The result of single-argument
	crossprod methods now inherits from symmetricMatrix.

2006-05-15  Douglas Bates  <>

	* R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
	generics lowerTriMatrix and upperTriMatrix along with methods for
	the Csparse virtual class.  Also added a C function Csparse_band
	that implements these methods by calling cholmod_band.

2006-05-15  Martin Maechler  <>

	* R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
	erased when it was NULL.  This led to invalid subselections!

2006-04-25  Douglas Bates  <>

	* R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
	in method for "t" so as not to lose the unit diagonal property.

2006-04-19  Douglas Bates  <>

	* R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
	and methods.  This is now an option to the ranef method for the
	mer class.

	* src/cs_utils.c: Ensure that the nz component is -1 for a
	compressed column-oriented matrix.  Minor formatting cleanup.

	* man/lmer-class.Rd: Document the qqmath method for ranef.lmer

2006-04-19  Martin Maechler  <>

	* R/Auxiliaries.R (diagU2N): new for the solve() methods in
	* R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".

2006-04-15  Douglas Bates  <>

	* src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
	in cs.[ch] and utilities to interface to that code in cs_utils.[ch].

	* R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
	for the dtCMatrix class.

2006-04-12  Douglas Bates  <>

	* R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
	and methods for it.

2006-04-12  Martin Maechler  <>

	* R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
	arguments, such that M %*% 1:6 now works
	* Tests/matprod.R: test the above

2006-04-03  Douglas Bates  <>

	* R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
	the ranef.lmer class.

	* R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
	methods to extract the posterior variances from the bVar slot.

2006-03-30  Martin Maechler  <>

	* R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
	* R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.

	* R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
	* tests/simple: (extended)

	* R/sparseMatrix.R (isTriangular): now using much improved
	* R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix

2006-03-23  Douglas Bates  <>

	* src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
	(problem report from Franklin Parlamis).  This should be done

2006-03-21  Douglas Bates  <>

	* R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
	ranef.lmer (like summary.lmer).  Add the coef.lmer class and
	update the plot methods.

2006-03-20  Douglas Bates  <>

	* R/lmer.R (resid and ranef methods):  Added methods for the
	"residuals" and "resid" generic but only for linear mixed model
	fits.  Changed the ranef method to return a list of data frames so
	that the plot methods now work.

2006-03-16  Douglas Bates  <bates@bates2>

	* src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
	dpotrf - otherwise the BLAS on Mac OS X complains and quits.

	* DESCRIPTION (Date): New release

2006-03-15  Martin Maechler  <>

	* DESCRIPTION (Version): 0.995-6  -- to be released to CRAN

	* data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
	* man/KNex.Rd: and other help files
	* tests/*.R: several ones needed adaption
	* inst/doc/Comparisons.Rnw: dito

2006-03-11  Martin Maechler  <>

	* R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix

	* tests/indexing.R: tests for new [<- methods for sparse matrices.

2006-03-10  Martin Maechler  <>

	* R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix

	* R/Tsparse.R (.ind.prep): fix out-of-range indexing

2006-03-08  Martin Maechler  <>

	* R/dMatrix.R: enable things like  M [ M < 10 ]
	* R/dgeMatrix.R: implement it

2006-03-06  Martin Maechler  <>

	* R/AllClass.R: define "summary.mer" and "*.lmer"
	* R/lmer.R (summary): summary(<mer>) computes & returns the above;
	* R/lmer.R (show): now works with summary()

2006-03-04  Martin Maechler  <>

	* R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
	* R/Auxiliaries.R (WhichintersectInd): and other utilities to
		support the above

2006-02-07  Douglas Bates  <>

	* R/lmer.R (lmer): fix initial values of offset and weights for
	Use glmFit$prior.weights for weights in a glmm.
	Allow an option usePQL = FALSE to skip the PQL steps for the
	Laplace method (and, in time, the AGQ method).

	* src/lmer.c (mer_factor): Move downdating and factoring of XtX
	into a separate function internal_mer_Xfactor to be able to call
	it from internal_bhat.

2006-01-23  Martin Maechler  <>

	* tests/Class+Meth.R (tstMatrixClass): function for much better
	testing; now again of all actual classes.

		use macros and define make_d_matrix_* and make_i_matrix_*
		where _i_ is for the ldense routines:

	* src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
	* src/ldense.c (lsyMatrix_as_lgeMatrix):

	* R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")

2006-01-16  Martin Maechler  <>

	* R/Matrix.R (Matrix): has become much "smarter" now auto-producing
		many different kinds of matrices.
	* R/*.R: quite a few new methods were needed for R CMD check with
		new Matrix().  Very good for users playing around.

2006-01-15  Martin Maechler  <>

	* src/dgeMatrix.c (dMatrix_validate): new
	* src/Mutils.c (dense_nonpacked_validate): new

	* src/dtrMatrix.c (dtrMatrix_validate): improved/fixed

2006-01-14  Douglas Bates  <>

	* R/AllClass.R (compMatrix), (generalMatrix): new virtual classes

2006-01-07  Douglas Bates  <>

	* DESCRIPTION (Version): 0.99-6 released to CRAN

	* src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
	segfault in cases with multiple non-nested grouping factors.

2006-01-03  Martin Maechler  <>

	* DESCRIPTION (Version): 0.99-4 to be released to CRAN
		(Depends): also on 'utils'

	* R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
	* R/diagMatrix.R (Diagonal): constructor and methods for
	diagonal matrices

	* R/ltTMatrix.R: new "minimal methods"

2005-12-12  Martin Maechler  <>

	* R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
	all methods (and help files).

2005-12-09  Martin Maechler  <>

	* R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
		for case (dimn.	 op  no_dimn.)

2005-11-14  Douglas Bates  <>

	* DESCRIPTION (Version): 0.99-2	 released to CRAN

2005-10-21  Douglas Bates  <>

	* R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
	by Julian Faraway.

2005-10-06  Martin Maechler  <>

	* R/Auxiliaries.R (try_as): new utility
	* R/sparseMatrix.R: use try_as() in coercion to original class

2005-09-30  Martin Maechler  <>

	* src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()

2005-09-29  Martin Maechler  <>

	* R/Auxiliaries.R (dimNamesCheck): added

	* R/Matrix.R (as.array), (as.vector): new

2005-09-28  Martin Maechler  <>

	* R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
	* R/AllClass.R: move 'factors' slot toplevel "Matrix";
		"pMatrix" now contains "sparseMatrix"

2005-09-26  Martin Maechler  <>

	* tests/Class+Meth.R: new tests; t(t(m)) == m

	* src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot

	* src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
	* src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new

	* R/dspMatrix.R: typo in "t" method

2005-09-18  Douglas Bates  <>

	* R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
	* R/Tsparse.R: instead of R/gTMatrix.R
	* R/Csparse.R: new
	* src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
	* src/Tsparse.c: new; many trivial methods calling cholmod_()
	* src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
			via cholmod

2005-09-16  Martin Maechler  <>

	* R/Auxiliaries.R (non0ind): new function using new C code
	* src/dgCMatrix.c (compressed_non_0_ij): new utility

2005-09-15  Douglas Bates  <bates@localhost.localdomain>

	* src/chm_common.h: header file required by all C sources that
	call CHOLMOD functions.	 It defines a cholmod_common structure
	called 'c' whose address is passed as the last argument to
	(virtually) every CHOLMOD function.

	* src/Pattern.c: Simple example of the use of CHOLMOD.

	* src/init.c: initialize and finalize the cholmod_common structure.

	* src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
	LDL and CCOLAMD from the U. of Florida sparse matrix library.

2005-09-08  Martin Maechler  <>

	* inst/test-tools.R: new file collecting the utility functions used
		in ./tests/*.R

	* R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
	* R/Matrix.R (cbind2): methods for NULL and missing

2005-08-31  Martin Maechler  <>

	* R/AllClass.R: new "index" class for "[" and "[<-":
		First cut at "symmetricMatrix" and "triangularMatrix"
	* R/gTMatrix.R (.ind.prep): new function;
		Logical and character indexing now work too.
	* R/Matrix.R: cheap "[<-" methods for denseMatrix now work
	* tests/indexing.R: new, including *
	* tests/dgTMatrix.R: new

2005-08-29  Douglas Bates  <>

	* src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
	indicator pos not being updated.  Also enforced upper triangular
	for symmetric case.  Need to coerce edges component of elements of
	edge list - grr! (Why don't they define their classes cleanly?)

2005-08-26  Martin Maechler  <>

	* R/Matrix.R:  added first "[<-" methods; not yet functional
	* R/denseMatrix.R: dito
	* man/Subassign-methods.Rd: new help file for these

2005-08-25  Martin Maechler  <>

	* DESCRIPTION (Version): 0.98-6

	* R/denseMatrix.R: new file for "[" fallback methods for all dense

2005-08-19  Martin Maechler  <>

	* src/lgCMatrix.c (lcsc_to_matrix): new; need for
		as( <logical>, "matrix")

	* R/pMatrix.R: coercion to "lgTMatrix"

	* R/gTMatrix.R: new virtual class to define "[" methods for.
	* man/gTMatrix-class.Rd:
	* General slight re-organization of where "[" methods are defined.
	  more to come.

2005-08-18  Douglas Bates  <>

	* DESCRIPTION (Version): 0.98-5	 released to CRAN

	* src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
	* .....

2005-08-18  Douglas Bates  <bates@localhost.localdomain>

	* R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
	or glmer objects.

2005-08-17  Martin Maechler  <>

	* DESCRIPTION (Version): 0.98-4 : upload to CRAN

2005-08-16  Douglas Bates  <bates@localhost.localdomain>

	* R/HBMM.R: finish re-writing R-only code.

2005-08-15  Douglas Bates  <bates@localhost.localdomain>

	* man/externalFormats.Rd: move documentation for writeHB and
	writeMM here.

	* src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
	(suggested by Paul Roecker).

	* tests/validObj.R (assertError): Comment out test that is failing
	after recent changes in r-devel.

2005-08-11  Martin Maechler  <>

	* R/AllClass.R: intermediate virtual class "denseMatrix"
	* man/denseMatrix-class.Rd
	* NAMESPACE: export it, and also export
	* man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"

2005-08-10  Douglas Bates  <>

	* DESCRIPTION (Version): 0.98-3 to CRAN

	* src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
	matrix_solve code (which was really, really wrong).

2005-08-07  Douglas Bates  <>

	* DESCRIPTION (Version): 0.98-2

	* R/HBMM.R (readHB), (readMM): read Matrix Market formats

	* R/lmer.R (abbrvNms): new
	* R/lmer.R (mcmcsamp): allow transformed parameters
	* src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
	for the Harwell-Boeing and the MatrixMarket formats.

2005-08-04  Martin Maechler  <>

	* man/dtrMatrix-class.Rd: add examples
	* man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM

	* TODO: note the dtpMatrix (docu) bug

	* R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
	in order to ensure that new as.matrix() is used by old functions,
	e.g., svd(), qr(), eigen(), dist(),..;
	      apply(), also matplot() or pairs().

2005-08-03  Martin Maechler  <>

	* R/lmer.R: add 'fixme' comments and move the linear vs glm check;
	  add comments about 'control' / lmerControl() arguments

2005-07-27  Douglas Bates  <>

	* man/sleepstudy.Rd: Added the sleep data set.
	* DESCRIPTION (Version): 0.98-1	 released to CRAN

2005-07-12  Douglas Bates  <>
	* man/sleepstudy.Rd: Added the sleep data set.

	* R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
	.Call calls that were producing spurious output.

2005-07-05  Douglas Bates  <>

	* R/lmer.R (lmer): stored updated variance component estimates in
	mer object for the generalized model.  (Bug reported by Renaud

2005-07-03  Douglas Bates  <>

	* src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
	unidimensional case.

2005-06-08  Douglas Bates  <>

	* DESCRIPTION (Version): 0.96-1

	* moved	 lmer-class' R and C code moved from lme4 to here

2005-06-04  Douglas Bates  <>

	* R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
	(reported by Guissepe Ragusa <>)

2005-06-02  Douglas Bates  <>

	* src/ Forgot to update this when Makefile changed.

2005-05-11  Douglas Bates  <>

	* src/dgCMatrix.c (csc_transpose): Simplified function fixing a
	bug reported by Kurt Hornik and Michael Hahsler.

2005-05-10  Douglas Bates  <>

	* src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
	logical sparse matrices.  These will also be used in the symbolic
	analysis for lmer objects.

	* src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
	of b to the result.  Fixes bug reported by

2005-05-06  Douglas Bates  <>

	* src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
	colMeans, colSums, rowMeans and rowSums.

2005-04-18  Douglas Bates  <>

	* src/lgCMatrix.[ch]: code for _validate method and stub for
	multiplication operation.

	* src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
	to dgetrs.

	* src/init.c: Fix cut-and-paste error in definition of

	* src/{many files}: Tighten code by using ALLOC_SLOT.

2005-04-15  Douglas Bates  <>

	* R/AllClass.R: Add lgTMatrix and lgCMatrix classes

	* DESCRIPTION: Eliminate import of stats.

2005-04-06  Douglas Bates  <>

	* R/AllClass.R : add logical sparse matrix classes

2005-04-01  Martin Maechler  <>

	* R/dgTMatrix.R: add "[" method for triplet matrices
	* R/sparseMatrix.R: and other sparse ones; --> add show() for sparse

2005-03-31  Douglas Bates  <>

	* DESCRIPTION (Version): release 0.95-5 to CRAN

	* R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
	* R/sparseMatrix.R: %*%, crossprod()
	* R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
	* man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
	* src/lmer.c (lmer_fitted): fix thinko

2005-03-26  Martin Maechler  <>

	* R/AllClass.R: add two virtual sparse classes ``on top''

2005-03-24  Martin Maechler  <>

	* R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
		correspondingly fix examples and tests/ since new()
		doesn't work for virtual classes.

2005-03-17  Martin Maechler  <>

	* R/Matrix.R (as.matrix): method and one for unname()
	* tests/dpoMatrix.R: tests should now be less platform dependent;
	  also run for R 2.1.0; using as.matrix()

2005-03-15  Douglas Bates  <>

	* R/pMatrix.R: "pMatrix" class added
	* ....

2005-03-14  Douglas Bates  <>

	* R/dtpMatrix.R: Add unpack method and an example.

	* src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
	of general symmetric matrices and associated S4 methods.

2005-03-10  Martin Maechler  <>
2005-03-05  Martin Maechler  <>

	* R/dgeMatrix.R (setAs): and many other files: more coercion,
	  crossprod() and "%*%" methods added; tests, too.
	* tests/matprod.R: new, for testing these

2005-03-03  Douglas Bates  <>

	* src/lmer.c (lmer_fitted): Added.

2005-03-02  Douglas Bates  <>

	* R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix

2005-02-28  Douglas Bates  <>

	* src/*.c,po/,inst/po: Internationalization and localization of
	the package.

	* src/ldl.[ch]: Removed these as their contents are referenced in the
	R_ldl.c file.

	* src/flame.[ch]: Removed these source files.

	* src/dtrMatrix.c (make_array_triangular): Move to Mutils

	* src/LU.[ch],src/init.c: absorb in factorizations

	* src/Mutils.h: prepare for internationalization

	* src/cblas.h: move the enum definitions to Mutils.h and remove
	this file

2005-02-26  Martin Maechler  <>

	* R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods

	* R/dtrMatrix.R: fix t() method

	* R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
	* NAMESPACE: export them (and import generics from "methods")
	* tests/group-methods.R : and test them.

	* src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
	border case

2005-02-24  Douglas Bates  <>

	* DESCRIPTION (Version): 0.95-2	 released to CRAN

	* src/dgBCMatrix.c:
	* src/lmer.c: many changes
	* ...

2005-02-04  Martin Maechler  <>

	* R/Matrix.R: add more sophisticated show() method.

2005-02-02  Douglas Bates  <>

	* */* : almost complete reorganization of classes.

2005-01-26  Douglas Bates  <>

	* R/AllGeneric.R: Added matrix exponential generic expm and a method
	for the geMatrix class.

2005-01-24  Douglas Bates  <>

	* src/Makefile (clean): Remove *.a and *.so

	* man/cscBlocked-class.Rd: Remove reference to the lmer-class.

2005-01-23  Douglas Bates  <>

	* src/lmer.c (Lind): Definition of Lind was backwards.	This only
	had an effect in cases with more than 2 grouping factors.

2005-01-03  Douglas Bates  <>

	* src/lmeRep.c (lmer_variances): change from lmeRep to lmer

2004-12-23  Douglas Bates  <>

	* src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
	and R_useDynamicSymbols (suggested by B.D.Ripley).

2004-12-14  Douglas Bates  <>

	* R/sscMatrix.R: Add determinant methods

	* src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
	for tripletMatrix to matrix.

2004-12-13  Douglas Bates  <>

	* R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
	no longer used.

	* src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
	with dynamic allocation of scratch arrays.

	* src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
	for multivariate random effects with multiple grouping factors.
	Fixes part but not all of #15.

2004-12-03  Douglas Bates  <>

	* src/lmeRep.c (lmeRep_factor): order of operations for multiple
	scalar grouping factors corrected.

2004-11-29  Douglas Bates  <>

	* src/bCrosstab.c: remove diag_update which is no longer used

2004-11-16  Douglas Bates  <>

	* src/Metis_utils.c: Move metis.h include to C sources so that the
	.h file can be included.

2004-11-12  Douglas Bates  <>

	* src/LU.c,geMatrix.c,trMatrix.c, etc.:
	Complete allocation of slots in NEW_OBJECT.

	* src/Mutils.h: Moved list of symbols to an include file

2004-11-11  Douglas Bates  <>

	* src/geMutils.c (Matrix_init): remove unused function

2004-11-10  Douglas Bates  <>

	* src/cscMatrix.c (csc_to_imagemat): removed unused function

2004-11-05  Douglas Bates  <>

	* src/ (SOURCES_C): Keep consistent with Makefile

2004-10-27  Douglas Bates  <>

	* R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls

2004-10-04  Douglas Bates  <>

	* src/init.c: Created R_init_Matrix and added registration of C

2004-10-02  Douglas Bates  <>

	* R/tripletMatrix.R: Force a require(lattice) for the image methods.

2004-06-15  Douglas Bates  <>

	* man/trMatrix-class.Rd: Escape the % chars in .Rd files.

2004-04-20  Douglas Bates  <>

	* src/ ($(SHLIB)): Modifications per Uwe Ligges.

2004-04-19  Douglas Bates  <>

	* src/ssclme.c (ssclme_update_mm): fix logic error in

2004-04-18  Douglas Bates  <>

	* src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
	in the order of unconstrained and constrained parameters.
	(ssclme_gradient): Added the gradients (not yet correct for
	multidimensional, unconstrained case).

2004-04-14  Douglas Bates  <>

	* src/ssclme.c (ssclme_EMsteps): Fix logic in REML update

	* src/ Remove unneeded ranlib call

2004-04-12  Douglas Bates  <>

	* DESCRIPTION (Version): New release

	* src/ Update to umfpack removal.

2004-04-05  Douglas Bates  <bates@bates2_home>

	* src/triplet_to_col.c: Create triplet_to_col as a native
	function, not the version from umfpack.	 There were problems with
	the configuration of UMFPACK for 64-bit processors and there was
	only one umfpack routine being used so I moved it here.

2004-04-04  Douglas Bates  <bates@bates2_home>

	* src/ssclme.c (ssclme_variances): New function.

2004-03-28  Douglas Bates  <bates@bates2_home>

	* src/ssclme.c (ssclme_fitted): Added function.

2004-03-27  Douglas Bates  <bates@bates2_home>

	* src/ssclme.c (ssclme_transfer_dimnames): Add new function to
	store the dimnames in the XtX and bVar slots
	(ssclme_update_mm): Change the dimensions of the bVar slot
	components and the returned value from ssclme_ranef.

2004-03-18  Douglas Bates  <>

	* R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
	Moved the pdMat classes from the lme4 package.

2004-03-02  Douglas Bates  <>

	* man/ssclme-class.Rd: Update definition and documentation of the
	ssclme class to include the DIsqrt slot.

	* src/ssclme.c (ssclme_deviance): Modify order of computation
	(much faster using dsyrk, a level 3 BLAS routine).

	* src/Makefile (SUBLIBS): Change definition (K. Hornik)

2004-02-28  Douglas Bates  <>

	* tests/ssclme.R: Modify the test to account for the permutation
	of the levels of the grouping factors.

2004-02-23  Douglas Bates  <>

	* R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
	directly into the ssclme class definition.

2004-02-22  Douglas Bates  <>

	* DESCRIPTION (Date): New release

	* man/ssclme-class.Rd: new file.

	* src/ssclme.c (ssclme_loglik): major revisions in design.  It
	works and it's fast!

2004-02-17  Douglas Bates  <>

	* src/taucs/ (lib): Change "ar" to "$(AR)" (B.Ripley)

2004-02-16  Douglas Bates  <>

	* DESCRIPTION (Date): New release

	* NAMESPACE: Don't export ssclme.

	* data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
	school data.

2004-02-11  Douglas Bates  <>

	* src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
	keep track of the fixed-effects and the response.  Counts also
	gets an extra element, which is always one.

	* src/ldl.c: Include these routines from Tim Davis' LDL package.

2004-02-10  Douglas Bates  <>

	* src/cscMatrix.c (csc_transpose): new function

	* src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
	(csc_components_transpose): new function

2004-02-06  Douglas Bates  <>

	* src/triplet.c (triplet_validate): Fix Dim slot on generated

2004-01-30  Douglas Bates  <>

	* R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.

	* src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
	and all other .h files in src.

	* src/ This and other files contributed
	by Brian Ripley.

2004-01-27  Douglas Bates  <>

	* R/syMatrix.R: Added methods for "%*%".

	* R/Hilbert.R (Hilbert): Changed Hilbert function to return a
	poMatrix object.

2004-01-26  Douglas Bates  <>

	* man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.

2004-01-25  Douglas Bates  <bates@bates2_home>

	* inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.

	* R/csc.R: Convert all cscMatrix classes to use Dim slot instead
	of nrow.

2003-12-31  Douglas Bates  <>

	* src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into

2003-12-08  Douglas Bates  <>

	* src/taucs.h: Accidently referred to global header files
	instead of local files.

2003-12-04  Douglas Bates  <>

	* R/AllClass.R: Lots of changes.  Removed all the lapack++ code
	and methods and replaced all classes with S4 classes.

2003-04-19  Douglas Bates  <>

	* R/det.R,man/det.Rd: Change name of det generic to determinant

	* src/ Change method of calculating determinants

2003-02-03  Douglas Bates  <>

	* DESCRIPTION (Version): removed empty data directory as requested
	by CRAN maintainers.  Changed version number and date.

2002-10-23  Douglas Bates  <>

	* src/laindex.h: Applied patches from Brian Ripley for compilation
	under Windows.

	* Added and src/ as requested by Brian

2002-05-03  Douglas Bates  <>

	* src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt

2002-04-24  Douglas Bates  <>

	* Replaced with
	contributed by Kurt Hornik.

	* aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
	version for R-1.5.0

2001-12-10  Douglas Bates  <>

	* man/eigen.Rd: Removed the .Alias in the example
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