The R Project SVN R-packages

2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>

    * DESCRIPTION (Date, Version): 0.9975-10 with new date.

    * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
    * tests/simple.R: test the above and some of these coercions:

    * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
        be careful to avoid infinite recursion, using new coercions in
    * R/ngCMatrix.R and nsC... and ntC...
    * R/lsparseMatrix.R: ditto

    * R/SparseM-conv.R: more conversion, notably for triplet matrices.

    * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
    * R/Rsparse.R: reactivate .Call()s

    * tests/Class+Meth.R: a bit more on actual classes

2007-02-04  Douglas Bates  <bates@stat.wisc.edu>

    * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()

2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>

    * DESCRIPTION (Version): 0.9975-10 to upload

    * tests/Class+Meth.R (tstMatrixClass): require coercions to
    specific classes less unconditionally.

    * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()

    * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()

    * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
    * R/Rsparse.R (.R.2.C): R-level workaround since C-level
    R_to_CMatrix segfaults on one platform.
    Eliminate most coercion method to *specific* classes, and replace
    with virtual classes coercions.


2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>

    * src/init.c: export the CHM...._validate() placeholders, since
    they *are* called.

    * tests/Class+Meth.R (classCanCoerce): and starting to test
    all as(<from>, <to>)

2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Tsparse.R ([): more care when subsetting triangular Tsparse
    * tests/indexing.R: tested now
    * tests/indexing.Rout.save: updated

    * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
    * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
    appropriate.

    * NAMESPACE: export a trivial
    * R/Matrix.R: drop() Matrix-method

    * R/AllClass.R: moved all prototypes to virtual super classes.

    * R/Rsparse.R: many more coercions to have less exceptions in
    * tests/Class+Meth.R:

    * R/Ops.R (Compare): tweak for case with NA
    * tests/simpl.R: hence another 'FIXME' eliminated

2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
    objects.

    * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
      and more of "!", "&", "|", all, any; coercions

    * R/Rsparse.R: many coercions (which enable quite a few other
    methods), thanks to enhancements in
    * src/dgCMatrix.c (R_to_CMatrix): new, and
    * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
    symmetric & triangular and ..RMatrix objects.

    * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
    renamed file from src/dsTMatrix.c;
    now dealing with symmetric and triangular Tsparse coercions, both
    to dense and general.

2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>

    * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.

    * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
    where sensible when the <numeric> is of length > 1.

2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Matrix.R ([<-): for M[] <- value: fix length

2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Auxiliaries.R (n2l_Matrix): new, to be used in
    * R/ndenseMatrix.R: new coercions n* -> l*

2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/triangularMatrix.R: new file; simple triu() and tril() methods.

    * R/Ops.R ("Logic"): and other "Ops", many updates

2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>

    * src/Mutils.h (SET_DimNames): new utility

    * R/Auxiliaries.R (nnzero): improved and now exported via

    * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects

2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/diagMatrix.R (!): fix typo.

2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Auxiliaries.R (as_Csparse): and quite a few others:
        allow to pass class definition --> speedup
    * R/sparseMatrix.R: apply the above

    * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.

    * src/Mutils.h (mMatrix_as_geMatrix): new, based on
    * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
    old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".

    * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()

    * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
    and use it for "sparse*" as well, since it's faster than the
    as_Csparse(.) way.

2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.

2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
    as method for   M[ ij ] <- v
    * R/Csparse.R:: go via Tsparse for "M[ij] <- v"

    * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
    FALSE answer

    * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
    * tests/indexing.R: test it, and some of the above

2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Auxiliaries.R (is_duplicatedT): new utility

2007-01-05  Douglas Bates  <bates@stat.wisc.edu>

    * src/init.c (R_init_Matrix): export cholmod_scale

2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
    base::as.matrix to (x, ...)

2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
    file; start using "Logic", hence

    * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
    * NAMESPACE: import and export "Logic"

2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>

    * src/zpotfr.f and dependencies: use LAPACK 3.1 version
    only needed previously to R version 2.5.0.

2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>

    * DESCRIPTION (Date, Version): 0.9975-8, ready for release

    * R/Tsparse.R (replTmat): fix subassignment of triangular
    * R/Csparse.R (replCmat): ditto
    * tests/indexing.R: more tests, incl the above fix

2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Auxiliaries.R (drop0): extend for non CSparse
    * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix

    * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
        use uplo correctly (!); other places: use uplo_P() macro

    * R/Csparse.R (replCmat): call diagU2N() when needed
    * R/Tsparse.R (replTmat): ditto

    * src/dtCMatrix.c (tCMatrix_validate): new
    * src/dtTMatrix.c (tTMatrix_validate): new, used in
    * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.

    * R/diagMatrix.R (replDiag): to use in [<-

2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
        also more general diagU2N().

2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/bind2.R: new file for all cbind2(), rbind() methods moved here
    from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.

2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>

    * tests/bind.R: a few more cases
    * R/Auxiliaries.R (.M.kind): also work for atomic vectors

    * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
    * R/ddenseMatrix.R (cbind2/rbind2)
    * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
    * tests/indexing.R
    * tests/indexing.Rout.save: updated

2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
    * tests/indexing.R

2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
    align with proper position of "0", i.e., right for integers.
    argument 'align' by default is "fancy".

2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
    * R/Csparse.R: and fix "Compare" for more cases.
    * tests/Class+Meth.R: test some of these (m == m, m != m)

2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/lsparseMatrix.R: all() and any() methods
    * R/ldenseMatrix.R:  ditto
    * NAMESPACE, R/Matrix.R: ditto

    * man/all-methods.Rd: document them minimally

    * tests/simple.R: add a few examples for these

2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Tsparse.R ([): fix long standing typo in symmetric case
    * man/dsCMatrix-class.Rd: add example exhibiting the above case

2006-12-10  Douglas Bates  <bates@stat.wisc.edu>

    * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
    to LL before converting to a sparse matrix. (The LDL form can be
    converted to a sparse matrix but it is implicitly a unit
    triangular matrix and a diagonal matrix overwritten on the diagonal.)

2006-12-09  Douglas Bates  <bates@stat.wisc.edu>

    * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.

2006-12-08  Douglas Bates  <bates@stat.wisc.edu>

    * DESCRIPTION (Version): updated -> release 0.9975-7
    * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p

2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method

2006-11-29  Douglas Bates  <bates@stat.wisc.edu>

    * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
    * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
    is exactly singular.

2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>

    * DESCRIPTION (Date): updated -> release 0.9975-6

2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
    now returns symmetric.

    * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x

    * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
    * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value

    * R/Auxiliaries.R (.type.kind): added

2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>

    * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
    running src/CSparse_install.sh

    * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.

2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>

    * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
    * R/dsCMatrix.R (solve): "fully-sparse" using the above.

    * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"

    * tests/Class+Meth.R (tstMatrixClass): now assure
    the (important in method programming) property :

        ###>>  Every "Matrix" is either
        ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"

        (where "*" stands for "Matrix")

    * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>

    * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
    * tests/validObj.R: checks for "comparison"

    * R/sparseMatrix.R ([): improved indexing for sparse;
        trying to keep <symmetric>[ n, n] symmmetric

    * tests/indexing.R: indexing for logical sparse now ok


2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>

        * src/Tsparse.c: use xTsparse_validate() , and hence remove

        * src/{ltC,lsC,lgT}Matrix.[ch]: removed

2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/AllClass.R (Matrix-class): check length of dimnames in validity.

    * tests/simple.R: validObject() checking the above.

    * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
    replacing both dgCMatrix_validate and lgCM*.

    * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
    fix dimnames setting in other places.
    * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames

2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)

    * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
    symmetry test, via
    * R/Auxiliaries.R (.as.dgC.0.factors):

2006-11-01  Douglas Bates  <bates@r-project.org>

    * R/Csparse.R,src/Csparse.c,tests/matprod.R,
    man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
    <CsparseMatrix>) added

2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>

    * tests/matprod.R: add a variation of Harri's example

    * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
    recursive infinitely.

    * R/dgCMatrix.R: + solve(<sparse>, <sparse>)

    * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R

2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>

    * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
    matrix if possible; test m+m == 2*m; now test dgRMatrix.
    * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
    satisfy the above test.

2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added

    * R/dgCMatrix.R: solve(a, b="missing") based on
    * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
    RHS = NULL.

    * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
    add more (needed) [t]crossprod() methods.

    * man/ddiMatrix-class.Rd: more info, notably on 'diag'

    * R/Auxiliaries.R (as_CspClass): cleanup
    (drop0): internal utility for "Csparse_drop(*, 0)"
    (.bail.out.2): encourage active feedback

2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/dMatrix.R(Compare): new(), then slots [no validity check]

    * src/Csparse.c (Csparse_validate): fixed (and more efficient in
    non-valid or 'sorted' case).

    * R/dsparseMatrix.R: add "chol" method.
    * R/ddenseMatrix.R: ditto

    * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
    * NAMESPACE (Ops)
    * R/diagMatrix.R (diag2T): simple utility used "higher level"
    coercion; deprecating direct lower level coercions.

    * R/*.R (seq): use seq_len() and seq_along() where possible.


2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>

    * DESCRIPTION (Version): 0.9975-5 ready for release

2006-10-20  Douglas Bates  <bates@stat.wisc.edu>

    * src/init.c (R_init_Matrix): export more cholmod CCallable functions.

2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/AllClass.R (corMatrix): add 'validity' check;
        comment out unused "LDL" class definition
    * NAMESPACE: mention, but do not export "LDL" class
    * R/corMatrix.R: new (simple), needed for R-devel with
    * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
      coerce and t() exceptions for all 5 'Mat.MatFact' classes.

2006-10-19  Douglas Bates  <bates@stat.wisc.edu>

    * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
    use Rprintf and R's error handling.

2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
    * tests/matprod.R: add tests for the bug fixed.

2006-10-11  Douglas Bates  <bates@stat.wisc.edu>

    * src/HBMM.[ch]: remove HarwellBoeing format for writing.
    * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c

2006-10-06  Douglas Bates  <bates@stat.wisc.edu>

    * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.

2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>

    * DESCRIPTION (Version): 0.9975-3

    * R/diagMatrix.R (bdiag): new function constructing block diagonal
    (sparse) matrices.
    * man/bdiag.Rd: docu + examples

    * R/Csparse.R (replCmat): calling new Csparse_drop() now.

    * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
    * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)

    * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
    that result is sparse or diagonal (and not dense).

    * man/Subassign-methods.Rd: fix examples

    * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
    should always return a sparse (and not sometimes a diagonal) matrix.

2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Matrix.R ([<-): also for value "Matrix" or "matrix"

2006-10-04  Douglas Bates  <bates@stat.wisc.edu>

    * DESCRIPTION (Version): 0.9975-2

    * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols

2006-10-02  Douglas Bates  <bates@R-project.org>

    * tests/dg_Matrix.R: Simplify test taking into account new code.

2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases

    * R/lsTMatrix.R: new files w/ missing methods
    * R/nsTMatrix.R:  "  'for completeness'

    * tests/Class+Meth.R: a bit less 'not.ok.classes'

    * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"


2006-09-28  Douglas Bates  <bates@R-project.org>

    * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
    included.

    * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
    Export C-callable functions used in Zt_create in lme4.

2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>

    * DESCRIPTION (Version): 0.9975-1

    * tests/simple.R: less checks fail; using NA, found that our
        kronecker() is not base-compatible with NA's.

    * R/dMatrix.R: "Compare" method now implemented for all cases

    * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility

    * man/dtpMatrix-class.Rd: mention length of 'x' slot

    * src/dtpMatrix.c (dtpMatrix_validate): fix check
    * src/dspMatrix.c (dspMatrix_validate): ditto

    * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
      including coercion to [nl]tTMatrix.

    * R/diagMatrix.R (show): print a header line as for other classes.

2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>

    * src/Makefile.win (SUBDIRS): fix typo

2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>

    * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN

2006-09-18  Douglas Bates  <bates@stat.wisc.edu>

    * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
    symmetric and y missing in R code using %*% (cholmod_aat doesn't
    accept a symmetric matrix).
    * tests/group-methods.R: Uncomment test of crossprod applied to
    lsCMatrix objects.

2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/AllClass.R (symmetricMatrix): add validity method (available
    in C for a long time). Many "n..Matrix": drop (wrong) validity arg.

    * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)

    * tests/indexing.Rout.save:
    * tests/indexing.R: additions, mainly for 'lsparse'

    * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
    case.

    * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()

2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
        as 'N' (1-letter - Ok?)

    * tests/group-methods.R: add test for logical + NAs

    * R/dMatrix.R ("Compare"): fix to work with NA's

    * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.

    * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
        which is implemented.

2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>

    * src/chm_common.c: coerce logical <-> double instead of
    typecasting;  needed for "l" matrix handling in cholmod.

    * tests/other-pkgs.R (graph): small extension in "graph" checks.

    * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
    (Tsp2grNEL): other fixes needed

2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
        Matrices, since "lMatrix", also "lsparseM" can have NA
    * R/ndenseMatrix.R, etc: new source files
    * man/nsparseMatrix-classes.Rd, etc: new help files
    * tests/: adaptions
    * src/chm_common.c (chm_dense_to_SEXP): and others:
        new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
    * src/Csparse.c, etc: ditto

2006-09-11  Douglas Bates  <bates@R-project.org>

    * src/Mutils.[ch],init.c inst/include/*.h: Move the
    alloc_d**Matrix functions to the lme4 package.

2006-09-09  Douglas Bates  <bates@R-project.org>

    * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
    fixed

2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/lMatrix.R: new

    * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()

    * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
    * man/tcrossprod.Rd: ditto

2006-09-08  Douglas Bates  <bates@stat.wisc.edu>

    * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
    for exported functions
    * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
    Remove partitioning algorithms for sparse matrix reordering.  The
    copyright on the Metis code was problematic and the methods were
    rarely used.
    * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
    operations are now done entirely in CHOLMOD code.

2006-09-06  Douglas Bates  <bates@R-project.org>

    * src/Mutils.h: Remove functions that are no longer used.

2006-09-04  Douglas Bates  <bates@R-project.org>

    * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
    * src/DEPS.mkf: update

2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>

    * created branches/Matrix-for-R-2.3.x;  on trunk: do
    * DESCRIPTION (Version): 0.9975-0
    (Depends): R (>= 2.4.0)

2006-09-01  Douglas Bates  <bates@R-project.org>

    * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL

2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
    * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"

    * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]

2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/sparseMatrix.R (Arith): moved Arith group method one-level up
    from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
    * R/dsparseMatrix.R: ditto
    * R/Csparse.R: ditto

2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/dMatrix.R (Compare): improve availability of "<", etc
    * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)

2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
    of a 0-index which was used as 1-index (..hmm)

    * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix

    * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
    * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
    (.is.diagonal): ditto

    * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's

    * R/Matrix.R (Matrix): also work for NA data

2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
    in all cases.

2006-08-27  Douglas Bates  <bates@R-project.org>

    * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
    (ddense_band): Added triu, tril and band for ddenseMatrix objects.

2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

    * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
    subclasses of "ddenseMatrix"
    * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
    * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
    instead of half dozen specialized ones.

2006-08-25  Douglas Bates  <bates@R-project.org>

    * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
    <tillard@cirad.fr> - ordering standard errors to match effects.

2006-08-24  Douglas Bates  <bates@R-project.org>

    * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
    on R_ldl.
    * R/lCholCMatrix.R,
    src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
    * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
    * many files in ./R and ./src: Use more general version of
    dup_mMatrix_as_dgeMatrix to simplify method definitions.
    * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
    dtpMatrix, dspMatrix and dppMatrix conversions.


2006-08-23  Douglas Bates  <bates@R-project.org>

    * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
    Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
    * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
    dgeMatrix_crossprod (may need to do this in other places).
    * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
    generic and method for dsCMatrix.  Use CHOLMOD for chol().

2006-08-22  Douglas Bates  <bates@R-project.org>

    * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
    types of classed Matrices, matrices or numeric or logical vectors.
    * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
    * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
    to Mutils.h (as an inline) and change name to Matrix_check_class;
    fixes in as_cholmod_factor and chm_factor_to_SEXP.
    * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
    dsCMatrix_matrix_solve.  Comment out vestigial functions.
    * src/Csparse.c: use diag_P and uplo_P macros.

2006-08-21  Douglas Bates  <bates@R-project.org>

    * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
    valgrind.
    * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
    inverses.
    * src/sparseQR.c (sparseQR_validate): add new validation test, fix
    -Wall warnings.
    * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
    Use dup_mMatrix_as_dgeMatrix.

2006-08-20  Douglas Bates  <bates@R-project.org>

    * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
    * tests/sparseQR.R: Added
    * man/sparseQR-class.Rd: Document methods for qr.* generics
    * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors

2006-08-19  Douglas Bates  <bates@R-project.org>

    * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
    Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
    and qr.fitted.
    * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
    * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR

2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
    the base version has no "..." argument.

    * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.

    * R/Matrix.R: define and
    * NAMESPACE: export as.numeric() and as.logical() methods.
        Let's hope these do not badly slow down something...
    Finally export the zapsmall() method.

2006-08-17  Douglas Bates  <bates@R-project.org>

    * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
    R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
    * src/dtCMatrix.c :Remove code that is no longer used
    * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes

2006-08-14  Douglas Bates  <bates@R-project.org>

    * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
    Csparse_to_logical and Csparse_symmetric_to_general.
    * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
    coercion methods between CsparseMatrix and TsparseMatrix.

2006-08-14  Douglas Bates  <bates@R-project.org>

    * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
    Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
    for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
    possible.

2006-08-12  Douglas Bates  <bates@R-project.org>

    * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
      dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
      Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
      generalize conversions between TsparseMatrix, CsparseMatrix,
      denseMatrix and matrix.  Preserve triangularity property and
      propagate Dimnames in the easy cases.

2006-08-10  Douglas Bates  <bates@R-project.org>

    * src/lmer.c: adjust checks in glmer_init for S4SXP
    * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
    before S4SXP but for the wrong reasons.

2006-08-08  Douglas Bates  <bates@R-project.org>

    * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
    Later modified to return the upper triangle only.
    * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.

2006-08-07  Douglas Bates  <bates@R-project.org>

    * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
    R-level conversion to a sparse symmetric class.
    * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
    Remove conversion to sparse symmetric classes (now done in C code).

2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
    * man/band.Rd:  adapt the \dontshow{} unit test.

2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>

    * DESCRIPTION (Version): 0.995-14  for CRAN

    * tests/other-pkgs.R: oops: library(Matrix) outside *if* !

    * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
    * tests/other-pkgs.R:  more checks, sparseMatrix -> graph

    * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
    * R/Tsparse.R (tril, triu, band): methods
    * R/dgRMatrix.R (tril, ...):    ditto
    * man/band.Rd:          ditto

2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Matrix.R (head, tail): directly use utils:::head.matrix
        to be up-to-date automatically.

2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>

    * DESCRIPTION (Version): 0.995-13 to be released to CRAN

    * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
    * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
    * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
    such that the S4 objects are always created by the current version
    of R and 'Matrix' class definitions.

2006-08-01  Douglas Bates  <bates@R-project.org>

    * R/lmer.R (LMEoptimize method), tests/lmer.R,
    inst/external/test3comp.rda: Added warnings for convergence on
    boundary and test cases.

    * src/lmer.c (mer_postVar): Modified to return the variances that
    are marginal to the fixed effects, not conditional on them (which
    is what the bVar slot contents represent).

2006-07-31  Douglas Bates  <bates@R-project.org>

    * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
    function which calls the C function mer_hat_trace2.

    * man/ranef.Rd: Include description of "postVar" argument and
    producing a caterpillar plot.

2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>

    * NAMESPACE:    change  "correlation" to "corMatrix"
    * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
    * R/dpoMatrix.R: ditto
    * R/lmer.R:  ditto

2006-07-28  Douglas Bates  <bates@R-project.org>

    * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
    RZXinv slot's contents into a separate internal function that can
    be used in mer_hat_trace.

2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
    via new smart
    * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
    utility functions.


2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Csparse.R (tril, triu, band): do return *triangular* classed
    matrices when appropriate; band() even symmetric ones.
    (replCmat): extend to potentially all "CsparseMatrix"
    * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
    allow subassignment for special sparse matrices.

    * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality

    * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
    argument; in glmer_*(): print only if(verbose).

    speed-optimize a few places by moving REAL(.) out of loops.

    * src/lmer.h, src/init.h, R/lmer.R:  related to above.

2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
        since that wrongly triggers also for M[ logi , ]

    * R/denseMatrix.R: "[" methods now also work e.g. when indexing
    a symmetric matrix that results in a non-symmetric one.
    * R/Auxiliaries.R (as_geClass): new function used in "[" above.

    * R/dMatrix.R: make round(M) work as round(M, 0)

    * R/dgTMatrix.R (image): coordinate system and axis now use
    1-based indices, not 0-based ones.

    * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
    * tests/indexing.R: test it.

    * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
    * man/isSymmetric-methods.Rd: and document it.

    * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
    * man/SparseM-conv.Rd: docu them

    * tests/other-pkgs.R: renamed from tests/graph.R and add example
        for 'SparseM' conversions

2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>

    * R/Matrix.R (head): added head() and tail() methods.

2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>

    * DESCRIPTION (Version): 0.995-12 released to CRAN

2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>

    * tests/simple.R: add check for correct dsT -> dgT coercion;
        add check for correct printing of symmetric sparse matrices.

    * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
    for sparse symmetric matrices.

    * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
    diagonal twice.

2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>

    * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
    being applied to the x slot (detected by Brian Ripley).

2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>

    * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.

    * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)

2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>

    * src/lgCMatrix.c (lgCMatrix_diag): new function
    * R/lgCMatrix.R (diag): for new method

    * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
         ==> construction of illegal "*gTMatrix" via new() should
         now be much less easy:
    * tests/Class+Meth.R: assertError() for some illegal "dgT*"

    * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
        directly.
    * man/Matrix.Rd: documents it.

2006-07-06  Douglas Bates  <bates@R-project.org>

    * src/pedigree.c (pedigree_inbreeding): Correction in
    initialization.  This function is not currently being used and is
    not fully tested.

    * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
    Introduced the glmer class.  Added code for mcmcmsamp on glmer
    objects.  Modified validity check on pedigree objects to account
    for nonparallel patterns of missingness of parents.

    * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
    class.

2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/pMatrix.R: coercion pMatrix -> Tsparse

2006-06-12  Douglas Bates  <bates@R-project.org>

    * DESCRIPTION (Version): 0.995-11 released to CRAN

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

2006-06-10  Douglas Bates  <bates@R-project.org>

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

2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
    classes.
    * R/sparseMatrix.R etc: multiplication of diagonal and sparse

2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>

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

2006-06-01  Douglas Bates  <bates@stat.wisc.edu>

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

2006-05-30  Douglas Bates  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

    * 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  <maechler@stat.math.ethz.ch>

    * 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: ditto (also: src/init.c src/dgTMatrix.h)


2006-05-17  Douglas Bates  <bates@stat.wisc.edu>

    *  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  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

    * 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  <maechler@stat.math.ethz.ch>

    * 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  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

    * 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
    objects.

2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>

    * 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  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

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

2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>

    * 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  <bates@stat.wisc.edu>

    * 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  <maechler@stat.math.ethz.ch>

    * 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  <bates@stat.wisc.edu>

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

2006-03-21  Douglas Bates  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

    * 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  <maechler@stat.math.ethz.ch>

    * 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: ditto

2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>

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

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

2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>

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

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

2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>

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

2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>

    * 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  <maechler@stat.math.ethz.ch>

    * 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  <bates@stat.wisc.edu>

    * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
    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  <maechler@stat.math.ethz.ch>

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

    * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
        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  <maechler@stat.math.ethz.ch>

    * 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  <maechler@stat.math.ethz.ch>

    * 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  <bates@stat.wisc.edu>

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

2006-01-07  Douglas Bates  <bates@stat.wisc.edu>

    * 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  <maechler@stat.math.ethz.ch>

    * 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  <maechler@stat.math.ethz.ch>

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

2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>

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

2005-11-14  Douglas Bates  <bates@stat.wisc.edu>

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

2005-10-21  Douglas Bates  <bates@stat.wisc.edu>

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

2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>

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

2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>

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

2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>

    * R/Auxiliaries.R (dimNamesCheck): added

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

2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>

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

2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>

    * 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  <bates@wisc.edu>

    * 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  <maechler@stat.math.ethz.ch>

    * 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  <maechler@stat.math.ethz.ch>

    * 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  <maechler@stat.math.ethz.ch>

    * 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 *.Rout.save
    * tests/dgTMatrix.R: new

2005-08-29  Douglas Bates  <bates@wisc.edu>

    * 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  <maechler@stat.math.ethz.ch>

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

2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

    * DESCRIPTION (Version): 0.98-6

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

2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>

    * 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  <bates@wisc.edu>

    * 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  <maechler@stat.math.ethz.ch>

    * 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  <maechler@stat.math.ethz.ch>

    * 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  <bates@wisc.edu>

    * 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  <bates@wisc.edu>

    * 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  <maechler@stat.math.ethz.ch>

    * 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  <maechler@stat.math.ethz.ch>

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

2005-07-27  Douglas Bates  <bates@wisc.edu>

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

2005-07-12  Douglas Bates  <bates@wisc.edu>
    * 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  <bates@wisc.edu>

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

2005-07-03  Douglas Bates  <bates@wisc.edu>

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

2005-06-08  Douglas Bates  <bates@wisc.edu>

    * DESCRIPTION (Version): 0.96-1

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

2005-06-04  Douglas Bates  <bates@wisc.edu>

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

2005-06-02  Douglas Bates  <bates@wisc.edu>

    * src/Makefile.win: Forgot to update this when Makefile changed.

2005-05-11  Douglas Bates  <bates@wisc.edu>

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

2005-05-10  Douglas Bates  <bates@wisc.edu>

    * 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 Jean.Coursol@math.u-psud.fr

2005-05-06  Douglas Bates  <bates@wisc.edu>

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

2005-04-18  Douglas Bates  <bates@wisc.edu>

    * 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
    dgeMatrix_matrix_solve

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

2005-04-15  Douglas Bates  <bates@wisc.edu>

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

    * DESCRIPTION: Eliminate import of stats.


2005-04-06  Douglas Bates  <bates@wisc.edu>

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

2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>

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

2005-03-31  Douglas Bates  <bates@wisc.edu>

    * 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  <maechler@stat.math.ethz.ch>

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

2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>

    * 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  <maechler@stat.math.ethz.ch>

    * 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  <bates@wisc.edu>

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

2005-03-14  Douglas Bates  <bates@wisc.edu>

    * 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  <maechler@stat.math.ethz.ch>
    +
2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>

    * 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  <bates@wisc.edu>

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

2005-03-02  Douglas Bates  <bates@wisc.edu>

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

2005-02-28  Douglas Bates  <bates@wisc.edu>

    * 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  <maechler@stat.math.ethz.ch>

    * 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  <bates@stat.wisc.edu>

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

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

2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>

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

2005-02-02  Douglas Bates  <bates@stat.wisc.edu>

    * */* : almost complete reorganization of classes.

2005-01-26  Douglas Bates  <bates@wisc.edu>

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

2005-01-24  Douglas Bates  <bates@wisc.edu>

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

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

2005-01-23  Douglas Bates  <bates@wisc.edu>

    * 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  <bates@wisc.edu>

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

2004-12-23  Douglas Bates  <bates@wisc.edu>

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

2004-12-14  Douglas Bates  <bates@wisc.edu>

    * 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  <bates@wisc.edu>

    * 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  <bates@wisc.edu>

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

2004-11-29  Douglas Bates  <bates@wisc.edu>

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

2004-11-16  Douglas Bates  <bates@wisc.edu>

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

2004-11-12  Douglas Bates  <bates@wisc.edu>

    * 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  <bates@wisc.edu>

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

2004-11-10  Douglas Bates  <bates@wisc.edu>

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

2004-11-05  Douglas Bates  <bates@wisc.edu>

    * src/Makefile.win (SOURCES_C): Keep consistent with Makefile

2004-10-27  Douglas Bates  <bates@wisc.edu>

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

2004-10-04  Douglas Bates  <bates@wisc.edu>

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

2004-10-02  Douglas Bates  <bates@wisc.edu>

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

2004-06-15  Douglas Bates  <bates@wisc.edu>

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

2004-04-20  Douglas Bates  <bates@stat.wisc.edu>

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

2004-04-19  Douglas Bates  <bates@stat.wisc.edu>

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

2004-04-18  Douglas Bates  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

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

    * src/Makefile.win: Remove unneeded ranlib call

2004-04-12  Douglas Bates  <bates@stat.wisc.edu>

    * DESCRIPTION (Version): New release

    * src/Makefile.win: Update Makefile.win 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  <bates@stat.wisc.edu>

    * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
      src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
      tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
      man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
      pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
      pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
      pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
      pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
    Moved the pdMat classes from the lme4 package.

2004-03-02  Douglas Bates  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

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

2004-02-23  Douglas Bates  <bates@stat.wisc.edu>

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

2004-02-22  Douglas Bates  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

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

2004-02-16  Douglas Bates  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

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

2004-01-30  Douglas Bates  <bates@stat.wisc.edu>

    * 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/Makefile.win: This and other Makefile.win files contributed
    by Brian Ripley.

2004-01-27  Douglas Bates  <bates@stat.wisc.edu>

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

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

2004-01-26  Douglas Bates  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

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

2003-12-08  Douglas Bates  <bates@stat.wisc.edu>

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

2003-12-04  Douglas Bates  <bates@stat.wisc.edu>

    * 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  <bates@stat.wisc.edu>

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

    * src/R_LapackPP.cc: Change method of calculating determinants

2003-02-03  Douglas Bates  <bates@stat.wisc.edu>

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

2002-10-23  Douglas Bates  <bates@stat.wisc.edu>

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

    * Added configure.win and src/Makevars.win as requested by Brian
    Ripley.

2002-05-03  Douglas Bates  <bates@stat.wisc.edu>

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

2002-04-24  Douglas Bates  <bates@stat.wisc.edu>

    * configure.ac: Replaced configure.in with configure.ac
    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  <bates@stat.wisc.edu>

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