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ChangeLog
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2015-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
* inst/NEWS.Rd: Moving ChangeLog to new (markup) NEWS file
2015-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Auxiliaries.R (anyDuplicatedT): renamed from is_duplicatedT(),
and exported. uniqTsparse(): exported too.
2014-06-15 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.1-4, released to CRAN on 2014-06-14
* src/dsyMatrix.c (dsyMatrix_matrix_mm): fix crossprod(<vec>, <dsyMatrix>) bug
2014-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
* new rsparsematrix()
2014-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.1-3, released to CRAN on 2014-03-30
2014-03-12 Martin Maechler <maechler@stat.math.ethz.ch>
* R/dgTMatrix.R (image): fix bug in default ylim computation.
2014-01-28 Martin Maechler <maechler@stat.math.ethz.ch>
* R/products.R: matrix products overhauled; should work with sparseVectors;
speedup of crossprod(v, <sparseM>), thanks to nudge by Niels Richard Hansen.
* man/matrix-products.Rd: all matrix products documented in one file.
* tests/matprod.R: more extensive testing
2014-01-20 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.1-2, released to CRAN on 2014-01-28
* NAMESPACE: export fast power-user coercion utilities
.dsy2mat(), .dxC2mat(), .T2Cmat(), ..2dge().
2013-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
* R/dgTMatrix.R (image): (xlim, ylim) get a slightly changed
default, plus ylim := sort(ylim, "decreasing").
This is strictly not back-compatible but should never harm.
2013-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
* R/spModels.R (fac2sparse, fac2Sparse): newly exported; plus
'giveCsparse' option.
2013-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
* src/scripts/0get-SuiteSparse.sh: new download script, for
* src/CHOLMOD/*, src/AMD/*, ...: getting SuiteSparse version 4.2.1
* R/zzz.R (.SuiteSparse_version): new function
2013-09-13 Martin Maechler <maechler@stat.math.ethz.ch>
* R/dsCMatrix.R (solve.dsC.*): finally fix the long-lasting
undetected solve(<dsC>) bug (only in case Cholmod fails) [r2908].
* DESCRIPTION (Version): 1.0-15, CRAN-*non*-released 2013-09-26
2013-09-12 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.0-14, CRAN-released 2013-09-12
* R/dgCMatrix.R: "stop gap fix" for R 3.0.2: partly revert
solve(<sparse>,*) changes in 1.0-13.
2013-08-27 Fabian Scheipl <fabian.scheipl@stat.uni-muenchen.de>
* man/indMatrix-class.Rd: new "indMatrix" class, a natural
superclass of "pMatrix". Many methods moved from "pMatrix" to
"indMatrix".
2013-05-09 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.0-13, CRAN-released 2013-09-10
* R/KhatriRao.R: Efficient KhatriRao() by Michael Cysouw
2013-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.0-12, CRAN-released 2013-03-26
2012-11-10 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.0-11, CRAN-released 2013-02-02
* R/SparseM-conv.R: as(<csr>, "dgCMatrix") now works again
* tests/other-pkgs.R: test that.
* src/Mutils.c: do *not* use '#if R_VERSION < ..' so this also
*runs* in older R when installed in R >= 2.15.2.
2012-10-15 Martin Maechler <maechler@stat.math.ethz.ch>
* src/Mutils.c (Mmatrix): new, to be used by .External()
in order to replace .Internal(matrix(....))
2012-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
* R/diagMatrix.R (.sparseDiagonal): new 'unitri' argument;
more flexibility; new: solve(<dsCMatrix>, <missing>)
2012-09-10 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.0-10, CRAN-released: 2012-10-16, r2845
2012-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseVector.R (sparseVector): new constructor
* inst/test-tools-Matrix.R (rspMat): smarter; also useful for large
dimensions.
2012-07-23 Martin Maechler <maechler@stat.math.ethz.ch>
* tests/group-methods.R: now do much more testing, notably <Ops> of
pairs of matrices ... however only when 'doExtras' is true, which
it is not by default, e.g., on CRAN.
2012-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Ops.R, R/diagMatrix.R: many fixes, notably for rare operations
that were not triggered before.
* R/Auxiliaries.R (allTrueMat): new utility.
2012-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
* R/dsparseMatrix.R, R/sparseVector.R, ...: Newly defined
is.finite() and is.infinite() methods for all our *Matrix and *sparseVector.
2012-07-14 Martin Maechler <maechler@stat.math.ethz.ch>
* R/d??Matrix.R (diag<-): many "diag<-" methods, which preserve
symmetricity, triangularity (even uni-triangularity sometimes);
Partly by also making A[cbind(i,i)] preserve such properties.
* src/Mutils.c (SET_packed_setDiag) {and similar}:
*_setDiag() C functions implementing "diag<-" R methods.
2012-06-30 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Ops.R (Ops.x.x): now, dense symmetric and triangular matrices
are preserved for many arithmetic and logic binary operators.
* src/ldense.c (lsyMatrix_as_lspMatrix, ..): more coercions keep
the dimnames().
* R/symmetricMatrix.R (pack, unpack): new pack() {"inverse" of
unpack(), including pack(<matrix>)}; new unpack() methods.
2012-06-20 Douglas Bates <bates@stat.wisc.edu>
* src/scripts/DEPS.mkf, ...
* src/*.c: Update to version 4.0.0 of SuiteSparse
2012-06-19 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.0-8, CRAN-released: 2012-06-20, r2789
* R/CHMfactor.R (update): *DO* allow non-symmetric parent.
* man/CHMfactor-class.Rd: be more clear about the two ways.
* tests/factorizing.R: more update(<Chol>) testing
2012-06-12 Martin Maechler <maechler@stat.math.ethz.ch>
* tests/matprod.R (chkDnProd): new testing function
2012-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
* R/CHMfactor.R (update): now *warn* when parent is not formally
symmetric and coerce it.
2012-06-05 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Auxiliaries.R (chk.s): "check dots" - new utility -- possibly
for base R ?
2012-04-16 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseMatrix.R (sparseMatrix): now also works for
'symmetric=TRUE' and lower triangular indices.
2012-04-15 Martin Maechler <maechler@stat.math.ethz.ch>
* R/CHMfactor.R (updown): new generic and methods,
* man/updown.Rd: provided by Nicholas Nagle.
2012-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.0-7, CRAN-released: for a few days only.
2012-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.0-6, CRAN-released: 2012-03-30, r2775
* DESCRIPTION (Depends): R >= 2.15.0
2012-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
* R/spModels.R (sparseInt.r): recursion free (which does not help much).
2012-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
* src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer use Alloca()
here.
* tests/factorizing.R (checkSchur): check against segfault example.
* R/Matrix.R (chol2inv(<diagonalMatrix>)) new method.
2012-03-01 Martin Maechler <maechler@stat.math.ethz.ch>
* R/spModels.R (sparse.model.matrix, model.spmatrix): add 'verbose'
argument in order to show to the user what's going on.
* man/sparse.model.matrix.Rd: ditto
2012-02-27 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Ops.R (A.M.n, A.n.M): <sparse> o <numeric> now correct, newly
via sparseVector.
2012-02-25 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.0-5, CRAN-released: 2012-03-15, r2773
* src/chm_common.c (chm_factor_to_SEXP): in case of failure,
* src/dsCMatrix.c (internal_chm_factor): ensure memory cleanup;
memory leak reported by Kasper Kristensen at dtu.dk.
2012-02-17 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.0-4, CRAN-released: 2012-02-21, r2765
* R/Ops.R: Fix "-" method for diagonalMatrix types.
2012-01-12 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Suggests): MASS, as we use a data set in a vignette
2011-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.0-3, CRAN-released: 2012-01-12, r2749
* R/diagMatrix.R (.bdiag): now works correctly when all blocks are "lMatrix"
2011-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
* R/zzz.R (.onLoad): when R version >= 2.15.0, no longer
need to assignInNamespace( ns = "base"), methods provides S4 generic.
2011-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.0-2, CRAN-released: 2011-11-19, r2739
* tests/other-pkgs.R: print more, don't run SparseM on Solaris for now.
* tests/Simple.R: encoding warning should not be promoted to error.
2011-10-22 Martin Maechler <maechler@stat.math.ethz.ch>
* R/rankMatrix.R (rankMatrix): 'method = "qrLINPACK"' now also
works for sparse matrices, but using \code{sparseQR()}.
* man/sparseQR-class.Rd: document options "Matrix.quiet" (old) and
new "Matrix.quiet.qr.R" for suppressiong the permutation warning.
* R/sparseQR.R:
2011-10-17 Douglas Bates <bates@stat.wisc.edu>
* src/Csparse.c (Csparse_submatrix): plugging memory leak
2011-10-08 Martin Maechler <maechler@stat.math.ethz.ch>
* R/bind2.R (cbind2Sparse, rbind2Sparse): auxiliaries,
used, also in new methods for <sparse, dense>.
* tests/bind.R: testing some of these.
* R/Matrix.R, man/Matrix.Rd: optional argument 'doDiag'.
* DESCRIPTION (Version): 1.0-1, CRAN-released: 2011-10-18, r2732
2011-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 1.0-0 -- to be released for R 2.14.0
2011-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
* R/dsCMatrix.R (solve.dsC.mat): new utility which calls lu() if
CHOLMOD'S Cholesky() errors (when matrix is not pos.def.).
2011-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
* R/bandSparse.R (bandSparse): and
* R/sparseMatrix.R (sparseMatrix): add 'giveCsparse = TRUE'
argument and allow returning Tsparse*, useful e.g. when used in
bdiag().
2011-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
* NAMESPACE: export diagN2U() & diagU2N(). They were "missing" for
at least one user (GG).
* man/diagU2N.Rd: docu + example.
* DESCRIPTION (Version): 0.9996875-4 (*not* yet released)
2011-08-12 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.9996875-3, for CRAN
2011-08-05 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseVector.R (head): method; used in a few cases, eliminating
two FIXMEs.
* DESCRIPTION (Version): 0.9996875-1
* R/ngTMatrix.R: stop() instead of warning() when NA's are coerced.
* R/Csparse.R, R/Tsparse.R
* src/t_Csparse_subassign.c, src/Csparse.c: <Csparse>[..] <- val
now works via .Call(*Csparse_subassign, ...) and no longer suffers
from unnecessary memory-blowup.
2011-07-29 Martin Maechler <maechler@stat.math.ethz.ch>
* R/dgTMatrix.R (image): add 'useRaster = FALSE' argument,
providing the possibility of using raster (instead of rectangle
drawing vector) images.
2011-07-27 Martin Maechler <maechler@stat.math.ethz.ch>
* R/nearPD.R: allow 'ensureSymmetry' argument for speedup.
2011-06-10 Martin Maechler <maechler@stat.math.ethz.ch>
* R/diagMatrix.R (Cspdiagprod, diagCspprod): fixup for symmetric
sparse, and non constant-diagonal.
2011-05-20 Martin Maechler <maechler@stat.math.ethz.ch>
* R/dsCMatrix.R (determinant(<dsCMatrix>): fix for Matrix(0, 1) case.
2011-05-18 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseMatrix.R (sparseMatrix): add 'symmetric' argument.
2011-04-04 Martin Maechler <maechler@stat.math.ethz.ch>
* src/Csparse.c (Csparse_subassign): unfinished prototype
* src/....: Finally no longer hack "UFlong := int", but rather
* src/UFconfig/UFconfig.h: use standard CHOLMOD headers
* DESCRIPTION (Version): 0.9996875-0
2011-03-31 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-49
2011-03-30 Douglas Bates <bates@stat.wisc.edu>
* Matrix/src/chm_common.c: [r2658] Install symbols first -
{preventing seg.fault under -gct}
2011-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-48
*only* difference to CRAN released *-47, is the work around Sweave bug
in inst/doc/sparseModels.Rnw.
2011-02-23 Martin Maechler <maechler@stat.math.ethz.ch>
* src/factorizations.c (LU_expand): now also works for non-square (m x n)
* tests/factorizing.R: testing that
2011-02-22 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Auxiliaries.R (t_geMatrix): drop 'factors', as they can be
wrong.
2011-02-18 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Tsparse.R (replTmat): fix bug for M[i,j] <- v,
when j had duplicated entries.
* tests/indexing.R (chkAssign): new function; testing the above.
2011-02-17 Martin Maechler <maechler@stat.math.ethz.ch>
* R/AllClass.R, R/sparseVector.R, man/sparseVector-class.Rd: now
require explicitly that i-slot must be sorted for sparseVectors.
2011-02-16 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseMatrix.R (formatSparseM): align="right" accidentally did
not use zero.print at all.
print/format sparse Matrix: fix align="right" and improve docu
2011-02-17 Douglas Bates <bates@stat.wisc.edu>
* DESCRIPTION: Remove Encoding: directive.
2011-02-10 Martin Maechler <maechler@stat.math.ethz.ch>
* inst/doc/sparseModels.Rnw: use png for large graphics (suggestion from
Brian)
2011-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
* man/symmpart.Rd: update, thanks to Spencer Graves' prompting.
2011-01-07 Martin Maechler <maechler@stat.math.ethz.ch>
* R/CHMfactor.R (determinant(<CHMfactor>)): no longer warn about
incompatible change of 2009-09-01.
2011-01-04 Martin Maechler <maechler@stat.math.ethz.ch>
* R/nearPD.R (nearPD): better error message when all eigenvalues
are (at least close to) negative.
2010-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-47, CRAN-released: 2011-02-23, r2653
* R/spModels.R, NAMESPACE: remove model.Matrix();
we had deprecated it for about four months now.
2010-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
* R/eigen.R,...: use full argument names;
* R/*.R: get rid of more from
checkUsagePackage("Matrix", suppressPartialMatchArgs = FALSE)
2010-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-46, CRAN-released: 2010-12-14, r2633
* R/products.R: dimension fixing in some Matrix o vector [t]crossprod()s.
* src/Csparse.c (nz2Csparse, nz_pattern_to_Csparse): new utilities,
callable from C and R.
(Csparse_dense_prod): check pattern matrix and coerce to "d..".
* tests/Simple.R: testing <n.Matrix> %*% <dense>
* R/ngCMatrix.R, R/nsCMatrix.R, .. : use the new fast coercions.
2010-10-08 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-45, CRAN-released: 2010-11-10, r2624
* R/sparseMatrix.R (graph.wgtMatrix): add 'graph::' in a few
places; as 'graph' package is not imported and may well be loaded
only.
2010-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseMatrix.R (setAs): graph |-> Matrix: via CsparseMatrix
2010-08-21 Martin Maechler <maechler@stat.math.ethz.ch>
* R/spModels.R (sparse.model.matrix): argument 'drop.unused.levels = FALSE'
NB: was *true* implicitly, before. Compatibility with model.matrix().
* R/sparseMatrix.R (formatSpMatrix, formatSparseM): factored out of
printSpMatrix(); export as potentially useful for standard
matrices, even.
2010-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
* R/eigen.R (Schur): correct setMethod() such that
Schur(<dgCMatrix>) works.
2010-08-10 Martin Maechler <maechler@stat.math.ethz.ch>
* R/diagMatrix.R, man/bdiag.Rd, NAMESPACE: export .bdiag() as well.
2010-08-09 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-44, CRAN-released: 2010-09-11, r2618
* R/diagMatrix.R (diagCspprod, Cspdiagprod): drop (possibly wrong) @factors
* R/Ops.R (.Arith.CM.atom, .Arith.atom.CM, A.M.n, A.n.M): ditto
* tests/factorizing.R: check some of the above.
2010-08-04 Douglas Bates <bates@stat.wisc.edu>
* R/spModels.R (fac2sparse): Fix name resolution problem
(R-SIG-Mixed-Models post by Florent Duyme).
2010-07-25 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Depends): require R >= 2.10.0 --> can clean up
* R/spModels.R: prepare to move most parts to new package
MatrixModels
2010-07-23 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Auxiliaries.R (prMatrix): add " (unitriangular)" as we already
have for sparse matrices.
2010-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Auxiliaries.R (.diagU2N): implement for "dtpMatrix" = old 'FIXME';
(.dense.diagU2N): new utility, called from .diagU2N()
2010-07-19 Martin Maechler <maechler@stat.math.ethz.ch>
* src/dtrMatrix.c (dtrMatrix_dtrMatrix_mm): new for tri %*% tri
* R/products.R (%*%): ditto
* tests/matprod.R: test it
2010-07-16 Martin Maechler <maechler@stat.math.ethz.ch>
* R/spModels.R (do.defaults): add 'nonMatched.action' with default
ensuring that typos are caught.
2010-07-16 Douglas Bates <bates@stat.wisc.edu>
* R/spModels.R (do.defaults): utility function; TODO: move to R
2010-07-16 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-43, CRAN-released: 2010-08-05, r 2599
* R/AllClass.R (Model): as mother class (of "glpModel")
* R/spModels.R (IRLS): more options()
(updateModel): update(<glm4>)
2010-07-13 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-42, CRAN-released: 2010-07-15, r 2566
* R/spModels.R (glm4, IRLS): glm4 [was 'glm1']; tweaks.
2010-07-12 Martin Maechler <maechler@stat.math.ethz.ch>
* NAMESPACE: rename, export and
* man/glpModel-class.Rd: document Doug's new "glpModel" class.
2010-07-08 Douglas Bates <bates@stat.wisc.edu>
* R/AllClass.R: new "lpMod" class (-> later =: "glpModel"), and
working function:
* R/spModels.R (glm1): using linear pred.Model class, and
Bates-Watts convergence criterion.
2010-07-06 Martin Maechler <maechler@stat.math.ethz.ch>
* R/lMatrix.R (whichDense): use arrayInd()
* R/zzz.R (arrayInd): provide for older R versions
2010-07-05 Martin Maechler <maechler@stat.math.ethz.ch>
* src/chm_common.c (chm_triplet_to_SEXP): deal more carefully with
NAs, needed e.g., on Solaris; thanks to Ruth and Brian Ripley.
* R/Ops.R (Compare <Csparse>): fix bug uncovered by "alongside" the
above.
2010-07-02 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseMatrix.R (x[] <- 0): fix shortcut code.
* tests/indexing.R: and test
* R/nearPD.R (nearPD): 'doDykstra = TRUE' and *do* use Dykstra's
correction which was *not* used in Jens' code; thanks to Bernhard
Spangl for a report
2010-06-26 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Matrix.R: fix mean() method; add sparse one, remaining sparse
at least for trim = 0.
2010-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-41, CRAN-released: 2010-07-03, r 2555
* R/sparseVector.R (spV2M): enable sparseVector -> (sparse)Matrix
as(*,.) coercion.
2010-06-07 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Tsparse.R (.TM.repl.i.mat): renamed from .TM.repl.i.2col().
* R/Matrix.R (.repl.i.lSMat): implement logical sparse
sub-assignment: M[<lsparseMatrix>] <- v; ditto for dense & nsparse.
* R/Csparse.R (.CM.repl.i.lSMat, ..): direct logical sparse
sub-assignment for "Csparse".
2010-06-04 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseMatrix.R (sparseMatrix): re-enable 'dimnames' argument.
2010-06-03 Martin Maechler <maechler@stat.math.ethz.ch>
* R/spModels.R (model.Matrix): tweak for NULL contrasts in dense case.
2010-06-02 Martin Maechler <maechler@stat.math.ethz.ch>
* tests/spModel.matrix.R (Sparse.model.matrix): adapt to the fact, that
sparse.model.matrix() returns not just a dgCMatrix.
2010-05-29 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-40, CRAN-released: 2010-06-04, r 2546
* R/AllClass.R: new classes "ModelMatrix", "sparseModelMatrix", etc.
* R/spModels.R (sparse.model.matrix): now return
"dsparseModelMatrix" object, notably with 'assign' slot.
* R/spModels.R (model.spmatrix): faster, using lower level
cbind2/rbind2 directly.
* R/spModels.R (model.Matrix): new function,
returning "ddenseModelMatrix".
* NAMESPACE: export new classes.
2010-05-18 Martin Maechler <maechler@stat.math.ethz.ch>
* src/Csparse.c (Csparse_horzcat, Csparse_vertcat): ensure that
rBind()/cBind() i.e., rbind2()/cbind2() return logical sparse
matrices when the components are.
* tests/bind.R: test
2010-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseMatrix.R: A[] <- v ; differentiate dense & sparse
* R/pMatrix.R: disallow <pMatrix>[] <- v more consequently
* tests/indexing.R: test above
2010-05-08 Martin Maechler <maechler@stat.math.ethz.ch>
* R/spModels.R (model.spmatrix): deal with "AsIs" components
* tests/spModel.matrix.R: test that
2010-05-01 Martin Maechler <maechler@stat.math.ethz.ch>
* R/condest.R (onenormest, condest): allow to estimate condition
number for large sparse matrices.
* condest.Rd: docu
* R/pMatrix.R (.inv.perm): utility; add [t]crossprod() methods
* man/sparseLU-class.Rd: A = P'LUQ; add examples, with "identities"
* R/Auxiliaries.R (mmultCheck): new arg. 'kind'
2010-04-28 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-39, CRAN-released: 2010-05-19, r 2540
* R/spModels.R (fac2sparse): using names(formals(new))[[1]] to
adapt to a future change in new()'s first argument *name*.
2010-03-31 Martin Maechler <maechler@stat.math.ethz.ch>
* R/spModels.R (lm.fit.sparse): update, allowing weights; also
return residuals, notably for "cholesky" case.
* man/lm.fit.sparse.Rd: examples; comparing with dense case.
* src/dgCMatrix.c (dgCMatrix_cholsol): comments; also compute
residuals.
2010-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
* R/spModels.R (sparse.model.matrix, model.spmatrix): border case
'~ 1' should also work. Add 'transpose = FALSE' argument.
* tests/spModel.matrix.R: test that.
2010-03-27 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseMatrix.R (printSpMatrix): ensure returning original argument
2010-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseVector.R (coercion from TsparseMatrix): diagU2N() when
needed.
* inst/test-tools.R (checkMatrix): explicit which() test for
"l" and "nMatrix". New sparseVector (coercion "and back") check.
2010-03-25 Martin Maechler <maechler@stat.math.ethz.ch>
* R/lMatrix.R (which): define methods for which(<[ln]Matrix>).
* inst/test-tools.R (Q.eq.symmpart): new utility, now called in
checkMatrix().
* R/nearPD.R: use symmpart() for non-symmetric x
* man/nearPD.Rd: improve title
2010-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
* R/colSums.R (.diag.Mean): define methods for "diagonalMatrix"
* src/Mutils.c (m_encodeInd, do_ii_FILL):
coerce ij to integer if necessary; check that ij are within "dim[]"
values. Parametrize do_ii_FILL() to be used in m_encodeInd2() as well:
* src/Mutils.c (m_encodeInd2): also check bounds (if desired).
* tests/indexing.R: test the above.
2010-03-19 Martin Maechler <maechler@stat.math.ethz.ch>
* src/dgeMatrix.c (dgeMatrix_solve): compute the recip.cond.number
and also bail out for *computational* singularity {as "base R"
does}, from (code) suggestion by Daniel Sabanés Bové.
* tests/dg_Matrix.R: "test" the above.
2010-03-01 Martin Maechler <maechler@stat.math.ethz.ch>
* man/rep2abI.Rd: rep2abI() utility is exported now.
* R/Csparse.R (subCsp_cols, subCsp_rows, subCsp_ij): dimnames() <-
fix for character subsetting.
* tests/indexing.R: testing it.
2010-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
* R/spModels.R (model.spmatrix): warn and coerce to sparseMatrix if
result would end up dense (e.g., in case of *no* factors in formula).
* tests/spModel.matrix.R: test the above.
2010-02-12 Martin Maechler <maechler@stat.math.ethz.ch>
* R/dtrMatrix.R: add solve(<dtrMatrix>, <dMatrix>): e.g., for
solve(<Cholesky>, <dgCMatrix>) in lme4.
2010-02-09 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-38, CRAN-released: 2010-03-31, r 2529
* NAMESPACE, R/AllGeneric.R, R/zzz.R: change det() into a regularly exported
function (masking base::det) instead of load-time hack.
* man/Matrix-class.Rd: \alias, docu
2010-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-37, CRAN-released: 2010-02-05
* inst/test-tools.R (Qidentical.DN): new
(Qidentical): all Qidentical.DN(<dimnames>)
* R/Csparse.R (subCsp_ij, subCsp_cols, subCsp_rows): use
CHOLMOD's submatrix C code, instead of matrix multiplication;
now *do* keep dimnames of result, wherever classical matrix
subsetting does.
2010-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-36, CRAN-released: 2010-02-04
* R/Csparse.R (subCsp_ij): Fix <sparse>[0,0] bug
2010-02-03 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Tsparse.R (.TM.repl.i.2col): <nsparse>[ <ij> ] <- FALSE fix
* tests/indexing.R, *.Rout.save: test that
2010-01-28 Martin Maechler <maechler@stat.math.ethz.ch>
* src/Csparse.c (Csparse_crossprod): PROTECT() Tsparse_diagU2N()
result, from a suggestion by Andrew Runnalls.
2010-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
* R/SparseM-conv.R (setAs(., "matrix.csc")): fix typo in method.
2010-01-20 Martin Maechler <maechler@stat.math.ethz.ch>
* R/AllGeneric.R: nnzero() is now generic,
* R/nnzero.R: newly containing all nnzero() methods.
* R/zzz.R (det): assign base::det such that it uses S4 generic kronecker.
2010-01-18 Martin Maechler <maechler@stat.math.ethz.ch>
* R/spModels.R (contr.poly): [the back-compatible-only version]:
do not use a default for 'scores'; rather rely on stats::contr.poly.
* tests/spModel.matrix.R: test that case
2009-12-28 Douglas Bates <bates@stat.wisc.edu>
* DESCRIPTION (Version): 0.999375-35, CRAN-released: 2010-02-03
* src/init.c, inst/include/Matrix_stubs.c: cholmod_band_inplace()
exported.
2009-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
* tests/indexing.R: slightly adapt to the very slight [] changes.
* inst/test-tools.R (Q.C.identical): + checkClass
* R/Tsparse.R ([-methods): for now go via "Csparse" and drop
all the sophisticated code dealing with the many cases.
* R/Csparse.R (subCsp_cols, etc): faster [i,j] via matrix
multiplication, thanks to suggestions by Greg Jorstad.
* R/Auxiliaries.R (paste0): more use of paste0()
2009-12-22 Martin Maechler <maechler@stat.math.ethz.ch>
* R/diagMatrix.R (.sparseDiagonal): made more general, allowing
to directly build the equivalent of Diagonal(n)[, j]
* man/Diagonal.Rd: document .sparseDiagonal() as well.
2009-12-21 Martin Maechler <maechler@stat.math.ethz.ch>
* R/AllClass.R: abIndex@x and rleDiff@first are now "numLike",
such that also logical can be converted to "abIndex".
* R/abIndex.R (.diff): new utility, used in num2abI()
2009-12-19 Martin Maechler <maechler@stat.math.ethz.ch>
* src/abIndex.c: include new
* src/t_Matrix_rle.c (Matrix_RLE_): is template for
Matrix_rle_i() and Matrix_rle_d(); now obeys a 'force' argument.
* R/abIndex.R: implement <Arith> methods, at least with scalars.
(all.equal.abI): add also all.equal() methods.
* tests/abIndex-tsts.R: testing <Arith>, using all.equal().
* R/AllClass.R: classUnion "numLike" := {"numeric", "logical"}
2009-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
* src/abIndex.c (Matrix_int_rle): UNPROTECT() needed in trivial case.
* R/abIndex.R (abIseq1, abIseq): new functions for building
"abIndex" vectors.
* tests/abIndex-tsts.R (tst.c.abI): test new c("<abIndex>") method.
* DESCRIPTION (Version): 0.999375-34, CRAN-released: -never-
* R/Ops.R: use prod(d) instead of d[1]*d[2], as the latter may
integer overflow; fixes <large sparseMatrix> o <sparseVector>
* tests/Simple.R: test that.
2009-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseVector.R (TsparseM* -> sparseV): symmetricMatrix needs to
be expanded. This fixes a bug reported by Yu-Sung Su.
* tests/indexing.R: testing the fix.
* inst/test-tools.R (all.equalX): new util
2009-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Ops.R (A.n.M, A.n.M): <sparseMatrix> o <numeric> : remain
sparse also when *majority* (instead of all) of 0 o v is 0.
* tests/group-methods.R: test one such case.
2009-12-06 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-33, CRAN-released: 2009-12-11
* R/Ops.R (Compare<Csp><Csp>): fix case with NA x.
* R/not.R: fix "typo" in !<sparseVector>
* R/Ops.R (Ops.spV.spV): fix thinko
2009-12-05 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseVector.R: setAs(nsparseV*, lsparseV*) etc
* R/Ops.R (Ops.spM.spV, Ops.spV.spM): sparseVec. o sparseMat.
2009-11-20 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Ops.R (Ops.spV.spV): enable sparseVector operations in more cases.
* R/sparseVector.R (is.na): methods defined.
* R/sparseVector.R (intIv): also accept "sparseVector"s
* tests/Simple.R: check the above
2009-11-19 Martin Maechler <maechler@stat.math.ethz.ch>
* R/sparseVector.R (newSpV, newSpVec): new utility, dropping 0 "on the fly".
* R/sparseVector.R (atomic -> sparse*): fix for NA case.
* R/Ops.R (<spV>): using newSpVec()
* R/not.R: fix thinko in !<sparseVector>
2009-11-17 Martin Maechler <maechler@stat.math.ethz.ch>
* tests/other-pkgs.R: detach(*, unload) Rgraphviz too
2009-11-14 Martin Maechler <maechler@stat.math.ethz.ch>
* R/AllClass.R: "abIndex" (and "rleDiff") class
* R/abIndex.R: with some methods; commit these finally, even if
it's mostly unfinished.
* src/abIndex.[ch]: new: currently only for .Call(Matrix_int_rle,*)
* tests/abIndex-tsts.R: basic consistency checks for "abIndex".
* R/diagMatrix.R (diagOdiag): "exploding" Matrix.msg() only level 2;
* tests/indexing.Rout.save: update
2009-11-11 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-32, CRAN-released: 2009-11-20
* src/Csparse.c (Csparse_Csparse_prod, Csparse_Csparse_crossprod):
PROTECT(.) the dimnames; thanks to Kaspar Kristensen
2009-10-24 Martin Maechler <maechler@stat.math.ethz.ch>
* R/Ops.R (Logic.lCMat): to be used for lsC* and ltC* as well,
effectively replacing previous suboptimal methods.
* src/chm_common.c (chm2Ralloc): Fix unidiagonal ntC segfault:
assign 'x' only when non-pattern.
* src/chm_common.c (as_cholmod_triplet): reallocate now in a way
that works; fix documentation about return value in diagU2N case;
ditto for
* src/chm_common.c (as_cholmod_sparse):
* R/sparseMatrix.R (printSpMatrix): add 'cld' argument, typically
passed from printSpMatrix2; and indicate "unit-diagonal"
2009-10-22 Martin Maechler <maechler@stat.math.ethz.ch>
* R/lsparseMatrix.R (C2l): fix for case with NA.
* R/Csparse.R (replCmat): drop "stale" cached @factors
factorizations after sub-assignments.
* R/Tsparse.R (replTmat, .TM.repl.i.2col): ditto
2009-10-19 Martin Maechler <maechler@stat.math.ethz.ch>
* src/dgCMatrix.c (dgCMatrix_LU): new boolean argument
'error_on_sing' to allow no error in case of singularity;
needed for determinant(), e.g.
* R/Auxiliaries.R (detSparseLU): using lu(*, errSing=FALSE)
* R/dgCMatrix.R, R/dsparseMatrix.R: lu() methods, using 'errSing'
* R/sparseMatrix.R (printSpMatrix): fix bug introduced on *-09-10
* tests/Simple.R: test for that.
2009-10-18 Martin Maechler <maechler@stat.math.ethz.ch>
* src/dgeMatrix.c (dgeMatrix_crossprod): do not fail in 0-column case.
* inst/test-tools.R (Q.eq): new utility
(checkMatrix): minimally check %*%, crossprod() and tcrossprod()
* R/products.R: more '%*%' methods for "[ln]?Matrix", "missing"
2009-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
* DESCRIPTION (Version): 0.999375-31, CRAN-released: 2009-10-06
* inst/include/Matrix_stubs.c (M_R_cholmod_error): revert (2009-09-18),
i.e., no longer restore cholmod_common. {{M_cholmod_defaults()
still seems not usable from lme4's init.c}}
2009-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
* src/dtrMatrix.c (dtrMatrix_chol2inv): use "dpoMatrix" instead of "dsy"
* R/dtrMatrix.R: make use of implicit generic for chol2inv() in
newer R versions.
2009-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
* R/CHMfactor.R (solve): fix methods for "ddiMatrix" and "missing" RHS.
* tests/factorizing.R: test these
* R/Matrix.R (image): fix Matrix method to work for "ddiMatrix"
* R/diagMatrix.R: coercion to "dsparse*"
* tests/Simple.R: test image(<ddiMatrix>)
2009-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
* R/AllGeneric.R: rcond is implicit generic in latest versions of R