2008-04-02 Martin Maechler * src/dense.c (dense_to_Csparse): all declarations *before* R_CheckStack(); needed e.g. for ancient gcc 2.96. 2008-03-29 Martin Maechler * DESCRIPTION (Version): 0.999375-9 --- need to release for R-devel (and R 2.7.0 alpha soon). * R/AllClass.R: drop "double" from "atomicVector" class union * R/AllGeneric.R (rcond): check for base::rcond instead of R version * R/dgeMatrix.R: ditto * R/sparseMatrix.R (summary): count NAs * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction. 2008-03-28 Martin Maechler * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in order to become compatible to new R 2.7.0 base::rcond(). 2008-03-25 Martin Maechler * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o * inst/test-tools.R (isValid): new utility, used much in * tests/simple.R: * man/BunchKaufman-methods.Rd: added too 2008-03-24 Martin Maechler * R/dsyMatrix.R: add BunchKaufman() methods. * R/dspMatrix.R: * src/init.c: add dsyMatrix_trf 2008-03-23 Douglas Bates * DESCRIPTION (Version): release 0.999375-7 * src/CHMfactor.c (CHMfactor_update): fix 2008-03-22 Martin Maechler * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using internal_chm_factor(). * R/AllGeneric.R: do *not* define a "chol" generic (but rather use the implicit one *without* making pivot part of the signature) * R/*.R: drop the 'pivot' from chol's signature and make 'pivot=FALSE' a default argument of method definitions. * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released version of Matrix 2008-03-18 Martin Maechler * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix" * R/sparseMatrix.R (is.na): new simple method * R/denseMatrix.R (is.na): ditto. * R/diagMatrix.R (.symDiagonal): newly exported utility. * R/diagMatrix.R (Ops): * should not become dgeMatrix! * src/UFsparse_download.sh: --> * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007) 2008-03-17 Martin Maechler * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same functionality; barely tested in * tests/factorizing.R * src/Csparse.c (diag_tC): new functionality to enable faster determinant(, .) in * R/dsCMatrix.R 2008-03-17 18:53 Douglas Bates * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c, src/CHMfactor.c, src/CHMfactor.h, man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R: Log-determinant of the parent matrix from a CHMfactor object as chm_factor_ldetL2; documentation and support 2008-03-15 Martin Maechler * R/dsCMatrix.R: enable determinant(, .) via chol(.) 2008-03-14 Martin Maechler * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation warning. 2008-03-13 Martin Maechler * DESCRIPTION (Version, Date): bug-fix release 0.999375-6 * R/diagMatrix.R (diag2tT.u): utility to be smarter in o setAs(., "nMatrix") added. * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps new argument 'checkDense = FALSE'. 2008-03-07 Martin Maechler * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the back-permutation of the matrix exponential. * tests/matr-exp.R: test the fix (for an example where expm() was wrong). * DESCRIPTION (Date,Version): ready to release 0.999375-5 * tests/simple.R: testing diagN2U 2008-03-06 Martin Maechler * R/Auxiliaries.R (diagN2U): interface to * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U() * tests/matprod.R: test for triangularity preserving %*% 2008-03-05 Martin Maechler * src/chm_common.c (chm_diagN2U): new utility. * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod): make use of chm_diagN2U() and hence now preserve triangularity and unit-triangularity. * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical" 2008-03-04 Martin Maechler * R/diagMatrix.R (subDiag): fix when x[..] became a vector * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g. * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !! * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N * R/Ops.R ("-" ()): use diagU2N() * src/chm_common.c (AS_CHM_FINISH): add note about problem for triangular (diag = "U"). 2008-02-21 Martin Maechler * R/Auxiliaries.R (as_Csparse2): drop this, replacing by * R/bind.R: .Call(dense_to_Csparse, *) 2008-02-20 Martin Maechler * R/Matrix.R (Matrix): no longer use coercions to specific classes (since we are discouraging them in user code). * tests/*.R: also replaces coercions to specific classes by coercions to super classes. * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric() 2008-02-19 Martin Maechler * man/CAex.Rd: example: coerce to symmetric*, not dsC* * src/dense.c (dense_band): generalized from ddense_band * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense): now for "denseMatrix" (instead of just "ddense*"); much simplified setMethod()s for these. * src/dense.c (dense_to_symmetric): generalized from ddense_* 2008-02-18 Martin Maechler * R/AllGeneric.R: forceSymmetric() generic: fast no-checking version of as(*, "symmetricMatric"). * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix" 2008-02-16 Martin Maechler * R/Matrix.R (subset.ij): utility, as first step to faster M [ ] indexing. * R/Matrix.R (.M.sub.i.logical): M[ ] : try better. * src/dense.c (ddense_symmpart, ddense_skewpart): new functions for more efficient symmpart() and skewpart() methods. * src/Mutils.c (equal_string_vectors): utility * src/dense.c (ddense_to_symmetric): new function used in * R/symmetricMatrix.R: setAs(., "symmetricMatrix") * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in order to match the generic (and evade .local(..)). * R/dsCMatrix.R: dgC -> dsC: use C code! * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions as per TODO * R/Auxiliaries.R (setZero, all0Matrix): new utilities * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods 2008-02-15 Martin Maechler * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular * R/Auxiliaries.R (non0.i): take out of non0ind * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense): make tril(), triu(), band() work for "matrix" and all "dense*" * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*) * tests/simple.R: test the fix above * R/sparseMatrix.R ([): simplification: no coerce to before we use as(., )[...] anyway * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR() * R/triangularMatrix.R (isTriangular): methods for all subclasses instead of "triangularMatrix" -- just to disambiguate 2008-02-14 Martin Maechler * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO} * tests/indexing.R: example that fails above 2008-01-26 Martin Maechler * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto; now, M[lower.tri(M)] and M[lower.tri(M)] <- v work better * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility. * src/Tsparse.h, init.c: ditto * R/Auxiliaries.R (isTriT): new; faster than going via Csparse both isTriC() and isTriT() now return TRUE with "kind" or FALSE. * R/sparseMatrix.R (isTriangular): hence simplified 2008-01-24 Martin Maechler * R/Ops.R (.Arith.Csparse): new utility factored out of former o , extended for triangular and also used in o . 2008-01-23 Martin Maechler * tests/factorizing.R (checkSchur): and more tests for checking Schur() * inst/test-tools.R (isOrthogonal): new function; also file restructured 2008-01-22 Martin Maechler * R/ngTMatrix.R: allow as(, "ngTMatrix") and hence coercion to "nMatrix" and "pMatrix" * R/AllClass.R: "Schur" class; "number" class union * man/number-class.Rd: * man/Schur-class.Rd: * R/eigen.R (.dgeSchur): utility, and return "Schur" class (.simpleSchur): Schur() method for diagonal matrices (.triSchur): Schur() method for triangular matrices (Schur.sym): Schur() for symmetric matrices {building on eigen()}. 2008-01-21 Martin Maechler * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc) 2008-01-15 Martin Maechler * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY" in order to ensure 'system = *' is not lost; formals()$system instead of cut&paste. * tests/factorizing.R: test solve(, ) 2008-01-11 Martin Maechler * DESCRIPTION (Date): make ready for release --> 0.999375-4 * R/dgeMatrix.R: fix rcond() method for "dgeMatrix". 2007-12-08 Martin Maechler * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix, and hence does as.vector(.). * man/pMatrix-class.Rd: docs * R/sparseMatrix.R: fix for printing "integer sparse" * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc * R/Matrix.R and others: use "exact" function argument list for both "[" : (x, i,j, ..., drop) and "[<-" : (x, i,j, ..., value) * R/denseMatrix.R: M[i] and M[i] <- v (i vector) now work * R/Tsparse.R (replTmat): ditto * R/diagMatrix.R (replDiag): ditto * R/Csparse.R (replCmat): ditto {was it worth the pain?} * tests/indexing.R: testing the above 2007-12-07 Martin Maechler * R/sparseMatrix.R (cov2cor): method for sparse matrices * R/diagMatrix.R ([<-): fix D[ cbind(i,j) ] <- v * R/bind2.R: fix for Rsparse* and rbind2(dense,dense) * tests/Class+Meth.R: test cbind2, rbind2 and diag<- 2007-12-06 Martin Maechler * R/Matrix.R: "generic" cov2cor() method * R/nearPD.R: new 'only.values', 'keepDiag' arguments; speed up Q %*% D %*% t(Q) * tests/dpoMatrix.R: test nearPD() 2007-12-05 Doug Bates and Martin Maechler * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of stats::xtabs() allowing to create sparse matrices. 2007-10-08 Martin Maechler * DESCRIPTION (Version): *-4 (released *-3 two days ago) 2007-10-06 Martin Maechler * R/pMatrix.R: solve(, ) 2007-10-05 Martin Maechler * R/LU.R: solve() method for "denseLU" 2007-10-01 Martin Maechler * DESCRIPTION (Version): 0.999375-3 preparing for release * R/AllGeneric.R: simplify if(.) .. else .. for R <= 2.5.1 * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0 2007-09-26 Martin Maechler * R/pMatrix.R (.m.mult.pMat): fix %*% , thanks to Kasper Kristensen. * tests/matprod.R: regression test for that. 2007-09-23 17:32 Douglas Bates * [r4778] R/AllGeneric.R: Check R version before defining generics for primitives 2007-09-13 Martin Maechler * R/denseMatrix.R (rcond): method * R/sparseQR.R (rcond): method, use x or t(x) 2007-09-12 Martin Maechler * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square matrices. * R/sparseMatrix.R: Ditto for all other rcond() method definitions. * man/rcond.Rd: mention the more general definition, and add example for non-square matrices. * man/chol.Rd: new file, for the S4 chol() generic and all methods. 2007-09-11 Martin Maechler * R/sparseQR.R: add qr.R() method [to be used for rcond()] 2007-09-01 Martin Maechler * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc * tests/indexing.R: add new regression for the above cases. 2007-08-30 Martin Maechler * src/Mutils.h (__sun): clause for alloca.h on Solaris 2007-08-16 Martin Maechler * DESCRIPTION (Date, Version): 0.999375-2 2007-08-15 Martin Maechler * R/HBMM.R (readMM): make work for pattern matrices as well 2007-08-14 13:07 Douglas Bates * [r4730] src/Mutils.h: declare alloca * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R, R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R, man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf, src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c, src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its methods; switch writeMM to use CHOLMOD code; repair readMM 2007-08-14 Martin Maechler * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens Oehlschlaegel's ... result type still to be discussed! 2007-08-10 Martin Maechler * man/image-methods.Rd: new, combining all image() methods 2007-08-09 Martin Maechler * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix" to work via dgC... * R/Matrix.R (Matrix): special treatment for "table" (S3) 2007-08-07 Martin Maechler * R/dgTMatrix.R (image): change defaults to aspect = "iso", colorkey = FALSE 2007-08-06 Martin Maechler * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix; must copy its *expanded* x slot before LAPACK call. * tests/matprod.R: test the last days' changes. 2007-08-06 16:43 Douglas Bates * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs as well as in sources * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before Lapack call 2007-08-03 Martin Maechler * R/Matrix.R (%*%, crossprod, tcrossprod): add method for ("Matrix", "matrix") which is needed in some cases. Ditto for solve(). * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid infinite recursion in dispatch for some cases. 2007-08-02 08:48 Martin Maechler * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just so pointers match 2007-08-02 Martin Maechler * DESCRIPTION (Date): set ready for release -- 0.999375-1 2007-08-01 15:44 Douglas Bates * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c, src/chm_common.c, src/chm_common.h: Change API for numeric_as_chm_dense and N_AS_CHM_DN 2007-08-01 Martin Maechler * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!) * tests/matprod.R: regr.test for it 2007-07-20 Martin Maechler * R/dMatrix.R: fix from Brian for Math2(., digits = "missing") * tests/group-methods.R: and regression-test it 2007-07-19 19:45 Douglas Bates * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c, inst/include/cholmod.h, src/chm_common.c, src/init.c: Export triplet_to_sparse, documentation, use typedefs 2007-07-18 Martin Maechler * man/dpoMatrix-class.Rd: added 'corMatrix' example * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto * R/lsparseMatrix.R: bug fix in "all" method * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names * R/ngTMatrix.R (coerce->ngTMatrix): ditto; + matrix |-> nMatrix coercion * R/pMatrix.R: + setAs() to dMatrix and from nMatrix * man/pMatrix-class.Rd: ditto * R/Matrix.R (Summary): method for non-dMatrix * tests/Class+Meth.R (extraValid): new check about "dirty" slots * tests/Class+Meth.R (tstMatrixClass): test norm(.); test all Summary methods. 2007-07-16 Martin Maechler * R/dgeMatrix.R (norm, rcond): methods for 'matrix' 2007-07-14 Martin Maechler * R/sparseMatrix.R (norm): simple methods for sparseMatrix * R/pMatrix.R (t?crossprod): methods for pMatrix 2007-07-10 Douglas Bates * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight. 2007-07-09 20:45 Douglas Bates * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums trying to fix a subtle bug - which has been somewhere else. 2007-07-09 19:43 Martin Maechler * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not solve the bug 2007-07-08 Martin Maechler * src/dgCMatrix.c (compressed_to_TMatrix): 2007-07-07 Martin Maechler * src/Csparse.c (Rsparse_validate): new, to have some validity checking for RsparseMatrix * src/dgCMatrix.c (xRMatrix_validate): ditto * src/dtCMatrix.c (tRMatrix_validate): ditto 2007-07-07 Douglas Bates * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in lgRMatrix * [r4568] DESCRIPTION: Prepare for bug-fix release * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h for declaration of cholmod_symmetry 2007-07-06 Martin Maechler * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for release. 2007-07-06 14:11 Douglas Bates * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output functions - no longer used * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c, src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c, src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by Alloca 2007-07-06 13:14 Martin Maechler * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c, src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c, src/t_gCMatrix_colSums.c: more R_CheckStack()s 2007-07-05 18:12 Douglas Bates * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca" the required amount of memory then call M_numeric_as_chm_dense. * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro (like Calloc but calling alloca) 2007-07-05 Martin Maechler * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix() and extended with more sophisticated 'col.names' option. * NAMESPACE: export printSparseMatrix() * man/printSpMatrix.Rd: document, incl. examples 2007-07-04 16:21 Douglas Bates * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c, src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro AS_CSP. API change - pass the empty structure to Matrix_as_cs. 2007-07-04 Martin Maechler * DESCRIPTION (Version): 0.99875-4 * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test some dimnames perservation. * R/dsTMatrix.R (t-method): keep dimnames * R/dtTMatrix.R: ditto * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial and ncol(.) < 10 * src/cs_utils.c: drop check_class() and use Matrix_check_class() from Mutils.h * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames, e.g. in as(, "matrix") 2007-07-01 13:27 Douglas Bates * [r4529] .: Create a branch for the API changes from the 0.99875 series to the 0.999375 series * [r4530] DESCRIPTION, inst/include/Matrix.h, inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c, src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/t_gCMatrix_colSums.c: API change - pass the empty structure to the as_cholmod_x functions 2007-06-30 09:05 Martin Maechler * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE, trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info to Comparisons >>>>>>> .merge-right.r4561 2007-06-29 Martin Maechler * DESCRIPTION (Version): 0.99875-3 ready to be released. * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way that should also work in a future version of R. 2007-06-21 Martin Maechler * NAMESPACE, R/AllClass.R: "xsparseVector" class union. * R/sparseVector.R: more *sparseVector coercions, notably for non - double ones. 2007-06-19 Martin Maechler * R/colSums.R: new file for all (col|row)(Sums|Means) methods, notably the new ones building on the new .Call(.)s: * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define all 4 of [dlin]gCMatrix_colSums(). 2007-06-18 16:12 Douglas Bates * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector result 2007-06-16 Martin Maechler * R/kronecker.R: fix typo (could lead to inf.recursion) * test/simple.R: testing that * R/sparseMatrix.R (prSpMatrix): change to be used as print() method as well (which can have arguments, show() can't). 2007-06-16 15:52 Douglas Bates * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c: added dgCMatrix_colSums for [col,row][Sums,Means] 2007-06-15 23:15 Douglas Bates * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported), coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators" class * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd, man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the row names to store the levels - duh! Added an example. 2007-06-14 Martin Maechler * src/Csparse.c (Csparse_validate): check for *repeated* entries thanks to example from Christian Buchta; with a test here: * tests/simple.R: 2007-06-07 Martin Maechler * R/Auxiliaries.R (callGeneric): another fix, needed for some cases of colSums(*, sparseResult = TRUE) 2007-06-06 Martin Maechler * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to 'na.rm = FALSE' as "everywhere" else in R. 2007-06-05 Douglas Bates * [r4421] src/CSparse_install.sh: Modify for new organization of CSparse package * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of SuiteSparse * [r4426] src/Makefile: add ./UFconfig to the include path for compilation * [r4427] src/cs.[ch]: update to CSparse version 2.2.0 * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/* src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse 2007-06-05 Martin Maechler * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in * R/sparseMatrix.R (prSpMatrix): now gives a message about suppressed column names. 2007-06-04 17:13 Douglas Bates * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c, src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c, src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h, src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c: Remove warnings after change to const char* CHAR 2007-06-04 17:11 Douglas Bates * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected type of M_cholmod_ssmult 2007-06-03 14:42 Douglas Bates * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h, src/init.c: Yet another cholmod export - cholmod_ssmult 2007-05-23 Martin Maechler * NAMESPACE: exported drop0(), since * man/drop0.Rd: I have seen several cases, I really wanted to use it, so our users may want too. 2007-05-22 Martin Maechler * man/colSums.Rd: separately document colSums() etc, since these have the extra argument 'sparseResult'. 2007-05-21 Martin Maechler * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor; * man/spMatrix.Rd: docu., including examples * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(), in order to make colMeans() etc fast *and* correct. * R/sparseVector.R (replSPvec): "[<-" functionality for sparseVectors; tested in * tests/simple.R: 2007-05-19 Martin Maechler * R/sparseMatrix.R (print.sparseSummary): and summary() method for (very) sparse Matrices; output similar to Matlab's print(). 2007-05-17 Douglas Bates * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not 0-based, indices (Jose Quesada ). 2007-05-16 Douglas Bates * R/CHMfactor.R: Added solve methods for a CHMfactor object. 2007-05-16 Martin Maechler * R/Auxiliaries.R (sparsapply): new utility, much faster than tapply1() for large sparse matrices. 2007-05-15 Martin Maechler * R/Matrix.R (dim<-): reshape now via sparseVector. * R/sparseVector.R: methods and function for * R/AllClass.R: new "sparseVector" class and daughters. * NAMESPACE: export new classes 2007-05-14 Martin Maechler * DESCRIPTION (Version): 0.99875-1 * src/Makefile.win: also remove Lapack code from here (cf. 04-25). 2007-05-11 Martin Maechler * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric indexing * tests/indexing.R: test set for that. 2007-05-08 Martin Maechler * R/Tsparse.R (replTmat): fix the case of *duplicated* index entries. * tests/indexing.R(out): add regression test for it 2007-04-30 Martin Maechler * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument name for "!" method definitions. 2007-04-26 Martin Maechler * R/Tsparse.R (intI): new utility, used for "[" : Cleanup up there, and fixes for duplicated indices - more TODO! * tests/indexing.R(out): more tests 2007-04-25 Douglas Bates * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack code that is now part of the R Lapack library. * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export cholmod_factorize_p (used in lme4 for GLMMs and NLMMs). 2007-04-21 Martin Maechler * R/Matrix.R (image): method for all Matrices, not just sparse ones. 2007-04-17 Martin Maechler * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end up with extraneous names '0'...'' 2007-04-12 Martin Maechler * R/dgTMatrix.R (mat2dgT): care about NAs 2007-04-11 Martin Maechler * R/kronecker.R: triangularity preserving methods 2007-03-27 Martin Maechler * R/kronecker.R: new file collecting kronecker() methods in one place. Goal: become much faster! 2007-03-23 Martin Maechler * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper Kristensen based cs_spsolve() instead of _lsolve & _usolve which can be much faster. * tests/matprod.R: add regression tests for these (upper & lower). 2007-03-19 Martin Maechler * R/Matrix.R (diff): method for our Matrices. * R/sparseMatrix.R (isDiagonal): check dim()! 2007-03-17 Martin Maechler * R/Matrix.R (dim<-): new method for "reshape()" built on a proposal from Tamas Papp. 2007-03-16 Martin Maechler * R/AllGeneric.R: remove all if(!isGeneric(.)) clauses * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE); rather define and export cBind() and rBind() only. --> useRs *must* change code that used to have cbind()/rbind() !! * R/bind.R: change tests from cbind() to cBind() and similarly to rBind() * R/bind.Rout.save: ditto 2007-02-16 Douglas Bates * DESCRIPTION (Date, Version): 0.9975-11 with new date * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove const modifier on declaration of the array 'valid' 2007-02-12 Douglas Bates * R/CHMfactor.R: Add image method (coercion to sparseMatrix). 2007-02-05 Martin Maechler * 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 * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup() 2007-02-03 Martin Maechler * 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 * src/init.c: export the CHM...._validate() placeholders, since they *are* called. * tests/Class+Meth.R (classCanCoerce): and starting to test all as(, ) 2007-01-30 Martin Maechler * 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 * 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 * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones. * R/Ops.R (Arith): o now remains sparse where sensible when the is of length > 1. 2007-01-26 Martin Maechler * R/Matrix.R ([<-): for M[] <- value: fix length 2007-01-25 Martin Maechler * R/Auxiliaries.R (n2l_Matrix): new, to be used in * R/ndenseMatrix.R: new coercions n* -> l* 2007-01-22 Martin Maechler * R/triangularMatrix.R: new file; simple triu() and tril() methods. * R/Ops.R ("Logic"): and other "Ops", many updates 2007-01-18 Martin Maechler * 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 * R/diagMatrix.R (!): fix typo. 2007-01-16 Martin Maechler * 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 * R/Ops.R ("Logic"): more methods, notably an o one. 2007-01-12 Martin Maechler * 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 * R/Auxiliaries.R (is_duplicatedT): new utility 2007-01-05 Douglas Bates * src/init.c (R_init_Matrix): export cholmod_scale 2006-12-30 Martin Maechler * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our base::as.matrix to (x, ...) 2006-12-28 Martin Maechler * 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 * src/zpotfr.f and dependencies: use LAPACK 3.1 version only needed previously to R version 2.5.0. 2006-12-26 Martin Maechler * 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 * 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 * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions; also more general diagU2N(). 2006-12-21 Martin Maechler * R/bind2.R: new file for all cbind2(), rbind() methods moved here from R/Matrix.R files. Better diagonal & improved sparse methods. 2006-12-20 Martin Maechler * 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 * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in * tests/indexing.R 2006-12-15 Martin Maechler * 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 * 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 * 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 * 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 * 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 * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot. 2006-12-08 Douglas Bates * DESCRIPTION (Version): updated -> release 0.9975-7 * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p 2006-11-30 Martin Maechler * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method 2006-11-29 Douglas Bates * 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 * DESCRIPTION (Date): updated -> release 0.9975-6 2006-11-06 Martin Maechler * 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 * 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 * 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 * R/dMatrix.R (Compare(,): update and * tests/validObj.R: checks for "comparison" * R/sparseMatrix.R ([): improved indexing for sparse; trying to keep [ n, n] symmmetric * tests/indexing.R: indexing for logical sparse now ok 2006-11-02 Martin Maechler * src/Tsparse.c: use xTsparse_validate() , and hence remove * src/{ltC,lsC,lgT}Matrix.[ch]: removed 2006-11-02 Martin Maechler * 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 * R/Csparse.R,src/Csparse.c, etc: tcrossprod(,) * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for symmetry test, via * R/Auxiliaries.R (.as.dgC.0.factors): 2006-11-01 Douglas Bates * R/Csparse.R,src/Csparse.c,tests/matprod.R, man/CsparseMatrix-class.Rd: crossprod(, ) added 2006-10-30 Martin Maechler * tests/matprod.R: add a variation of Harri's example * R/dsparseMatrix.R: fix crossprod(, ) to *not* recursive infinitely. * R/dgCMatrix.R: + solve(, ) * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R 2006-10-28 Martin Maechler * 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 * R/Matrix.R (Ops): o 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 * 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 o * 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 * DESCRIPTION (Version): 0.9975-5 ready for release 2006-10-20 Douglas Bates * src/init.c (R_init_Matrix): export more cholmod CCallable functions. 2006-10-20 Martin Maechler * 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 * src/chm_common.h: Add R_cholmod_start to initialize cholmod to use Rprintf and R's error handling. 2006-10-17 Martin Maechler * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal. * tests/matprod.R: add tests for the bug fixed. 2006-10-11 Douglas Bates * src/HBMM.[ch]: remove HarwellBoeing format for writing. * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c 2006-10-06 Douglas Bates * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead. 2006-10-06 Martin Maechler * 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 * R/Matrix.R ([<-): also for value "Matrix" or "matrix" 2006-10-04 Douglas Bates * DESCRIPTION (Version): 0.9975-2 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols 2006-10-02 Douglas Bates * tests/dg_Matrix.R: Simplify test taking into account new code. 2006-09-29 Martin Maechler * 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 * 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 * 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 * src/Makefile.win (SUBDIRS): fix typo 2006-09-19 Martin Maechler * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN 2006-09-18 Douglas Bates * 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 * 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 * 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 * 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 * 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 * src/Mutils.[ch],init.c inst/include/*.h: Move the alloc_d**Matrix functions to the lme4 package. 2006-09-09 Douglas Bates * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now fixed 2006-09-09 Martin Maechler * 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 * 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 * src/Mutils.h: Remove functions that are no longer used. 2006-09-04 Douglas Bates * src/dtCMatrix.c (dtCMatrix_validate): rename functions. * src/DEPS.mkf: update 2006-09-02 Martin Maechler * 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 * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL 2006-09-01 Martin Maechler * 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 * 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 * 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 * R/dgCMatrix.R: aargh: "Arith(, 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 * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting in all cases. 2006-08-27 Douglas Bates * 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 * 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 * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard - ordering standard errors to match effects. 2006-08-24 Douglas Bates * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods * man/band.Rd: adapt the \dontshow{} unit test. 2006-08-07 Martin Maechler * 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 * R/Matrix.R (head, tail): directly use utils:::head.matrix to be up-to-date automatically. 2006-08-03 Martin Maechler * 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 * 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 * 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 * 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 * 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 * 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 * 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 * 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() 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 * R/Matrix.R (head): added head() and tail() methods. 2006-07-17 Martin Maechler * DESCRIPTION (Version): 0.995-12 released to CRAN 2006-07-15 Martin Maechler * 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 * 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 * 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 * 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 * 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 * R/pMatrix.R: coercion pMatrix -> Tsparse 2006-06-12 Douglas Bates * 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 * R/lmer.R (simulestimate): added C code for calculating the trace of the hat matrix. 2006-06-09 Martin Maechler * R/diagMatrix.R (setAs): define coercion methods to sparse matrix classes. * R/sparseMatrix.R etc: multiplication of diagonal and sparse 2006-06-08 Martin Maechler * R/dgTMatrix.R (colSums): etc. All four of colSums(), rowSums(), colMeans(), rowMeans() now should work for all "Matrices". 2006-06-01 Douglas Bates * R/lmer.R (panel.ci): Add a reference line at zero and a background grid to the qqmath plot of ranef.lmer. 2006-05-30 Douglas Bates * R/lmer.R (expandSlash): Functions (non-exported) to allow nested grouping factors to be specified in the formula as (1|foo/bar). 2006-05-27 Douglas Bates * R/lmer.R (findbars and others): Change check of is.numeric to !is.language to resolve the bug reported by Jacob Wegelin. * src/pedigree.c (pedigree_inbreeding): Initial implementation of code to evaluate inbreeding coefficients without calculating T, based on code in Sargolzaei and Iwaisaki's paper. 2006-05-27 Douglas Bates * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local generic and mer methods for isNested and denomDF. This denomDF was an attempt to emulate that in lme but I don't think that makes sense. Use the trace of the hat matrix instead. 2006-05-17 Martin Maechler * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use the C code depending on a slot structure that's no longer valid. * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h) 2006-05-17 Douglas Bates * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name of lowerTriMatrix generic and methods to tril (also upper to triu) and added a general band extractor. 2006-05-16 Douglas Bates * R/pedigree.R (pedigree): Replace sire and dam values outside the allowable range with NAs. Added a corresponding check in the validity check for the pedigree class. * R/[CT]sparse.R ([t]crossprod): The result of single-argument crossprod methods now inherits from symmetricMatrix. 2006-05-15 Douglas Bates * R/AllGeneric.R (lowerTriMatrix): Added (but did not export) generics lowerTriMatrix and upperTriMatrix along with methods for the Csparse virtual class. Also added a C function Csparse_band that implements these methods by calling cholmod_band. 2006-05-15 Martin Maechler * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got erased when it was NULL. This led to invalid subselections! 2006-04-25 Douglas Bates * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix in method for "t" so as not to lose the unit diagonal property. 2006-04-19 Douglas Bates * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic and methods. This is now an option to the ranef method for the mer class. * src/cs_utils.c: Ensure that the nz component is -1 for a compressed column-oriented matrix. Minor formatting cleanup. * man/lmer-class.Rd: Document the qqmath method for ranef.lmer objects. 2006-04-19 Martin Maechler * R/Auxiliaries.R (diagU2N): new for the solve() methods in * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U". 2006-04-15 Douglas Bates * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library in cs.[ch] and utilities to interface to that code in cs_utils.[ch]. * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods for the dtCMatrix class. 2006-04-12 Douglas Bates * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class and methods for it. 2006-04-12 Martin Maechler * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix" arguments, such that M %*% 1:6 now works * Tests/matprod.R: test the above 2006-04-03 Douglas Bates * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for the ranef.lmer class. * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and methods to extract the posterior variances from the bVar slot. 2006-03-30 Martin Maechler * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*) * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices. * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in * tests/simple: (extended) * R/sparseMatrix.R (isTriangular): now using much improved * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix 2006-03-23 Douglas Bates * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames (problem report from Franklin Parlamis). This should be done generally. 2006-03-21 Douglas Bates * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to ranef.lmer (like summary.lmer). Add the coef.lmer class and update the plot methods. 2006-03-20 Douglas Bates * R/lmer.R (resid and ranef methods): Added methods for the "residuals" and "resid" generic but only for linear mixed model fits. Changed the ranef method to return a list of data frames so that the plot methods now work. 2006-03-16 Douglas Bates * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to dpotrf - otherwise the BLAS on Mac OS X complains and quits. * DESCRIPTION (Date): New release 2006-03-15 Martin Maechler * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y) * man/KNex.Rd: and other help files * tests/*.R: several ones needed adaption * inst/doc/Comparisons.Rnw: ditto 2006-03-11 Martin Maechler * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix * tests/indexing.R: tests for new [<- methods for sparse matrices. 2006-03-10 Martin Maechler * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix * R/Tsparse.R (.ind.prep): fix out-of-range indexing 2006-03-08 Martin Maechler * R/dMatrix.R: enable things like M [ M < 10 ] * R/dgeMatrix.R: implement it 2006-03-06 Martin Maechler * R/AllClass.R: define "summary.mer" and "*.lmer" * R/lmer.R (summary): summary() computes & returns the above; * R/lmer.R (show): now works with summary() 2006-03-04 Martin Maechler * R/dgCMatrix.R: finally direct "Arith" dgC o dgC * R/Auxiliaries.R (WhichintersectInd): and other utilities to support the above 2006-02-07 Douglas Bates * R/lmer.R (lmer): fix initial values of offset and weights for 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 * 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 * R/Matrix.R (Matrix): has become much "smarter" now auto-producing many different kinds of matrices. * R/*.R: quite a few new methods were needed for R CMD check with new Matrix(). Very good for users playing around. 2006-01-15 Martin Maechler * src/dgeMatrix.c (dMatrix_validate): new * src/Mutils.c (dense_nonpacked_validate): new * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed 2006-01-14 Douglas Bates * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes 2006-01-07 Douglas Bates * DESCRIPTION (Version): 0.99-6 released to CRAN * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for segfault in cases with multiple non-nested grouping factors. 2006-01-03 Martin Maechler * DESCRIPTION (Version): 0.99-4 to be released to CRAN (Depends): also on 'utils' * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*" * R/diagMatrix.R (Diagonal): constructor and methods for diagonal matrices * R/ltTMatrix.R: new "minimal methods" 2005-12-12 Martin Maechler * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for all methods (and help files). 2005-12-09 Martin Maechler * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug for case (dimn. op no_dimn.) 2005-11-14 Douglas Bates * DESCRIPTION (Version): 0.99-2 released to CRAN 2005-10-21 Douglas Bates * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported by Julian Faraway. 2005-10-06 Martin Maechler * R/Auxiliaries.R (try_as): new utility * R/sparseMatrix.R: use try_as() in coercion to original class 2005-09-30 Martin Maechler * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc() 2005-09-29 Martin Maechler * R/Auxiliaries.R (dimNamesCheck): added * R/Matrix.R (as.array), (as.vector): new 2005-09-28 Martin Maechler * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart default. * R/AllClass.R: move 'factors' slot toplevel "Matrix"; "pMatrix" now contains "sparseMatrix" 2005-09-26 Martin Maechler * tests/Class+Meth.R: new tests; t(t(m)) == m * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!) * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new * R/dspMatrix.R: typo in "t" method 2005-09-18 Douglas Bates * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM* * R/Tsparse.R: instead of R/gTMatrix.R * R/Csparse.R: new * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_() * src/Tsparse.c: new; many trivial methods calling cholmod_() * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod: via cholmod 2005-09-16 Martin Maechler * R/Auxiliaries.R (non0ind): new function using new C code * src/dgCMatrix.c (compressed_non_0_ij): new utility 2005-09-15 Douglas Bates * src/chm_common.h: header file required by all C sources that call CHOLMOD functions. It defines a cholmod_common structure called 'c' whose address is passed as the last argument to (virtually) every CHOLMOD function. * src/Pattern.c: Simple example of the use of CHOLMOD. * src/init.c: initialize and finalize the cholmod_common structure. * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD LDL and CCOLAMD from the U. of Florida sparse matrix library. 2005-09-08 Martin Maechler * inst/test-tools.R: new file collecting the utility functions used in ./tests/*.R * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix" * R/Matrix.R (cbind2): methods for NULL and missing 2005-08-31 Martin Maechler * R/AllClass.R: new "index" class for "[" and "[<-": First cut at "symmetricMatrix" and "triangularMatrix" * R/gTMatrix.R (.ind.prep): new function; Logical and character indexing now work too. * R/Matrix.R: cheap "[<-" methods for denseMatrix now work * tests/indexing.R: new, including *.Rout.save * tests/dgTMatrix.R: new 2005-08-29 Douglas Bates * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position indicator pos not being updated. Also enforced upper triangular for symmetric case. Need to coerce edges component of elements of edge list - grr! (Why don't they define their classes cleanly?) 2005-08-26 Martin Maechler * R/Matrix.R: added first "[<-" methods; not yet functional * R/denseMatrix.R: ditto * man/Subassign-methods.Rd: new help file for these 2005-08-25 Martin Maechler * DESCRIPTION (Version): 0.98-6 * R/denseMatrix.R: new file for "[" fallback methods for all dense matrices. 2005-08-19 Martin Maechler * src/lgCMatrix.c (lcsc_to_matrix): new; need for as( , "matrix") * R/pMatrix.R: coercion to "lgTMatrix" * R/gTMatrix.R: new virtual class to define "[" methods for. * man/gTMatrix-class.Rd: * General slight re-organization of where "[" methods are defined. more to come. 2005-08-18 Douglas Bates * DESCRIPTION (Version): 0.98-5 released to CRAN * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods * ..... 2005-08-18 Douglas Bates * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer or glmer objects. 2005-08-17 Martin Maechler * DESCRIPTION (Version): 0.98-4 : upload to CRAN 2005-08-16 Douglas Bates * R/HBMM.R: finish re-writing R-only code. 2005-08-15 Douglas Bates * man/externalFormats.Rd: move documentation for writeHB and writeMM here. * src/mmio.c: replace inclusion of by (suggested by Paul Roecker). * tests/validObj.R (assertError): Comment out test that is failing after recent changes in r-devel. 2005-08-11 Martin Maechler * R/AllClass.R: intermediate virtual class "denseMatrix" * man/denseMatrix-class.Rd * NAMESPACE: export it, and also export * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix" 2005-08-10 Douglas Bates * DESCRIPTION (Version): 0.98-3 to CRAN * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and matrix_solve code (which was really, really wrong). 2005-08-07 Douglas Bates * DESCRIPTION (Version): 0.98-2 * R/HBMM.R (readHB), (readMM): read Matrix Market formats * R/lmer.R (abbrvNms): new * R/lmer.R (mcmcsamp): allow transformed parameters * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines for the Harwell-Boeing and the MatrixMarket formats. 2005-08-04 Martin Maechler * man/dtrMatrix-class.Rd: add examples * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM * TODO: note the dtpMatrix (docu) bug * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base") in order to ensure that new as.matrix() is used by old functions, e.g., svd(), qr(), eigen(), dist(),..; apply(), also matplot() or pairs(). 2005-08-03 Martin Maechler * R/lmer.R: add 'fixme' comments and move the linear vs glm check; add comments about 'control' / lmerControl() arguments 2005-07-27 Douglas Bates * man/sleepstudy.Rd: Added the sleep data set. * DESCRIPTION (Version): 0.98-1 released to CRAN 2005-07-12 Douglas Bates * man/sleepstudy.Rd: Added the sleep data set. * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of .Call calls that were producing spurious output. 2005-07-05 Douglas Bates * R/lmer.R (lmer): stored updated variance component estimates in mer object for the generalized model. (Bug reported by Renaud Lancelot). 2005-07-03 Douglas Bates * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor, unidimensional case. 2005-06-08 Douglas Bates * DESCRIPTION (Version): 0.96-1 * moved lmer-class' R and C code moved from lme4 to here 2005-06-04 Douglas Bates * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments (reported by Guissepe Ragusa ) 2005-06-02 Douglas Bates * src/Makefile.win: Forgot to update this when Makefile changed. 2005-05-11 Douglas Bates * src/dgCMatrix.c (csc_transpose): Simplified function fixing a bug reported by Kurt Hornik and Michael Hahsler. 2005-05-10 Douglas Bates * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for logical sparse matrices. These will also be used in the symbolic analysis for lmer objects. * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr 2005-05-06 Douglas Bates * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of colMeans, colSums, rowMeans and rowSums. 2005-04-18 Douglas Bates * src/lgCMatrix.[ch]: code for _validate method and stub for multiplication operation. * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument to dgetrs. * src/init.c: Fix cut-and-paste error in definition of dgeMatrix_matrix_solve * src/{many files}: Tighten code by using ALLOC_SLOT. 2005-04-15 Douglas Bates * R/AllClass.R: Add lgTMatrix and lgCMatrix classes * DESCRIPTION: Eliminate import of stats. 2005-04-06 Douglas Bates * R/AllClass.R : add logical sparse matrix classes 2005-04-01 Martin Maechler * R/dgTMatrix.R: add "[" method for triplet matrices * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse 2005-03-31 Douglas Bates * DESCRIPTION (Version): release 0.95-5 to CRAN * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods * R/sparseMatrix.R: %*%, crossprod() * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix' * src/lmer.c (lmer_fitted): fix thinko 2005-03-26 Martin Maechler * R/AllClass.R: add two virtual sparse classes ``on top'' 2005-03-24 Martin Maechler * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes; correspondingly fix examples and tests/ since new() doesn't work for virtual classes. 2005-03-17 Martin Maechler * R/Matrix.R (as.matrix): method and one for unname() * tests/dpoMatrix.R: tests should now be less platform dependent; also run for R 2.1.0; using as.matrix() 2005-03-15 Douglas Bates * R/pMatrix.R: "pMatrix" class added * .... 2005-03-14 Douglas Bates * R/dtpMatrix.R: Add unpack method and an example. * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization of general symmetric matrices and associated S4 methods. 2005-03-10 Martin Maechler + 2005-03-05 Martin Maechler * R/dgeMatrix.R (setAs): and many other files: more coercion, crossprod() and "%*%" methods added; tests, too. * tests/matprod.R: new, for testing these 2005-03-03 Douglas Bates * src/lmer.c (lmer_fitted): Added. 2005-03-02 Douglas Bates * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix 2005-02-28 Douglas Bates * src/*.c,po/,inst/po: Internationalization and localization of the package. * src/ldl.[ch]: Removed these as their contents are referenced in the R_ldl.c file. * src/flame.[ch]: Removed these source files. * src/dtrMatrix.c (make_array_triangular): Move to Mutils * src/LU.[ch],src/init.c: absorb in factorizations * src/Mutils.h: prepare for internationalization * src/cblas.h: move the enum definitions to Mutils.h and remove this file 2005-02-26 Martin Maechler * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods * R/dtrMatrix.R: fix t() method * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2" * NAMESPACE: export them (and import generics from "methods") * tests/group-methods.R : and test them. * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in border case 2005-02-24 Douglas Bates * DESCRIPTION (Version): 0.95-2 released to CRAN * src/dgBCMatrix.c: * src/lmer.c: many changes * ... 2005-02-04 Martin Maechler * R/Matrix.R: add more sophisticated show() method. 2005-02-02 Douglas Bates * */* : almost complete reorganization of classes. 2005-01-26 Douglas Bates * R/AllGeneric.R: Added matrix exponential generic expm and a method for the geMatrix class. 2005-01-24 Douglas Bates * src/Makefile (clean): Remove *.a and *.so * man/cscBlocked-class.Rd: Remove reference to the lmer-class. 2005-01-23 Douglas Bates * src/lmer.c (Lind): Definition of Lind was backwards. This only had an effect in cases with more than 2 grouping factors. 2005-01-03 Douglas Bates * src/lmeRep.c (lmer_variances): change from lmeRep to lmer 2004-12-23 Douglas Bates * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines and R_useDynamicSymbols (suggested by B.D.Ripley). 2004-12-14 Douglas Bates * R/sscMatrix.R: Add determinant methods * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion for tripletMatrix to matrix. 2004-12-13 Douglas Bates * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is no longer used. * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files with dynamic allocation of scratch arrays. * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ for multivariate random effects with multiple grouping factors. Fixes part but not all of #15. 2004-12-03 Douglas Bates * src/lmeRep.c (lmeRep_factor): order of operations for multiple scalar grouping factors corrected. 2004-11-29 Douglas Bates * src/bCrosstab.c: remove diag_update which is no longer used 2004-11-16 Douglas Bates