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: dito * man/Subassign-methods.Rd: new help file for these 2005-08-25 Martin Maechler * DESCRIPTION (Version): 0.98-6 * R/denseMatrix.R: new file for "[" fallback methods for all dense 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 * src/Metis_utils.c: Move metis.h include to C sources so that the .h file can be included. 2004-11-12 Douglas Bates * src/LU.c,geMatrix.c,trMatrix.c, etc.: Complete allocation of slots in NEW_OBJECT. * src/Mutils.h: Moved list of symbols to an include file 2004-11-11 Douglas Bates * src/geMutils.c (Matrix_init): remove unused function 2004-11-10 Douglas Bates * src/cscMatrix.c (csc_to_imagemat): removed unused function 2004-11-05 Douglas Bates * src/Makefile.win (SOURCES_C): Keep consistent with Makefile 2004-10-27 Douglas Bates * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls 2004-10-04 Douglas Bates * src/init.c: Created R_init_Matrix and added registration of C routines. 2004-10-02 Douglas Bates * R/tripletMatrix.R: Force a require(lattice) for the image methods. 2004-06-15 Douglas Bates * man/trMatrix-class.Rd: Escape the % chars in .Rd files. 2004-04-20 Douglas Bates * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges. 2004-04-19 Douglas Bates * src/ssclme.c (ssclme_update_mm): fix logic error in ssclme_update_mm 2004-04-18 Douglas Bates * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency in the order of unconstrained and constrained parameters. (ssclme_gradient): Added the gradients (not yet correct for multidimensional, unconstrained case). 2004-04-14 Douglas Bates * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update * src/Makefile.win: Remove unneeded ranlib call 2004-04-12 Douglas Bates * DESCRIPTION (Version): New release * src/Makefile.win: Update Makefile.win to umfpack removal. 2004-04-05 Douglas Bates * src/triplet_to_col.c: Create triplet_to_col as a native function, not the version from umfpack. There were problems with the configuration of UMFPACK for 64-bit processors and there was only one umfpack routine being used so I moved it here. 2004-04-04 Douglas Bates * src/ssclme.c (ssclme_variances): New function. 2004-03-28 Douglas Bates * src/ssclme.c (ssclme_fitted): Added function. 2004-03-27 Douglas Bates * src/ssclme.c (ssclme_transfer_dimnames): Add new function to store the dimnames in the XtX and bVar slots (ssclme_update_mm): Change the dimensions of the bVar slot components and the returned value from ssclme_ranef. 2004-03-18 Douglas Bates * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R}, src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c}, tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R}, man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd, pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd, pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd, pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd, pdBlocked-class.Rd},AllClass.R,AllGeneric.R: Moved the pdMat classes from the lme4 package. 2004-03-02 Douglas Bates * man/ssclme-class.Rd: Update definition and documentation of the ssclme class to include the DIsqrt slot. * src/ssclme.c (ssclme_deviance): Modify order of computation (much faster using dsyrk, a level 3 BLAS routine). * src/Makefile (SUBLIBS): Change definition (K. Hornik) 2004-02-28 Douglas Bates * tests/ssclme.R: Modify the test to account for the permutation of the levels of the grouping factors. 2004-02-23 Douglas Bates * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot directly into the ssclme class definition. 2004-02-22 Douglas Bates * DESCRIPTION (Date): New release * man/ssclme-class.Rd: new file. * src/ssclme.c (ssclme_loglik): major revisions in design. It works and it's fast! 2004-02-17 Douglas Bates * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley) 2004-02-16 Douglas Bates * DESCRIPTION (Date): New release * NAMESPACE: Don't export ssclme. * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary school data. 2004-02-11 Douglas Bates * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to keep track of the fixed-effects and the response. Counts also gets an extra element, which is always one. * src/ldl.c: Include these routines from Tim Davis' LDL package. 2004-02-10 Douglas Bates * src/cscMatrix.c (csc_transpose): new function * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected (csc_components_transpose): new function 2004-02-06 Douglas Bates * src/triplet.c (triplet_validate): Fix Dim slot on generated triplets 2004-01-30 Douglas Bates * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function. * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this and all other .h files in src. * src/Makefile.win: This and other Makefile.win files contributed by Brian Ripley. 2004-01-27 Douglas Bates * R/syMatrix.R: Added methods for "%*%". * R/Hilbert.R (Hilbert): Changed Hilbert function to return a poMatrix object. 2004-01-26 Douglas Bates * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages. 2004-01-25 Douglas Bates * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes. * R/csc.R: Convert all cscMatrix classes to use Dim slot instead of nrow. 2003-12-31 Douglas Bates * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into subdirectories. 2003-12-08 Douglas Bates * src/taucs.h: Accidently referred to global header files instead of local files. 2003-12-04 Douglas Bates * R/AllClass.R: Lots of changes. Removed all the lapack++ code and methods and replaced all classes with S4 classes. 2003-04-19 Douglas Bates * R/det.R,man/det.Rd: Change name of det generic to determinant * src/R_LapackPP.cc: Change method of calculating determinants 2003-02-03 Douglas Bates * DESCRIPTION (Version): removed empty data directory as requested by CRAN maintainers. Changed version number and date. 2002-10-23 Douglas Bates * src/laindex.h: Applied patches from Brian Ripley for compilation under Windows. * Added configure.win and src/Makevars.win as requested by Brian Ripley. 2002-05-03 Douglas Bates * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt Hornik. 2002-04-24 Douglas Bates * configure.ac: Replaced configure.in with configure.ac contributed by Kurt Hornik. * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's version for R-1.5.0 2001-12-10 Douglas Bates * man/eigen.Rd: Removed the .Alias in the example