 pkg/ChangeLog 2004/11/23 15:39:45 350
+++ pkg/ChangeLog 2006/08/07 09:05:42 1349
@@ 1,41 +1,932 @@
20041116 Douglas Bates
+20060807 Martin Maechler
+
+ * DESCRIPTION (Version): 0.99514 for CRAN
+
+ * tests/otherpkgs.R: oops: library(Matrix) outside *if* !
+
+ * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse > graph coercion
+ * tests/otherpkgs.R: more checks, sparseMatrix > graph
+
+ * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
+ * R/Tsparse.R (tril, triu, band): methods
+ * R/dgRMatrix.R (tril, ...): dito
+ * man/band.Rd: dito
+
+20060804 Martin Maechler
+
+ * R/Matrix.R (head, tail): directly use utils:::head.matrix
+ to be uptodate automatically.
+
+20060803 Martin Maechler
+
+ * DESCRIPTION (Version): 0.99513 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.
+
+20060801 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).
+
+20060731 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.
+
+20060731 Martin Maechler
+
+ * NAMESPACE: change "correlation" to "corMatrix"
+ * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
+ * R/dpoMatrix.R: dito
+ * R/lmer.R: dito
+
+20060728 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.
+
+20060722 Martin Maechler
+
+ * R/Matrix.R: Coercions "Matrix" > (sparsedense)Matrix
+ via new smart
+ * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
+ utility functions.
+
+
+20060721 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).
+
+ speedoptimize a few places by moving REAL(.) out of loops.
+
+ * src/lmer.h, src/init.h, R/lmer.R: related to above.
+
+20060720 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 nonsymmetric 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
+ 1based indices, not 0based 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/isSymmetricmethods.Rd: and document it.
+
+ * R/SparseMconv.R: added coercion methods for some 'SparseM' matrices.
+ * man/SparseMconv.Rd: docu them
+
+ * tests/otherpkgs.R: renamed from tests/graph.R and add example
+ for 'SparseM' conversions
+
+20060717 Douglas Bates
+
+ * R/Matrix.R (head): added head() and tail() methods.
+
+20060717 Martin Maechler
+
+ * DESCRIPTION (Version): 0.99512 released to CRAN
+
+20060715 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* non0 entry indices also
+ for sparse symmetric matrices.
+
+ * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
+ diagonal twice.
+
+20060711 Douglas Bates
+
+ * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
+ being applied to the x slot (detected by Brian Ripley).
+
+20060710 Martin Maechler
+
+ * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
+
+ * R/Auxiliaries.R (isTriC): fix buglet (we were 1based!)
+
+20060708 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.
+
+20060706 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/{lmerclass.Rd,mcmcsamp.Rd}: Update documentation for glmer
+ class.
+
+20060701 Martin Maechler
+
+ * R/pMatrix.R: coercion pMatrix > Tsparse
+
+20060612 Douglas Bates
+
+ * DESCRIPTION (Version): 0.99511 released to CRAN
+
+ * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
+ the output from mcmcsamp.
+
+20060610 Douglas Bates
+
+ * R/lmer.R (simulestimate): added C code for calculating the trace
+ of the hat matrix.
+
+20060609 Martin Maechler
+
+ * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
+ classes.
+ * R/sparseMatrix.R etc: multiplication of diagonal and sparse
+
+20060608 Martin Maechler
+
+ * R/dgTMatrix.R (colSums): etc. All four of
+ colSums(), rowSums(), colMeans(), rowMeans() now should work for
+ all "Matrices".
+
+20060601 Douglas Bates
+
+ * R/lmer.R (panel.ci): Add a reference line at zero and a
+ background grid to the qqmath plot of ranef.lmer.
+
+20060530 Douglas Bates
+
+ * R/lmer.R (expandSlash): Functions (nonexported) to allow nested
+ grouping factors to be specified in the formula as (1foo/bar).
+
+20060527 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.
+
+20060527 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.
+
+20060517 Martin Maechler
+
+ * R/sparseMatrix.R: Matrix <> graph methods: can no longer use
+ the C code depending on a slot structure that's no longer valid.
+ * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
+
+
+20060517 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.
+
+20060516 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 singleargument
+ crossprod methods now inherits from symmetricMatrix.
+
+20060515 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.
+
+20060515 Martin Maechler
+
+ * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
+ erased when it was NULL. This led to invalid subselections!
+
+20060425 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.
+
+20060419 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 columnoriented matrix. Minor formatting cleanup.
+
+ * man/lmerclass.Rd: Document the qqmath method for ranef.lmer
+ objects.
+
+20060419 Martin Maechler
+
+ * R/Auxiliaries.R (diagU2N): new for the solve() methods in
+ * R/dtCMatrix.R: where dgC > dgT coercion now preserves diag = "U".
+
+20060415 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] : CSparsebased solve methods
+ for the dtCMatrix class.
+
+20060412 Douglas Bates
+
+ * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
+ and methods for it.
+
+20060412 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
+
+20060403 Douglas Bates
+
+ * R/lmer.R (qqmath,ranef.lmermethod): 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.
+
+20060330 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
+
+20060323 Douglas Bates
+
+ * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
+ (problem report from Franklin Parlamis). This should be done
+ generally.
+
+20060321 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.
+
+20060320 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.
+
+20060316 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
+
+20060315 Martin Maechler
+
+ * DESCRIPTION (Version): 0.9956  to be released to CRAN
+
+ * data/KNex.rda: replacing 'mm' and 'y' by KNex < list(mm=mm, y=y)
+ * man/KNex.Rd: and other help files
+ * tests/*.R: several ones needed adaption
+ * inst/doc/Comparisons.Rnw: dito
+
+20060311 Martin Maechler
+
+ * R/dgCMatrix.R (replCmat): "[<" methods for dgCMatrix
+
+ * tests/indexing.R: tests for new [< methods for sparse matrices.
+
+20060310 Martin Maechler
+
+ * R/dgTMatrix.R (replTmat): "[<" methods for dgTMatrix
+
+ * R/Tsparse.R (.ind.prep): fix outofrange indexing
+
+20060308 Martin Maechler
+
+ * R/dMatrix.R: enable things like M [ M < 10 ]
+ * R/dgeMatrix.R: implement it
+
+20060306 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()
+
+20060304 Martin Maechler
+
+ * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
+ * R/Auxiliaries.R (WhichintersectInd): and other utilities to
+ support the above
+
+20060207 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.
+
+20060123 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")
+
+
+20060116 Martin Maechler
+
+ * R/Matrix.R (Matrix): has become much "smarter" now autoproducing
+ 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.
+
+
+20060115 Martin Maechler
+
+ * src/dgeMatrix.c (dMatrix_validate): new
+ * src/Mutils.c (dense_nonpacked_validate): new
+
+ * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
+
+
+20060114 Douglas Bates
+
+ * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
+
+20060107 Douglas Bates
+
+ * DESCRIPTION (Version): 0.996 released to CRAN
+
+ * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
+ segfault in cases with multiple nonnested grouping factors.
+
+20060103 Martin Maechler
+
+ * DESCRIPTION (Version): 0.994 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"
+
+20051212 Martin Maechler
+
+ * R/AllGeneric.R (tcrossprod): 2argument version; here, and for
+ all methods (and help files).
+
+20051209 Martin Maechler
+
+ * R/Auxiliaries.R (dimNamesCheck): fixed thinko > bug
+ for case (dimn. op no_dimn.)
+
+20051114 Douglas Bates
+
+ * DESCRIPTION (Version): 0.992 released to CRAN
+
+20051021 Douglas Bates
+
+ * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
+ by Julian Faraway.
+
+20051006 Martin Maechler
+
+ * R/Auxiliaries.R (try_as): new utility
+ * R/sparseMatrix.R: use try_as() in coercion to original class
+
+20050930 Martin Maechler
+
+ * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
+
+20050929 Martin Maechler
+
+ * R/Auxiliaries.R (dimNamesCheck): added
+
+ * R/Matrix.R (as.array), (as.vector): new
+
+20050928 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"
+
+20050926 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
+
+20050918 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, (matcross)prod:
+ via cholmod
+
+20050916 Martin Maechler
+
+ * R/Auxiliaries.R (non0ind): new function using new C code
+ * src/dgCMatrix.c (compressed_non_0_ij): new utility
+
+20050915 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.
+
+20050908 Martin Maechler
+
+ * inst/testtools.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
+
+20050831 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
+
+20050829 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?)
+
+20050826 Martin Maechler
+
+ * R/Matrix.R: added first "[<" methods; not yet functional
+ * R/denseMatrix.R: dito
+ * man/Subassignmethods.Rd: new help file for these
+
+20050825 Martin Maechler
+
+ * DESCRIPTION (Version): 0.986
+
+ * R/denseMatrix.R: new file for "[" fallback methods for all dense
+ matrices.
+
+20050819 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/gTMatrixclass.Rd:
+ * General slight reorganization of where "[" methods are defined.
+ more to come.
+
+20050818 Douglas Bates
+
+ * DESCRIPTION (Version): 0.985 released to CRAN
+
+ * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
+ * .....
+
+20050818 Douglas Bates
+
+ * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
+ or glmer objects.
+
+20050817 Martin Maechler
+
+ * DESCRIPTION (Version): 0.984 : upload to CRAN
+
+20050816 Douglas Bates
+
+ * R/HBMM.R: finish rewriting Ronly code.
+
+20050815 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 rdevel.
+
+
+20050811 Martin Maechler
+
+ * R/AllClass.R: intermediate virtual class "denseMatrix"
+ * man/denseMatrixclass.Rd
+ * NAMESPACE: export it, and also export
+ * man/unusedclasses.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
+
+20050810 Douglas Bates
+
+ * DESCRIPTION (Version): 0.983 to CRAN
+
+ * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
+ matrix_solve code (which was really, really wrong).
+
+20050807 Douglas Bates
+
+ * DESCRIPTION (Version): 0.982
+
+ * 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 HarwellBoeing and the MatrixMarket formats.
+
+20050804 Martin Maechler
+
+ * man/dtrMatrixclass.Rd: add examples
+ * man/dtpMatrixclass.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().
+
+
+20050803 Martin Maechler
+
+ * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
+ add comments about 'control' / lmerControl() arguments
+
+20050727 Douglas Bates
+
+ * man/sleepstudy.Rd: Added the sleep data set.
+ * DESCRIPTION (Version): 0.981 released to CRAN
+
+20050712 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.
+
+20050705 Douglas Bates
+
+ * R/lmer.R (lmer): stored updated variance component estimates in
+ mer object for the generalized model. (Bug reported by Renaud
+ Lancelot).
+
+20050703 Douglas Bates
+
+ * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
+ unidimensional case.
+
+20050608 Douglas Bates
+
+ * DESCRIPTION (Version): 0.961
+
+ * moved lmerclass' R and C code moved from lme4 to here
+
+20050604 Douglas Bates
+
+ * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
+ (reported by Guissepe Ragusa )
+
+20050602 Douglas Bates
+
+ * src/Makefile.win: Forgot to update this when Makefile changed.
+
+20050511 Douglas Bates
+
+ * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
+ bug reported by Kurt Hornik and Michael Hahsler.
+
+20050510 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.upsud.fr
+
+20050506 Douglas Bates
+
+ * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
+ colMeans, colSums, rowMeans and rowSums.
+
+20050418 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 cutandpaste error in definition of
+ dgeMatrix_matrix_solve
+
+ * src/{many files}: Tighten code by using ALLOC_SLOT.
+
+20050415 Douglas Bates
+
+ * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
+
+ * DESCRIPTION: Eliminate import of stats.
+
+
+20050406 Douglas Bates
+
+ * R/AllClass.R : add logical sparse matrix classes
+
+20050401 Martin Maechler
+
+ * R/dgTMatrix.R: add "[" method for triplet matrices
+ * R/sparseMatrix.R: and other sparse ones; > add show() for sparse
+
+20050331 Douglas Bates
+
+ * DESCRIPTION (Version): release 0.955 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
+
+20050326 Martin Maechler
+
+ * R/AllClass.R: add two virtual sparse classes ``on top''
+
+20050324 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.
+
+20050317 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()
+
+20050315 Douglas Bates
+
+ * R/pMatrix.R: "pMatrix" class added
+ * ....
+
+20050314 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.
+
+20050310 Martin Maechler
+ +
+20050305 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
+
+20050303 Douglas Bates
+
+ * src/lmer.c (lmer_fitted): Added.
+
+20050302 Douglas Bates
+
+ * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
+
+20050228 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
+
+20050226 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/groupmethods.R : and test them.
+
+ * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
+ border case
+
+20050224 Douglas Bates
+
+ * DESCRIPTION (Version): 0.952 released to CRAN
+
+ * src/dgBCMatrix.c:
+ * src/lmer.c: many changes
+ * ...
+
+20050204 Martin Maechler
+
+ * R/Matrix.R: add more sophisticated show() method.
+
+20050202 Douglas Bates
+
+ * */* : almost complete reorganization of classes.
+
+20050126 Douglas Bates
+
+ * R/AllGeneric.R: Added matrix exponential generic expm and a method
+ for the geMatrix class.
+
+20050124 Douglas Bates
+
+ * src/Makefile (clean): Remove *.a and *.so
+
+ * man/cscBlockedclass.Rd: Remove reference to the lmerclass.
+
+20050123 Douglas Bates
+
+ * src/lmer.c (Lind): Definition of Lind was backwards. This only
+ had an effect in cases with more than 2 grouping factors.
+
+20050103 Douglas Bates
+
+ * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
+
+20041223 Douglas Bates
+
+ * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
+ and R_useDynamicSymbols (suggested by B.D.Ripley).
+
+20041214 Douglas Bates
+
+ * R/sscMatrix.R: Add determinant methods
+
+ * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
+ for tripletMatrix to matrix.
+
+20041213 Douglas Bates
+
+ * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
+ no longer used.
+
+ * src/R_ldl.c: Created an Rspecific 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.
+
+20041203 Douglas Bates
+
+ * src/lmeRep.c (lmeRep_factor): order of operations for multiple
+ scalar grouping factors corrected.
+
+20041129 Douglas Bates
+
+ * src/bCrosstab.c: remove diag_update which is no longer used
+
+20041116 Douglas Bates
* src/Metis_utils.c: Move metis.h include to C sources so that the
.h file can be included.
20041112 Douglas Bates
+20041112 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
20041111 Douglas Bates
+20041111 Douglas Bates
* src/geMutils.c (Matrix_init): remove unused function
20041110 Douglas Bates
+20041110 Douglas Bates
* src/cscMatrix.c (csc_to_imagemat): removed unused function
20041105 Douglas Bates
+20041105 Douglas Bates
* src/Makefile.win (SOURCES_C): Keep consistent with Makefile
20041027 Douglas Bates
+20041027 Douglas Bates
* R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
20041004 Douglas Bates
+20041004 Douglas Bates
* src/init.c: Created R_init_Matrix and added registration of C
routines.
20041002 Douglas Bates
+20041002 Douglas Bates
* R/tripletMatrix.R: Force a require(lattice) for the image methods.
20040615 Douglas Bates
+20040615 Douglas Bates
* man/trMatrixclass.Rd: Escape the % chars in .Rd files.
@@ 70,7 +961,7 @@
20040405 Douglas Bates
* src/triplet_to_col.c: Create triplet_to_col as a native
 function, not the version from umfpack. There were problems with
+ function, not the version from umfpack. There were problems with
the configuration of UMFPACK for 64bit processors and there was
only one umfpack routine being used so I moved it here.
@@ 237,7 +1128,7 @@
* aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
version for R1.5.0

+
20011210 Douglas Bates