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
* 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