--- pkg/ChangeLog 2005/08/11 07:41:59 848
+++ pkg/ChangeLog 2006/08/07 18:31:12 1352
@@ -1,3 +1,623 @@
+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"
@@ -44,7 +664,7 @@
2005-07-27 Douglas Bates
* man/sleepstudy.Rd: Added the sleep data set.
- * DESCRIPTION (Version): 0.98-1 released to CRAN
+ * DESCRIPTION (Version): 0.98-1 released to CRAN
2005-07-12 Douglas Bates
* man/sleepstudy.Rd: Added the sleep data set.
@@ -67,7 +687,7 @@
* DESCRIPTION (Version): 0.96-1
- * moved lmer-class' R and C code moved from lme4 to here
+ * moved lmer-class' R and C code moved from lme4 to here
2005-06-04 Douglas Bates