--- pkg/ChangeLog 2006/02/07 23:44:07 1213
+++ pkg/ChangeLog 2006/07/17 13:08:04 1319
@@ -1,3 +1,265 @@
+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: dito (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: dito
+
+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.