--- pkg/ChangeLog 2006/06/01 20:41:20 1288
+++ pkg/ChangeLog 2006/08/07 16:51:14 1351
@@ -1,3 +1,205 @@
+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, ...): dito
+ * man/band.Rd: dito
+
+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: dito
+ * R/lmer.R: dito
+
+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