--- pkg/ChangeLog 2006/03/15 17:43:34 1228
+++ pkg/ChangeLog 2006/06/10 19:56:18 1298
@@ -1,3 +1,164 @@
+2006-06-10 Douglas Bates
+
+ * R/lmer.R (simulestimate): added
+
+2006-06-09 Martin Maechler
+
+ * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
+ classes.
+
+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+ the C code depending on a slot structure that's no longer valid.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