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revision 726, Thu May 12 14:59:04 2005 UTC revision 1725, Wed Jan 17 08:01:10 2007 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (!): fix typo.
4    
5    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Auxiliaries.R (as_Csparse): and quite a few others:
8                    allow to pass class definition --> speedup
9            * R/sparseMatrix.R: apply the above
10    
11            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
12    
13            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
14            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
15            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
16    
17            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
18    
19            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
20            and use it for "sparse*" as well, since it's faster than the
21            as_Csparse(.) way.
22    
23    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
26    
27    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
30            as method for   M[ ij ] <- v
31            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
32    
33            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
34            FALSE answer
35    
36            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
37            * tests/indexing.R: test it, and some of the above
38    
39    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Auxiliaries.R (is_duplicatedT): new utility
42    
43    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
44    
45            * src/init.c (R_init_Matrix): export cholmod_scale
46    
47    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
50            base::as.matrix to (x, ...)
51    
52    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
55            file; start using "Logic", hence
56    
57            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
58            * NAMESPACE: import and export "Logic"
59    
60    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
63            only needed previously to R version 2.5.0.
64    
65    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
68    
69            * R/Tsparse.R (replTmat): fix subassignment of triangular
70            * R/Csparse.R (replCmat): ditto
71            * tests/indexing.R: more tests, incl the above fix
72    
73    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Auxiliaries.R (drop0): extend for non CSparse
76            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
77    
78            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
79                    use uplo correctly (!); other places: use uplo_P() macro
80    
81            * R/Csparse.R (replCmat): call diagU2N() when needed
82            * R/Tsparse.R (replTmat): ditto
83    
84            * src/dtCMatrix.c (tCMatrix_validate): new
85            * src/dtTMatrix.c (tTMatrix_validate): new, used in
86            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
87    
88            * R/diagMatrix.R (replDiag): to use in [<-
89    
90    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
93                    also more general diagU2N().
94    
95    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
98            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
99    
100    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * tests/bind.R: a few more cases
103            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
104    
105            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
106            * R/ddenseMatrix.R (cbind2/rbind2)
107            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
108            * tests/indexing.R
109            * tests/indexing.Rout.save: updated
110    
111    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
114            * tests/indexing.R
115    
116    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
119            align with proper position of "0", i.e., right for integers.
120            argument 'align' by default is "fancy".
121    
122    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
125            * R/Csparse.R: and fix "Compare" for more cases.
126            * tests/Class+Meth.R: test some of these (m == m, m != m)
127    
128    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/lsparseMatrix.R: all() and any() methods
131            * R/ldenseMatrix.R:      ditto
132            * NAMESPACE, R/Matrix.R: ditto
133    
134            * man/all-methods.Rd: document them minimally
135    
136            * tests/simple.R: add a few examples for these
137    
138    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Tsparse.R ([): fix long standing typo in symmetric case
141            * man/dsCMatrix-class.Rd: add example exhibiting the above case
142    
143    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
144    
145            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
146            to LL before converting to a sparse matrix. (The LDL form can be
147            converted to a sparse matrix but it is implicitly a unit
148            triangular matrix and a diagonal matrix overwritten on the diagonal.)
149    
150    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
151    
152            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
153    
154    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
155    
156            * DESCRIPTION (Version): updated -> release 0.9975-7
157            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
158    
159    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
162    
163    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
164    
165            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
166            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
167            is exactly singular.
168    
169    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * DESCRIPTION (Date): updated -> release 0.9975-6
172    
173    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
176            now returns symmetric.
177    
178            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
179    
180            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
181            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
182    
183            * R/Auxiliaries.R (.type.kind): added
184    
185    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
188            running src/CSparse_install.sh
189    
190            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
191    
192    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
195            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
196    
197            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
198    
199            * tests/Class+Meth.R (tstMatrixClass): now assure
200            the (important in method programming) property :
201    
202                    ###>>  Every "Matrix" is either
203                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
204    
205                    (where "*" stands for "Matrix")
206    
207            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
208    
209            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
210            * tests/validObj.R: checks for "comparison"
211    
212            * R/sparseMatrix.R ([): improved indexing for sparse;
213                    trying to keep <symmetric>[ n, n] symmmetric
214    
215            * tests/indexing.R: indexing for logical sparse now ok
216    
217    
218    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * src/Tsparse.c: use xTsparse_validate() , and hence remove
221    
222            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
223    
224    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
227    
228            * tests/simple.R: validObject() checking the above.
229    
230            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
231            replacing both dgCMatrix_validate and lgCM*.
232    
233            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
234            fix dimnames setting in other places.
235            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
236    
237    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
240    
241            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
242            symmetry test, via
243            * R/Auxiliaries.R (.as.dgC.0.factors):
244    
245    2006-11-01  Douglas Bates  <bates@r-project.org>
246    
247            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
248            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
249            <CsparseMatrix>) added
250    
251    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * tests/matprod.R: add a variation of Harri's example
254    
255            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
256            recursive infinitely.
257    
258            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
259    
260            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
261    
262    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
265            matrix if possible; test m+m == 2*m; now test dgRMatrix.
266            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
267            satisfy the above test.
268    
269    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
272    
273            * R/dgCMatrix.R: solve(a, b="missing") based on
274            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
275            RHS = NULL.
276    
277            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
278            add more (needed) [t]crossprod() methods.
279    
280            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
281    
282            * R/Auxiliaries.R (as_CspClass): cleanup
283            (drop0): internal utility for "Csparse_drop(*, 0)"
284            (.bail.out.2): encourage active feedback
285    
286    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/dMatrix.R(Compare): new(), then slots [no validity check]
289    
290            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
291            non-valid or 'sorted' case).
292    
293            * R/dsparseMatrix.R: add "chol" method.
294            * R/ddenseMatrix.R: ditto
295    
296            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
297            * NAMESPACE (Ops)
298            * R/diagMatrix.R (diag2T): simple utility used "higher level"
299            coercion; deprecating direct lower level coercions.
300    
301            * R/*.R (seq): use seq_len() and seq_along() where possible.
302    
303    
304    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * DESCRIPTION (Version): 0.9975-5 ready for release
307    
308    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
309    
310            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
311    
312    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/AllClass.R (corMatrix): add 'validity' check;
315                    comment out unused "LDL" class definition
316            * NAMESPACE: mention, but do not export "LDL" class
317            * R/corMatrix.R: new (simple), needed for R-devel with
318            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
319              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
320    
321    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
322    
323            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
324            use Rprintf and R's error handling.
325    
326    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
329            * tests/matprod.R: add tests for the bug fixed.
330    
331    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
332    
333            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
334            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
335    
336    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
337    
338            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
339    
340    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * DESCRIPTION (Version): 0.9975-3
343    
344            * R/diagMatrix.R (bdiag): new function constructing block diagonal
345            (sparse) matrices.
346            * man/bdiag.Rd: docu + examples
347    
348            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
349    
350            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
351            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
352    
353            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
354            that result is sparse or diagonal (and not dense).
355    
356            * man/Subassign-methods.Rd: fix examples
357    
358            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
359            should always return a sparse (and not sometimes a diagonal) matrix.
360    
361    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
364    
365    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
366    
367            * DESCRIPTION (Version): 0.9975-2
368    
369            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
370    
371    2006-10-02  Douglas Bates  <bates@R-project.org>
372    
373            * tests/dg_Matrix.R: Simplify test taking into account new code.
374    
375    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
378    
379            * R/lsTMatrix.R: new files w/ missing methods
380            * R/nsTMatrix.R:  "  'for completeness'
381    
382            * tests/Class+Meth.R: a bit less 'not.ok.classes'
383    
384            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
385    
386    
387    2006-09-28  Douglas Bates  <bates@R-project.org>
388    
389            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
390            included.
391    
392            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
393            Export C-callable functions used in Zt_create in lme4.
394    
395    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * DESCRIPTION (Version): 0.9975-1
398    
399            * tests/simple.R: less checks fail; using NA, found that our
400                    kronecker() is not base-compatible with NA's.
401    
402            * R/dMatrix.R: "Compare" method now implemented for all cases
403    
404            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
405    
406            * man/dtpMatrix-class.Rd: mention length of 'x' slot
407    
408            * src/dtpMatrix.c (dtpMatrix_validate): fix check
409            * src/dspMatrix.c (dspMatrix_validate): ditto
410    
411            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
412              including coercion to [nl]tTMatrix.
413    
414            * R/diagMatrix.R (show): print a header line as for other classes.
415    
416    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * src/Makefile.win (SUBDIRS): fix typo
419    
420    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
423    
424    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
425    
426            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
427            symmetric and y missing in R code using %*% (cholmod_aat doesn't
428            accept a symmetric matrix).
429            * tests/group-methods.R: Uncomment test of crossprod applied to
430            lsCMatrix objects.
431    
432    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * R/AllClass.R (symmetricMatrix): add validity method (available
435            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
436    
437            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
438    
439            * tests/indexing.Rout.save:
440            * tests/indexing.R: additions, mainly for 'lsparse'
441    
442            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
443            case.
444    
445            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
446    
447    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
450                    as 'N' (1-letter - Ok?)
451    
452            * tests/group-methods.R: add test for logical + NAs
453    
454            * R/dMatrix.R ("Compare"): fix to work with NA's
455    
456            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
457    
458            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
459                    which is implemented.
460    
461    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * src/chm_common.c: coerce logical <-> double instead of
464            typecasting;  needed for "l" matrix handling in cholmod.
465    
466            * tests/other-pkgs.R (graph): small extension in "graph" checks.
467    
468            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
469            (Tsp2grNEL): other fixes needed
470    
471    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
474                    Matrices, since "lMatrix", also "lsparseM" can have NA
475            * R/ndenseMatrix.R, etc: new source files
476            * man/nsparseMatrix-classes.Rd, etc: new help files
477            * tests/: adaptions
478            * src/chm_common.c (chm_dense_to_SEXP): and others:
479                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
480            * src/Csparse.c, etc: ditto
481    
482    2006-09-11  Douglas Bates  <bates@R-project.org>
483    
484            * src/Mutils.[ch],init.c inst/include/*.h: Move the
485            alloc_d**Matrix functions to the lme4 package.
486    
487    2006-09-09  Douglas Bates  <bates@R-project.org>
488    
489            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
490            fixed
491    
492    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/lMatrix.R: new
495    
496            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
497    
498            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
499            * man/tcrossprod.Rd: ditto
500    
501    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
502    
503            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
504            for exported functions
505            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
506            Remove partitioning algorithms for sparse matrix reordering.  The
507            copyright on the Metis code was problematic and the methods were
508            rarely used.
509            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
510            operations are now done entirely in CHOLMOD code.
511    
512    2006-09-06  Douglas Bates  <bates@R-project.org>
513    
514            * src/Mutils.h: Remove functions that are no longer used.
515    
516    2006-09-04  Douglas Bates  <bates@R-project.org>
517    
518            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
519            * src/DEPS.mkf: update
520    
521    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * created branches/Matrix-for-R-2.3.x;  on trunk: do
524            * DESCRIPTION (Version): 0.9975-0
525            (Depends): R (>= 2.4.0)
526    
527    2006-09-01  Douglas Bates  <bates@R-project.org>
528    
529            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
530    
531    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
534            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
535    
536            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
537    
538    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
539    
540            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
541            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
542            * R/dsparseMatrix.R: ditto
543            * R/Csparse.R: ditto
544    
545    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * R/dMatrix.R (Compare): improve availability of "<", etc
548            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
549    
550    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
553            of a 0-index which was used as 1-index (..hmm)
554    
555            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
556    
557            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
558            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
559            (.is.diagonal): ditto
560    
561            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
562    
563            * R/Matrix.R (Matrix): also work for NA data
564    
565    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
568            in all cases.
569    
570    2006-08-27  Douglas Bates  <bates@R-project.org>
571    
572            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
573            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
574    
575    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
578            subclasses of "ddenseMatrix"
579            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
580            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
581            instead of half dozen specialized ones.
582    
583    2006-08-25  Douglas Bates  <bates@R-project.org>
584    
585            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
586            <tillard@cirad.fr> - ordering standard errors to match effects.
587    
588    2006-08-24  Douglas Bates  <bates@R-project.org>
589    
590            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
591            on R_ldl.
592            * R/lCholCMatrix.R,
593            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
594            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
595            * many files in ./R and ./src: Use more general version of
596            dup_mMatrix_as_dgeMatrix to simplify method definitions.
597            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
598            dtpMatrix, dspMatrix and dppMatrix conversions.
599    
600    
601    2006-08-23  Douglas Bates  <bates@R-project.org>
602    
603            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
604            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
605            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
606            dgeMatrix_crossprod (may need to do this in other places).
607            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
608            generic and method for dsCMatrix.  Use CHOLMOD for chol().
609    
610    2006-08-22  Douglas Bates  <bates@R-project.org>
611    
612            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
613            types of classed Matrices, matrices or numeric or logical vectors.
614            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
615            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
616            to Mutils.h (as an inline) and change name to Matrix_check_class;
617            fixes in as_cholmod_factor and chm_factor_to_SEXP.
618            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
619            dsCMatrix_matrix_solve.  Comment out vestigial functions.
620            * src/Csparse.c: use diag_P and uplo_P macros.
621    
622    2006-08-21  Douglas Bates  <bates@R-project.org>
623    
624            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
625            valgrind.
626            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
627            inverses.
628            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
629            -Wall warnings.
630            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
631            Use dup_mMatrix_as_dgeMatrix.
632    
633    2006-08-20  Douglas Bates  <bates@R-project.org>
634    
635            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
636            * tests/sparseQR.R: Added
637            * man/sparseQR-class.Rd: Document methods for qr.* generics
638            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
639    
640    2006-08-19  Douglas Bates  <bates@R-project.org>
641    
642            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
643            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
644            and qr.fitted.
645            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
646            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
647    
648    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
651            the base version has no "..." argument.
652    
653            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
654    
655            * R/Matrix.R: define and
656            * NAMESPACE: export as.numeric() and as.logical() methods.
657                    Let's hope these do not badly slow down something...
658            Finally export the zapsmall() method.
659    
660    2006-08-17  Douglas Bates  <bates@R-project.org>
661    
662            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
663            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
664            * src/dtCMatrix.c :Remove code that is no longer used
665            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
666    
667    2006-08-14  Douglas Bates  <bates@R-project.org>
668    
669            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
670            Csparse_to_logical and Csparse_symmetric_to_general.
671            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
672            coercion methods between CsparseMatrix and TsparseMatrix.
673    
674    2006-08-14  Douglas Bates  <bates@R-project.org>
675    
676            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
677            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
678            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
679            possible.
680    
681    2006-08-12  Douglas Bates  <bates@R-project.org>
682    
683            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
684              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
685              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
686              generalize conversions between TsparseMatrix, CsparseMatrix,
687              denseMatrix and matrix.  Preserve triangularity property and
688              propagate Dimnames in the easy cases.
689    
690    2006-08-10  Douglas Bates  <bates@R-project.org>
691    
692            * src/lmer.c: adjust checks in glmer_init for S4SXP
693            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
694            before S4SXP but for the wrong reasons.
695    
696    2006-08-08  Douglas Bates  <bates@R-project.org>
697    
698            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
699            Later modified to return the upper triangle only.
700            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
701    
702    2006-08-07  Douglas Bates  <bates@R-project.org>
703    
704            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
705            R-level conversion to a sparse symmetric class.
706            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
707            Remove conversion to sparse symmetric classes (now done in C code).
708    
709    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
712            * man/band.Rd:  adapt the \dontshow{} unit test.
713    
714    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * DESCRIPTION (Version): 0.995-14  for CRAN
717    
718            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
719    
720            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
721            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
722    
723            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
724            * R/Tsparse.R (tril, triu, band): methods
725            * R/dgRMatrix.R (tril, ...):    ditto
726            * man/band.Rd:                  ditto
727    
728    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
729    
730            * R/Matrix.R (head, tail): directly use utils:::head.matrix
731                    to be up-to-date automatically.
732    
733    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
736    
737            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
738            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
739            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
740            such that the S4 objects are always created by the current version
741            of R and 'Matrix' class definitions.
742    
743    2006-08-01  Douglas Bates  <bates@R-project.org>
744    
745            * R/lmer.R (LMEoptimize method), tests/lmer.R,
746            inst/external/test3comp.rda: Added warnings for convergence on
747            boundary and test cases.
748    
749            * src/lmer.c (mer_postVar): Modified to return the variances that
750            are marginal to the fixed effects, not conditional on them (which
751            is what the bVar slot contents represent).
752    
753    2006-07-31  Douglas Bates  <bates@R-project.org>
754    
755            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
756            function which calls the C function mer_hat_trace2.
757    
758            * man/ranef.Rd: Include description of "postVar" argument and
759            producing a caterpillar plot.
760    
761    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * NAMESPACE:    change  "correlation" to "corMatrix"
764            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
765            * R/dpoMatrix.R: ditto
766            * R/lmer.R:      ditto
767    
768    2006-07-28  Douglas Bates  <bates@R-project.org>
769    
770            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
771            RZXinv slot's contents into a separate internal function that can
772            be used in mer_hat_trace.
773    
774    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
775    
776            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
777            via new smart
778            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
779            utility functions.
780    
781    
782    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * R/Csparse.R (tril, triu, band): do return *triangular* classed
785            matrices when appropriate; band() even symmetric ones.
786            (replCmat): extend to potentially all "CsparseMatrix"
787            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
788            allow subassignment for special sparse matrices.
789    
790            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
791    
792            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
793            argument; in glmer_*(): print only if(verbose).
794    
795            speed-optimize a few places by moving REAL(.) out of loops.
796    
797            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
798    
799    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
802                    since that wrongly triggers also for M[ logi , ]
803    
804            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
805            a symmetric matrix that results in a non-symmetric one.
806            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
807    
808            * R/dMatrix.R: make round(M) work as round(M, 0)
809    
810            * R/dgTMatrix.R (image): coordinate system and axis now use
811            1-based indices, not 0-based ones.
812    
813            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
814            * tests/indexing.R: test it.
815    
816            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
817            * man/isSymmetric-methods.Rd: and document it.
818    
819            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
820            * man/SparseM-conv.Rd: docu them
821    
822            * tests/other-pkgs.R: renamed from tests/graph.R and add example
823                    for 'SparseM' conversions
824    
825    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
826    
827            * R/Matrix.R (head): added head() and tail() methods.
828    
829    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * DESCRIPTION (Version): 0.995-12 released to CRAN
832    
833    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
834    
835            * tests/simple.R: add check for correct dsT -> dgT coercion;
836                    add check for correct printing of symmetric sparse matrices.
837    
838            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
839            for sparse symmetric matrices.
840    
841            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
842            diagonal twice.
843    
844    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
845    
846            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
847            being applied to the x slot (detected by Brian Ripley).
848    
849    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
850    
851            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
852    
853            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
854    
855    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * src/lgCMatrix.c (lgCMatrix_diag): new function
858            * R/lgCMatrix.R (diag): for new method
859    
860            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
861                 ==> construction of illegal "*gTMatrix" via new() should
862                 now be much less easy:
863            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
864    
865            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
866                    directly.
867            * man/Matrix.Rd: documents it.
868    
869    2006-07-06  Douglas Bates  <bates@R-project.org>
870    
871            * src/pedigree.c (pedigree_inbreeding): Correction in
872            initialization.  This function is not currently being used and is
873            not fully tested.
874    
875            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
876            Introduced the glmer class.  Added code for mcmcmsamp on glmer
877            objects.  Modified validity check on pedigree objects to account
878            for nonparallel patterns of missingness of parents.
879    
880            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
881            class.
882    
883    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
884    
885            * R/pMatrix.R: coercion pMatrix -> Tsparse
886    
887    2006-06-12  Douglas Bates  <bates@R-project.org>
888    
889            * DESCRIPTION (Version): 0.995-11 released to CRAN
890    
891            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
892            the output from mcmcsamp.
893    
894    2006-06-10  Douglas Bates  <bates@R-project.org>
895    
896            * R/lmer.R (simulestimate): added C code for calculating the trace
897            of the hat matrix.
898    
899    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
902            classes.
903            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
904    
905    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * R/dgTMatrix.R (colSums): etc. All four of
908            colSums(), rowSums(), colMeans(), rowMeans() now should work for
909            all "Matrices".
910    
911    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
912    
913            * R/lmer.R (panel.ci): Add a reference line at zero and a
914            background grid to the qqmath plot of ranef.lmer.
915    
916    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
917    
918            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
919            grouping factors to be specified in the formula as (1|foo/bar).
920    
921    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
922    
923            * R/lmer.R (findbars and others): Change check of is.numeric to
924            !is.language to resolve the bug reported by Jacob Wegelin.
925    
926            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
927            code to evaluate inbreeding coefficients without calculating T,
928            based on code in Sargolzaei and Iwaisaki's paper.
929    
930    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
931    
932            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
933            generic and mer methods for isNested and denomDF. This denomDF was
934            an attempt to emulate that in lme but I don't think that makes
935            sense.  Use the trace of the hat matrix instead.
936    
937    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
938    
939            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
940            the C code depending on a slot structure that's no longer valid.
941            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
942    
943    
944    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
945    
946            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
947            of lowerTriMatrix generic and methods to tril (also upper to triu)
948            and added a general band extractor.
949    
950    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
951    
952            * R/pedigree.R (pedigree): Replace sire and dam values outside the
953            allowable range with NAs. Added a corresponding check in the
954            validity check for the pedigree class.
955    
956            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
957            crossprod methods now inherits from symmetricMatrix.
958    
959    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
960    
961            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
962            generics lowerTriMatrix and upperTriMatrix along with methods for
963            the Csparse virtual class.  Also added a C function Csparse_band
964            that implements these methods by calling cholmod_band.
965    
966    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
967    
968            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
969            erased when it was NULL.  This led to invalid subselections!
970    
971    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
972    
973            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
974            in method for "t" so as not to lose the unit diagonal property.
975    
976    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
977    
978            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
979            and methods.  This is now an option to the ranef method for the
980            mer class.
981    
982            * src/cs_utils.c: Ensure that the nz component is -1 for a
983            compressed column-oriented matrix.  Minor formatting cleanup.
984    
985            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
986            objects.
987    
988    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
989    
990            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
991            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
992    
993    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
994    
995            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
996            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
997    
998            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
999            for the dtCMatrix class.
1000    
1001    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1002    
1003            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1004            and methods for it.
1005    
1006    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1007    
1008            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1009            arguments, such that M %*% 1:6 now works
1010            * Tests/matprod.R: test the above
1011    
1012    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1013    
1014            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1015            the ranef.lmer class.
1016    
1017            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1018            methods to extract the posterior variances from the bVar slot.
1019    
1020    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1021    
1022            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1023            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1024    
1025            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1026            * tests/simple: (extended)
1027    
1028            * R/sparseMatrix.R (isTriangular): now using much improved
1029            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1030    
1031    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1032    
1033            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1034            (problem report from Franklin Parlamis).  This should be done
1035            generally.
1036    
1037    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1038    
1039            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1040            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1041            update the plot methods.
1042    
1043    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1044    
1045            * R/lmer.R (resid and ranef methods):  Added methods for the
1046            "residuals" and "resid" generic but only for linear mixed model
1047            fits.  Changed the ranef method to return a list of data frames so
1048            that the plot methods now work.
1049    
1050    2006-03-16  Douglas Bates  <bates@bates2>
1051    
1052            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1053            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1054    
1055            * DESCRIPTION (Date): New release
1056    
1057    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1058    
1059            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1060    
1061            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1062            * man/KNex.Rd: and other help files
1063            * tests/*.R: several ones needed adaption
1064            * inst/doc/Comparisons.Rnw: ditto
1065    
1066    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1067    
1068            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1069    
1070            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1071    
1072    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1073    
1074            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1075    
1076            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1077    
1078    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1079    
1080            * R/dMatrix.R: enable things like  M [ M < 10 ]
1081            * R/dgeMatrix.R: implement it
1082    
1083    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1084    
1085            * R/AllClass.R: define "summary.mer" and "*.lmer"
1086            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1087            * R/lmer.R (show): now works with summary()
1088    
1089    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1090    
1091            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1092            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1093                    support the above
1094    
1095    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1096    
1097            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1098            Use glmFit$prior.weights for weights in a glmm.
1099            Allow an option usePQL = FALSE to skip the PQL steps for the
1100            Laplace method (and, in time, the AGQ method).
1101    
1102            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1103            into a separate function internal_mer_Xfactor to be able to call
1104            it from internal_bhat.
1105    
1106    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1107    
1108            * tests/Class+Meth.R (tstMatrixClass): function for much better
1109            testing; now again of all actual classes.
1110    
1111            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1112                    use macros and define make_d_matrix_* and make_i_matrix_*
1113                    where _i_ is for the ldense routines:
1114    
1115            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1116            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1117    
1118            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1119    
1120    
1121    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1122    
1123            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1124                    many different kinds of matrices.
1125            * R/*.R: quite a few new methods were needed for R CMD check with
1126                    new Matrix().  Very good for users playing around.
1127    
1128    
1129    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1130    
1131            * src/dgeMatrix.c (dMatrix_validate): new
1132            * src/Mutils.c (dense_nonpacked_validate): new
1133    
1134            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1135    
1136    
1137    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1138    
1139            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1140    
1141    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1142    
1143            * DESCRIPTION (Version): 0.99-6 released to CRAN
1144    
1145            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1146            segfault in cases with multiple non-nested grouping factors.
1147    
1148    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1149    
1150            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1151                    (Depends): also on 'utils'
1152    
1153            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1154            * R/diagMatrix.R (Diagonal): constructor and methods for
1155            diagonal matrices
1156    
1157            * R/ltTMatrix.R: new "minimal methods"
1158    
1159    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1160    
1161            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1162            all methods (and help files).
1163    
1164    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1165    
1166            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1167                    for case (dimn.  op  no_dimn.)
1168    
1169    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1170    
1171            * DESCRIPTION (Version): 0.99-2  released to CRAN
1172    
1173    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1174    
1175            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1176            by Julian Faraway.
1177    
1178    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1179    
1180            * R/Auxiliaries.R (try_as): new utility
1181            * R/sparseMatrix.R: use try_as() in coercion to original class
1182    
1183    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1184    
1185            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1186    
1187    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1188    
1189            * R/Auxiliaries.R (dimNamesCheck): added
1190    
1191            * R/Matrix.R (as.array), (as.vector): new
1192    
1193    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1194    
1195            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1196                    default.
1197            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1198                    "pMatrix" now contains "sparseMatrix"
1199    
1200    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1201    
1202            * tests/Class+Meth.R: new tests; t(t(m)) == m
1203    
1204            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1205    
1206            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1207            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1208    
1209            * R/dspMatrix.R: typo in "t" method
1210    
1211    2005-09-18  Douglas Bates  <bates@wisc.edu>
1212    
1213            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1214            * R/Tsparse.R: instead of R/gTMatrix.R
1215            * R/Csparse.R: new
1216            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1217            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1218            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1219                            via cholmod
1220    
1221    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1222    
1223            * R/Auxiliaries.R (non0ind): new function using new C code
1224            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1225    
1226    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1227    
1228            * src/chm_common.h: header file required by all C sources that
1229            call CHOLMOD functions.  It defines a cholmod_common structure
1230            called 'c' whose address is passed as the last argument to
1231            (virtually) every CHOLMOD function.
1232    
1233            * src/Pattern.c: Simple example of the use of CHOLMOD.
1234    
1235            * src/init.c: initialize and finalize the cholmod_common structure.
1236    
1237            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1238            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1239    
1240    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1241    
1242            * inst/test-tools.R: new file collecting the utility functions used
1243                    in ./tests/*.R
1244    
1245            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1246            * R/Matrix.R (cbind2): methods for NULL and missing
1247    
1248    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1249    
1250            * R/AllClass.R: new "index" class for "[" and "[<-":
1251                    First cut at "symmetricMatrix" and "triangularMatrix"
1252            * R/gTMatrix.R (.ind.prep): new function;
1253                    Logical and character indexing now work too.
1254            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1255            * tests/indexing.R: new, including *.Rout.save
1256            * tests/dgTMatrix.R: new
1257    
1258    2005-08-29  Douglas Bates  <bates@wisc.edu>
1259    
1260            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1261            indicator pos not being updated.  Also enforced upper triangular
1262            for symmetric case.  Need to coerce edges component of elements of
1263            edge list - grr! (Why don't they define their classes cleanly?)
1264    
1265    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1266    
1267            * R/Matrix.R:  added first "[<-" methods; not yet functional
1268            * R/denseMatrix.R: ditto
1269            * man/Subassign-methods.Rd: new help file for these
1270    
1271    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1272    
1273            * DESCRIPTION (Version): 0.98-6
1274    
1275            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1276            matrices.
1277    
1278    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1279    
1280            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1281                    as( <logical>, "matrix")
1282    
1283            * R/pMatrix.R: coercion to "lgTMatrix"
1284    
1285            * R/gTMatrix.R: new virtual class to define "[" methods for.
1286            * man/gTMatrix-class.Rd:
1287            * General slight re-organization of where "[" methods are defined.
1288              more to come.
1289    
1290    2005-08-18  Douglas Bates  <bates@wisc.edu>
1291    
1292            * DESCRIPTION (Version): 0.98-5  released to CRAN
1293    
1294            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1295            * .....
1296    
1297    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1298    
1299            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1300            or glmer objects.
1301    
1302    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1303    
1304            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1305    
1306    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1307    
1308            * R/HBMM.R: finish re-writing R-only code.
1309    
1310    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1311    
1312            * man/externalFormats.Rd: move documentation for writeHB and
1313            writeMM here.
1314    
1315            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1316            (suggested by Paul Roecker).
1317    
1318            * tests/validObj.R (assertError): Comment out test that is failing
1319            after recent changes in r-devel.
1320    
1321    
1322    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1323    
1324            * R/AllClass.R: intermediate virtual class "denseMatrix"
1325            * man/denseMatrix-class.Rd
1326            * NAMESPACE: export it, and also export
1327            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1328    
1329    2005-08-10  Douglas Bates  <bates@wisc.edu>
1330    
1331            * DESCRIPTION (Version): 0.98-3 to CRAN
1332    
1333            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1334            matrix_solve code (which was really, really wrong).
1335    
1336    2005-08-07  Douglas Bates  <bates@wisc.edu>
1337    
1338            * DESCRIPTION (Version): 0.98-2
1339    
1340            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1341    
1342            * R/lmer.R (abbrvNms): new
1343            * R/lmer.R (mcmcsamp): allow transformed parameters
1344            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1345            for the Harwell-Boeing and the MatrixMarket formats.
1346    
1347    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1348    
1349            * man/dtrMatrix-class.Rd: add examples
1350            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1351    
1352            * TODO: note the dtpMatrix (docu) bug
1353    
1354            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1355            in order to ensure that new as.matrix() is used by old functions,
1356            e.g., svd(), qr(), eigen(), dist(),..;
1357                  apply(), also matplot() or pairs().
1358    
1359    
1360    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1361    
1362            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1363              add comments about 'control' / lmerControl() arguments
1364    
1365    2005-07-27  Douglas Bates  <bates@wisc.edu>
1366    
1367            * man/sleepstudy.Rd: Added the sleep data set.
1368            * DESCRIPTION (Version): 0.98-1  released to CRAN
1369    
1370    2005-07-12  Douglas Bates  <bates@wisc.edu>
1371            * man/sleepstudy.Rd: Added the sleep data set.
1372    
1373            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1374            .Call calls that were producing spurious output.
1375    
1376    2005-07-05  Douglas Bates  <bates@wisc.edu>
1377    
1378            * R/lmer.R (lmer): stored updated variance component estimates in
1379            mer object for the generalized model.  (Bug reported by Renaud
1380            Lancelot).
1381    
1382    2005-07-03  Douglas Bates  <bates@wisc.edu>
1383    
1384            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1385            unidimensional case.
1386    
1387    2005-06-08  Douglas Bates  <bates@wisc.edu>
1388    
1389            * DESCRIPTION (Version): 0.96-1
1390    
1391            * moved  lmer-class' R and C code moved from lme4 to here
1392    
1393    2005-06-04  Douglas Bates  <bates@wisc.edu>
1394    
1395            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1396            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1397    
1398    2005-06-02  Douglas Bates  <bates@wisc.edu>
1399    
1400            * src/Makefile.win: Forgot to update this when Makefile changed.
1401    
1402    2005-05-11  Douglas Bates  <bates@wisc.edu>
1403    
1404          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1405          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
1406    
1407  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
1408    
1409          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1410          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 1413 
1413          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1414          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1415    
1416  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
1417    
1418          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1419          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
1420    
1421  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
1422    
1423          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
1424          multiplication operation.          multiplication operation.
# Line 30  Line 1431 
1431    
1432          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
1433    
1434  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
1435    
1436          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1437    
1438          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
1439    
1440    
1441  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
1442    
1443          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
1444    
# Line 46  Line 1447 
1447          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1448          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1449    
1450  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1451    
1452          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1453    
# Line 72  Line 1473 
1473          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
1474            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
1475    
1476  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
1477    
1478          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
1479          * ....          * ....
1480    
1481  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
1482    
1483          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1484    
# Line 92  Line 1493 
1493            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1494          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1495    
1496  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1497    
1498          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1499    
1500  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1501    
1502          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1503    
1504  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1505    
1506          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1507          the package.          the package.
# Line 148  Line 1549 
1549    
1550          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1551    
1552  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1553    
1554          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1555          for the geMatrix class.          for the geMatrix class.
1556    
1557  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1558    
1559          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1560    
1561          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1562    
1563  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1564    
1565          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1566          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1567    
1568  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1569    
1570          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1571    
1572  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1573    
1574          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1575          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1576    
1577  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1578    
1579          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1580    
1581          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1582          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1583    
1584  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1585    
1586          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1587          no longer used.          no longer used.
# Line 192  Line 1593 
1593          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1594          Fixes part but not all of #15.          Fixes part but not all of #15.
1595    
1596  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1597    
1598          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1599          scalar grouping factors corrected.          scalar grouping factors corrected.
1600    
1601  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1602    
1603          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1604    
1605  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1606    
1607          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
1608          .h file can be included.          .h file can be included.
1609    
1610  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1611    
1612          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1613          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1614    
1615          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1616    
1617  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1618    
1619          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1620    
1621  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1622    
1623          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1624    
1625  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1626    
1627          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1628    
1629  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1630    
1631          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1632    
1633  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1634    
1635          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1636          routines.          routines.
1637    
1638  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1639    
1640          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1641    
1642  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1643    
1644          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1645    

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