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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1960, Fri Jul 6 16:54:43 2007 UTC
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1    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
4              functions - no longer used
5            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
6              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
7              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
8              Alloca
9    
10    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
11    
12            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
13              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
14              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
15              src/t_gCMatrix_colSums.c: more R_CheckStack()s
16    
17    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
18    
19            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
20              the required amount of memory then call M_numeric_as_chm_dense.
21            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
22              (like Calloc but calling alloca)
23    
24    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
27            and extended with more sophisticated 'col.names' option.
28            * NAMESPACE: export  printSparseMatrix()
29            * man/printSpMatrix.Rd: document, incl. examples
30    
31    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
32    
33            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
34              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
35              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
36    
37    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * DESCRIPTION (Version): 0.99875-4
40    
41            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
42            some dimnames perservation.
43    
44            * R/dsTMatrix.R (t-method): keep dimnames
45            * R/dtTMatrix.R:  ditto
46    
47            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
48            and ncol(.) < 10
49    
50            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
51            from Mutils.h
52    
53            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
54            e.g. in as(<ngCMatrix>, "matrix")
55    
56    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
57    
58            * [r4529] .: Create a branch for the API changes from the 0.99875
59              series to the 0.999375 series
60            * [r4530] DESCRIPTION, inst/include/Matrix.h,
61              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
62              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
63              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
64              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
65              as_cholmod_x functions
66    
67    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
68    
69            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
70              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
71              to Comparisons
72    
73    >>>>>>> .merge-right.r4561
74    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * DESCRIPTION (Version): 0.99875-3 ready to be released.
77    
78            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
79    
80            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
81            that should also work in a future version of R.
82    
83    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
86    
87            * R/sparseVector.R: more *sparseVector coercions, notably for
88            non - double ones.
89    
90    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
93              notably the new ones building on the new .Call(.)s:
94    
95            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
96            all 4 of [dlin]gCMatrix_colSums().
97    
98    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
99    
100            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
101            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
102              result
103    
104    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/kronecker.R: fix typo (could lead to inf.recursion)
107            * test/simple.R: testing that
108    
109            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
110            method as well (which can have arguments, show() can't).
111    
112    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
113    
114            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
115              added dgCMatrix_colSums for [col,row][Sums,Means]
116    
117    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
118    
119            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
120              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
121              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
122            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
123              class
124            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
125              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
126              row names to store the levels - duh!  Added an example.
127    
128    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * src/Csparse.c (Csparse_validate): check for *repeated* entries
131            thanks to example from Christian Buchta; with a test here:
132            * tests/simple.R:
133    
134    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
137            of colSums(*, sparseResult = TRUE)
138    
139    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
142            'na.rm = FALSE' as "everywhere" else in R.
143    
144    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
145    
146            * [r4421] src/CSparse_install.sh: Modify for new organization of
147              CSparse package
148            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
149              SuiteSparse
150            * [r4426] src/Makefile: add ./UFconfig to the include path for
151              compilation
152            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
153            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
154              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
155    
156    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
159            * R/sparseMatrix.R (prSpMatrix): now gives a message about
160            suppressed column names.
161    
162    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
163    
164            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
165              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
166              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
167              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
168              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
169              Remove warnings after change to const char* CHAR
170    
171    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
172    
173            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
174              type of M_cholmod_ssmult
175    
176    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
177    
178            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
179              src/init.c: Yet another cholmod export - cholmod_ssmult
180    
181    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * NAMESPACE: exported drop0(), since
184            * man/drop0.Rd: I have seen several cases, I really wanted to use
185            it, so our users may want too.
186    
187    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * man/colSums.Rd: separately document colSums() etc, since these
190            have the extra argument 'sparseResult'.
191    
192    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
195            * man/spMatrix.Rd: docu., including examples
196    
197            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
198            in order to make colMeans() etc fast *and* correct.
199            * R/sparseVector.R (replSPvec): "[<-" functionality for
200            sparseVectors; tested in
201            * tests/simple.R:
202    
203    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
206            (very) sparse Matrices; output similar to Matlab's print().
207    
208    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
209    
210            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
211            0-based, indices (Jose Quesada <quesada@gmail.com>).
212    
213    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
214    
215            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
216    
217    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Auxiliaries.R (sparsapply): new utility, much faster than
220            tapply1() for large sparse matrices.
221    
222    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Matrix.R (dim<-): reshape now via sparseVector.
225    
226            * R/sparseVector.R: methods and function for
227            * R/AllClass.R: new "sparseVector" class and daughters.
228            * NAMESPACE: export new classes
229    
230    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * DESCRIPTION (Version): 0.99875-1
233            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
234    
235    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
238            indexing
239            * tests/indexing.R: test set for that.
240    
241    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
244            entries.
245            * tests/indexing.R(out): add regression test for it
246    
247    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
250            name for "!" method definitions.
251    
252    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/Tsparse.R (intI): new utility, used for "[" :
255                    Cleanup up there, and fixes for duplicated indices - more TODO!
256    
257            * tests/indexing.R(out): more tests
258    
259    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
260    
261            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
262            code that is now part of the R Lapack library.
263    
264            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
265            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
266    
267    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
270    
271    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
274            up with extraneous names '0'...'<n-1>'
275    
276    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/dgTMatrix.R (mat2dgT): care about NAs
279    
280    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/kronecker.R: triangularity preserving methods
283    
284    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/kronecker.R: new file collecting kronecker() methods in one
287                    place.  Goal: become much faster!
288    
289    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
292            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
293            can be much faster.
294    
295            * tests/matprod.R: add regression tests for these (upper & lower).
296    
297    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/Matrix.R (diff): method for our Matrices.
300    
301            * R/sparseMatrix.R (isDiagonal): check dim()!
302    
303    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/Matrix.R (dim<-): new method for "reshape()" built on a
306            proposal from Tamas Papp.
307    
308    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
311    
312            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
313            rather define and export  cBind() and rBind() only.
314            --> useRs *must* change code that used to have cbind()/rbind() !!
315    
316            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
317            * R/bind.Rout.save: ditto
318    
319    2007-02-16  Douglas Bates  <bates@r-project.org>
320    
321            * DESCRIPTION (Date, Version): 0.9975-11 with new date
322            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
323            const modifier on declaration of the array 'valid'
324    
325    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
326    
327            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
328    
329    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
332    
333            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
334            * tests/simple.R: test the above and some of these coercions:
335    
336            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
337                    be careful to avoid infinite recursion, using new coercions in
338            * R/ngCMatrix.R and nsC... and ntC...
339            * R/lsparseMatrix.R: ditto
340    
341            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
342    
343            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
344            * R/Rsparse.R: reactivate .Call()s
345    
346            * tests/Class+Meth.R: a bit more on actual classes
347    
348    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
349    
350            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
351    
352    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * DESCRIPTION (Version): 0.9975-10 to upload
355    
356            * tests/Class+Meth.R (tstMatrixClass): require coercions to
357            specific classes less unconditionally.
358    
359            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
360    
361            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
362    
363            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
364            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
365            R_to_CMatrix segfaults on one platform.
366            Eliminate most coercion method to *specific* classes, and replace
367            with virtual classes coercions.
368    
369    
370    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
371    
372            * src/init.c: export the CHM...._validate() placeholders, since
373            they *are* called.
374    
375            * tests/Class+Meth.R (classCanCoerce): and starting to test
376            all as(<from>, <to>)
377    
378    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
381            * tests/indexing.R: tested now
382            * tests/indexing.Rout.save: updated
383    
384            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
385            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
386            appropriate.
387    
388            * NAMESPACE: export a trivial
389            * R/Matrix.R: drop() Matrix-method
390    
391            * R/AllClass.R: moved all prototypes to virtual super classes.
392    
393            * R/Rsparse.R: many more coercions to have less exceptions in
394            * tests/Class+Meth.R:
395    
396            * R/Ops.R (Compare): tweak for case with NA
397            * tests/simpl.R: hence another 'FIXME' eliminated
398    
399    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
402            objects.
403    
404            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
405              and more of "!", "&", "|", all, any; coercions
406    
407            * R/Rsparse.R: many coercions (which enable quite a few other
408            methods), thanks to enhancements in
409            * src/dgCMatrix.c (R_to_CMatrix): new, and
410            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
411            symmetric & triangular and ..RMatrix objects.
412    
413            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
414            renamed file from src/dsTMatrix.c;
415            now dealing with symmetric and triangular Tsparse coercions, both
416            to dense and general.
417    
418    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
421    
422            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
423            where sensible when the <numeric> is of length > 1.
424    
425    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/Matrix.R ([<-): for M[] <- value: fix length
428    
429    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
432            * R/ndenseMatrix.R: new coercions n* -> l*
433    
434    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
437    
438            * R/Ops.R ("Logic"): and other "Ops", many updates
439    
440    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * src/Mutils.h (SET_DimNames): new utility
443    
444            * R/Auxiliaries.R (nnzero): improved and now exported via
445    
446            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
447    
448    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * R/diagMatrix.R (!): fix typo.
451    
452    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/Auxiliaries.R (as_Csparse): and quite a few others:
455                    allow to pass class definition --> speedup
456            * R/sparseMatrix.R: apply the above
457    
458            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
459    
460            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
461            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
462            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
463    
464            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
465    
466            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
467            and use it for "sparse*" as well, since it's faster than the
468            as_Csparse(.) way.
469    
470    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
473    
474    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
477            as method for   M[ ij ] <- v
478            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
479    
480            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
481            FALSE answer
482    
483            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
484            * tests/indexing.R: test it, and some of the above
485    
486    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/Auxiliaries.R (is_duplicatedT): new utility
489    
490    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
491    
492            * src/init.c (R_init_Matrix): export cholmod_scale
493    
494    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
497            base::as.matrix to (x, ...)
498    
499    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
502            file; start using "Logic", hence
503    
504            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
505            * NAMESPACE: import and export "Logic"
506    
507    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
510            only needed previously to R version 2.5.0.
511    
512    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
515    
516            * R/Tsparse.R (replTmat): fix subassignment of triangular
517            * R/Csparse.R (replCmat): ditto
518            * tests/indexing.R: more tests, incl the above fix
519    
520    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * R/Auxiliaries.R (drop0): extend for non CSparse
523            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
524    
525            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
526                    use uplo correctly (!); other places: use uplo_P() macro
527    
528            * R/Csparse.R (replCmat): call diagU2N() when needed
529            * R/Tsparse.R (replTmat): ditto
530    
531            * src/dtCMatrix.c (tCMatrix_validate): new
532            * src/dtTMatrix.c (tTMatrix_validate): new, used in
533            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
534    
535            * R/diagMatrix.R (replDiag): to use in [<-
536    
537    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
540                    also more general diagU2N().
541    
542    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
545            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
546    
547    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * tests/bind.R: a few more cases
550            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
551    
552            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
553            * R/ddenseMatrix.R (cbind2/rbind2)
554            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
555            * tests/indexing.R
556            * tests/indexing.Rout.save: updated
557    
558    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
561            * tests/indexing.R
562    
563    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
566            align with proper position of "0", i.e., right for integers.
567            argument 'align' by default is "fancy".
568    
569    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
572            * R/Csparse.R: and fix "Compare" for more cases.
573            * tests/Class+Meth.R: test some of these (m == m, m != m)
574    
575    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * R/lsparseMatrix.R: all() and any() methods
578            * R/ldenseMatrix.R:      ditto
579            * NAMESPACE, R/Matrix.R: ditto
580    
581            * man/all-methods.Rd: document them minimally
582    
583            * tests/simple.R: add a few examples for these
584    
585    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/Tsparse.R ([): fix long standing typo in symmetric case
588            * man/dsCMatrix-class.Rd: add example exhibiting the above case
589    
590    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
591    
592            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
593            to LL before converting to a sparse matrix. (The LDL form can be
594            converted to a sparse matrix but it is implicitly a unit
595            triangular matrix and a diagonal matrix overwritten on the diagonal.)
596    
597    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
598    
599            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
600    
601    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
602    
603            * DESCRIPTION (Version): updated -> release 0.9975-7
604            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
605    
606    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
609    
610    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
611    
612            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
613            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
614            is exactly singular.
615    
616    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * DESCRIPTION (Date): updated -> release 0.9975-6
619    
620    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
623            now returns symmetric.
624    
625            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
626    
627            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
628            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
629    
630            * R/Auxiliaries.R (.type.kind): added
631    
632    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
635            running src/CSparse_install.sh
636    
637            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
638    
639    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
642            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
643    
644            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
645    
646            * tests/Class+Meth.R (tstMatrixClass): now assure
647            the (important in method programming) property :
648    
649                    ###>>  Every "Matrix" is either
650                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
651    
652                    (where "*" stands for "Matrix")
653    
654            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
655    
656            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
657            * tests/validObj.R: checks for "comparison"
658    
659            * R/sparseMatrix.R ([): improved indexing for sparse;
660                    trying to keep <symmetric>[ n, n] symmmetric
661    
662            * tests/indexing.R: indexing for logical sparse now ok
663    
664    
665    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
666    
667            * src/Tsparse.c: use xTsparse_validate() , and hence remove
668    
669            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
670    
671    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
674    
675            * tests/simple.R: validObject() checking the above.
676    
677            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
678            replacing both dgCMatrix_validate and lgCM*.
679    
680            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
681            fix dimnames setting in other places.
682            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
683    
684    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
687    
688            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
689            symmetry test, via
690            * R/Auxiliaries.R (.as.dgC.0.factors):
691    
692    2006-11-01  Douglas Bates  <bates@r-project.org>
693    
694            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
695            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
696            <CsparseMatrix>) added
697    
698    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * tests/matprod.R: add a variation of Harri's example
701    
702            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
703            recursive infinitely.
704    
705            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
706    
707            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
708    
709    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
712            matrix if possible; test m+m == 2*m; now test dgRMatrix.
713            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
714            satisfy the above test.
715    
716    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
719    
720            * R/dgCMatrix.R: solve(a, b="missing") based on
721            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
722            RHS = NULL.
723    
724            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
725            add more (needed) [t]crossprod() methods.
726    
727            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
728    
729            * R/Auxiliaries.R (as_CspClass): cleanup
730            (drop0): internal utility for "Csparse_drop(*, 0)"
731            (.bail.out.2): encourage active feedback
732    
733    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/dMatrix.R(Compare): new(), then slots [no validity check]
736    
737            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
738            non-valid or 'sorted' case).
739    
740            * R/dsparseMatrix.R: add "chol" method.
741            * R/ddenseMatrix.R: ditto
742    
743            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
744            * NAMESPACE (Ops)
745            * R/diagMatrix.R (diag2T): simple utility used "higher level"
746            coercion; deprecating direct lower level coercions.
747    
748            * R/*.R (seq): use seq_len() and seq_along() where possible.
749    
750    
751    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * DESCRIPTION (Version): 0.9975-5 ready for release
754    
755    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
756    
757            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
758    
759    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
760    
761            * R/AllClass.R (corMatrix): add 'validity' check;
762                    comment out unused "LDL" class definition
763            * NAMESPACE: mention, but do not export "LDL" class
764            * R/corMatrix.R: new (simple), needed for R-devel with
765            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
766              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
767    
768    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
769    
770            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
771            use Rprintf and R's error handling.
772    
773    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
776            * tests/matprod.R: add tests for the bug fixed.
777    
778    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
779    
780            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
781            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
782    
783    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
784    
785            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
786    
787    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
788    
789            * DESCRIPTION (Version): 0.9975-3
790    
791            * R/diagMatrix.R (bdiag): new function constructing block diagonal
792            (sparse) matrices.
793            * man/bdiag.Rd: docu + examples
794    
795            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
796    
797            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
798            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
799    
800            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
801            that result is sparse or diagonal (and not dense).
802    
803            * man/Subassign-methods.Rd: fix examples
804    
805            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
806            should always return a sparse (and not sometimes a diagonal) matrix.
807    
808    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
811    
812    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
813    
814            * DESCRIPTION (Version): 0.9975-2
815    
816            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
817    
818    2006-10-02  Douglas Bates  <bates@R-project.org>
819    
820            * tests/dg_Matrix.R: Simplify test taking into account new code.
821    
822    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
825    
826            * R/lsTMatrix.R: new files w/ missing methods
827            * R/nsTMatrix.R:  "  'for completeness'
828    
829            * tests/Class+Meth.R: a bit less 'not.ok.classes'
830    
831            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
832    
833    
834    2006-09-28  Douglas Bates  <bates@R-project.org>
835    
836            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
837            included.
838    
839            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
840            Export C-callable functions used in Zt_create in lme4.
841    
842    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844            * DESCRIPTION (Version): 0.9975-1
845    
846            * tests/simple.R: less checks fail; using NA, found that our
847                    kronecker() is not base-compatible with NA's.
848    
849            * R/dMatrix.R: "Compare" method now implemented for all cases
850    
851            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
852    
853            * man/dtpMatrix-class.Rd: mention length of 'x' slot
854    
855            * src/dtpMatrix.c (dtpMatrix_validate): fix check
856            * src/dspMatrix.c (dspMatrix_validate): ditto
857    
858            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
859              including coercion to [nl]tTMatrix.
860    
861            * R/diagMatrix.R (show): print a header line as for other classes.
862    
863    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
864    
865            * src/Makefile.win (SUBDIRS): fix typo
866    
867    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
868    
869            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
870    
871    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
872    
873            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
874            symmetric and y missing in R code using %*% (cholmod_aat doesn't
875            accept a symmetric matrix).
876            * tests/group-methods.R: Uncomment test of crossprod applied to
877            lsCMatrix objects.
878    
879    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
880    
881            * R/AllClass.R (symmetricMatrix): add validity method (available
882            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
883    
884            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
885    
886            * tests/indexing.Rout.save:
887            * tests/indexing.R: additions, mainly for 'lsparse'
888    
889            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
890            case.
891    
892            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
893    
894    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
895    
896            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
897                    as 'N' (1-letter - Ok?)
898    
899            * tests/group-methods.R: add test for logical + NAs
900    
901            * R/dMatrix.R ("Compare"): fix to work with NA's
902    
903            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
904    
905            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
906                    which is implemented.
907    
908    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
909    
910            * src/chm_common.c: coerce logical <-> double instead of
911            typecasting;  needed for "l" matrix handling in cholmod.
912    
913            * tests/other-pkgs.R (graph): small extension in "graph" checks.
914    
915            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
916            (Tsp2grNEL): other fixes needed
917    
918    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
921                    Matrices, since "lMatrix", also "lsparseM" can have NA
922            * R/ndenseMatrix.R, etc: new source files
923            * man/nsparseMatrix-classes.Rd, etc: new help files
924            * tests/: adaptions
925            * src/chm_common.c (chm_dense_to_SEXP): and others:
926                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
927            * src/Csparse.c, etc: ditto
928    
929    2006-09-11  Douglas Bates  <bates@R-project.org>
930    
931            * src/Mutils.[ch],init.c inst/include/*.h: Move the
932            alloc_d**Matrix functions to the lme4 package.
933    
934    2006-09-09  Douglas Bates  <bates@R-project.org>
935    
936            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
937            fixed
938    
939    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
940    
941            * R/lMatrix.R: new
942    
943            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
944    
945            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
946            * man/tcrossprod.Rd: ditto
947    
948    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
949    
950            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
951            for exported functions
952            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
953            Remove partitioning algorithms for sparse matrix reordering.  The
954            copyright on the Metis code was problematic and the methods were
955            rarely used.
956            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
957            operations are now done entirely in CHOLMOD code.
958    
959    2006-09-06  Douglas Bates  <bates@R-project.org>
960    
961            * src/Mutils.h: Remove functions that are no longer used.
962    
963    2006-09-04  Douglas Bates  <bates@R-project.org>
964    
965            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
966            * src/DEPS.mkf: update
967    
968    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
969    
970            * created branches/Matrix-for-R-2.3.x;  on trunk: do
971            * DESCRIPTION (Version): 0.9975-0
972            (Depends): R (>= 2.4.0)
973    
974    2006-09-01  Douglas Bates  <bates@R-project.org>
975    
976            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
977    
978    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
979    
980            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
981            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
982    
983            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
984    
985    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
986    
987            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
988            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
989            * R/dsparseMatrix.R: ditto
990            * R/Csparse.R: ditto
991    
992    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
993    
994            * R/dMatrix.R (Compare): improve availability of "<", etc
995            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
996    
997    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
998    
999            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1000            of a 0-index which was used as 1-index (..hmm)
1001    
1002            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1003    
1004            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1005            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1006            (.is.diagonal): ditto
1007    
1008            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1009    
1010            * R/Matrix.R (Matrix): also work for NA data
1011    
1012    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1015            in all cases.
1016    
1017    2006-08-27  Douglas Bates  <bates@R-project.org>
1018    
1019            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1020            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1021    
1022    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1023    
1024            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1025            subclasses of "ddenseMatrix"
1026            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1027            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1028            instead of half dozen specialized ones.
1029    
1030    2006-08-25  Douglas Bates  <bates@R-project.org>
1031    
1032            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1033            <tillard@cirad.fr> - ordering standard errors to match effects.
1034    
1035    2006-08-24  Douglas Bates  <bates@R-project.org>
1036    
1037            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1038            on R_ldl.
1039            * R/lCholCMatrix.R,
1040            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1041            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1042            * many files in ./R and ./src: Use more general version of
1043            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1044            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1045            dtpMatrix, dspMatrix and dppMatrix conversions.
1046    
1047    
1048    2006-08-23  Douglas Bates  <bates@R-project.org>
1049    
1050            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1051            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1052            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1053            dgeMatrix_crossprod (may need to do this in other places).
1054            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1055            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1056    
1057    2006-08-22  Douglas Bates  <bates@R-project.org>
1058    
1059            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1060            types of classed Matrices, matrices or numeric or logical vectors.
1061            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1062            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1063            to Mutils.h (as an inline) and change name to Matrix_check_class;
1064            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1065            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1066            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1067            * src/Csparse.c: use diag_P and uplo_P macros.
1068    
1069    2006-08-21  Douglas Bates  <bates@R-project.org>
1070    
1071            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1072            valgrind.
1073            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1074            inverses.
1075            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1076            -Wall warnings.
1077            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1078            Use dup_mMatrix_as_dgeMatrix.
1079    
1080    2006-08-20  Douglas Bates  <bates@R-project.org>
1081    
1082            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1083            * tests/sparseQR.R: Added
1084            * man/sparseQR-class.Rd: Document methods for qr.* generics
1085            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1086    
1087    2006-08-19  Douglas Bates  <bates@R-project.org>
1088    
1089            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1090            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1091            and qr.fitted.
1092            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1093            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1094    
1095    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1096    
1097            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1098            the base version has no "..." argument.
1099    
1100            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1101    
1102            * R/Matrix.R: define and
1103            * NAMESPACE: export as.numeric() and as.logical() methods.
1104                    Let's hope these do not badly slow down something...
1105            Finally export the zapsmall() method.
1106    
1107    2006-08-17  Douglas Bates  <bates@R-project.org>
1108    
1109            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1110            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1111            * src/dtCMatrix.c :Remove code that is no longer used
1112            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1113    
1114    2006-08-14  Douglas Bates  <bates@R-project.org>
1115    
1116            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1117            Csparse_to_logical and Csparse_symmetric_to_general.
1118            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1119            coercion methods between CsparseMatrix and TsparseMatrix.
1120    
1121    2006-08-14  Douglas Bates  <bates@R-project.org>
1122    
1123            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1124            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1125            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1126            possible.
1127    
1128    2006-08-12  Douglas Bates  <bates@R-project.org>
1129    
1130            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1131              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1132              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1133              generalize conversions between TsparseMatrix, CsparseMatrix,
1134              denseMatrix and matrix.  Preserve triangularity property and
1135              propagate Dimnames in the easy cases.
1136    
1137    2006-08-10  Douglas Bates  <bates@R-project.org>
1138    
1139            * src/lmer.c: adjust checks in glmer_init for S4SXP
1140            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1141            before S4SXP but for the wrong reasons.
1142    
1143    2006-08-08  Douglas Bates  <bates@R-project.org>
1144    
1145            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1146            Later modified to return the upper triangle only.
1147            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1148    
1149    2006-08-07  Douglas Bates  <bates@R-project.org>
1150    
1151            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1152            R-level conversion to a sparse symmetric class.
1153            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1154            Remove conversion to sparse symmetric classes (now done in C code).
1155    
1156    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1157    
1158            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1159            * man/band.Rd:  adapt the \dontshow{} unit test.
1160    
1161    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1162    
1163            * DESCRIPTION (Version): 0.995-14  for CRAN
1164    
1165            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1166    
1167            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1168            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1169    
1170            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1171            * R/Tsparse.R (tril, triu, band): methods
1172            * R/dgRMatrix.R (tril, ...):    ditto
1173            * man/band.Rd:                  ditto
1174    
1175    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1176    
1177            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1178                    to be up-to-date automatically.
1179    
1180    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1181    
1182            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1183    
1184            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1185            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1186            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1187            such that the S4 objects are always created by the current version
1188            of R and 'Matrix' class definitions.
1189    
1190    2006-08-01  Douglas Bates  <bates@R-project.org>
1191    
1192            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1193            inst/external/test3comp.rda: Added warnings for convergence on
1194            boundary and test cases.
1195    
1196            * src/lmer.c (mer_postVar): Modified to return the variances that
1197            are marginal to the fixed effects, not conditional on them (which
1198            is what the bVar slot contents represent).
1199    
1200    2006-07-31  Douglas Bates  <bates@R-project.org>
1201    
1202            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1203            function which calls the C function mer_hat_trace2.
1204    
1205            * man/ranef.Rd: Include description of "postVar" argument and
1206            producing a caterpillar plot.
1207    
1208    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1209    
1210            * NAMESPACE:    change  "correlation" to "corMatrix"
1211            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1212            * R/dpoMatrix.R: ditto
1213            * R/lmer.R:      ditto
1214    
1215    2006-07-28  Douglas Bates  <bates@R-project.org>
1216    
1217            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1218            RZXinv slot's contents into a separate internal function that can
1219            be used in mer_hat_trace.
1220    
1221    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1222    
1223            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1224            via new smart
1225            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1226            utility functions.
1227    
1228    
1229    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1230    
1231            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1232            matrices when appropriate; band() even symmetric ones.
1233            (replCmat): extend to potentially all "CsparseMatrix"
1234            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1235            allow subassignment for special sparse matrices.
1236    
1237            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1238    
1239            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1240            argument; in glmer_*(): print only if(verbose).
1241    
1242            speed-optimize a few places by moving REAL(.) out of loops.
1243    
1244            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1245    
1246    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1247    
1248            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1249                    since that wrongly triggers also for M[ logi , ]
1250    
1251            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1252            a symmetric matrix that results in a non-symmetric one.
1253            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1254    
1255            * R/dMatrix.R: make round(M) work as round(M, 0)
1256    
1257            * R/dgTMatrix.R (image): coordinate system and axis now use
1258            1-based indices, not 0-based ones.
1259    
1260            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1261            * tests/indexing.R: test it.
1262    
1263            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1264            * man/isSymmetric-methods.Rd: and document it.
1265    
1266            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1267            * man/SparseM-conv.Rd: docu them
1268    
1269            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1270                    for 'SparseM' conversions
1271    
1272    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1273    
1274            * R/Matrix.R (head): added head() and tail() methods.
1275    
1276    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1277    
1278            * DESCRIPTION (Version): 0.995-12 released to CRAN
1279    
1280    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1281    
1282            * tests/simple.R: add check for correct dsT -> dgT coercion;
1283                    add check for correct printing of symmetric sparse matrices.
1284    
1285            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1286            for sparse symmetric matrices.
1287    
1288            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1289            diagonal twice.
1290    
1291    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1292    
1293            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1294            being applied to the x slot (detected by Brian Ripley).
1295    
1296    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1297    
1298            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1299    
1300            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1301    
1302    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1303    
1304            * src/lgCMatrix.c (lgCMatrix_diag): new function
1305            * R/lgCMatrix.R (diag): for new method
1306    
1307            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1308                 ==> construction of illegal "*gTMatrix" via new() should
1309                 now be much less easy:
1310            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1311    
1312            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1313                    directly.
1314            * man/Matrix.Rd: documents it.
1315    
1316    2006-07-06  Douglas Bates  <bates@R-project.org>
1317    
1318            * src/pedigree.c (pedigree_inbreeding): Correction in
1319            initialization.  This function is not currently being used and is
1320            not fully tested.
1321    
1322            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1323            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1324            objects.  Modified validity check on pedigree objects to account
1325            for nonparallel patterns of missingness of parents.
1326    
1327            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1328            class.
1329    
1330    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1331    
1332            * R/pMatrix.R: coercion pMatrix -> Tsparse
1333    
1334    2006-06-12  Douglas Bates  <bates@R-project.org>
1335    
1336            * DESCRIPTION (Version): 0.995-11 released to CRAN
1337    
1338            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1339            the output from mcmcsamp.
1340    
1341    2006-06-10  Douglas Bates  <bates@R-project.org>
1342    
1343            * R/lmer.R (simulestimate): added C code for calculating the trace
1344            of the hat matrix.
1345    
1346    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1347    
1348            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1349            classes.
1350            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1351    
1352    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1353    
1354            * R/dgTMatrix.R (colSums): etc. All four of
1355            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1356            all "Matrices".
1357    
1358    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1359    
1360            * R/lmer.R (panel.ci): Add a reference line at zero and a
1361            background grid to the qqmath plot of ranef.lmer.
1362    
1363    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1364    
1365            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1366            grouping factors to be specified in the formula as (1|foo/bar).
1367    
1368    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1369    
1370            * R/lmer.R (findbars and others): Change check of is.numeric to
1371            !is.language to resolve the bug reported by Jacob Wegelin.
1372    
1373            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1374            code to evaluate inbreeding coefficients without calculating T,
1375            based on code in Sargolzaei and Iwaisaki's paper.
1376    
1377    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1378    
1379            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1380            generic and mer methods for isNested and denomDF. This denomDF was
1381            an attempt to emulate that in lme but I don't think that makes
1382            sense.  Use the trace of the hat matrix instead.
1383    
1384    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1385    
1386            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1387            the C code depending on a slot structure that's no longer valid.
1388            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1389    
1390    
1391    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1392    
1393            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1394            of lowerTriMatrix generic and methods to tril (also upper to triu)
1395            and added a general band extractor.
1396    
1397    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1398    
1399            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1400            allowable range with NAs. Added a corresponding check in the
1401            validity check for the pedigree class.
1402    
1403            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1404            crossprod methods now inherits from symmetricMatrix.
1405    
1406    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1407    
1408            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1409            generics lowerTriMatrix and upperTriMatrix along with methods for
1410            the Csparse virtual class.  Also added a C function Csparse_band
1411            that implements these methods by calling cholmod_band.
1412    
1413    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1414    
1415            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1416            erased when it was NULL.  This led to invalid subselections!
1417    
1418    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1419    
1420            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1421            in method for "t" so as not to lose the unit diagonal property.
1422    
1423    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1424    
1425            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1426            and methods.  This is now an option to the ranef method for the
1427            mer class.
1428    
1429            * src/cs_utils.c: Ensure that the nz component is -1 for a
1430            compressed column-oriented matrix.  Minor formatting cleanup.
1431    
1432            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1433            objects.
1434    
1435    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1436    
1437            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1438            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1439    
1440    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1441    
1442            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1443            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1444    
1445            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1446            for the dtCMatrix class.
1447    
1448    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1449    
1450            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1451            and methods for it.
1452    
1453    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1454    
1455            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1456            arguments, such that M %*% 1:6 now works
1457            * Tests/matprod.R: test the above
1458    
1459    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1460    
1461            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1462            the ranef.lmer class.
1463    
1464            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1465            methods to extract the posterior variances from the bVar slot.
1466    
1467    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1468    
1469            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1470            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1471    
1472            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1473            * tests/simple: (extended)
1474    
1475            * R/sparseMatrix.R (isTriangular): now using much improved
1476            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1477    
1478    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1479    
1480            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1481            (problem report from Franklin Parlamis).  This should be done
1482            generally.
1483    
1484    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1485    
1486            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1487            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1488            update the plot methods.
1489    
1490    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1491    
1492            * R/lmer.R (resid and ranef methods):  Added methods for the
1493            "residuals" and "resid" generic but only for linear mixed model
1494            fits.  Changed the ranef method to return a list of data frames so
1495            that the plot methods now work.
1496    
1497    2006-03-16  Douglas Bates  <bates@bates2>
1498    
1499            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1500            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1501    
1502            * DESCRIPTION (Date): New release
1503    
1504    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1505    
1506            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1507    
1508            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1509            * man/KNex.Rd: and other help files
1510            * tests/*.R: several ones needed adaption
1511            * inst/doc/Comparisons.Rnw: ditto
1512    
1513    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1514    
1515            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1516    
1517            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1518    
1519    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1520    
1521            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1522    
1523            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1524    
1525    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1526    
1527            * R/dMatrix.R: enable things like  M [ M < 10 ]
1528            * R/dgeMatrix.R: implement it
1529    
1530    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1531    
1532            * R/AllClass.R: define "summary.mer" and "*.lmer"
1533            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1534            * R/lmer.R (show): now works with summary()
1535    
1536    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1537    
1538            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1539            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1540                    support the above
1541    
1542  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1543    
1544          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
# Line 171  Line 1712 
1712  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1713    
1714          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1715          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1716          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1717    
1718  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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