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revision 726, Thu May 12 14:59:04 2005 UTC revision 1987, Tue Jul 10 19:31:18 2007 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
4    
5    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
6    
7            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
8              to fix a subtle bug (Kurt Hornik and Ingo Feinerer)
9    
10    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
11    
12            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
13              solve the bug
14    
15    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * src/dgCMatrix.c (compressed_to_TMatrix):
18    
19    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * src/Csparse.c (Rsparse_validate): new, to have some validity
22            checking for RsparseMatrix
23            * src/dgCMatrix.c (xRMatrix_validate): ditto
24            * src/dtCMatrix.c (tRMatrix_validate): ditto
25    
26    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
27    
28            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
29              lgRMatrix
30            * [r4568] DESCRIPTION: Prepare for bug-fix release
31            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
32              for declaration of cholmod_symmetry
33    
34    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
37            release.
38    
39    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
40    
41            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
42              functions - no longer used
43            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
44              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
45              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
46              Alloca
47    
48    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
49    
50            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
51              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
52              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
53              src/t_gCMatrix_colSums.c: more R_CheckStack()s
54    
55    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
56    
57            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
58              the required amount of memory then call M_numeric_as_chm_dense.
59            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
60              (like Calloc but calling alloca)
61    
62    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
65            and extended with more sophisticated 'col.names' option.
66            * NAMESPACE: export  printSparseMatrix()
67            * man/printSpMatrix.Rd: document, incl. examples
68    
69    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
70    
71            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
72              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
73              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
74    
75    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * DESCRIPTION (Version): 0.99875-4
78    
79            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
80            some dimnames perservation.
81    
82            * R/dsTMatrix.R (t-method): keep dimnames
83            * R/dtTMatrix.R:  ditto
84    
85            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
86            and ncol(.) < 10
87    
88            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
89            from Mutils.h
90    
91            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
92            e.g. in as(<ngCMatrix>, "matrix")
93    
94    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
95    
96            * [r4529] .: Create a branch for the API changes from the 0.99875
97              series to the 0.999375 series
98            * [r4530] DESCRIPTION, inst/include/Matrix.h,
99              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
100              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
101              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
102              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
103              as_cholmod_x functions
104    
105    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
106    
107            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
108              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
109              to Comparisons
110    
111    >>>>>>> .merge-right.r4561
112    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * DESCRIPTION (Version): 0.99875-3 ready to be released.
115    
116            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
117    
118            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
119            that should also work in a future version of R.
120    
121    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
124    
125            * R/sparseVector.R: more *sparseVector coercions, notably for
126            non - double ones.
127    
128    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
131              notably the new ones building on the new .Call(.)s:
132    
133            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
134            all 4 of [dlin]gCMatrix_colSums().
135    
136    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
137    
138            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
139            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
140              result
141    
142    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/kronecker.R: fix typo (could lead to inf.recursion)
145            * test/simple.R: testing that
146    
147            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
148            method as well (which can have arguments, show() can't).
149    
150    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
151    
152            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
153              added dgCMatrix_colSums for [col,row][Sums,Means]
154    
155    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
156    
157            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
158              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
159              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
160            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
161              class
162            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
163              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
164              row names to store the levels - duh!  Added an example.
165    
166    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * src/Csparse.c (Csparse_validate): check for *repeated* entries
169            thanks to example from Christian Buchta; with a test here:
170            * tests/simple.R:
171    
172    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
175            of colSums(*, sparseResult = TRUE)
176    
177    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
180            'na.rm = FALSE' as "everywhere" else in R.
181    
182    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
183    
184            * [r4421] src/CSparse_install.sh: Modify for new organization of
185              CSparse package
186            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
187              SuiteSparse
188            * [r4426] src/Makefile: add ./UFconfig to the include path for
189              compilation
190            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
191            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
192              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
193    
194    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
197            * R/sparseMatrix.R (prSpMatrix): now gives a message about
198            suppressed column names.
199    
200    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
201    
202            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
203              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
204              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
205              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
206              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
207              Remove warnings after change to const char* CHAR
208    
209    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
210    
211            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
212              type of M_cholmod_ssmult
213    
214    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
215    
216            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
217              src/init.c: Yet another cholmod export - cholmod_ssmult
218    
219    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * NAMESPACE: exported drop0(), since
222            * man/drop0.Rd: I have seen several cases, I really wanted to use
223            it, so our users may want too.
224    
225    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * man/colSums.Rd: separately document colSums() etc, since these
228            have the extra argument 'sparseResult'.
229    
230    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
233            * man/spMatrix.Rd: docu., including examples
234    
235            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
236            in order to make colMeans() etc fast *and* correct.
237            * R/sparseVector.R (replSPvec): "[<-" functionality for
238            sparseVectors; tested in
239            * tests/simple.R:
240    
241    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
244            (very) sparse Matrices; output similar to Matlab's print().
245    
246    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
247    
248            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
249            0-based, indices (Jose Quesada <quesada@gmail.com>).
250    
251    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
252    
253            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
254    
255    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * R/Auxiliaries.R (sparsapply): new utility, much faster than
258            tapply1() for large sparse matrices.
259    
260    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/Matrix.R (dim<-): reshape now via sparseVector.
263    
264            * R/sparseVector.R: methods and function for
265            * R/AllClass.R: new "sparseVector" class and daughters.
266            * NAMESPACE: export new classes
267    
268    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * DESCRIPTION (Version): 0.99875-1
271            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
272    
273    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
276            indexing
277            * tests/indexing.R: test set for that.
278    
279    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
282            entries.
283            * tests/indexing.R(out): add regression test for it
284    
285    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
288            name for "!" method definitions.
289    
290    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/Tsparse.R (intI): new utility, used for "[" :
293                    Cleanup up there, and fixes for duplicated indices - more TODO!
294    
295            * tests/indexing.R(out): more tests
296    
297    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
298    
299            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
300            code that is now part of the R Lapack library.
301    
302            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
303            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
304    
305    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
308    
309    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
312            up with extraneous names '0'...'<n-1>'
313    
314    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/dgTMatrix.R (mat2dgT): care about NAs
317    
318    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/kronecker.R: triangularity preserving methods
321    
322    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/kronecker.R: new file collecting kronecker() methods in one
325                    place.  Goal: become much faster!
326    
327    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
330            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
331            can be much faster.
332    
333            * tests/matprod.R: add regression tests for these (upper & lower).
334    
335    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/Matrix.R (diff): method for our Matrices.
338    
339            * R/sparseMatrix.R (isDiagonal): check dim()!
340    
341    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/Matrix.R (dim<-): new method for "reshape()" built on a
344            proposal from Tamas Papp.
345    
346    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
349    
350            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
351            rather define and export  cBind() and rBind() only.
352            --> useRs *must* change code that used to have cbind()/rbind() !!
353    
354            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
355            * R/bind.Rout.save: ditto
356    
357    2007-02-16  Douglas Bates  <bates@r-project.org>
358    
359            * DESCRIPTION (Date, Version): 0.9975-11 with new date
360            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
361            const modifier on declaration of the array 'valid'
362    
363    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
364    
365            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
366    
367    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
370    
371            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
372            * tests/simple.R: test the above and some of these coercions:
373    
374            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
375                    be careful to avoid infinite recursion, using new coercions in
376            * R/ngCMatrix.R and nsC... and ntC...
377            * R/lsparseMatrix.R: ditto
378    
379            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
380    
381            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
382            * R/Rsparse.R: reactivate .Call()s
383    
384            * tests/Class+Meth.R: a bit more on actual classes
385    
386    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
387    
388            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
389    
390    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * DESCRIPTION (Version): 0.9975-10 to upload
393    
394            * tests/Class+Meth.R (tstMatrixClass): require coercions to
395            specific classes less unconditionally.
396    
397            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
398    
399            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
400    
401            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
402            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
403            R_to_CMatrix segfaults on one platform.
404            Eliminate most coercion method to *specific* classes, and replace
405            with virtual classes coercions.
406    
407    
408    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
409    
410            * src/init.c: export the CHM...._validate() placeholders, since
411            they *are* called.
412    
413            * tests/Class+Meth.R (classCanCoerce): and starting to test
414            all as(<from>, <to>)
415    
416    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
419            * tests/indexing.R: tested now
420            * tests/indexing.Rout.save: updated
421    
422            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
423            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
424            appropriate.
425    
426            * NAMESPACE: export a trivial
427            * R/Matrix.R: drop() Matrix-method
428    
429            * R/AllClass.R: moved all prototypes to virtual super classes.
430    
431            * R/Rsparse.R: many more coercions to have less exceptions in
432            * tests/Class+Meth.R:
433    
434            * R/Ops.R (Compare): tweak for case with NA
435            * tests/simpl.R: hence another 'FIXME' eliminated
436    
437    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
440            objects.
441    
442            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
443              and more of "!", "&", "|", all, any; coercions
444    
445            * R/Rsparse.R: many coercions (which enable quite a few other
446            methods), thanks to enhancements in
447            * src/dgCMatrix.c (R_to_CMatrix): new, and
448            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
449            symmetric & triangular and ..RMatrix objects.
450    
451            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
452            renamed file from src/dsTMatrix.c;
453            now dealing with symmetric and triangular Tsparse coercions, both
454            to dense and general.
455    
456    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
459    
460            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
461            where sensible when the <numeric> is of length > 1.
462    
463    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * R/Matrix.R ([<-): for M[] <- value: fix length
466    
467    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
470            * R/ndenseMatrix.R: new coercions n* -> l*
471    
472    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
475    
476            * R/Ops.R ("Logic"): and other "Ops", many updates
477    
478    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * src/Mutils.h (SET_DimNames): new utility
481    
482            * R/Auxiliaries.R (nnzero): improved and now exported via
483    
484            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
485    
486    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/diagMatrix.R (!): fix typo.
489    
490    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/Auxiliaries.R (as_Csparse): and quite a few others:
493                    allow to pass class definition --> speedup
494            * R/sparseMatrix.R: apply the above
495    
496            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
497    
498            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
499            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
500            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
501    
502            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
503    
504            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
505            and use it for "sparse*" as well, since it's faster than the
506            as_Csparse(.) way.
507    
508    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
511    
512    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
515            as method for   M[ ij ] <- v
516            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
517    
518            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
519            FALSE answer
520    
521            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
522            * tests/indexing.R: test it, and some of the above
523    
524    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/Auxiliaries.R (is_duplicatedT): new utility
527    
528    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
529    
530            * src/init.c (R_init_Matrix): export cholmod_scale
531    
532    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
535            base::as.matrix to (x, ...)
536    
537    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
540            file; start using "Logic", hence
541    
542            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
543            * NAMESPACE: import and export "Logic"
544    
545    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
548            only needed previously to R version 2.5.0.
549    
550    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
553    
554            * R/Tsparse.R (replTmat): fix subassignment of triangular
555            * R/Csparse.R (replCmat): ditto
556            * tests/indexing.R: more tests, incl the above fix
557    
558    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * R/Auxiliaries.R (drop0): extend for non CSparse
561            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
562    
563            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
564                    use uplo correctly (!); other places: use uplo_P() macro
565    
566            * R/Csparse.R (replCmat): call diagU2N() when needed
567            * R/Tsparse.R (replTmat): ditto
568    
569            * src/dtCMatrix.c (tCMatrix_validate): new
570            * src/dtTMatrix.c (tTMatrix_validate): new, used in
571            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
572    
573            * R/diagMatrix.R (replDiag): to use in [<-
574    
575    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
578                    also more general diagU2N().
579    
580    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
583            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
584    
585    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * tests/bind.R: a few more cases
588            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
589    
590            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
591            * R/ddenseMatrix.R (cbind2/rbind2)
592            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
593            * tests/indexing.R
594            * tests/indexing.Rout.save: updated
595    
596    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
599            * tests/indexing.R
600    
601    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
604            align with proper position of "0", i.e., right for integers.
605            argument 'align' by default is "fancy".
606    
607    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
610            * R/Csparse.R: and fix "Compare" for more cases.
611            * tests/Class+Meth.R: test some of these (m == m, m != m)
612    
613    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/lsparseMatrix.R: all() and any() methods
616            * R/ldenseMatrix.R:      ditto
617            * NAMESPACE, R/Matrix.R: ditto
618    
619            * man/all-methods.Rd: document them minimally
620    
621            * tests/simple.R: add a few examples for these
622    
623    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * R/Tsparse.R ([): fix long standing typo in symmetric case
626            * man/dsCMatrix-class.Rd: add example exhibiting the above case
627    
628    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
629    
630            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
631            to LL before converting to a sparse matrix. (The LDL form can be
632            converted to a sparse matrix but it is implicitly a unit
633            triangular matrix and a diagonal matrix overwritten on the diagonal.)
634    
635    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
636    
637            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
638    
639    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
640    
641            * DESCRIPTION (Version): updated -> release 0.9975-7
642            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
643    
644    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
647    
648    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
649    
650            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
651            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
652            is exactly singular.
653    
654    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
655    
656            * DESCRIPTION (Date): updated -> release 0.9975-6
657    
658    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
661            now returns symmetric.
662    
663            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
664    
665            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
666            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
667    
668            * R/Auxiliaries.R (.type.kind): added
669    
670    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
671    
672            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
673            running src/CSparse_install.sh
674    
675            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
676    
677    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
678    
679            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
680            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
681    
682            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
683    
684            * tests/Class+Meth.R (tstMatrixClass): now assure
685            the (important in method programming) property :
686    
687                    ###>>  Every "Matrix" is either
688                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
689    
690                    (where "*" stands for "Matrix")
691    
692            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
693    
694            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
695            * tests/validObj.R: checks for "comparison"
696    
697            * R/sparseMatrix.R ([): improved indexing for sparse;
698                    trying to keep <symmetric>[ n, n] symmmetric
699    
700            * tests/indexing.R: indexing for logical sparse now ok
701    
702    
703    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * src/Tsparse.c: use xTsparse_validate() , and hence remove
706    
707            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
708    
709    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
712    
713            * tests/simple.R: validObject() checking the above.
714    
715            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
716            replacing both dgCMatrix_validate and lgCM*.
717    
718            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
719            fix dimnames setting in other places.
720            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
721    
722    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
725    
726            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
727            symmetry test, via
728            * R/Auxiliaries.R (.as.dgC.0.factors):
729    
730    2006-11-01  Douglas Bates  <bates@r-project.org>
731    
732            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
733            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
734            <CsparseMatrix>) added
735    
736    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * tests/matprod.R: add a variation of Harri's example
739    
740            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
741            recursive infinitely.
742    
743            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
744    
745            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
746    
747    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
750            matrix if possible; test m+m == 2*m; now test dgRMatrix.
751            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
752            satisfy the above test.
753    
754    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
755    
756            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
757    
758            * R/dgCMatrix.R: solve(a, b="missing") based on
759            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
760            RHS = NULL.
761    
762            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
763            add more (needed) [t]crossprod() methods.
764    
765            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
766    
767            * R/Auxiliaries.R (as_CspClass): cleanup
768            (drop0): internal utility for "Csparse_drop(*, 0)"
769            (.bail.out.2): encourage active feedback
770    
771    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * R/dMatrix.R(Compare): new(), then slots [no validity check]
774    
775            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
776            non-valid or 'sorted' case).
777    
778            * R/dsparseMatrix.R: add "chol" method.
779            * R/ddenseMatrix.R: ditto
780    
781            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
782            * NAMESPACE (Ops)
783            * R/diagMatrix.R (diag2T): simple utility used "higher level"
784            coercion; deprecating direct lower level coercions.
785    
786            * R/*.R (seq): use seq_len() and seq_along() where possible.
787    
788    
789    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * DESCRIPTION (Version): 0.9975-5 ready for release
792    
793    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
794    
795            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
796    
797    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * R/AllClass.R (corMatrix): add 'validity' check;
800                    comment out unused "LDL" class definition
801            * NAMESPACE: mention, but do not export "LDL" class
802            * R/corMatrix.R: new (simple), needed for R-devel with
803            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
804              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
805    
806    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
807    
808            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
809            use Rprintf and R's error handling.
810    
811    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
812    
813            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
814            * tests/matprod.R: add tests for the bug fixed.
815    
816    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
817    
818            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
819            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
820    
821    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
822    
823            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
824    
825    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
826    
827            * DESCRIPTION (Version): 0.9975-3
828    
829            * R/diagMatrix.R (bdiag): new function constructing block diagonal
830            (sparse) matrices.
831            * man/bdiag.Rd: docu + examples
832    
833            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
834    
835            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
836            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
837    
838            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
839            that result is sparse or diagonal (and not dense).
840    
841            * man/Subassign-methods.Rd: fix examples
842    
843            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
844            should always return a sparse (and not sometimes a diagonal) matrix.
845    
846    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
849    
850    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
851    
852            * DESCRIPTION (Version): 0.9975-2
853    
854            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
855    
856    2006-10-02  Douglas Bates  <bates@R-project.org>
857    
858            * tests/dg_Matrix.R: Simplify test taking into account new code.
859    
860    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
861    
862            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
863    
864            * R/lsTMatrix.R: new files w/ missing methods
865            * R/nsTMatrix.R:  "  'for completeness'
866    
867            * tests/Class+Meth.R: a bit less 'not.ok.classes'
868    
869            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
870    
871    
872    2006-09-28  Douglas Bates  <bates@R-project.org>
873    
874            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
875            included.
876    
877            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
878            Export C-callable functions used in Zt_create in lme4.
879    
880    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
881    
882            * DESCRIPTION (Version): 0.9975-1
883    
884            * tests/simple.R: less checks fail; using NA, found that our
885                    kronecker() is not base-compatible with NA's.
886    
887            * R/dMatrix.R: "Compare" method now implemented for all cases
888    
889            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
890    
891            * man/dtpMatrix-class.Rd: mention length of 'x' slot
892    
893            * src/dtpMatrix.c (dtpMatrix_validate): fix check
894            * src/dspMatrix.c (dspMatrix_validate): ditto
895    
896            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
897              including coercion to [nl]tTMatrix.
898    
899            * R/diagMatrix.R (show): print a header line as for other classes.
900    
901    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
902    
903            * src/Makefile.win (SUBDIRS): fix typo
904    
905    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
908    
909    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
910    
911            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
912            symmetric and y missing in R code using %*% (cholmod_aat doesn't
913            accept a symmetric matrix).
914            * tests/group-methods.R: Uncomment test of crossprod applied to
915            lsCMatrix objects.
916    
917    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
918    
919            * R/AllClass.R (symmetricMatrix): add validity method (available
920            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
921    
922            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
923    
924            * tests/indexing.Rout.save:
925            * tests/indexing.R: additions, mainly for 'lsparse'
926    
927            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
928            case.
929    
930            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
931    
932    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
933    
934            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
935                    as 'N' (1-letter - Ok?)
936    
937            * tests/group-methods.R: add test for logical + NAs
938    
939            * R/dMatrix.R ("Compare"): fix to work with NA's
940    
941            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
942    
943            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
944                    which is implemented.
945    
946    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
947    
948            * src/chm_common.c: coerce logical <-> double instead of
949            typecasting;  needed for "l" matrix handling in cholmod.
950    
951            * tests/other-pkgs.R (graph): small extension in "graph" checks.
952    
953            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
954            (Tsp2grNEL): other fixes needed
955    
956    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
957    
958            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
959                    Matrices, since "lMatrix", also "lsparseM" can have NA
960            * R/ndenseMatrix.R, etc: new source files
961            * man/nsparseMatrix-classes.Rd, etc: new help files
962            * tests/: adaptions
963            * src/chm_common.c (chm_dense_to_SEXP): and others:
964                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
965            * src/Csparse.c, etc: ditto
966    
967    2006-09-11  Douglas Bates  <bates@R-project.org>
968    
969            * src/Mutils.[ch],init.c inst/include/*.h: Move the
970            alloc_d**Matrix functions to the lme4 package.
971    
972    2006-09-09  Douglas Bates  <bates@R-project.org>
973    
974            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
975            fixed
976    
977    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
978    
979            * R/lMatrix.R: new
980    
981            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
982    
983            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
984            * man/tcrossprod.Rd: ditto
985    
986    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
987    
988            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
989            for exported functions
990            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
991            Remove partitioning algorithms for sparse matrix reordering.  The
992            copyright on the Metis code was problematic and the methods were
993            rarely used.
994            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
995            operations are now done entirely in CHOLMOD code.
996    
997    2006-09-06  Douglas Bates  <bates@R-project.org>
998    
999            * src/Mutils.h: Remove functions that are no longer used.
1000    
1001    2006-09-04  Douglas Bates  <bates@R-project.org>
1002    
1003            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1004            * src/DEPS.mkf: update
1005    
1006    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1007    
1008            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1009            * DESCRIPTION (Version): 0.9975-0
1010            (Depends): R (>= 2.4.0)
1011    
1012    2006-09-01  Douglas Bates  <bates@R-project.org>
1013    
1014            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1015    
1016    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1017    
1018            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1019            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1020    
1021            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1022    
1023    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1024    
1025            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1026            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1027            * R/dsparseMatrix.R: ditto
1028            * R/Csparse.R: ditto
1029    
1030    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1031    
1032            * R/dMatrix.R (Compare): improve availability of "<", etc
1033            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1034    
1035    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1036    
1037            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1038            of a 0-index which was used as 1-index (..hmm)
1039    
1040            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1041    
1042            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1043            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1044            (.is.diagonal): ditto
1045    
1046            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1047    
1048            * R/Matrix.R (Matrix): also work for NA data
1049    
1050    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1051    
1052            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1053            in all cases.
1054    
1055    2006-08-27  Douglas Bates  <bates@R-project.org>
1056    
1057            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1058            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1059    
1060    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1061    
1062            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1063            subclasses of "ddenseMatrix"
1064            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1065            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1066            instead of half dozen specialized ones.
1067    
1068    2006-08-25  Douglas Bates  <bates@R-project.org>
1069    
1070            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1071            <tillard@cirad.fr> - ordering standard errors to match effects.
1072    
1073    2006-08-24  Douglas Bates  <bates@R-project.org>
1074    
1075            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1076            on R_ldl.
1077            * R/lCholCMatrix.R,
1078            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1079            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1080            * many files in ./R and ./src: Use more general version of
1081            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1082            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1083            dtpMatrix, dspMatrix and dppMatrix conversions.
1084    
1085    
1086    2006-08-23  Douglas Bates  <bates@R-project.org>
1087    
1088            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1089            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1090            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1091            dgeMatrix_crossprod (may need to do this in other places).
1092            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1093            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1094    
1095    2006-08-22  Douglas Bates  <bates@R-project.org>
1096    
1097            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1098            types of classed Matrices, matrices or numeric or logical vectors.
1099            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1100            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1101            to Mutils.h (as an inline) and change name to Matrix_check_class;
1102            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1103            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1104            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1105            * src/Csparse.c: use diag_P and uplo_P macros.
1106    
1107    2006-08-21  Douglas Bates  <bates@R-project.org>
1108    
1109            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1110            valgrind.
1111            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1112            inverses.
1113            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1114            -Wall warnings.
1115            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1116            Use dup_mMatrix_as_dgeMatrix.
1117    
1118    2006-08-20  Douglas Bates  <bates@R-project.org>
1119    
1120            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1121            * tests/sparseQR.R: Added
1122            * man/sparseQR-class.Rd: Document methods for qr.* generics
1123            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1124    
1125    2006-08-19  Douglas Bates  <bates@R-project.org>
1126    
1127            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1128            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1129            and qr.fitted.
1130            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1131            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1132    
1133    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1134    
1135            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1136            the base version has no "..." argument.
1137    
1138            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1139    
1140            * R/Matrix.R: define and
1141            * NAMESPACE: export as.numeric() and as.logical() methods.
1142                    Let's hope these do not badly slow down something...
1143            Finally export the zapsmall() method.
1144    
1145    2006-08-17  Douglas Bates  <bates@R-project.org>
1146    
1147            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1148            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1149            * src/dtCMatrix.c :Remove code that is no longer used
1150            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1151    
1152    2006-08-14  Douglas Bates  <bates@R-project.org>
1153    
1154            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1155            Csparse_to_logical and Csparse_symmetric_to_general.
1156            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1157            coercion methods between CsparseMatrix and TsparseMatrix.
1158    
1159    2006-08-14  Douglas Bates  <bates@R-project.org>
1160    
1161            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1162            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1163            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1164            possible.
1165    
1166    2006-08-12  Douglas Bates  <bates@R-project.org>
1167    
1168            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1169              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1170              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1171              generalize conversions between TsparseMatrix, CsparseMatrix,
1172              denseMatrix and matrix.  Preserve triangularity property and
1173              propagate Dimnames in the easy cases.
1174    
1175    2006-08-10  Douglas Bates  <bates@R-project.org>
1176    
1177            * src/lmer.c: adjust checks in glmer_init for S4SXP
1178            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1179            before S4SXP but for the wrong reasons.
1180    
1181    2006-08-08  Douglas Bates  <bates@R-project.org>
1182    
1183            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1184            Later modified to return the upper triangle only.
1185            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1186    
1187    2006-08-07  Douglas Bates  <bates@R-project.org>
1188    
1189            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1190            R-level conversion to a sparse symmetric class.
1191            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1192            Remove conversion to sparse symmetric classes (now done in C code).
1193    
1194    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1195    
1196            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1197            * man/band.Rd:  adapt the \dontshow{} unit test.
1198    
1199    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1200    
1201            * DESCRIPTION (Version): 0.995-14  for CRAN
1202    
1203            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1204    
1205            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1206            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1207    
1208            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1209            * R/Tsparse.R (tril, triu, band): methods
1210            * R/dgRMatrix.R (tril, ...):    ditto
1211            * man/band.Rd:                  ditto
1212    
1213    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1214    
1215            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1216                    to be up-to-date automatically.
1217    
1218    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1219    
1220            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1221    
1222            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1223            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1224            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1225            such that the S4 objects are always created by the current version
1226            of R and 'Matrix' class definitions.
1227    
1228    2006-08-01  Douglas Bates  <bates@R-project.org>
1229    
1230            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1231            inst/external/test3comp.rda: Added warnings for convergence on
1232            boundary and test cases.
1233    
1234            * src/lmer.c (mer_postVar): Modified to return the variances that
1235            are marginal to the fixed effects, not conditional on them (which
1236            is what the bVar slot contents represent).
1237    
1238    2006-07-31  Douglas Bates  <bates@R-project.org>
1239    
1240            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1241            function which calls the C function mer_hat_trace2.
1242    
1243            * man/ranef.Rd: Include description of "postVar" argument and
1244            producing a caterpillar plot.
1245    
1246    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1247    
1248            * NAMESPACE:    change  "correlation" to "corMatrix"
1249            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1250            * R/dpoMatrix.R: ditto
1251            * R/lmer.R:      ditto
1252    
1253    2006-07-28  Douglas Bates  <bates@R-project.org>
1254    
1255            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1256            RZXinv slot's contents into a separate internal function that can
1257            be used in mer_hat_trace.
1258    
1259    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1260    
1261            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1262            via new smart
1263            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1264            utility functions.
1265    
1266    
1267    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1268    
1269            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1270            matrices when appropriate; band() even symmetric ones.
1271            (replCmat): extend to potentially all "CsparseMatrix"
1272            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1273            allow subassignment for special sparse matrices.
1274    
1275            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1276    
1277            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1278            argument; in glmer_*(): print only if(verbose).
1279    
1280            speed-optimize a few places by moving REAL(.) out of loops.
1281    
1282            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1283    
1284    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1285    
1286            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1287                    since that wrongly triggers also for M[ logi , ]
1288    
1289            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1290            a symmetric matrix that results in a non-symmetric one.
1291            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1292    
1293            * R/dMatrix.R: make round(M) work as round(M, 0)
1294    
1295            * R/dgTMatrix.R (image): coordinate system and axis now use
1296            1-based indices, not 0-based ones.
1297    
1298            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1299            * tests/indexing.R: test it.
1300    
1301            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1302            * man/isSymmetric-methods.Rd: and document it.
1303    
1304            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1305            * man/SparseM-conv.Rd: docu them
1306    
1307            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1308                    for 'SparseM' conversions
1309    
1310    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1311    
1312            * R/Matrix.R (head): added head() and tail() methods.
1313    
1314    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1315    
1316            * DESCRIPTION (Version): 0.995-12 released to CRAN
1317    
1318    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1319    
1320            * tests/simple.R: add check for correct dsT -> dgT coercion;
1321                    add check for correct printing of symmetric sparse matrices.
1322    
1323            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1324            for sparse symmetric matrices.
1325    
1326            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1327            diagonal twice.
1328    
1329    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1330    
1331            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1332            being applied to the x slot (detected by Brian Ripley).
1333    
1334    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1335    
1336            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1337    
1338            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1339    
1340    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1341    
1342            * src/lgCMatrix.c (lgCMatrix_diag): new function
1343            * R/lgCMatrix.R (diag): for new method
1344    
1345            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1346                 ==> construction of illegal "*gTMatrix" via new() should
1347                 now be much less easy:
1348            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1349    
1350            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1351                    directly.
1352            * man/Matrix.Rd: documents it.
1353    
1354    2006-07-06  Douglas Bates  <bates@R-project.org>
1355    
1356            * src/pedigree.c (pedigree_inbreeding): Correction in
1357            initialization.  This function is not currently being used and is
1358            not fully tested.
1359    
1360            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1361            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1362            objects.  Modified validity check on pedigree objects to account
1363            for nonparallel patterns of missingness of parents.
1364    
1365            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1366            class.
1367    
1368    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1369    
1370            * R/pMatrix.R: coercion pMatrix -> Tsparse
1371    
1372    2006-06-12  Douglas Bates  <bates@R-project.org>
1373    
1374            * DESCRIPTION (Version): 0.995-11 released to CRAN
1375    
1376            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1377            the output from mcmcsamp.
1378    
1379    2006-06-10  Douglas Bates  <bates@R-project.org>
1380    
1381            * R/lmer.R (simulestimate): added C code for calculating the trace
1382            of the hat matrix.
1383    
1384    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1385    
1386            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1387            classes.
1388            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1389    
1390    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1391    
1392            * R/dgTMatrix.R (colSums): etc. All four of
1393            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1394            all "Matrices".
1395    
1396    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1397    
1398            * R/lmer.R (panel.ci): Add a reference line at zero and a
1399            background grid to the qqmath plot of ranef.lmer.
1400    
1401    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1402    
1403            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1404            grouping factors to be specified in the formula as (1|foo/bar).
1405    
1406    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1407    
1408            * R/lmer.R (findbars and others): Change check of is.numeric to
1409            !is.language to resolve the bug reported by Jacob Wegelin.
1410    
1411            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1412            code to evaluate inbreeding coefficients without calculating T,
1413            based on code in Sargolzaei and Iwaisaki's paper.
1414    
1415    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1416    
1417            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1418            generic and mer methods for isNested and denomDF. This denomDF was
1419            an attempt to emulate that in lme but I don't think that makes
1420            sense.  Use the trace of the hat matrix instead.
1421    
1422    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1423    
1424            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1425            the C code depending on a slot structure that's no longer valid.
1426            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1427    
1428    
1429    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1430    
1431            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1432            of lowerTriMatrix generic and methods to tril (also upper to triu)
1433            and added a general band extractor.
1434    
1435    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1436    
1437            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1438            allowable range with NAs. Added a corresponding check in the
1439            validity check for the pedigree class.
1440    
1441            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1442            crossprod methods now inherits from symmetricMatrix.
1443    
1444    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1445    
1446            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1447            generics lowerTriMatrix and upperTriMatrix along with methods for
1448            the Csparse virtual class.  Also added a C function Csparse_band
1449            that implements these methods by calling cholmod_band.
1450    
1451    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1452    
1453            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1454            erased when it was NULL.  This led to invalid subselections!
1455    
1456    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1457    
1458            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1459            in method for "t" so as not to lose the unit diagonal property.
1460    
1461    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1462    
1463            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1464            and methods.  This is now an option to the ranef method for the
1465            mer class.
1466    
1467            * src/cs_utils.c: Ensure that the nz component is -1 for a
1468            compressed column-oriented matrix.  Minor formatting cleanup.
1469    
1470            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1471            objects.
1472    
1473    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1474    
1475            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1476            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1477    
1478    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1479    
1480            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1481            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1482    
1483            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1484            for the dtCMatrix class.
1485    
1486    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1487    
1488            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1489            and methods for it.
1490    
1491    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1492    
1493            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1494            arguments, such that M %*% 1:6 now works
1495            * Tests/matprod.R: test the above
1496    
1497    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1498    
1499            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1500            the ranef.lmer class.
1501    
1502            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1503            methods to extract the posterior variances from the bVar slot.
1504    
1505    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1506    
1507            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1508            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1509    
1510            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1511            * tests/simple: (extended)
1512    
1513            * R/sparseMatrix.R (isTriangular): now using much improved
1514            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1515    
1516    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1517    
1518            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1519            (problem report from Franklin Parlamis).  This should be done
1520            generally.
1521    
1522    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1523    
1524            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1525            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1526            update the plot methods.
1527    
1528    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1529    
1530            * R/lmer.R (resid and ranef methods):  Added methods for the
1531            "residuals" and "resid" generic but only for linear mixed model
1532            fits.  Changed the ranef method to return a list of data frames so
1533            that the plot methods now work.
1534    
1535    2006-03-16  Douglas Bates  <bates@bates2>
1536    
1537            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1538            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1539    
1540            * DESCRIPTION (Date): New release
1541    
1542    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1543    
1544            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1545    
1546            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1547            * man/KNex.Rd: and other help files
1548            * tests/*.R: several ones needed adaption
1549            * inst/doc/Comparisons.Rnw: ditto
1550    
1551    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1552    
1553            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1554    
1555            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1556    
1557    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1558    
1559            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1560    
1561            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1562    
1563    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1564    
1565            * R/dMatrix.R: enable things like  M [ M < 10 ]
1566            * R/dgeMatrix.R: implement it
1567    
1568    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1569    
1570            * R/AllClass.R: define "summary.mer" and "*.lmer"
1571            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1572            * R/lmer.R (show): now works with summary()
1573    
1574    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1575    
1576            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1577            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1578                    support the above
1579    
1580    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1581    
1582            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1583            Use glmFit$prior.weights for weights in a glmm.
1584            Allow an option usePQL = FALSE to skip the PQL steps for the
1585            Laplace method (and, in time, the AGQ method).
1586    
1587            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1588            into a separate function internal_mer_Xfactor to be able to call
1589            it from internal_bhat.
1590    
1591    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1592    
1593            * tests/Class+Meth.R (tstMatrixClass): function for much better
1594            testing; now again of all actual classes.
1595    
1596            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1597                    use macros and define make_d_matrix_* and make_i_matrix_*
1598                    where _i_ is for the ldense routines:
1599    
1600            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1601            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1602    
1603            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1604    
1605    
1606    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1607    
1608            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1609                    many different kinds of matrices.
1610            * R/*.R: quite a few new methods were needed for R CMD check with
1611                    new Matrix().  Very good for users playing around.
1612    
1613    
1614    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1615    
1616            * src/dgeMatrix.c (dMatrix_validate): new
1617            * src/Mutils.c (dense_nonpacked_validate): new
1618    
1619            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1620    
1621    
1622    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1623    
1624            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1625    
1626    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1627    
1628            * DESCRIPTION (Version): 0.99-6 released to CRAN
1629    
1630            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1631            segfault in cases with multiple non-nested grouping factors.
1632    
1633    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1634    
1635            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1636                    (Depends): also on 'utils'
1637    
1638            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1639            * R/diagMatrix.R (Diagonal): constructor and methods for
1640            diagonal matrices
1641    
1642            * R/ltTMatrix.R: new "minimal methods"
1643    
1644    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1645    
1646            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1647            all methods (and help files).
1648    
1649    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1650    
1651            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1652                    for case (dimn.  op  no_dimn.)
1653    
1654    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1655    
1656            * DESCRIPTION (Version): 0.99-2  released to CRAN
1657    
1658    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1659    
1660            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1661            by Julian Faraway.
1662    
1663    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1664    
1665            * R/Auxiliaries.R (try_as): new utility
1666            * R/sparseMatrix.R: use try_as() in coercion to original class
1667    
1668    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1669    
1670            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1671    
1672    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1673    
1674            * R/Auxiliaries.R (dimNamesCheck): added
1675    
1676            * R/Matrix.R (as.array), (as.vector): new
1677    
1678    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1679    
1680            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1681                    default.
1682            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1683                    "pMatrix" now contains "sparseMatrix"
1684    
1685    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1686    
1687            * tests/Class+Meth.R: new tests; t(t(m)) == m
1688    
1689            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1690    
1691            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1692            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1693    
1694            * R/dspMatrix.R: typo in "t" method
1695    
1696    2005-09-18  Douglas Bates  <bates@wisc.edu>
1697    
1698            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1699            * R/Tsparse.R: instead of R/gTMatrix.R
1700            * R/Csparse.R: new
1701            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1702            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1703            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1704                            via cholmod
1705    
1706    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1707    
1708            * R/Auxiliaries.R (non0ind): new function using new C code
1709            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1710    
1711    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1712    
1713            * src/chm_common.h: header file required by all C sources that
1714            call CHOLMOD functions.  It defines a cholmod_common structure
1715            called 'c' whose address is passed as the last argument to
1716            (virtually) every CHOLMOD function.
1717    
1718            * src/Pattern.c: Simple example of the use of CHOLMOD.
1719    
1720            * src/init.c: initialize and finalize the cholmod_common structure.
1721    
1722            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1723            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1724    
1725    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1726    
1727            * inst/test-tools.R: new file collecting the utility functions used
1728                    in ./tests/*.R
1729    
1730            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1731            * R/Matrix.R (cbind2): methods for NULL and missing
1732    
1733    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1734    
1735            * R/AllClass.R: new "index" class for "[" and "[<-":
1736                    First cut at "symmetricMatrix" and "triangularMatrix"
1737            * R/gTMatrix.R (.ind.prep): new function;
1738                    Logical and character indexing now work too.
1739            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1740            * tests/indexing.R: new, including *.Rout.save
1741            * tests/dgTMatrix.R: new
1742    
1743    2005-08-29  Douglas Bates  <bates@wisc.edu>
1744    
1745            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1746            indicator pos not being updated.  Also enforced upper triangular
1747            for symmetric case.  Need to coerce edges component of elements of
1748            edge list - grr! (Why don't they define their classes cleanly?)
1749    
1750    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1751    
1752            * R/Matrix.R:  added first "[<-" methods; not yet functional
1753            * R/denseMatrix.R: ditto
1754            * man/Subassign-methods.Rd: new help file for these
1755    
1756    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1757    
1758            * DESCRIPTION (Version): 0.98-6
1759    
1760            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1761            matrices.
1762    
1763    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1764    
1765            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1766                    as( <logical>, "matrix")
1767    
1768            * R/pMatrix.R: coercion to "lgTMatrix"
1769    
1770            * R/gTMatrix.R: new virtual class to define "[" methods for.
1771            * man/gTMatrix-class.Rd:
1772            * General slight re-organization of where "[" methods are defined.
1773              more to come.
1774    
1775    2005-08-18  Douglas Bates  <bates@wisc.edu>
1776    
1777            * DESCRIPTION (Version): 0.98-5  released to CRAN
1778    
1779            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1780            * .....
1781    
1782    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1783    
1784            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1785            or glmer objects.
1786    
1787    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1788    
1789            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1790    
1791    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1792    
1793            * R/HBMM.R: finish re-writing R-only code.
1794    
1795    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1796    
1797            * man/externalFormats.Rd: move documentation for writeHB and
1798            writeMM here.
1799    
1800            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1801            (suggested by Paul Roecker).
1802    
1803            * tests/validObj.R (assertError): Comment out test that is failing
1804            after recent changes in r-devel.
1805    
1806    
1807    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1808    
1809            * R/AllClass.R: intermediate virtual class "denseMatrix"
1810            * man/denseMatrix-class.Rd
1811            * NAMESPACE: export it, and also export
1812            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1813    
1814    2005-08-10  Douglas Bates  <bates@wisc.edu>
1815    
1816            * DESCRIPTION (Version): 0.98-3 to CRAN
1817    
1818            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1819            matrix_solve code (which was really, really wrong).
1820    
1821    2005-08-07  Douglas Bates  <bates@wisc.edu>
1822    
1823            * DESCRIPTION (Version): 0.98-2
1824    
1825            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1826    
1827            * R/lmer.R (abbrvNms): new
1828            * R/lmer.R (mcmcsamp): allow transformed parameters
1829            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1830            for the Harwell-Boeing and the MatrixMarket formats.
1831    
1832    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1833    
1834            * man/dtrMatrix-class.Rd: add examples
1835            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1836    
1837            * TODO: note the dtpMatrix (docu) bug
1838    
1839            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1840            in order to ensure that new as.matrix() is used by old functions,
1841            e.g., svd(), qr(), eigen(), dist(),..;
1842                  apply(), also matplot() or pairs().
1843    
1844    
1845    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1846    
1847            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1848              add comments about 'control' / lmerControl() arguments
1849    
1850    2005-07-27  Douglas Bates  <bates@wisc.edu>
1851    
1852            * man/sleepstudy.Rd: Added the sleep data set.
1853            * DESCRIPTION (Version): 0.98-1  released to CRAN
1854    
1855    2005-07-12  Douglas Bates  <bates@wisc.edu>
1856            * man/sleepstudy.Rd: Added the sleep data set.
1857    
1858            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1859            .Call calls that were producing spurious output.
1860    
1861    2005-07-05  Douglas Bates  <bates@wisc.edu>
1862    
1863            * R/lmer.R (lmer): stored updated variance component estimates in
1864            mer object for the generalized model.  (Bug reported by Renaud
1865            Lancelot).
1866    
1867    2005-07-03  Douglas Bates  <bates@wisc.edu>
1868    
1869            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1870            unidimensional case.
1871    
1872    2005-06-08  Douglas Bates  <bates@wisc.edu>
1873    
1874            * DESCRIPTION (Version): 0.96-1
1875    
1876            * moved  lmer-class' R and C code moved from lme4 to here
1877    
1878    2005-06-04  Douglas Bates  <bates@wisc.edu>
1879    
1880            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1881            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1882    
1883    2005-06-02  Douglas Bates  <bates@wisc.edu>
1884    
1885            * src/Makefile.win: Forgot to update this when Makefile changed.
1886    
1887    2005-05-11  Douglas Bates  <bates@wisc.edu>
1888    
1889          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1890          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
1891    
1892  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
1893    
1894          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1895          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 1898 
1898          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1899          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
1900    
1901  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
1902    
1903          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1904          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
1905    
1906  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
1907    
1908          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
1909          multiplication operation.          multiplication operation.
# Line 30  Line 1916 
1916    
1917          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
1918    
1919  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
1920    
1921          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1922    
1923          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
1924    
1925    
1926  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
1927    
1928          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
1929    
# Line 46  Line 1932 
1932          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1933          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1934    
1935  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1936    
1937          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1938    
# Line 72  Line 1958 
1958          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
1959            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
1960    
1961  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
1962    
1963          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
1964          * ....          * ....
1965    
1966  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
1967    
1968          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1969    
# Line 92  Line 1978 
1978            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1979          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1980    
1981  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1982    
1983          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1984    
1985  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1986    
1987          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1988    
1989  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1990    
1991          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1992          the package.          the package.
# Line 148  Line 2034 
2034    
2035          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
2036    
2037  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
2038    
2039          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
2040          for the geMatrix class.          for the geMatrix class.
2041    
2042  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
2043    
2044          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
2045    
2046          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2047    
2048  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
2049    
2050          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
2051          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
2052    
2053  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
2054    
2055          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2056    
2057  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
2058    
2059          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2060          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
2061    
2062  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
2063    
2064          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
2065    
2066          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2067          for tripletMatrix to matrix.          for tripletMatrix to matrix.
2068    
2069  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
2070    
2071          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2072          no longer used.          no longer used.
# Line 192  Line 2078 
2078          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
2079          Fixes part but not all of #15.          Fixes part but not all of #15.
2080    
2081  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
2082    
2083          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2084          scalar grouping factors corrected.          scalar grouping factors corrected.
2085    
2086  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
2087    
2088          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
2089    
2090  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
2091    
2092          * 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
2093          .h file can be included.          .h file can be included.
2094    
2095  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
2096    
2097          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2098          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
2099    
2100          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
2101    
2102  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
2103    
2104          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
2105    
2106  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
2107    
2108          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
2109    
2110  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
2111    
2112          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2113    
2114  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
2115    
2116          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2117    
2118  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
2119    
2120          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
2121          routines.          routines.
2122    
2123  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
2124    
2125          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2126    
2127  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
2128    
2129          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2130    

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