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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1844, Wed May 16 20:40:34 2007 UTC
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1    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
4    
5    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * DESCRIPTION (Version): 0.99875-1
8            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
9    
10    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
13            indexing
14            * tests/indexing.R: test set for that.
15    
16    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
19            entries.
20            * tests/indexing.R(out): add regression test for it
21    
22    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
25            name for "!" method definitions.
26    
27    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Tsparse.R (intI): new utility, used for "[" :
30                    Cleanup up there, and fixes for duplicated indices - more TODO!
31    
32            * tests/indexing.R(out): more tests
33    
34    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
35    
36            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
37            code that is now part of the R Lapack library.
38    
39            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
40            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
41    
42    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
45    
46    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
49            up with extraneous names '0'...'<n-1>'
50    
51    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/dgTMatrix.R (mat2dgT): care about NAs
54    
55    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/kronecker.R: triangularity preserving methods
58    
59    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/kronecker.R: new file collecting kronecker() methods in one
62                    place.  Goal: become much faster!
63    
64    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
67            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
68            can be much faster.
69    
70            * tests/matprod.R: add regression tests for these (upper & lower).
71    
72    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/Matrix.R (diff): method for our Matrices.
75    
76            * R/sparseMatrix.R (isDiagonal): check dim()!
77    
78    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/Matrix.R (dim<-): new method for "reshape()" built on a
81            proposal from Tamas Papp.
82    
83    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
86    
87            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
88            rather define and export  cBind() and rBind() only.
89            --> useRs *must* change code that used to have cbind()/rbind() !!
90    
91            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
92            * R/bind.Rout.save: ditto
93    
94    2007-02-16  Douglas Bates  <bates@r-project.org>
95    
96            * DESCRIPTION (Date, Version): 0.9975-11 with new date
97            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
98            const modifier on declaration of the array 'valid'
99    
100    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
101    
102            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
103    
104    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
107    
108            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
109            * tests/simple.R: test the above and some of these coercions:
110    
111            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
112                    be careful to avoid infinite recursion, using new coercions in
113            * R/ngCMatrix.R and nsC... and ntC...
114            * R/lsparseMatrix.R: ditto
115    
116            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
117    
118            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
119            * R/Rsparse.R: reactivate .Call()s
120    
121            * tests/Class+Meth.R: a bit more on actual classes
122    
123    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
124    
125            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
126    
127    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * DESCRIPTION (Version): 0.9975-10 to upload
130    
131            * tests/Class+Meth.R (tstMatrixClass): require coercions to
132            specific classes less unconditionally.
133    
134            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
135    
136            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
137    
138            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
139            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
140            R_to_CMatrix segfaults on one platform.
141            Eliminate most coercion method to *specific* classes, and replace
142            with virtual classes coercions.
143    
144    
145    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
146    
147            * src/init.c: export the CHM...._validate() placeholders, since
148            they *are* called.
149    
150            * tests/Class+Meth.R (classCanCoerce): and starting to test
151            all as(<from>, <to>)
152    
153    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
156            * tests/indexing.R: tested now
157            * tests/indexing.Rout.save: updated
158    
159            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
160            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
161            appropriate.
162    
163            * NAMESPACE: export a trivial
164            * R/Matrix.R: drop() Matrix-method
165    
166            * R/AllClass.R: moved all prototypes to virtual super classes.
167    
168            * R/Rsparse.R: many more coercions to have less exceptions in
169            * tests/Class+Meth.R:
170    
171            * R/Ops.R (Compare): tweak for case with NA
172            * tests/simpl.R: hence another 'FIXME' eliminated
173    
174    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
177            objects.
178    
179            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
180              and more of "!", "&", "|", all, any; coercions
181    
182            * R/Rsparse.R: many coercions (which enable quite a few other
183            methods), thanks to enhancements in
184            * src/dgCMatrix.c (R_to_CMatrix): new, and
185            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
186            symmetric & triangular and ..RMatrix objects.
187    
188            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
189            renamed file from src/dsTMatrix.c;
190            now dealing with symmetric and triangular Tsparse coercions, both
191            to dense and general.
192    
193    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
196    
197            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
198            where sensible when the <numeric> is of length > 1.
199    
200    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Matrix.R ([<-): for M[] <- value: fix length
203    
204    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
207            * R/ndenseMatrix.R: new coercions n* -> l*
208    
209    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
212    
213            * R/Ops.R ("Logic"): and other "Ops", many updates
214    
215    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * src/Mutils.h (SET_DimNames): new utility
218    
219            * R/Auxiliaries.R (nnzero): improved and now exported via
220    
221            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
222    
223    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/diagMatrix.R (!): fix typo.
226    
227    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/Auxiliaries.R (as_Csparse): and quite a few others:
230                    allow to pass class definition --> speedup
231            * R/sparseMatrix.R: apply the above
232    
233            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
234    
235            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
236            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
237            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
238    
239            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
240    
241            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
242            and use it for "sparse*" as well, since it's faster than the
243            as_Csparse(.) way.
244    
245    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
248    
249    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
252            as method for   M[ ij ] <- v
253            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
254    
255            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
256            FALSE answer
257    
258            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
259            * tests/indexing.R: test it, and some of the above
260    
261    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/Auxiliaries.R (is_duplicatedT): new utility
264    
265    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
266    
267            * src/init.c (R_init_Matrix): export cholmod_scale
268    
269    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
272            base::as.matrix to (x, ...)
273    
274    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
277            file; start using "Logic", hence
278    
279            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
280            * NAMESPACE: import and export "Logic"
281    
282    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
285            only needed previously to R version 2.5.0.
286    
287    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
290    
291            * R/Tsparse.R (replTmat): fix subassignment of triangular
292            * R/Csparse.R (replCmat): ditto
293            * tests/indexing.R: more tests, incl the above fix
294    
295    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/Auxiliaries.R (drop0): extend for non CSparse
298            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
299    
300            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
301                    use uplo correctly (!); other places: use uplo_P() macro
302    
303            * R/Csparse.R (replCmat): call diagU2N() when needed
304            * R/Tsparse.R (replTmat): ditto
305    
306            * src/dtCMatrix.c (tCMatrix_validate): new
307            * src/dtTMatrix.c (tTMatrix_validate): new, used in
308            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
309    
310            * R/diagMatrix.R (replDiag): to use in [<-
311    
312    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
315                    also more general diagU2N().
316    
317    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
320            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
321    
322    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * tests/bind.R: a few more cases
325            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
326    
327            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
328            * R/ddenseMatrix.R (cbind2/rbind2)
329            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
330            * tests/indexing.R
331            * tests/indexing.Rout.save: updated
332    
333    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
336            * tests/indexing.R
337    
338    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
341            align with proper position of "0", i.e., right for integers.
342            argument 'align' by default is "fancy".
343    
344    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
347            * R/Csparse.R: and fix "Compare" for more cases.
348            * tests/Class+Meth.R: test some of these (m == m, m != m)
349    
350    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/lsparseMatrix.R: all() and any() methods
353            * R/ldenseMatrix.R:      ditto
354            * NAMESPACE, R/Matrix.R: ditto
355    
356            * man/all-methods.Rd: document them minimally
357    
358            * tests/simple.R: add a few examples for these
359    
360    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * R/Tsparse.R ([): fix long standing typo in symmetric case
363            * man/dsCMatrix-class.Rd: add example exhibiting the above case
364    
365    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
366    
367            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
368            to LL before converting to a sparse matrix. (The LDL form can be
369            converted to a sparse matrix but it is implicitly a unit
370            triangular matrix and a diagonal matrix overwritten on the diagonal.)
371    
372    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
373    
374            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
375    
376    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
377    
378            * DESCRIPTION (Version): updated -> release 0.9975-7
379            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
380    
381    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
384    
385    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
386    
387            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
388            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
389            is exactly singular.
390    
391    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * DESCRIPTION (Date): updated -> release 0.9975-6
394    
395    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
398            now returns symmetric.
399    
400            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
401    
402            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
403            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
404    
405            * R/Auxiliaries.R (.type.kind): added
406    
407    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
410            running src/CSparse_install.sh
411    
412            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
413    
414    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
417            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
418    
419            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
420    
421            * tests/Class+Meth.R (tstMatrixClass): now assure
422            the (important in method programming) property :
423    
424                    ###>>  Every "Matrix" is either
425                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
426    
427                    (where "*" stands for "Matrix")
428    
429            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
430    
431            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
432            * tests/validObj.R: checks for "comparison"
433    
434            * R/sparseMatrix.R ([): improved indexing for sparse;
435                    trying to keep <symmetric>[ n, n] symmmetric
436    
437            * tests/indexing.R: indexing for logical sparse now ok
438    
439    
440    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * src/Tsparse.c: use xTsparse_validate() , and hence remove
443    
444            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
445    
446    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
449    
450            * tests/simple.R: validObject() checking the above.
451    
452            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
453            replacing both dgCMatrix_validate and lgCM*.
454    
455            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
456            fix dimnames setting in other places.
457            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
458    
459    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
462    
463            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
464            symmetry test, via
465            * R/Auxiliaries.R (.as.dgC.0.factors):
466    
467    2006-11-01  Douglas Bates  <bates@r-project.org>
468    
469            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
470            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
471            <CsparseMatrix>) added
472    
473    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
474    
475            * tests/matprod.R: add a variation of Harri's example
476    
477            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
478            recursive infinitely.
479    
480            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
481    
482            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
483    
484    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
487            matrix if possible; test m+m == 2*m; now test dgRMatrix.
488            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
489            satisfy the above test.
490    
491    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
494    
495            * R/dgCMatrix.R: solve(a, b="missing") based on
496            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
497            RHS = NULL.
498    
499            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
500            add more (needed) [t]crossprod() methods.
501    
502            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
503    
504            * R/Auxiliaries.R (as_CspClass): cleanup
505            (drop0): internal utility for "Csparse_drop(*, 0)"
506            (.bail.out.2): encourage active feedback
507    
508    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * R/dMatrix.R(Compare): new(), then slots [no validity check]
511    
512            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
513            non-valid or 'sorted' case).
514    
515            * R/dsparseMatrix.R: add "chol" method.
516            * R/ddenseMatrix.R: ditto
517    
518            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
519            * NAMESPACE (Ops)
520            * R/diagMatrix.R (diag2T): simple utility used "higher level"
521            coercion; deprecating direct lower level coercions.
522    
523            * R/*.R (seq): use seq_len() and seq_along() where possible.
524    
525    
526    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * DESCRIPTION (Version): 0.9975-5 ready for release
529    
530    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
531    
532            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
533    
534    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
535    
536            * R/AllClass.R (corMatrix): add 'validity' check;
537                    comment out unused "LDL" class definition
538            * NAMESPACE: mention, but do not export "LDL" class
539            * R/corMatrix.R: new (simple), needed for R-devel with
540            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
541              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
542    
543    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
544    
545            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
546            use Rprintf and R's error handling.
547    
548    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
551            * tests/matprod.R: add tests for the bug fixed.
552    
553    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
554    
555            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
556            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
557    
558    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
559    
560            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
561    
562    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * DESCRIPTION (Version): 0.9975-3
565    
566            * R/diagMatrix.R (bdiag): new function constructing block diagonal
567            (sparse) matrices.
568            * man/bdiag.Rd: docu + examples
569    
570            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
571    
572            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
573            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
574    
575            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
576            that result is sparse or diagonal (and not dense).
577    
578            * man/Subassign-methods.Rd: fix examples
579    
580            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
581            should always return a sparse (and not sometimes a diagonal) matrix.
582    
583    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
586    
587    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
588    
589            * DESCRIPTION (Version): 0.9975-2
590    
591            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
592    
593    2006-10-02  Douglas Bates  <bates@R-project.org>
594    
595            * tests/dg_Matrix.R: Simplify test taking into account new code.
596    
597    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
600    
601            * R/lsTMatrix.R: new files w/ missing methods
602            * R/nsTMatrix.R:  "  'for completeness'
603    
604            * tests/Class+Meth.R: a bit less 'not.ok.classes'
605    
606            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
607    
608    
609    2006-09-28  Douglas Bates  <bates@R-project.org>
610    
611            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
612            included.
613    
614            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
615            Export C-callable functions used in Zt_create in lme4.
616    
617    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * DESCRIPTION (Version): 0.9975-1
620    
621            * tests/simple.R: less checks fail; using NA, found that our
622                    kronecker() is not base-compatible with NA's.
623    
624            * R/dMatrix.R: "Compare" method now implemented for all cases
625    
626            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
627    
628            * man/dtpMatrix-class.Rd: mention length of 'x' slot
629    
630            * src/dtpMatrix.c (dtpMatrix_validate): fix check
631            * src/dspMatrix.c (dspMatrix_validate): ditto
632    
633            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
634              including coercion to [nl]tTMatrix.
635    
636            * R/diagMatrix.R (show): print a header line as for other classes.
637    
638    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * src/Makefile.win (SUBDIRS): fix typo
641    
642    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
643    
644            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
645    
646    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
647    
648            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
649            symmetric and y missing in R code using %*% (cholmod_aat doesn't
650            accept a symmetric matrix).
651            * tests/group-methods.R: Uncomment test of crossprod applied to
652            lsCMatrix objects.
653    
654    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
655    
656            * R/AllClass.R (symmetricMatrix): add validity method (available
657            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
658    
659            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
660    
661            * tests/indexing.Rout.save:
662            * tests/indexing.R: additions, mainly for 'lsparse'
663    
664            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
665            case.
666    
667            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
668    
669    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
670    
671            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
672                    as 'N' (1-letter - Ok?)
673    
674            * tests/group-methods.R: add test for logical + NAs
675    
676            * R/dMatrix.R ("Compare"): fix to work with NA's
677    
678            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
679    
680            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
681                    which is implemented.
682    
683    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * src/chm_common.c: coerce logical <-> double instead of
686            typecasting;  needed for "l" matrix handling in cholmod.
687    
688            * tests/other-pkgs.R (graph): small extension in "graph" checks.
689    
690            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
691            (Tsp2grNEL): other fixes needed
692    
693    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
696                    Matrices, since "lMatrix", also "lsparseM" can have NA
697            * R/ndenseMatrix.R, etc: new source files
698            * man/nsparseMatrix-classes.Rd, etc: new help files
699            * tests/: adaptions
700            * src/chm_common.c (chm_dense_to_SEXP): and others:
701                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
702            * src/Csparse.c, etc: ditto
703    
704    2006-09-11  Douglas Bates  <bates@R-project.org>
705    
706            * src/Mutils.[ch],init.c inst/include/*.h: Move the
707            alloc_d**Matrix functions to the lme4 package.
708    
709    2006-09-09  Douglas Bates  <bates@R-project.org>
710    
711            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
712            fixed
713    
714    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * R/lMatrix.R: new
717    
718            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
719    
720            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
721            * man/tcrossprod.Rd: ditto
722    
723    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
724    
725            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
726            for exported functions
727            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
728            Remove partitioning algorithms for sparse matrix reordering.  The
729            copyright on the Metis code was problematic and the methods were
730            rarely used.
731            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
732            operations are now done entirely in CHOLMOD code.
733    
734    2006-09-06  Douglas Bates  <bates@R-project.org>
735    
736            * src/Mutils.h: Remove functions that are no longer used.
737    
738    2006-09-04  Douglas Bates  <bates@R-project.org>
739    
740            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
741            * src/DEPS.mkf: update
742    
743    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
745            * created branches/Matrix-for-R-2.3.x;  on trunk: do
746            * DESCRIPTION (Version): 0.9975-0
747            (Depends): R (>= 2.4.0)
748    
749    2006-09-01  Douglas Bates  <bates@R-project.org>
750    
751            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
752    
753    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
756            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
757    
758            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
759    
760    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
763            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
764            * R/dsparseMatrix.R: ditto
765            * R/Csparse.R: ditto
766    
767    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
768    
769            * R/dMatrix.R (Compare): improve availability of "<", etc
770            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
771    
772    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
775            of a 0-index which was used as 1-index (..hmm)
776    
777            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
778    
779            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
780            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
781            (.is.diagonal): ditto
782    
783            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
784    
785            * R/Matrix.R (Matrix): also work for NA data
786    
787    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
788    
789            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
790            in all cases.
791    
792    2006-08-27  Douglas Bates  <bates@R-project.org>
793    
794            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
795            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
796    
797    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
800            subclasses of "ddenseMatrix"
801            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
802            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
803            instead of half dozen specialized ones.
804    
805    2006-08-25  Douglas Bates  <bates@R-project.org>
806    
807            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
808            <tillard@cirad.fr> - ordering standard errors to match effects.
809    
810    2006-08-24  Douglas Bates  <bates@R-project.org>
811    
812            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
813            on R_ldl.
814            * R/lCholCMatrix.R,
815            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
816            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
817            * many files in ./R and ./src: Use more general version of
818            dup_mMatrix_as_dgeMatrix to simplify method definitions.
819            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
820            dtpMatrix, dspMatrix and dppMatrix conversions.
821    
822    
823    2006-08-23  Douglas Bates  <bates@R-project.org>
824    
825            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
826            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
827            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
828            dgeMatrix_crossprod (may need to do this in other places).
829            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
830            generic and method for dsCMatrix.  Use CHOLMOD for chol().
831    
832    2006-08-22  Douglas Bates  <bates@R-project.org>
833    
834            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
835            types of classed Matrices, matrices or numeric or logical vectors.
836            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
837            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
838            to Mutils.h (as an inline) and change name to Matrix_check_class;
839            fixes in as_cholmod_factor and chm_factor_to_SEXP.
840            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
841            dsCMatrix_matrix_solve.  Comment out vestigial functions.
842            * src/Csparse.c: use diag_P and uplo_P macros.
843    
844    2006-08-21  Douglas Bates  <bates@R-project.org>
845    
846            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
847            valgrind.
848            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
849            inverses.
850            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
851            -Wall warnings.
852            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
853            Use dup_mMatrix_as_dgeMatrix.
854    
855    2006-08-20  Douglas Bates  <bates@R-project.org>
856    
857            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
858            * tests/sparseQR.R: Added
859            * man/sparseQR-class.Rd: Document methods for qr.* generics
860            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
861    
862    2006-08-19  Douglas Bates  <bates@R-project.org>
863    
864            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
865            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
866            and qr.fitted.
867            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
868            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
869    
870    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
871    
872            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
873            the base version has no "..." argument.
874    
875            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
876    
877            * R/Matrix.R: define and
878            * NAMESPACE: export as.numeric() and as.logical() methods.
879                    Let's hope these do not badly slow down something...
880            Finally export the zapsmall() method.
881    
882    2006-08-17  Douglas Bates  <bates@R-project.org>
883    
884            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
885            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
886            * src/dtCMatrix.c :Remove code that is no longer used
887            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
888    
889    2006-08-14  Douglas Bates  <bates@R-project.org>
890    
891            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
892            Csparse_to_logical and Csparse_symmetric_to_general.
893            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
894            coercion methods between CsparseMatrix and TsparseMatrix.
895    
896    2006-08-14  Douglas Bates  <bates@R-project.org>
897    
898            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
899            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
900            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
901            possible.
902    
903  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
904    
905          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,

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