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revision 1411, Tue Aug 22 01:01:23 2006 UTC revision 1827, Wed Apr 25 22:22:41 2007 UTC
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1    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
4            code that is now part of the R Lapack library.
5    
6            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
7            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
8    
9    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/dgTMatrix.R (mat2dgT): care about NAs
12    
13    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/kronecker.R: triangularity preserving methods
16    
17    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/kronecker.R: new file collecting kronecker() methods in one
20                    place.  Goal: become much faster!
21    
22    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
25            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
26            can be much faster.
27    
28            * tests/matprod.R: add regression tests for these (upper & lower).
29    
30    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/Matrix.R (diff): method for our Matrices.
33    
34            * R/sparseMatrix.R (isDiagonal): check dim()!
35    
36    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Matrix.R (dim<-): new method for "reshape()" built on a
39            proposal from Tamas Papp.
40    
41    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
44    
45            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
46            rather define and export  cBind() and rBind() only.
47            --> useRs *must* change code that used to have cbind()/rbind() !!
48    
49            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
50            * R/bind.Rout.save: ditto
51    
52    2007-02-16  Douglas Bates  <bates@r-project.org>
53    
54            * DESCRIPTION (Date, Version): 0.9975-11 with new date
55            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
56            const modifier on declaration of the array 'valid'
57    
58    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
59    
60            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
61    
62    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
65    
66            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
67            * tests/simple.R: test the above and some of these coercions:
68    
69            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
70                    be careful to avoid infinite recursion, using new coercions in
71            * R/ngCMatrix.R and nsC... and ntC...
72            * R/lsparseMatrix.R: ditto
73    
74            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
75    
76            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
77            * R/Rsparse.R: reactivate .Call()s
78    
79            * tests/Class+Meth.R: a bit more on actual classes
80    
81    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
84    
85    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * DESCRIPTION (Version): 0.9975-10 to upload
88    
89            * tests/Class+Meth.R (tstMatrixClass): require coercions to
90            specific classes less unconditionally.
91    
92            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
93    
94            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
95    
96            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
97            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
98            R_to_CMatrix segfaults on one platform.
99            Eliminate most coercion method to *specific* classes, and replace
100            with virtual classes coercions.
101    
102    
103    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
104    
105            * src/init.c: export the CHM...._validate() placeholders, since
106            they *are* called.
107    
108            * tests/Class+Meth.R (classCanCoerce): and starting to test
109            all as(<from>, <to>)
110    
111    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
114            * tests/indexing.R: tested now
115            * tests/indexing.Rout.save: updated
116    
117            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
118            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
119            appropriate.
120    
121            * NAMESPACE: export a trivial
122            * R/Matrix.R: drop() Matrix-method
123    
124            * R/AllClass.R: moved all prototypes to virtual super classes.
125    
126            * R/Rsparse.R: many more coercions to have less exceptions in
127            * tests/Class+Meth.R:
128    
129            * R/Ops.R (Compare): tweak for case with NA
130            * tests/simpl.R: hence another 'FIXME' eliminated
131    
132    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
135            objects.
136    
137            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
138              and more of "!", "&", "|", all, any; coercions
139    
140            * R/Rsparse.R: many coercions (which enable quite a few other
141            methods), thanks to enhancements in
142            * src/dgCMatrix.c (R_to_CMatrix): new, and
143            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
144            symmetric & triangular and ..RMatrix objects.
145    
146            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
147            renamed file from src/dsTMatrix.c;
148            now dealing with symmetric and triangular Tsparse coercions, both
149            to dense and general.
150    
151    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
154    
155            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
156            where sensible when the <numeric> is of length > 1.
157    
158    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/Matrix.R ([<-): for M[] <- value: fix length
161    
162    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
165            * R/ndenseMatrix.R: new coercions n* -> l*
166    
167    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
170    
171            * R/Ops.R ("Logic"): and other "Ops", many updates
172    
173    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * src/Mutils.h (SET_DimNames): new utility
176    
177            * R/Auxiliaries.R (nnzero): improved and now exported via
178    
179            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
180    
181    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/diagMatrix.R (!): fix typo.
184    
185    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/Auxiliaries.R (as_Csparse): and quite a few others:
188                    allow to pass class definition --> speedup
189            * R/sparseMatrix.R: apply the above
190    
191            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
192    
193            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
194            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
195            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
196    
197            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
198    
199            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
200            and use it for "sparse*" as well, since it's faster than the
201            as_Csparse(.) way.
202    
203    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
206    
207    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
210            as method for   M[ ij ] <- v
211            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
212    
213            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
214            FALSE answer
215    
216            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
217            * tests/indexing.R: test it, and some of the above
218    
219    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/Auxiliaries.R (is_duplicatedT): new utility
222    
223    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
224    
225            * src/init.c (R_init_Matrix): export cholmod_scale
226    
227    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
230            base::as.matrix to (x, ...)
231    
232    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
235            file; start using "Logic", hence
236    
237            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
238            * NAMESPACE: import and export "Logic"
239    
240    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
243            only needed previously to R version 2.5.0.
244    
245    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
248    
249            * R/Tsparse.R (replTmat): fix subassignment of triangular
250            * R/Csparse.R (replCmat): ditto
251            * tests/indexing.R: more tests, incl the above fix
252    
253    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/Auxiliaries.R (drop0): extend for non CSparse
256            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
257    
258            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
259                    use uplo correctly (!); other places: use uplo_P() macro
260    
261            * R/Csparse.R (replCmat): call diagU2N() when needed
262            * R/Tsparse.R (replTmat): ditto
263    
264            * src/dtCMatrix.c (tCMatrix_validate): new
265            * src/dtTMatrix.c (tTMatrix_validate): new, used in
266            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
267    
268            * R/diagMatrix.R (replDiag): to use in [<-
269    
270    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
273                    also more general diagU2N().
274    
275    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
278            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
279    
280    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * tests/bind.R: a few more cases
283            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
284    
285            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
286            * R/ddenseMatrix.R (cbind2/rbind2)
287            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
288            * tests/indexing.R
289            * tests/indexing.Rout.save: updated
290    
291    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
294            * tests/indexing.R
295    
296    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
299            align with proper position of "0", i.e., right for integers.
300            argument 'align' by default is "fancy".
301    
302    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
305            * R/Csparse.R: and fix "Compare" for more cases.
306            * tests/Class+Meth.R: test some of these (m == m, m != m)
307    
308    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/lsparseMatrix.R: all() and any() methods
311            * R/ldenseMatrix.R:      ditto
312            * NAMESPACE, R/Matrix.R: ditto
313    
314            * man/all-methods.Rd: document them minimally
315    
316            * tests/simple.R: add a few examples for these
317    
318    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/Tsparse.R ([): fix long standing typo in symmetric case
321            * man/dsCMatrix-class.Rd: add example exhibiting the above case
322    
323    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
324    
325            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
326            to LL before converting to a sparse matrix. (The LDL form can be
327            converted to a sparse matrix but it is implicitly a unit
328            triangular matrix and a diagonal matrix overwritten on the diagonal.)
329    
330    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
331    
332            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
333    
334    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
335    
336            * DESCRIPTION (Version): updated -> release 0.9975-7
337            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
338    
339    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
342    
343    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
344    
345            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
346            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
347            is exactly singular.
348    
349    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * DESCRIPTION (Date): updated -> release 0.9975-6
352    
353    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
356            now returns symmetric.
357    
358            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
359    
360            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
361            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
362    
363            * R/Auxiliaries.R (.type.kind): added
364    
365    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
368            running src/CSparse_install.sh
369    
370            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
371    
372    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
375            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
376    
377            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
378    
379            * tests/Class+Meth.R (tstMatrixClass): now assure
380            the (important in method programming) property :
381    
382                    ###>>  Every "Matrix" is either
383                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
384    
385                    (where "*" stands for "Matrix")
386    
387            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
388    
389            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
390            * tests/validObj.R: checks for "comparison"
391    
392            * R/sparseMatrix.R ([): improved indexing for sparse;
393                    trying to keep <symmetric>[ n, n] symmmetric
394    
395            * tests/indexing.R: indexing for logical sparse now ok
396    
397    
398    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * src/Tsparse.c: use xTsparse_validate() , and hence remove
401    
402            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
403    
404    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
407    
408            * tests/simple.R: validObject() checking the above.
409    
410            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
411            replacing both dgCMatrix_validate and lgCM*.
412    
413            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
414            fix dimnames setting in other places.
415            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
416    
417    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
420    
421            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
422            symmetry test, via
423            * R/Auxiliaries.R (.as.dgC.0.factors):
424    
425    2006-11-01  Douglas Bates  <bates@r-project.org>
426    
427            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
428            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
429            <CsparseMatrix>) added
430    
431    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * tests/matprod.R: add a variation of Harri's example
434    
435            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
436            recursive infinitely.
437    
438            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
439    
440            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
441    
442    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
445            matrix if possible; test m+m == 2*m; now test dgRMatrix.
446            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
447            satisfy the above test.
448    
449    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
452    
453            * R/dgCMatrix.R: solve(a, b="missing") based on
454            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
455            RHS = NULL.
456    
457            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
458            add more (needed) [t]crossprod() methods.
459    
460            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
461    
462            * R/Auxiliaries.R (as_CspClass): cleanup
463            (drop0): internal utility for "Csparse_drop(*, 0)"
464            (.bail.out.2): encourage active feedback
465    
466    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/dMatrix.R(Compare): new(), then slots [no validity check]
469    
470            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
471            non-valid or 'sorted' case).
472    
473            * R/dsparseMatrix.R: add "chol" method.
474            * R/ddenseMatrix.R: ditto
475    
476            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
477            * NAMESPACE (Ops)
478            * R/diagMatrix.R (diag2T): simple utility used "higher level"
479            coercion; deprecating direct lower level coercions.
480    
481            * R/*.R (seq): use seq_len() and seq_along() where possible.
482    
483    
484    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * DESCRIPTION (Version): 0.9975-5 ready for release
487    
488    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
489    
490            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
491    
492    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/AllClass.R (corMatrix): add 'validity' check;
495                    comment out unused "LDL" class definition
496            * NAMESPACE: mention, but do not export "LDL" class
497            * R/corMatrix.R: new (simple), needed for R-devel with
498            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
499              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
500    
501    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
502    
503            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
504            use Rprintf and R's error handling.
505    
506    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
509            * tests/matprod.R: add tests for the bug fixed.
510    
511    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
512    
513            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
514            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
515    
516    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
517    
518            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
519    
520    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * DESCRIPTION (Version): 0.9975-3
523    
524            * R/diagMatrix.R (bdiag): new function constructing block diagonal
525            (sparse) matrices.
526            * man/bdiag.Rd: docu + examples
527    
528            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
529    
530            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
531            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
532    
533            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
534            that result is sparse or diagonal (and not dense).
535    
536            * man/Subassign-methods.Rd: fix examples
537    
538            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
539            should always return a sparse (and not sometimes a diagonal) matrix.
540    
541    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
544    
545    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
546    
547            * DESCRIPTION (Version): 0.9975-2
548    
549            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
550    
551    2006-10-02  Douglas Bates  <bates@R-project.org>
552    
553            * tests/dg_Matrix.R: Simplify test taking into account new code.
554    
555    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
558    
559            * R/lsTMatrix.R: new files w/ missing methods
560            * R/nsTMatrix.R:  "  'for completeness'
561    
562            * tests/Class+Meth.R: a bit less 'not.ok.classes'
563    
564            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
565    
566    
567    2006-09-28  Douglas Bates  <bates@R-project.org>
568    
569            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
570            included.
571    
572            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
573            Export C-callable functions used in Zt_create in lme4.
574    
575    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * DESCRIPTION (Version): 0.9975-1
578    
579            * tests/simple.R: less checks fail; using NA, found that our
580                    kronecker() is not base-compatible with NA's.
581    
582            * R/dMatrix.R: "Compare" method now implemented for all cases
583    
584            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
585    
586            * man/dtpMatrix-class.Rd: mention length of 'x' slot
587    
588            * src/dtpMatrix.c (dtpMatrix_validate): fix check
589            * src/dspMatrix.c (dspMatrix_validate): ditto
590    
591            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
592              including coercion to [nl]tTMatrix.
593    
594            * R/diagMatrix.R (show): print a header line as for other classes.
595    
596    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * src/Makefile.win (SUBDIRS): fix typo
599    
600    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
603    
604    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
605    
606            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
607            symmetric and y missing in R code using %*% (cholmod_aat doesn't
608            accept a symmetric matrix).
609            * tests/group-methods.R: Uncomment test of crossprod applied to
610            lsCMatrix objects.
611    
612    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * R/AllClass.R (symmetricMatrix): add validity method (available
615            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
616    
617            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
618    
619            * tests/indexing.Rout.save:
620            * tests/indexing.R: additions, mainly for 'lsparse'
621    
622            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
623            case.
624    
625            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
626    
627    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
630                    as 'N' (1-letter - Ok?)
631    
632            * tests/group-methods.R: add test for logical + NAs
633    
634            * R/dMatrix.R ("Compare"): fix to work with NA's
635    
636            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
637    
638            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
639                    which is implemented.
640    
641    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * src/chm_common.c: coerce logical <-> double instead of
644            typecasting;  needed for "l" matrix handling in cholmod.
645    
646            * tests/other-pkgs.R (graph): small extension in "graph" checks.
647    
648            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
649            (Tsp2grNEL): other fixes needed
650    
651    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
654                    Matrices, since "lMatrix", also "lsparseM" can have NA
655            * R/ndenseMatrix.R, etc: new source files
656            * man/nsparseMatrix-classes.Rd, etc: new help files
657            * tests/: adaptions
658            * src/chm_common.c (chm_dense_to_SEXP): and others:
659                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
660            * src/Csparse.c, etc: ditto
661    
662    2006-09-11  Douglas Bates  <bates@R-project.org>
663    
664            * src/Mutils.[ch],init.c inst/include/*.h: Move the
665            alloc_d**Matrix functions to the lme4 package.
666    
667    2006-09-09  Douglas Bates  <bates@R-project.org>
668    
669            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
670            fixed
671    
672    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/lMatrix.R: new
675    
676            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
677    
678            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
679            * man/tcrossprod.Rd: ditto
680    
681    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
682    
683            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
684            for exported functions
685            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
686            Remove partitioning algorithms for sparse matrix reordering.  The
687            copyright on the Metis code was problematic and the methods were
688            rarely used.
689            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
690            operations are now done entirely in CHOLMOD code.
691    
692    2006-09-06  Douglas Bates  <bates@R-project.org>
693    
694            * src/Mutils.h: Remove functions that are no longer used.
695    
696    2006-09-04  Douglas Bates  <bates@R-project.org>
697    
698            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
699            * src/DEPS.mkf: update
700    
701    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * created branches/Matrix-for-R-2.3.x;  on trunk: do
704            * DESCRIPTION (Version): 0.9975-0
705            (Depends): R (>= 2.4.0)
706    
707    2006-09-01  Douglas Bates  <bates@R-project.org>
708    
709            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
710    
711    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
712    
713            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
714            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
715    
716            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
717    
718    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
721            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
722            * R/dsparseMatrix.R: ditto
723            * R/Csparse.R: ditto
724    
725    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * R/dMatrix.R (Compare): improve availability of "<", etc
728            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
729    
730    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
733            of a 0-index which was used as 1-index (..hmm)
734    
735            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
736    
737            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
738            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
739            (.is.diagonal): ditto
740    
741            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
742    
743            * R/Matrix.R (Matrix): also work for NA data
744    
745    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
748            in all cases.
749    
750    2006-08-27  Douglas Bates  <bates@R-project.org>
751    
752            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
753            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
754    
755    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
756    
757            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
758            subclasses of "ddenseMatrix"
759            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
760            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
761            instead of half dozen specialized ones.
762    
763    2006-08-25  Douglas Bates  <bates@R-project.org>
764    
765            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
766            <tillard@cirad.fr> - ordering standard errors to match effects.
767    
768    2006-08-24  Douglas Bates  <bates@R-project.org>
769    
770            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
771            on R_ldl.
772            * R/lCholCMatrix.R,
773            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
774            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
775            * many files in ./R and ./src: Use more general version of
776            dup_mMatrix_as_dgeMatrix to simplify method definitions.
777            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
778            dtpMatrix, dspMatrix and dppMatrix conversions.
779    
780    
781    2006-08-23  Douglas Bates  <bates@R-project.org>
782    
783            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
784            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
785            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
786            dgeMatrix_crossprod (may need to do this in other places).
787            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
788            generic and method for dsCMatrix.  Use CHOLMOD for chol().
789    
790    2006-08-22  Douglas Bates  <bates@R-project.org>
791    
792            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
793            types of classed Matrices, matrices or numeric or logical vectors.
794            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
795            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
796            to Mutils.h (as an inline) and change name to Matrix_check_class;
797            fixes in as_cholmod_factor and chm_factor_to_SEXP.
798            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
799            dsCMatrix_matrix_solve.  Comment out vestigial functions.
800            * src/Csparse.c: use diag_P and uplo_P macros.
801    
802  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
803    
804          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by

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