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revision 1373, Mon Aug 14 21:15:38 2006 UTC revision 1767, Mon Feb 5 16:53:17 2007 UTC
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1    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
4            * tests/simple.R: test the above and some of these coercions:
5    
6            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
7                    be careful to avoid infinite recursion, using new coercions in
8            * R/ngCMatrix.R and nsC... and ntC...
9            * R/lsparseMatrix.R: ditto
10    
11            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
12    
13            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
14            * R/Rsparse.R: reactivate .Call()s
15    
16            * tests/Class+Meth.R: a bit more on actual classes
17    
18    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
19    
20            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
21    
22    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * DESCRIPTION (Version): 0.9975-10 to upload
25    
26            * tests/Class+Meth.R (tstMatrixClass): require coercions to
27            specific classes less unconditionally.
28    
29            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
30    
31            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
32    
33            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
34            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
35            R_to_CMatrix segfaults on one platform.
36            Eliminate most coercion method to *specific* classes, and replace
37            with virtual classes coercions.
38    
39    
40    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
41    
42            * src/init.c: export the CHM...._validate() placeholders, since
43            they *are* called.
44    
45            * tests/Class+Meth.R (classCanCoerce): and starting to test
46            all as(<from>, <to>)
47    
48    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
51            * tests/indexing.R: tested now
52            * tests/indexing.Rout.save: updated
53    
54            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
55            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
56            appropriate.
57    
58            * NAMESPACE: export a trivial
59            * R/Matrix.R: drop() Matrix-method
60    
61            * R/AllClass.R: moved all prototypes to virtual super classes.
62    
63            * R/Rsparse.R: many more coercions to have less exceptions in
64            * tests/Class+Meth.R:
65    
66            * R/Ops.R (Compare): tweak for case with NA
67            * tests/simpl.R: hence another 'FIXME' eliminated
68    
69    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
72            objects.
73    
74            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
75              and more of "!", "&", "|", all, any; coercions
76    
77            * R/Rsparse.R: many coercions (which enable quite a few other
78            methods), thanks to enhancements in
79            * src/dgCMatrix.c (R_to_CMatrix): new, and
80            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
81            symmetric & triangular and ..RMatrix objects.
82    
83            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
84            renamed file from src/dsTMatrix.c;
85            now dealing with symmetric and triangular Tsparse coercions, both
86            to dense and general.
87    
88    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
91    
92            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
93            where sensible when the <numeric> is of length > 1.
94    
95    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Matrix.R ([<-): for M[] <- value: fix length
98    
99    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
102            * R/ndenseMatrix.R: new coercions n* -> l*
103    
104    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
107    
108            * R/Ops.R ("Logic"): and other "Ops", many updates
109    
110    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * src/Mutils.h (SET_DimNames): new utility
113    
114            * R/Auxiliaries.R (nnzero): improved and now exported via
115    
116            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
117    
118    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/diagMatrix.R (!): fix typo.
121    
122    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Auxiliaries.R (as_Csparse): and quite a few others:
125                    allow to pass class definition --> speedup
126            * R/sparseMatrix.R: apply the above
127    
128            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
129    
130            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
131            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
132            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
133    
134            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
135    
136            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
137            and use it for "sparse*" as well, since it's faster than the
138            as_Csparse(.) way.
139    
140    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
143    
144    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
147            as method for   M[ ij ] <- v
148            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
149    
150            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
151            FALSE answer
152    
153            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
154            * tests/indexing.R: test it, and some of the above
155    
156    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Auxiliaries.R (is_duplicatedT): new utility
159    
160    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
161    
162            * src/init.c (R_init_Matrix): export cholmod_scale
163    
164    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
167            base::as.matrix to (x, ...)
168    
169    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
172            file; start using "Logic", hence
173    
174            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
175            * NAMESPACE: import and export "Logic"
176    
177    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
180            only needed previously to R version 2.5.0.
181    
182    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
185    
186            * R/Tsparse.R (replTmat): fix subassignment of triangular
187            * R/Csparse.R (replCmat): ditto
188            * tests/indexing.R: more tests, incl the above fix
189    
190    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/Auxiliaries.R (drop0): extend for non CSparse
193            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
194    
195            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
196                    use uplo correctly (!); other places: use uplo_P() macro
197    
198            * R/Csparse.R (replCmat): call diagU2N() when needed
199            * R/Tsparse.R (replTmat): ditto
200    
201            * src/dtCMatrix.c (tCMatrix_validate): new
202            * src/dtTMatrix.c (tTMatrix_validate): new, used in
203            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
204    
205            * R/diagMatrix.R (replDiag): to use in [<-
206    
207    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
210                    also more general diagU2N().
211    
212    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
215            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
216    
217    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * tests/bind.R: a few more cases
220            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
221    
222            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
223            * R/ddenseMatrix.R (cbind2/rbind2)
224            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
225            * tests/indexing.R
226            * tests/indexing.Rout.save: updated
227    
228    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
231            * tests/indexing.R
232    
233    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
236            align with proper position of "0", i.e., right for integers.
237            argument 'align' by default is "fancy".
238    
239    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
242            * R/Csparse.R: and fix "Compare" for more cases.
243            * tests/Class+Meth.R: test some of these (m == m, m != m)
244    
245    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/lsparseMatrix.R: all() and any() methods
248            * R/ldenseMatrix.R:      ditto
249            * NAMESPACE, R/Matrix.R: ditto
250    
251            * man/all-methods.Rd: document them minimally
252    
253            * tests/simple.R: add a few examples for these
254    
255    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * R/Tsparse.R ([): fix long standing typo in symmetric case
258            * man/dsCMatrix-class.Rd: add example exhibiting the above case
259    
260    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
261    
262            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
263            to LL before converting to a sparse matrix. (The LDL form can be
264            converted to a sparse matrix but it is implicitly a unit
265            triangular matrix and a diagonal matrix overwritten on the diagonal.)
266    
267    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
268    
269            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
270    
271    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
272    
273            * DESCRIPTION (Version): updated -> release 0.9975-7
274            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
275    
276    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
279    
280    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
281    
282            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
283            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
284            is exactly singular.
285    
286    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * DESCRIPTION (Date): updated -> release 0.9975-6
289    
290    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
293            now returns symmetric.
294    
295            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
296    
297            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
298            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
299    
300            * R/Auxiliaries.R (.type.kind): added
301    
302    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
305            running src/CSparse_install.sh
306    
307            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
308    
309    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
312            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
313    
314            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
315    
316            * tests/Class+Meth.R (tstMatrixClass): now assure
317            the (important in method programming) property :
318    
319                    ###>>  Every "Matrix" is either
320                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
321    
322                    (where "*" stands for "Matrix")
323    
324            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
325    
326            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
327            * tests/validObj.R: checks for "comparison"
328    
329            * R/sparseMatrix.R ([): improved indexing for sparse;
330                    trying to keep <symmetric>[ n, n] symmmetric
331    
332            * tests/indexing.R: indexing for logical sparse now ok
333    
334    
335    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * src/Tsparse.c: use xTsparse_validate() , and hence remove
338    
339            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
340    
341    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
344    
345            * tests/simple.R: validObject() checking the above.
346    
347            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
348            replacing both dgCMatrix_validate and lgCM*.
349    
350            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
351            fix dimnames setting in other places.
352            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
353    
354    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
357    
358            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
359            symmetry test, via
360            * R/Auxiliaries.R (.as.dgC.0.factors):
361    
362    2006-11-01  Douglas Bates  <bates@r-project.org>
363    
364            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
365            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
366            <CsparseMatrix>) added
367    
368    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * tests/matprod.R: add a variation of Harri's example
371    
372            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
373            recursive infinitely.
374    
375            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
376    
377            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
378    
379    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
382            matrix if possible; test m+m == 2*m; now test dgRMatrix.
383            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
384            satisfy the above test.
385    
386    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
389    
390            * R/dgCMatrix.R: solve(a, b="missing") based on
391            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
392            RHS = NULL.
393    
394            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
395            add more (needed) [t]crossprod() methods.
396    
397            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
398    
399            * R/Auxiliaries.R (as_CspClass): cleanup
400            (drop0): internal utility for "Csparse_drop(*, 0)"
401            (.bail.out.2): encourage active feedback
402    
403    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/dMatrix.R(Compare): new(), then slots [no validity check]
406    
407            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
408            non-valid or 'sorted' case).
409    
410            * R/dsparseMatrix.R: add "chol" method.
411            * R/ddenseMatrix.R: ditto
412    
413            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
414            * NAMESPACE (Ops)
415            * R/diagMatrix.R (diag2T): simple utility used "higher level"
416            coercion; deprecating direct lower level coercions.
417    
418            * R/*.R (seq): use seq_len() and seq_along() where possible.
419    
420    
421    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * DESCRIPTION (Version): 0.9975-5 ready for release
424    
425    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
426    
427            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
428    
429    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * R/AllClass.R (corMatrix): add 'validity' check;
432                    comment out unused "LDL" class definition
433            * NAMESPACE: mention, but do not export "LDL" class
434            * R/corMatrix.R: new (simple), needed for R-devel with
435            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
436              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
437    
438    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
439    
440            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
441            use Rprintf and R's error handling.
442    
443    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
444    
445            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
446            * tests/matprod.R: add tests for the bug fixed.
447    
448    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
449    
450            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
451            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
452    
453    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
454    
455            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
456    
457    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * DESCRIPTION (Version): 0.9975-3
460    
461            * R/diagMatrix.R (bdiag): new function constructing block diagonal
462            (sparse) matrices.
463            * man/bdiag.Rd: docu + examples
464    
465            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
466    
467            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
468            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
469    
470            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
471            that result is sparse or diagonal (and not dense).
472    
473            * man/Subassign-methods.Rd: fix examples
474    
475            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
476            should always return a sparse (and not sometimes a diagonal) matrix.
477    
478    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
481    
482    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
483    
484            * DESCRIPTION (Version): 0.9975-2
485    
486            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
487    
488    2006-10-02  Douglas Bates  <bates@R-project.org>
489    
490            * tests/dg_Matrix.R: Simplify test taking into account new code.
491    
492    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
495    
496            * R/lsTMatrix.R: new files w/ missing methods
497            * R/nsTMatrix.R:  "  'for completeness'
498    
499            * tests/Class+Meth.R: a bit less 'not.ok.classes'
500    
501            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
502    
503    
504    2006-09-28  Douglas Bates  <bates@R-project.org>
505    
506            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
507            included.
508    
509            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
510            Export C-callable functions used in Zt_create in lme4.
511    
512    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * DESCRIPTION (Version): 0.9975-1
515    
516            * tests/simple.R: less checks fail; using NA, found that our
517                    kronecker() is not base-compatible with NA's.
518    
519            * R/dMatrix.R: "Compare" method now implemented for all cases
520    
521            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
522    
523            * man/dtpMatrix-class.Rd: mention length of 'x' slot
524    
525            * src/dtpMatrix.c (dtpMatrix_validate): fix check
526            * src/dspMatrix.c (dspMatrix_validate): ditto
527    
528            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
529              including coercion to [nl]tTMatrix.
530    
531            * R/diagMatrix.R (show): print a header line as for other classes.
532    
533    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * src/Makefile.win (SUBDIRS): fix typo
536    
537    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
540    
541    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
542    
543            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
544            symmetric and y missing in R code using %*% (cholmod_aat doesn't
545            accept a symmetric matrix).
546            * tests/group-methods.R: Uncomment test of crossprod applied to
547            lsCMatrix objects.
548    
549    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/AllClass.R (symmetricMatrix): add validity method (available
552            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
553    
554            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
555    
556            * tests/indexing.Rout.save:
557            * tests/indexing.R: additions, mainly for 'lsparse'
558    
559            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
560            case.
561    
562            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
563    
564    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
565    
566            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
567                    as 'N' (1-letter - Ok?)
568    
569            * tests/group-methods.R: add test for logical + NAs
570    
571            * R/dMatrix.R ("Compare"): fix to work with NA's
572    
573            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
574    
575            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
576                    which is implemented.
577    
578    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * src/chm_common.c: coerce logical <-> double instead of
581            typecasting;  needed for "l" matrix handling in cholmod.
582    
583            * tests/other-pkgs.R (graph): small extension in "graph" checks.
584    
585            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
586            (Tsp2grNEL): other fixes needed
587    
588    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
591                    Matrices, since "lMatrix", also "lsparseM" can have NA
592            * R/ndenseMatrix.R, etc: new source files
593            * man/nsparseMatrix-classes.Rd, etc: new help files
594            * tests/: adaptions
595            * src/chm_common.c (chm_dense_to_SEXP): and others:
596                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
597            * src/Csparse.c, etc: ditto
598    
599    2006-09-11  Douglas Bates  <bates@R-project.org>
600    
601            * src/Mutils.[ch],init.c inst/include/*.h: Move the
602            alloc_d**Matrix functions to the lme4 package.
603    
604    2006-09-09  Douglas Bates  <bates@R-project.org>
605    
606            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
607            fixed
608    
609    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/lMatrix.R: new
612    
613            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
614    
615            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
616            * man/tcrossprod.Rd: ditto
617    
618    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
619    
620            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
621            for exported functions
622            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
623            Remove partitioning algorithms for sparse matrix reordering.  The
624            copyright on the Metis code was problematic and the methods were
625            rarely used.
626            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
627            operations are now done entirely in CHOLMOD code.
628    
629    2006-09-06  Douglas Bates  <bates@R-project.org>
630    
631            * src/Mutils.h: Remove functions that are no longer used.
632    
633    2006-09-04  Douglas Bates  <bates@R-project.org>
634    
635            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
636            * src/DEPS.mkf: update
637    
638    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * created branches/Matrix-for-R-2.3.x;  on trunk: do
641            * DESCRIPTION (Version): 0.9975-0
642            (Depends): R (>= 2.4.0)
643    
644    2006-09-01  Douglas Bates  <bates@R-project.org>
645    
646            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
647    
648    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
651            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
652    
653            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
654    
655    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
658            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
659            * R/dsparseMatrix.R: ditto
660            * R/Csparse.R: ditto
661    
662    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/dMatrix.R (Compare): improve availability of "<", etc
665            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
666    
667    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
670            of a 0-index which was used as 1-index (..hmm)
671    
672            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
673    
674            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
675            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
676            (.is.diagonal): ditto
677    
678            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
679    
680            * R/Matrix.R (Matrix): also work for NA data
681    
682    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
685            in all cases.
686    
687    2006-08-27  Douglas Bates  <bates@R-project.org>
688    
689            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
690            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
691    
692    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
693    
694            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
695            subclasses of "ddenseMatrix"
696            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
697            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
698            instead of half dozen specialized ones.
699    
700    2006-08-25  Douglas Bates  <bates@R-project.org>
701    
702            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
703            <tillard@cirad.fr> - ordering standard errors to match effects.
704    
705    2006-08-24  Douglas Bates  <bates@R-project.org>
706    
707            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
708            on R_ldl.
709            * R/lCholCMatrix.R,
710            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
711            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
712            * many files in ./R and ./src: Use more general version of
713            dup_mMatrix_as_dgeMatrix to simplify method definitions.
714            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
715            dtpMatrix, dspMatrix and dppMatrix conversions.
716    
717    
718    2006-08-23  Douglas Bates  <bates@R-project.org>
719    
720            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
721            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
722            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
723            dgeMatrix_crossprod (may need to do this in other places).
724            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
725            generic and method for dsCMatrix.  Use CHOLMOD for chol().
726    
727    2006-08-22  Douglas Bates  <bates@R-project.org>
728    
729            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
730            types of classed Matrices, matrices or numeric or logical vectors.
731            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
732            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
733            to Mutils.h (as an inline) and change name to Matrix_check_class;
734            fixes in as_cholmod_factor and chm_factor_to_SEXP.
735            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
736            dsCMatrix_matrix_solve.  Comment out vestigial functions.
737            * src/Csparse.c: use diag_P and uplo_P macros.
738    
739    2006-08-21  Douglas Bates  <bates@R-project.org>
740    
741            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
742            valgrind.
743            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
744            inverses.
745            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
746            -Wall warnings.
747            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
748            Use dup_mMatrix_as_dgeMatrix.
749    
750    2006-08-20  Douglas Bates  <bates@R-project.org>
751    
752            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
753            * tests/sparseQR.R: Added
754            * man/sparseQR-class.Rd: Document methods for qr.* generics
755            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
756    
757    2006-08-19  Douglas Bates  <bates@R-project.org>
758    
759            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
760            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
761            and qr.fitted.
762            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
763            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
764    
765    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
768            the base version has no "..." argument.
769    
770            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
771    
772            * R/Matrix.R: define and
773            * NAMESPACE: export as.numeric() and as.logical() methods.
774                    Let's hope these do not badly slow down something...
775            Finally export the zapsmall() method.
776    
777    2006-08-17  Douglas Bates  <bates@R-project.org>
778    
779            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
780            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
781            * src/dtCMatrix.c :Remove code that is no longer used
782            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
783    
784  2006-08-14  Douglas Bates  <bates@R-project.org>  2006-08-14  Douglas Bates  <bates@R-project.org>
785    
786          * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities          * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities

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