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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1787, Fri Feb 16 20:02:19 2007 UTC
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1    2007-02-16  Douglas Bates  <bates@r-project.org>
2    
3            * DESCRIPTION (Date, Version): 0.9975-11 with new date
4            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
5            const modifier on declaration of the array 'valid'
6    
7    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
8    
9            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
10    
11    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
14    
15            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
16            * tests/simple.R: test the above and some of these coercions:
17    
18            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
19                    be careful to avoid infinite recursion, using new coercions in
20            * R/ngCMatrix.R and nsC... and ntC...
21            * R/lsparseMatrix.R: ditto
22    
23            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
24    
25            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
26            * R/Rsparse.R: reactivate .Call()s
27    
28            * tests/Class+Meth.R: a bit more on actual classes
29    
30    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
31    
32            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
33    
34    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * DESCRIPTION (Version): 0.9975-10 to upload
37    
38            * tests/Class+Meth.R (tstMatrixClass): require coercions to
39            specific classes less unconditionally.
40    
41            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
42    
43            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
44    
45            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
46            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
47            R_to_CMatrix segfaults on one platform.
48            Eliminate most coercion method to *specific* classes, and replace
49            with virtual classes coercions.
50    
51    
52    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
53    
54            * src/init.c: export the CHM...._validate() placeholders, since
55            they *are* called.
56    
57            * tests/Class+Meth.R (classCanCoerce): and starting to test
58            all as(<from>, <to>)
59    
60    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
63            * tests/indexing.R: tested now
64            * tests/indexing.Rout.save: updated
65    
66            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
67            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
68            appropriate.
69    
70            * NAMESPACE: export a trivial
71            * R/Matrix.R: drop() Matrix-method
72    
73            * R/AllClass.R: moved all prototypes to virtual super classes.
74    
75            * R/Rsparse.R: many more coercions to have less exceptions in
76            * tests/Class+Meth.R:
77    
78            * R/Ops.R (Compare): tweak for case with NA
79            * tests/simpl.R: hence another 'FIXME' eliminated
80    
81    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
84            objects.
85    
86            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
87              and more of "!", "&", "|", all, any; coercions
88    
89            * R/Rsparse.R: many coercions (which enable quite a few other
90            methods), thanks to enhancements in
91            * src/dgCMatrix.c (R_to_CMatrix): new, and
92            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
93            symmetric & triangular and ..RMatrix objects.
94    
95            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
96            renamed file from src/dsTMatrix.c;
97            now dealing with symmetric and triangular Tsparse coercions, both
98            to dense and general.
99    
100    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
103    
104            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
105            where sensible when the <numeric> is of length > 1.
106    
107    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/Matrix.R ([<-): for M[] <- value: fix length
110    
111    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
114            * R/ndenseMatrix.R: new coercions n* -> l*
115    
116    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
119    
120            * R/Ops.R ("Logic"): and other "Ops", many updates
121    
122    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * src/Mutils.h (SET_DimNames): new utility
125    
126            * R/Auxiliaries.R (nnzero): improved and now exported via
127    
128            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
129    
130    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/diagMatrix.R (!): fix typo.
133    
134    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/Auxiliaries.R (as_Csparse): and quite a few others:
137                    allow to pass class definition --> speedup
138            * R/sparseMatrix.R: apply the above
139    
140            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
141    
142            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
143            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
144            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
145    
146            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
147    
148            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
149            and use it for "sparse*" as well, since it's faster than the
150            as_Csparse(.) way.
151    
152    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
155    
156    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
159            as method for   M[ ij ] <- v
160            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
161    
162            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
163            FALSE answer
164    
165            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
166            * tests/indexing.R: test it, and some of the above
167    
168    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Auxiliaries.R (is_duplicatedT): new utility
171    
172    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
173    
174            * src/init.c (R_init_Matrix): export cholmod_scale
175    
176    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
179            base::as.matrix to (x, ...)
180    
181    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
184            file; start using "Logic", hence
185    
186            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
187            * NAMESPACE: import and export "Logic"
188    
189    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
192            only needed previously to R version 2.5.0.
193    
194    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
197    
198            * R/Tsparse.R (replTmat): fix subassignment of triangular
199            * R/Csparse.R (replCmat): ditto
200            * tests/indexing.R: more tests, incl the above fix
201    
202    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/Auxiliaries.R (drop0): extend for non CSparse
205            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
206    
207            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
208                    use uplo correctly (!); other places: use uplo_P() macro
209    
210            * R/Csparse.R (replCmat): call diagU2N() when needed
211            * R/Tsparse.R (replTmat): ditto
212    
213            * src/dtCMatrix.c (tCMatrix_validate): new
214            * src/dtTMatrix.c (tTMatrix_validate): new, used in
215            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
216    
217            * R/diagMatrix.R (replDiag): to use in [<-
218    
219    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
222                    also more general diagU2N().
223    
224    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
227            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
228    
229    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * tests/bind.R: a few more cases
232            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
233    
234            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
235            * R/ddenseMatrix.R (cbind2/rbind2)
236            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
237            * tests/indexing.R
238            * tests/indexing.Rout.save: updated
239    
240    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
243            * tests/indexing.R
244    
245    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
248            align with proper position of "0", i.e., right for integers.
249            argument 'align' by default is "fancy".
250    
251    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
254            * R/Csparse.R: and fix "Compare" for more cases.
255            * tests/Class+Meth.R: test some of these (m == m, m != m)
256    
257    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/lsparseMatrix.R: all() and any() methods
260            * R/ldenseMatrix.R:      ditto
261            * NAMESPACE, R/Matrix.R: ditto
262    
263            * man/all-methods.Rd: document them minimally
264    
265            * tests/simple.R: add a few examples for these
266    
267    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/Tsparse.R ([): fix long standing typo in symmetric case
270            * man/dsCMatrix-class.Rd: add example exhibiting the above case
271    
272    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
273    
274            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
275            to LL before converting to a sparse matrix. (The LDL form can be
276            converted to a sparse matrix but it is implicitly a unit
277            triangular matrix and a diagonal matrix overwritten on the diagonal.)
278    
279    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
280    
281            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
282    
283    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
284    
285            * DESCRIPTION (Version): updated -> release 0.9975-7
286            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
287    
288    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
291    
292    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
293    
294            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
295            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
296            is exactly singular.
297    
298    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * DESCRIPTION (Date): updated -> release 0.9975-6
301    
302    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
305            now returns symmetric.
306    
307            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
308    
309            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
310            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
311    
312            * R/Auxiliaries.R (.type.kind): added
313    
314    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
317            running src/CSparse_install.sh
318    
319            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
320    
321    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
324            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
325    
326            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
327    
328            * tests/Class+Meth.R (tstMatrixClass): now assure
329            the (important in method programming) property :
330    
331                    ###>>  Every "Matrix" is either
332                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
333    
334                    (where "*" stands for "Matrix")
335    
336            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
337    
338            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
339            * tests/validObj.R: checks for "comparison"
340    
341            * R/sparseMatrix.R ([): improved indexing for sparse;
342                    trying to keep <symmetric>[ n, n] symmmetric
343    
344            * tests/indexing.R: indexing for logical sparse now ok
345    
346    
347    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * src/Tsparse.c: use xTsparse_validate() , and hence remove
350    
351            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
352    
353    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
356    
357            * tests/simple.R: validObject() checking the above.
358    
359            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
360            replacing both dgCMatrix_validate and lgCM*.
361    
362            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
363            fix dimnames setting in other places.
364            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
365    
366    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
369    
370            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
371            symmetry test, via
372            * R/Auxiliaries.R (.as.dgC.0.factors):
373    
374    2006-11-01  Douglas Bates  <bates@r-project.org>
375    
376            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
377            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
378            <CsparseMatrix>) added
379    
380    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * tests/matprod.R: add a variation of Harri's example
383    
384            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
385            recursive infinitely.
386    
387            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
388    
389            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
390    
391    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
394            matrix if possible; test m+m == 2*m; now test dgRMatrix.
395            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
396            satisfy the above test.
397    
398    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
401    
402            * R/dgCMatrix.R: solve(a, b="missing") based on
403            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
404            RHS = NULL.
405    
406            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
407            add more (needed) [t]crossprod() methods.
408    
409            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
410    
411            * R/Auxiliaries.R (as_CspClass): cleanup
412            (drop0): internal utility for "Csparse_drop(*, 0)"
413            (.bail.out.2): encourage active feedback
414    
415    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * R/dMatrix.R(Compare): new(), then slots [no validity check]
418    
419            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
420            non-valid or 'sorted' case).
421    
422            * R/dsparseMatrix.R: add "chol" method.
423            * R/ddenseMatrix.R: ditto
424    
425            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
426            * NAMESPACE (Ops)
427            * R/diagMatrix.R (diag2T): simple utility used "higher level"
428            coercion; deprecating direct lower level coercions.
429    
430            * R/*.R (seq): use seq_len() and seq_along() where possible.
431    
432    
433    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * DESCRIPTION (Version): 0.9975-5 ready for release
436    
437    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
438    
439            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
440    
441    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/AllClass.R (corMatrix): add 'validity' check;
444                    comment out unused "LDL" class definition
445            * NAMESPACE: mention, but do not export "LDL" class
446            * R/corMatrix.R: new (simple), needed for R-devel with
447            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
448              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
449    
450    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
451    
452            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
453            use Rprintf and R's error handling.
454    
455    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
458            * tests/matprod.R: add tests for the bug fixed.
459    
460    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
461    
462            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
463            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
464    
465    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
466    
467            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
468    
469    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * DESCRIPTION (Version): 0.9975-3
472    
473            * R/diagMatrix.R (bdiag): new function constructing block diagonal
474            (sparse) matrices.
475            * man/bdiag.Rd: docu + examples
476    
477            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
478    
479            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
480            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
481    
482            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
483            that result is sparse or diagonal (and not dense).
484    
485            * man/Subassign-methods.Rd: fix examples
486    
487            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
488            should always return a sparse (and not sometimes a diagonal) matrix.
489    
490    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
493    
494    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
495    
496            * DESCRIPTION (Version): 0.9975-2
497    
498            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
499    
500    2006-10-02  Douglas Bates  <bates@R-project.org>
501    
502            * tests/dg_Matrix.R: Simplify test taking into account new code.
503    
504    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
507    
508            * R/lsTMatrix.R: new files w/ missing methods
509            * R/nsTMatrix.R:  "  'for completeness'
510    
511            * tests/Class+Meth.R: a bit less 'not.ok.classes'
512    
513            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
514    
515    
516    2006-09-28  Douglas Bates  <bates@R-project.org>
517    
518            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
519            included.
520    
521            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
522            Export C-callable functions used in Zt_create in lme4.
523    
524    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * DESCRIPTION (Version): 0.9975-1
527    
528            * tests/simple.R: less checks fail; using NA, found that our
529                    kronecker() is not base-compatible with NA's.
530    
531            * R/dMatrix.R: "Compare" method now implemented for all cases
532    
533            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
534    
535            * man/dtpMatrix-class.Rd: mention length of 'x' slot
536    
537            * src/dtpMatrix.c (dtpMatrix_validate): fix check
538            * src/dspMatrix.c (dspMatrix_validate): ditto
539    
540            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
541              including coercion to [nl]tTMatrix.
542    
543            * R/diagMatrix.R (show): print a header line as for other classes.
544    
545    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * src/Makefile.win (SUBDIRS): fix typo
548    
549    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
552    
553    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
554    
555            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
556            symmetric and y missing in R code using %*% (cholmod_aat doesn't
557            accept a symmetric matrix).
558            * tests/group-methods.R: Uncomment test of crossprod applied to
559            lsCMatrix objects.
560    
561    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/AllClass.R (symmetricMatrix): add validity method (available
564            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
565    
566            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
567    
568            * tests/indexing.Rout.save:
569            * tests/indexing.R: additions, mainly for 'lsparse'
570    
571            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
572            case.
573    
574            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
575    
576    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
579                    as 'N' (1-letter - Ok?)
580    
581            * tests/group-methods.R: add test for logical + NAs
582    
583            * R/dMatrix.R ("Compare"): fix to work with NA's
584    
585            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
586    
587            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
588                    which is implemented.
589    
590    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * src/chm_common.c: coerce logical <-> double instead of
593            typecasting;  needed for "l" matrix handling in cholmod.
594    
595            * tests/other-pkgs.R (graph): small extension in "graph" checks.
596    
597            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
598            (Tsp2grNEL): other fixes needed
599    
600    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
603                    Matrices, since "lMatrix", also "lsparseM" can have NA
604            * R/ndenseMatrix.R, etc: new source files
605            * man/nsparseMatrix-classes.Rd, etc: new help files
606            * tests/: adaptions
607            * src/chm_common.c (chm_dense_to_SEXP): and others:
608                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
609            * src/Csparse.c, etc: ditto
610    
611    2006-09-11  Douglas Bates  <bates@R-project.org>
612    
613            * src/Mutils.[ch],init.c inst/include/*.h: Move the
614            alloc_d**Matrix functions to the lme4 package.
615    
616    2006-09-09  Douglas Bates  <bates@R-project.org>
617    
618            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
619            fixed
620    
621    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
622    
623            * R/lMatrix.R: new
624    
625            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
626    
627            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
628            * man/tcrossprod.Rd: ditto
629    
630    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
631    
632            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
633            for exported functions
634            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
635            Remove partitioning algorithms for sparse matrix reordering.  The
636            copyright on the Metis code was problematic and the methods were
637            rarely used.
638            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
639            operations are now done entirely in CHOLMOD code.
640    
641    2006-09-06  Douglas Bates  <bates@R-project.org>
642    
643            * src/Mutils.h: Remove functions that are no longer used.
644    
645    2006-09-04  Douglas Bates  <bates@R-project.org>
646    
647            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
648            * src/DEPS.mkf: update
649    
650    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * created branches/Matrix-for-R-2.3.x;  on trunk: do
653            * DESCRIPTION (Version): 0.9975-0
654            (Depends): R (>= 2.4.0)
655    
656    2006-09-01  Douglas Bates  <bates@R-project.org>
657    
658            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
659    
660    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
663            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
664    
665            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
666    
667    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
670            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
671            * R/dsparseMatrix.R: ditto
672            * R/Csparse.R: ditto
673    
674    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
675    
676            * R/dMatrix.R (Compare): improve availability of "<", etc
677            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
678    
679    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
680    
681            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
682            of a 0-index which was used as 1-index (..hmm)
683    
684            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
685    
686            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
687            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
688            (.is.diagonal): ditto
689    
690            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
691    
692            * R/Matrix.R (Matrix): also work for NA data
693    
694    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
695    
696            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
697            in all cases.
698    
699    2006-08-27  Douglas Bates  <bates@R-project.org>
700    
701            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
702            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
703    
704    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
705    
706            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
707            subclasses of "ddenseMatrix"
708            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
709            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
710            instead of half dozen specialized ones.
711    
712    2006-08-25  Douglas Bates  <bates@R-project.org>
713    
714            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
715            <tillard@cirad.fr> - ordering standard errors to match effects.
716    
717    2006-08-24  Douglas Bates  <bates@R-project.org>
718    
719            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
720            on R_ldl.
721            * R/lCholCMatrix.R,
722            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
723            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
724            * many files in ./R and ./src: Use more general version of
725            dup_mMatrix_as_dgeMatrix to simplify method definitions.
726            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
727            dtpMatrix, dspMatrix and dppMatrix conversions.
728    
729    
730    2006-08-23  Douglas Bates  <bates@R-project.org>
731    
732            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
733            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
734            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
735            dgeMatrix_crossprod (may need to do this in other places).
736            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
737            generic and method for dsCMatrix.  Use CHOLMOD for chol().
738    
739    2006-08-22  Douglas Bates  <bates@R-project.org>
740    
741            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
742            types of classed Matrices, matrices or numeric or logical vectors.
743            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
744            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
745            to Mutils.h (as an inline) and change name to Matrix_check_class;
746            fixes in as_cholmod_factor and chm_factor_to_SEXP.
747            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
748            dsCMatrix_matrix_solve.  Comment out vestigial functions.
749            * src/Csparse.c: use diag_P and uplo_P macros.
750    
751    2006-08-21  Douglas Bates  <bates@R-project.org>
752    
753            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
754            valgrind.
755            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
756            inverses.
757            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
758            -Wall warnings.
759            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
760            Use dup_mMatrix_as_dgeMatrix.
761    
762    2006-08-20  Douglas Bates  <bates@R-project.org>
763    
764            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
765            * tests/sparseQR.R: Added
766            * man/sparseQR-class.Rd: Document methods for qr.* generics
767            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
768    
769    2006-08-19  Douglas Bates  <bates@R-project.org>
770    
771            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
772            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
773            and qr.fitted.
774            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
775            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
776    
777    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
780            the base version has no "..." argument.
781    
782            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
783    
784            * R/Matrix.R: define and
785            * NAMESPACE: export as.numeric() and as.logical() methods.
786                    Let's hope these do not badly slow down something...
787            Finally export the zapsmall() method.
788    
789    2006-08-17  Douglas Bates  <bates@R-project.org>
790    
791            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
792            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
793            * src/dtCMatrix.c :Remove code that is no longer used
794            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
795    
796    2006-08-14  Douglas Bates  <bates@R-project.org>
797    
798            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
799            Csparse_to_logical and Csparse_symmetric_to_general.
800            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
801            coercion methods between CsparseMatrix and TsparseMatrix.
802    
803    2006-08-14  Douglas Bates  <bates@R-project.org>
804    
805            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
806            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
807            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
808            possible.
809    
810  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
811    
812          * 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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