SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 1897, Fri Jun 15 18:22:25 2007 UTC
# Line 1  Line 1 
1    2007-06-15 18:20  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
4              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
5              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
6            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
7              class
8    
9    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * src/Csparse.c (Csparse_validate): check for *repeated* entries
12            thanks to example from Christian Buchta; with a test here:
13            * tests/simple.R:
14    
15    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
18            of colSums(*, sparseResult = TRUE)
19    
20    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
23            'na.rm = FALSE' as "everywhere" else in R.
24    
25    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
26    
27            * [r4421] src/CSparse_install.sh: Modify for new organization of
28              CSparse package
29            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
30              SuiteSparse
31            * [r4426] src/Makefile: add ./UFconfig to the include path for
32              compilation
33            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
34            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
35              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
36    
37    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
40            * R/sparseMatrix.R (prSpMatrix): now gives a message about
41            suppressed column names.
42    
43    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
44    
45            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
46              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
47              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
48              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
49              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
50              Remove warnings after change to const char* CHAR
51    
52    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
53    
54            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
55              type of M_cholmod_ssmult
56    
57    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
58    
59            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
60              src/init.c: Yet another cholmod export - cholmod_ssmult
61    
62    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * NAMESPACE: exported drop0(), since
65            * man/drop0.Rd: I have seen several cases, I really wanted to use
66            it, so our users may want too.
67    
68    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * man/colSums.Rd: separately document colSums() etc, since these
71            have the extra argument 'sparseResult'.
72    
73    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
76            * man/spMatrix.Rd: docu., including examples
77    
78            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
79            in order to make colMeans() etc fast *and* correct.
80            * R/sparseVector.R (replSPvec): "[<-" functionality for
81            sparseVectors; tested in
82            * tests/simple.R:
83    
84    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
87            (very) sparse Matrices; output similar to Matlab's print().
88    
89    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
90    
91            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
92            0-based, indices (Jose Quesada <quesada@gmail.com>).
93    
94    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
95    
96            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
97    
98    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * R/Auxiliaries.R (sparsapply): new utility, much faster than
101            tapply1() for large sparse matrices.
102    
103    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/Matrix.R (dim<-): reshape now via sparseVector.
106    
107            * R/sparseVector.R: methods and function for
108            * R/AllClass.R: new "sparseVector" class and daughters.
109            * NAMESPACE: export new classes
110    
111    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * DESCRIPTION (Version): 0.99875-1
114            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
115    
116    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
119            indexing
120            * tests/indexing.R: test set for that.
121    
122    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
125            entries.
126            * tests/indexing.R(out): add regression test for it
127    
128    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
131            name for "!" method definitions.
132    
133    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/Tsparse.R (intI): new utility, used for "[" :
136                    Cleanup up there, and fixes for duplicated indices - more TODO!
137    
138            * tests/indexing.R(out): more tests
139    
140    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
141    
142            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
143            code that is now part of the R Lapack library.
144    
145            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
146            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
147    
148    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
151    
152    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
155            up with extraneous names '0'...'<n-1>'
156    
157    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/dgTMatrix.R (mat2dgT): care about NAs
160    
161    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/kronecker.R: triangularity preserving methods
164    
165    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/kronecker.R: new file collecting kronecker() methods in one
168                    place.  Goal: become much faster!
169    
170    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
173            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
174            can be much faster.
175    
176            * tests/matprod.R: add regression tests for these (upper & lower).
177    
178    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/Matrix.R (diff): method for our Matrices.
181    
182            * R/sparseMatrix.R (isDiagonal): check dim()!
183    
184    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/Matrix.R (dim<-): new method for "reshape()" built on a
187            proposal from Tamas Papp.
188    
189    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
192    
193            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
194            rather define and export  cBind() and rBind() only.
195            --> useRs *must* change code that used to have cbind()/rbind() !!
196    
197            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
198            * R/bind.Rout.save: ditto
199    
200    2007-02-16  Douglas Bates  <bates@r-project.org>
201    
202            * DESCRIPTION (Date, Version): 0.9975-11 with new date
203            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
204            const modifier on declaration of the array 'valid'
205    
206    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
207    
208            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
209    
210    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
213    
214            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
215            * tests/simple.R: test the above and some of these coercions:
216    
217            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
218                    be careful to avoid infinite recursion, using new coercions in
219            * R/ngCMatrix.R and nsC... and ntC...
220            * R/lsparseMatrix.R: ditto
221    
222            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
223    
224            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
225            * R/Rsparse.R: reactivate .Call()s
226    
227            * tests/Class+Meth.R: a bit more on actual classes
228    
229    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
230    
231            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
232    
233    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * DESCRIPTION (Version): 0.9975-10 to upload
236    
237            * tests/Class+Meth.R (tstMatrixClass): require coercions to
238            specific classes less unconditionally.
239    
240            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
241    
242            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
243    
244            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
245            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
246            R_to_CMatrix segfaults on one platform.
247            Eliminate most coercion method to *specific* classes, and replace
248            with virtual classes coercions.
249    
250    
251    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
252    
253            * src/init.c: export the CHM...._validate() placeholders, since
254            they *are* called.
255    
256            * tests/Class+Meth.R (classCanCoerce): and starting to test
257            all as(<from>, <to>)
258    
259    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
262            * tests/indexing.R: tested now
263            * tests/indexing.Rout.save: updated
264    
265            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
266            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
267            appropriate.
268    
269            * NAMESPACE: export a trivial
270            * R/Matrix.R: drop() Matrix-method
271    
272            * R/AllClass.R: moved all prototypes to virtual super classes.
273    
274            * R/Rsparse.R: many more coercions to have less exceptions in
275            * tests/Class+Meth.R:
276    
277            * R/Ops.R (Compare): tweak for case with NA
278            * tests/simpl.R: hence another 'FIXME' eliminated
279    
280    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
283            objects.
284    
285            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
286              and more of "!", "&", "|", all, any; coercions
287    
288            * R/Rsparse.R: many coercions (which enable quite a few other
289            methods), thanks to enhancements in
290            * src/dgCMatrix.c (R_to_CMatrix): new, and
291            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
292            symmetric & triangular and ..RMatrix objects.
293    
294            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
295            renamed file from src/dsTMatrix.c;
296            now dealing with symmetric and triangular Tsparse coercions, both
297            to dense and general.
298    
299    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
302    
303            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
304            where sensible when the <numeric> is of length > 1.
305    
306    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/Matrix.R ([<-): for M[] <- value: fix length
309    
310    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
313            * R/ndenseMatrix.R: new coercions n* -> l*
314    
315    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
318    
319            * R/Ops.R ("Logic"): and other "Ops", many updates
320    
321    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * src/Mutils.h (SET_DimNames): new utility
324    
325            * R/Auxiliaries.R (nnzero): improved and now exported via
326    
327            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
328    
329    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/diagMatrix.R (!): fix typo.
332    
333    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/Auxiliaries.R (as_Csparse): and quite a few others:
336                    allow to pass class definition --> speedup
337            * R/sparseMatrix.R: apply the above
338    
339            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
340    
341            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
342            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
343            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
344    
345            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
346    
347            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
348            and use it for "sparse*" as well, since it's faster than the
349            as_Csparse(.) way.
350    
351    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
354    
355    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
358            as method for   M[ ij ] <- v
359            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
360    
361            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
362            FALSE answer
363    
364            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
365            * tests/indexing.R: test it, and some of the above
366    
367    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/Auxiliaries.R (is_duplicatedT): new utility
370    
371    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
372    
373            * src/init.c (R_init_Matrix): export cholmod_scale
374    
375    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
378            base::as.matrix to (x, ...)
379    
380    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
383            file; start using "Logic", hence
384    
385            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
386            * NAMESPACE: import and export "Logic"
387    
388    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
391            only needed previously to R version 2.5.0.
392    
393    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
396    
397            * R/Tsparse.R (replTmat): fix subassignment of triangular
398            * R/Csparse.R (replCmat): ditto
399            * tests/indexing.R: more tests, incl the above fix
400    
401    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * R/Auxiliaries.R (drop0): extend for non CSparse
404            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
405    
406            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
407                    use uplo correctly (!); other places: use uplo_P() macro
408    
409            * R/Csparse.R (replCmat): call diagU2N() when needed
410            * R/Tsparse.R (replTmat): ditto
411    
412            * src/dtCMatrix.c (tCMatrix_validate): new
413            * src/dtTMatrix.c (tTMatrix_validate): new, used in
414            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
415    
416            * R/diagMatrix.R (replDiag): to use in [<-
417    
418    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
421                    also more general diagU2N().
422    
423    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
426            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
427    
428    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * tests/bind.R: a few more cases
431            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
432    
433            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
434            * R/ddenseMatrix.R (cbind2/rbind2)
435            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
436            * tests/indexing.R
437            * tests/indexing.Rout.save: updated
438    
439    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
442            * tests/indexing.R
443    
444    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
447            align with proper position of "0", i.e., right for integers.
448            argument 'align' by default is "fancy".
449    
450    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
453            * R/Csparse.R: and fix "Compare" for more cases.
454            * tests/Class+Meth.R: test some of these (m == m, m != m)
455    
456    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/lsparseMatrix.R: all() and any() methods
459            * R/ldenseMatrix.R:      ditto
460            * NAMESPACE, R/Matrix.R: ditto
461    
462            * man/all-methods.Rd: document them minimally
463    
464            * tests/simple.R: add a few examples for these
465    
466    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/Tsparse.R ([): fix long standing typo in symmetric case
469            * man/dsCMatrix-class.Rd: add example exhibiting the above case
470    
471    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
472    
473            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
474            to LL before converting to a sparse matrix. (The LDL form can be
475            converted to a sparse matrix but it is implicitly a unit
476            triangular matrix and a diagonal matrix overwritten on the diagonal.)
477    
478    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
479    
480            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
481    
482    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
483    
484            * DESCRIPTION (Version): updated -> release 0.9975-7
485            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
486    
487    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
490    
491    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
492    
493            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
494            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
495            is exactly singular.
496    
497    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * DESCRIPTION (Date): updated -> release 0.9975-6
500    
501    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
504            now returns symmetric.
505    
506            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
507    
508            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
509            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
510    
511            * R/Auxiliaries.R (.type.kind): added
512    
513    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
516            running src/CSparse_install.sh
517    
518            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
519    
520    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
523            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
524    
525            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
526    
527            * tests/Class+Meth.R (tstMatrixClass): now assure
528            the (important in method programming) property :
529    
530                    ###>>  Every "Matrix" is either
531                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
532    
533                    (where "*" stands for "Matrix")
534    
535            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
536    
537            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
538            * tests/validObj.R: checks for "comparison"
539    
540            * R/sparseMatrix.R ([): improved indexing for sparse;
541                    trying to keep <symmetric>[ n, n] symmmetric
542    
543            * tests/indexing.R: indexing for logical sparse now ok
544    
545    
546    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * src/Tsparse.c: use xTsparse_validate() , and hence remove
549    
550            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
551    
552    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
555    
556            * tests/simple.R: validObject() checking the above.
557    
558            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
559            replacing both dgCMatrix_validate and lgCM*.
560    
561            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
562            fix dimnames setting in other places.
563            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
564    
565    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
568    
569            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
570            symmetry test, via
571            * R/Auxiliaries.R (.as.dgC.0.factors):
572    
573    2006-11-01  Douglas Bates  <bates@r-project.org>
574    
575            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
576            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
577            <CsparseMatrix>) added
578    
579    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
580    
581            * tests/matprod.R: add a variation of Harri's example
582    
583            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
584            recursive infinitely.
585    
586            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
587    
588            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
589    
590    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
593            matrix if possible; test m+m == 2*m; now test dgRMatrix.
594            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
595            satisfy the above test.
596    
597    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
600    
601            * R/dgCMatrix.R: solve(a, b="missing") based on
602            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
603            RHS = NULL.
604    
605            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
606            add more (needed) [t]crossprod() methods.
607    
608            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
609    
610            * R/Auxiliaries.R (as_CspClass): cleanup
611            (drop0): internal utility for "Csparse_drop(*, 0)"
612            (.bail.out.2): encourage active feedback
613    
614    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/dMatrix.R(Compare): new(), then slots [no validity check]
617    
618            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
619            non-valid or 'sorted' case).
620    
621            * R/dsparseMatrix.R: add "chol" method.
622            * R/ddenseMatrix.R: ditto
623    
624            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
625            * NAMESPACE (Ops)
626            * R/diagMatrix.R (diag2T): simple utility used "higher level"
627            coercion; deprecating direct lower level coercions.
628    
629            * R/*.R (seq): use seq_len() and seq_along() where possible.
630    
631    
632    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * DESCRIPTION (Version): 0.9975-5 ready for release
635    
636    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
637    
638            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
639    
640    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * R/AllClass.R (corMatrix): add 'validity' check;
643                    comment out unused "LDL" class definition
644            * NAMESPACE: mention, but do not export "LDL" class
645            * R/corMatrix.R: new (simple), needed for R-devel with
646            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
647              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
648    
649    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
650    
651            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
652            use Rprintf and R's error handling.
653    
654    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
655    
656            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
657            * tests/matprod.R: add tests for the bug fixed.
658    
659    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
660    
661            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
662            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
663    
664    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
665    
666            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
667    
668    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
669    
670            * DESCRIPTION (Version): 0.9975-3
671    
672            * R/diagMatrix.R (bdiag): new function constructing block diagonal
673            (sparse) matrices.
674            * man/bdiag.Rd: docu + examples
675    
676            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
677    
678            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
679            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
680    
681            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
682            that result is sparse or diagonal (and not dense).
683    
684            * man/Subassign-methods.Rd: fix examples
685    
686            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
687            should always return a sparse (and not sometimes a diagonal) matrix.
688    
689    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
690    
691            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
692    
693    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
694    
695            * DESCRIPTION (Version): 0.9975-2
696    
697            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
698    
699    2006-10-02  Douglas Bates  <bates@R-project.org>
700    
701            * tests/dg_Matrix.R: Simplify test taking into account new code.
702    
703    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
706    
707            * R/lsTMatrix.R: new files w/ missing methods
708            * R/nsTMatrix.R:  "  'for completeness'
709    
710            * tests/Class+Meth.R: a bit less 'not.ok.classes'
711    
712            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
713    
714    
715    2006-09-28  Douglas Bates  <bates@R-project.org>
716    
717            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
718            included.
719    
720            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
721            Export C-callable functions used in Zt_create in lme4.
722    
723    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
724    
725            * DESCRIPTION (Version): 0.9975-1
726    
727            * tests/simple.R: less checks fail; using NA, found that our
728                    kronecker() is not base-compatible with NA's.
729    
730            * R/dMatrix.R: "Compare" method now implemented for all cases
731    
732            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
733    
734            * man/dtpMatrix-class.Rd: mention length of 'x' slot
735    
736            * src/dtpMatrix.c (dtpMatrix_validate): fix check
737            * src/dspMatrix.c (dspMatrix_validate): ditto
738    
739            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
740              including coercion to [nl]tTMatrix.
741    
742            * R/diagMatrix.R (show): print a header line as for other classes.
743    
744    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
745    
746            * src/Makefile.win (SUBDIRS): fix typo
747    
748    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
751    
752    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
753    
754            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
755            symmetric and y missing in R code using %*% (cholmod_aat doesn't
756            accept a symmetric matrix).
757            * tests/group-methods.R: Uncomment test of crossprod applied to
758            lsCMatrix objects.
759    
760    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * R/AllClass.R (symmetricMatrix): add validity method (available
763            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
764    
765            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
766    
767            * tests/indexing.Rout.save:
768            * tests/indexing.R: additions, mainly for 'lsparse'
769    
770            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
771            case.
772    
773            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
774    
775    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
778                    as 'N' (1-letter - Ok?)
779    
780            * tests/group-methods.R: add test for logical + NAs
781    
782            * R/dMatrix.R ("Compare"): fix to work with NA's
783    
784            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
785    
786            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
787                    which is implemented.
788    
789    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * src/chm_common.c: coerce logical <-> double instead of
792            typecasting;  needed for "l" matrix handling in cholmod.
793    
794            * tests/other-pkgs.R (graph): small extension in "graph" checks.
795    
796            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
797            (Tsp2grNEL): other fixes needed
798    
799    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
802                    Matrices, since "lMatrix", also "lsparseM" can have NA
803            * R/ndenseMatrix.R, etc: new source files
804            * man/nsparseMatrix-classes.Rd, etc: new help files
805            * tests/: adaptions
806            * src/chm_common.c (chm_dense_to_SEXP): and others:
807                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
808            * src/Csparse.c, etc: ditto
809    
810    2006-09-11  Douglas Bates  <bates@R-project.org>
811    
812            * src/Mutils.[ch],init.c inst/include/*.h: Move the
813            alloc_d**Matrix functions to the lme4 package.
814    
815    2006-09-09  Douglas Bates  <bates@R-project.org>
816    
817            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
818            fixed
819    
820    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * R/lMatrix.R: new
823    
824            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
825    
826            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
827            * man/tcrossprod.Rd: ditto
828    
829    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
830    
831            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
832            for exported functions
833            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
834            Remove partitioning algorithms for sparse matrix reordering.  The
835            copyright on the Metis code was problematic and the methods were
836            rarely used.
837            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
838            operations are now done entirely in CHOLMOD code.
839    
840    2006-09-06  Douglas Bates  <bates@R-project.org>
841    
842            * src/Mutils.h: Remove functions that are no longer used.
843    
844    2006-09-04  Douglas Bates  <bates@R-project.org>
845    
846            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
847            * src/DEPS.mkf: update
848    
849    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
850    
851            * created branches/Matrix-for-R-2.3.x;  on trunk: do
852            * DESCRIPTION (Version): 0.9975-0
853            (Depends): R (>= 2.4.0)
854    
855    2006-09-01  Douglas Bates  <bates@R-project.org>
856    
857            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
858    
859    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
862            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
863    
864            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
865    
866    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
869            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
870            * R/dsparseMatrix.R: ditto
871            * R/Csparse.R: ditto
872    
873    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
874    
875            * R/dMatrix.R (Compare): improve availability of "<", etc
876            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
877    
878    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
881            of a 0-index which was used as 1-index (..hmm)
882    
883            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
884    
885            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
886            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
887            (.is.diagonal): ditto
888    
889            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
890    
891            * R/Matrix.R (Matrix): also work for NA data
892    
893    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
894    
895            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
896            in all cases.
897    
898    2006-08-27  Douglas Bates  <bates@R-project.org>
899    
900            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
901            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
902    
903    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
904    
905            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
906            subclasses of "ddenseMatrix"
907            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
908            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
909            instead of half dozen specialized ones.
910    
911    2006-08-25  Douglas Bates  <bates@R-project.org>
912    
913            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
914            <tillard@cirad.fr> - ordering standard errors to match effects.
915    
916    2006-08-24  Douglas Bates  <bates@R-project.org>
917    
918            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
919            on R_ldl.
920            * R/lCholCMatrix.R,
921            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
922            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
923            * many files in ./R and ./src: Use more general version of
924            dup_mMatrix_as_dgeMatrix to simplify method definitions.
925            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
926            dtpMatrix, dspMatrix and dppMatrix conversions.
927    
928    
929    2006-08-23  Douglas Bates  <bates@R-project.org>
930    
931            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
932            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
933            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
934            dgeMatrix_crossprod (may need to do this in other places).
935            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
936            generic and method for dsCMatrix.  Use CHOLMOD for chol().
937    
938    2006-08-22  Douglas Bates  <bates@R-project.org>
939    
940            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
941            types of classed Matrices, matrices or numeric or logical vectors.
942            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
943            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
944            to Mutils.h (as an inline) and change name to Matrix_check_class;
945            fixes in as_cholmod_factor and chm_factor_to_SEXP.
946            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
947            dsCMatrix_matrix_solve.  Comment out vestigial functions.
948            * src/Csparse.c: use diag_P and uplo_P macros.
949    
950    2006-08-21  Douglas Bates  <bates@R-project.org>
951    
952            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
953            valgrind.
954            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
955            inverses.
956            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
957            -Wall warnings.
958            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
959            Use dup_mMatrix_as_dgeMatrix.
960    
961    2006-08-20  Douglas Bates  <bates@R-project.org>
962    
963            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
964            * tests/sparseQR.R: Added
965            * man/sparseQR-class.Rd: Document methods for qr.* generics
966            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
967    
968    2006-08-19  Douglas Bates  <bates@R-project.org>
969    
970            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
971            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
972            and qr.fitted.
973            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
974            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
975    
976    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
977    
978            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
979            the base version has no "..." argument.
980    
981            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
982    
983            * R/Matrix.R: define and
984            * NAMESPACE: export as.numeric() and as.logical() methods.
985                    Let's hope these do not badly slow down something...
986            Finally export the zapsmall() method.
987    
988    2006-08-17  Douglas Bates  <bates@R-project.org>
989    
990            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
991            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
992            * src/dtCMatrix.c :Remove code that is no longer used
993            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
994    
995    2006-08-14  Douglas Bates  <bates@R-project.org>
996    
997            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
998            Csparse_to_logical and Csparse_symmetric_to_general.
999            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1000            coercion methods between CsparseMatrix and TsparseMatrix.
1001    
1002    2006-08-14  Douglas Bates  <bates@R-project.org>
1003    
1004            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1005            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1006            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1007            possible.
1008    
1009  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
1010    
1011          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,

Legend:
Removed from v.1368  
changed lines
  Added in v.1897

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge