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revision 1315, Mon Jul 10 16:08:05 2006 UTC revision 1847, Sat May 19 19:23:28 2007 UTC
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1    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
4            0-based, indices (Jose Quesada <quesada@gmail.com>).
5    
6    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
9    
10    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Auxiliaries.R (sparsapply): new utility, much faster than
13            tapply1() for large sparse matrices.
14    
15    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Matrix.R (dim<-): reshape now via sparseVector.
18    
19            * R/sparseVector.R: methods and function for
20            * R/AllClass.R: new "sparseVector" class and daughters.
21            * NAMESPACE: export new classes
22    
23    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * DESCRIPTION (Version): 0.99875-1
26            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
27    
28    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
31            indexing
32            * tests/indexing.R: test set for that.
33    
34    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
37            entries.
38            * tests/indexing.R(out): add regression test for it
39    
40    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
43            name for "!" method definitions.
44    
45    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/Tsparse.R (intI): new utility, used for "[" :
48                    Cleanup up there, and fixes for duplicated indices - more TODO!
49    
50            * tests/indexing.R(out): more tests
51    
52    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
53    
54            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
55            code that is now part of the R Lapack library.
56    
57            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
58            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
59    
60    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
63    
64    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
67            up with extraneous names '0'...'<n-1>'
68    
69    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/dgTMatrix.R (mat2dgT): care about NAs
72    
73    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/kronecker.R: triangularity preserving methods
76    
77    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/kronecker.R: new file collecting kronecker() methods in one
80                    place.  Goal: become much faster!
81    
82    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
85            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
86            can be much faster.
87    
88            * tests/matprod.R: add regression tests for these (upper & lower).
89    
90    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/Matrix.R (diff): method for our Matrices.
93    
94            * R/sparseMatrix.R (isDiagonal): check dim()!
95    
96    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/Matrix.R (dim<-): new method for "reshape()" built on a
99            proposal from Tamas Papp.
100    
101    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
104    
105            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
106            rather define and export  cBind() and rBind() only.
107            --> useRs *must* change code that used to have cbind()/rbind() !!
108    
109            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
110            * R/bind.Rout.save: ditto
111    
112    2007-02-16  Douglas Bates  <bates@r-project.org>
113    
114            * DESCRIPTION (Date, Version): 0.9975-11 with new date
115            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
116            const modifier on declaration of the array 'valid'
117    
118    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
119    
120            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
121    
122    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
125    
126            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
127            * tests/simple.R: test the above and some of these coercions:
128    
129            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
130                    be careful to avoid infinite recursion, using new coercions in
131            * R/ngCMatrix.R and nsC... and ntC...
132            * R/lsparseMatrix.R: ditto
133    
134            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
135    
136            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
137            * R/Rsparse.R: reactivate .Call()s
138    
139            * tests/Class+Meth.R: a bit more on actual classes
140    
141    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
142    
143            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
144    
145    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * DESCRIPTION (Version): 0.9975-10 to upload
148    
149            * tests/Class+Meth.R (tstMatrixClass): require coercions to
150            specific classes less unconditionally.
151    
152            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
153    
154            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
155    
156            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
157            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
158            R_to_CMatrix segfaults on one platform.
159            Eliminate most coercion method to *specific* classes, and replace
160            with virtual classes coercions.
161    
162    
163    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
164    
165            * src/init.c: export the CHM...._validate() placeholders, since
166            they *are* called.
167    
168            * tests/Class+Meth.R (classCanCoerce): and starting to test
169            all as(<from>, <to>)
170    
171    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
174            * tests/indexing.R: tested now
175            * tests/indexing.Rout.save: updated
176    
177            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
178            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
179            appropriate.
180    
181            * NAMESPACE: export a trivial
182            * R/Matrix.R: drop() Matrix-method
183    
184            * R/AllClass.R: moved all prototypes to virtual super classes.
185    
186            * R/Rsparse.R: many more coercions to have less exceptions in
187            * tests/Class+Meth.R:
188    
189            * R/Ops.R (Compare): tweak for case with NA
190            * tests/simpl.R: hence another 'FIXME' eliminated
191    
192    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
195            objects.
196    
197            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
198              and more of "!", "&", "|", all, any; coercions
199    
200            * R/Rsparse.R: many coercions (which enable quite a few other
201            methods), thanks to enhancements in
202            * src/dgCMatrix.c (R_to_CMatrix): new, and
203            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
204            symmetric & triangular and ..RMatrix objects.
205    
206            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
207            renamed file from src/dsTMatrix.c;
208            now dealing with symmetric and triangular Tsparse coercions, both
209            to dense and general.
210    
211    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
214    
215            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
216            where sensible when the <numeric> is of length > 1.
217    
218    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/Matrix.R ([<-): for M[] <- value: fix length
221    
222    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
225            * R/ndenseMatrix.R: new coercions n* -> l*
226    
227    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
230    
231            * R/Ops.R ("Logic"): and other "Ops", many updates
232    
233    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * src/Mutils.h (SET_DimNames): new utility
236    
237            * R/Auxiliaries.R (nnzero): improved and now exported via
238    
239            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
240    
241    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/diagMatrix.R (!): fix typo.
244    
245    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Auxiliaries.R (as_Csparse): and quite a few others:
248                    allow to pass class definition --> speedup
249            * R/sparseMatrix.R: apply the above
250    
251            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
252    
253            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
254            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
255            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
256    
257            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
258    
259            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
260            and use it for "sparse*" as well, since it's faster than the
261            as_Csparse(.) way.
262    
263    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
266    
267    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
270            as method for   M[ ij ] <- v
271            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
272    
273            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
274            FALSE answer
275    
276            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
277            * tests/indexing.R: test it, and some of the above
278    
279    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Auxiliaries.R (is_duplicatedT): new utility
282    
283    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
284    
285            * src/init.c (R_init_Matrix): export cholmod_scale
286    
287    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
290            base::as.matrix to (x, ...)
291    
292    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
295            file; start using "Logic", hence
296    
297            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
298            * NAMESPACE: import and export "Logic"
299    
300    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
303            only needed previously to R version 2.5.0.
304    
305    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
308    
309            * R/Tsparse.R (replTmat): fix subassignment of triangular
310            * R/Csparse.R (replCmat): ditto
311            * tests/indexing.R: more tests, incl the above fix
312    
313    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/Auxiliaries.R (drop0): extend for non CSparse
316            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
317    
318            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
319                    use uplo correctly (!); other places: use uplo_P() macro
320    
321            * R/Csparse.R (replCmat): call diagU2N() when needed
322            * R/Tsparse.R (replTmat): ditto
323    
324            * src/dtCMatrix.c (tCMatrix_validate): new
325            * src/dtTMatrix.c (tTMatrix_validate): new, used in
326            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
327    
328            * R/diagMatrix.R (replDiag): to use in [<-
329    
330    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
333                    also more general diagU2N().
334    
335    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
338            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
339    
340    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * tests/bind.R: a few more cases
343            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
344    
345            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
346            * R/ddenseMatrix.R (cbind2/rbind2)
347            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
348            * tests/indexing.R
349            * tests/indexing.Rout.save: updated
350    
351    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
354            * tests/indexing.R
355    
356    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
359            align with proper position of "0", i.e., right for integers.
360            argument 'align' by default is "fancy".
361    
362    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
365            * R/Csparse.R: and fix "Compare" for more cases.
366            * tests/Class+Meth.R: test some of these (m == m, m != m)
367    
368    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/lsparseMatrix.R: all() and any() methods
371            * R/ldenseMatrix.R:      ditto
372            * NAMESPACE, R/Matrix.R: ditto
373    
374            * man/all-methods.Rd: document them minimally
375    
376            * tests/simple.R: add a few examples for these
377    
378    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/Tsparse.R ([): fix long standing typo in symmetric case
381            * man/dsCMatrix-class.Rd: add example exhibiting the above case
382    
383    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
384    
385            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
386            to LL before converting to a sparse matrix. (The LDL form can be
387            converted to a sparse matrix but it is implicitly a unit
388            triangular matrix and a diagonal matrix overwritten on the diagonal.)
389    
390    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
391    
392            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
393    
394    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
395    
396            * DESCRIPTION (Version): updated -> release 0.9975-7
397            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
398    
399    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
402    
403    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
404    
405            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
406            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
407            is exactly singular.
408    
409    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * DESCRIPTION (Date): updated -> release 0.9975-6
412    
413    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
416            now returns symmetric.
417    
418            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
419    
420            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
421            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
422    
423            * R/Auxiliaries.R (.type.kind): added
424    
425    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
428            running src/CSparse_install.sh
429    
430            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
431    
432    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
435            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
436    
437            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
438    
439            * tests/Class+Meth.R (tstMatrixClass): now assure
440            the (important in method programming) property :
441    
442                    ###>>  Every "Matrix" is either
443                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
444    
445                    (where "*" stands for "Matrix")
446    
447            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
448    
449            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
450            * tests/validObj.R: checks for "comparison"
451    
452            * R/sparseMatrix.R ([): improved indexing for sparse;
453                    trying to keep <symmetric>[ n, n] symmmetric
454    
455            * tests/indexing.R: indexing for logical sparse now ok
456    
457    
458    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * src/Tsparse.c: use xTsparse_validate() , and hence remove
461    
462            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
463    
464    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
467    
468            * tests/simple.R: validObject() checking the above.
469    
470            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
471            replacing both dgCMatrix_validate and lgCM*.
472    
473            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
474            fix dimnames setting in other places.
475            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
476    
477    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
478    
479            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
480    
481            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
482            symmetry test, via
483            * R/Auxiliaries.R (.as.dgC.0.factors):
484    
485    2006-11-01  Douglas Bates  <bates@r-project.org>
486    
487            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
488            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
489            <CsparseMatrix>) added
490    
491    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * tests/matprod.R: add a variation of Harri's example
494    
495            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
496            recursive infinitely.
497    
498            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
499    
500            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
501    
502    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
505            matrix if possible; test m+m == 2*m; now test dgRMatrix.
506            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
507            satisfy the above test.
508    
509    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
512    
513            * R/dgCMatrix.R: solve(a, b="missing") based on
514            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
515            RHS = NULL.
516    
517            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
518            add more (needed) [t]crossprod() methods.
519    
520            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
521    
522            * R/Auxiliaries.R (as_CspClass): cleanup
523            (drop0): internal utility for "Csparse_drop(*, 0)"
524            (.bail.out.2): encourage active feedback
525    
526    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * R/dMatrix.R(Compare): new(), then slots [no validity check]
529    
530            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
531            non-valid or 'sorted' case).
532    
533            * R/dsparseMatrix.R: add "chol" method.
534            * R/ddenseMatrix.R: ditto
535    
536            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
537            * NAMESPACE (Ops)
538            * R/diagMatrix.R (diag2T): simple utility used "higher level"
539            coercion; deprecating direct lower level coercions.
540    
541            * R/*.R (seq): use seq_len() and seq_along() where possible.
542    
543    
544    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * DESCRIPTION (Version): 0.9975-5 ready for release
547    
548    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
549    
550            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
551    
552    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * R/AllClass.R (corMatrix): add 'validity' check;
555                    comment out unused "LDL" class definition
556            * NAMESPACE: mention, but do not export "LDL" class
557            * R/corMatrix.R: new (simple), needed for R-devel with
558            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
559              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
560    
561    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
562    
563            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
564            use Rprintf and R's error handling.
565    
566    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
569            * tests/matprod.R: add tests for the bug fixed.
570    
571    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
572    
573            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
574            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
575    
576    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
577    
578            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
579    
580    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * DESCRIPTION (Version): 0.9975-3
583    
584            * R/diagMatrix.R (bdiag): new function constructing block diagonal
585            (sparse) matrices.
586            * man/bdiag.Rd: docu + examples
587    
588            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
589    
590            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
591            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
592    
593            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
594            that result is sparse or diagonal (and not dense).
595    
596            * man/Subassign-methods.Rd: fix examples
597    
598            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
599            should always return a sparse (and not sometimes a diagonal) matrix.
600    
601    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
604    
605    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
606    
607            * DESCRIPTION (Version): 0.9975-2
608    
609            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
610    
611    2006-10-02  Douglas Bates  <bates@R-project.org>
612    
613            * tests/dg_Matrix.R: Simplify test taking into account new code.
614    
615    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
616    
617            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
618    
619            * R/lsTMatrix.R: new files w/ missing methods
620            * R/nsTMatrix.R:  "  'for completeness'
621    
622            * tests/Class+Meth.R: a bit less 'not.ok.classes'
623    
624            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
625    
626    
627    2006-09-28  Douglas Bates  <bates@R-project.org>
628    
629            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
630            included.
631    
632            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
633            Export C-callable functions used in Zt_create in lme4.
634    
635    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
636    
637            * DESCRIPTION (Version): 0.9975-1
638    
639            * tests/simple.R: less checks fail; using NA, found that our
640                    kronecker() is not base-compatible with NA's.
641    
642            * R/dMatrix.R: "Compare" method now implemented for all cases
643    
644            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
645    
646            * man/dtpMatrix-class.Rd: mention length of 'x' slot
647    
648            * src/dtpMatrix.c (dtpMatrix_validate): fix check
649            * src/dspMatrix.c (dspMatrix_validate): ditto
650    
651            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
652              including coercion to [nl]tTMatrix.
653    
654            * R/diagMatrix.R (show): print a header line as for other classes.
655    
656    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * src/Makefile.win (SUBDIRS): fix typo
659    
660    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
663    
664    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
665    
666            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
667            symmetric and y missing in R code using %*% (cholmod_aat doesn't
668            accept a symmetric matrix).
669            * tests/group-methods.R: Uncomment test of crossprod applied to
670            lsCMatrix objects.
671    
672    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/AllClass.R (symmetricMatrix): add validity method (available
675            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
676    
677            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
678    
679            * tests/indexing.Rout.save:
680            * tests/indexing.R: additions, mainly for 'lsparse'
681    
682            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
683            case.
684    
685            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
686    
687    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
690                    as 'N' (1-letter - Ok?)
691    
692            * tests/group-methods.R: add test for logical + NAs
693    
694            * R/dMatrix.R ("Compare"): fix to work with NA's
695    
696            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
697    
698            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
699                    which is implemented.
700    
701    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * src/chm_common.c: coerce logical <-> double instead of
704            typecasting;  needed for "l" matrix handling in cholmod.
705    
706            * tests/other-pkgs.R (graph): small extension in "graph" checks.
707    
708            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
709            (Tsp2grNEL): other fixes needed
710    
711    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
712    
713            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
714                    Matrices, since "lMatrix", also "lsparseM" can have NA
715            * R/ndenseMatrix.R, etc: new source files
716            * man/nsparseMatrix-classes.Rd, etc: new help files
717            * tests/: adaptions
718            * src/chm_common.c (chm_dense_to_SEXP): and others:
719                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
720            * src/Csparse.c, etc: ditto
721    
722    2006-09-11  Douglas Bates  <bates@R-project.org>
723    
724            * src/Mutils.[ch],init.c inst/include/*.h: Move the
725            alloc_d**Matrix functions to the lme4 package.
726    
727    2006-09-09  Douglas Bates  <bates@R-project.org>
728    
729            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
730            fixed
731    
732    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * R/lMatrix.R: new
735    
736            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
737    
738            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
739            * man/tcrossprod.Rd: ditto
740    
741    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
742    
743            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
744            for exported functions
745            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
746            Remove partitioning algorithms for sparse matrix reordering.  The
747            copyright on the Metis code was problematic and the methods were
748            rarely used.
749            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
750            operations are now done entirely in CHOLMOD code.
751    
752    2006-09-06  Douglas Bates  <bates@R-project.org>
753    
754            * src/Mutils.h: Remove functions that are no longer used.
755    
756    2006-09-04  Douglas Bates  <bates@R-project.org>
757    
758            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
759            * src/DEPS.mkf: update
760    
761    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * created branches/Matrix-for-R-2.3.x;  on trunk: do
764            * DESCRIPTION (Version): 0.9975-0
765            (Depends): R (>= 2.4.0)
766    
767    2006-09-01  Douglas Bates  <bates@R-project.org>
768    
769            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
770    
771    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
774            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
775    
776            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
777    
778    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
781            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
782            * R/dsparseMatrix.R: ditto
783            * R/Csparse.R: ditto
784    
785    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * R/dMatrix.R (Compare): improve availability of "<", etc
788            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
789    
790    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
793            of a 0-index which was used as 1-index (..hmm)
794    
795            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
796    
797            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
798            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
799            (.is.diagonal): ditto
800    
801            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
802    
803            * R/Matrix.R (Matrix): also work for NA data
804    
805    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
806    
807            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
808            in all cases.
809    
810    2006-08-27  Douglas Bates  <bates@R-project.org>
811    
812            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
813            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
814    
815    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
816    
817            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
818            subclasses of "ddenseMatrix"
819            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
820            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
821            instead of half dozen specialized ones.
822    
823    2006-08-25  Douglas Bates  <bates@R-project.org>
824    
825            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
826            <tillard@cirad.fr> - ordering standard errors to match effects.
827    
828    2006-08-24  Douglas Bates  <bates@R-project.org>
829    
830            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
831            on R_ldl.
832            * R/lCholCMatrix.R,
833            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
834            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
835            * many files in ./R and ./src: Use more general version of
836            dup_mMatrix_as_dgeMatrix to simplify method definitions.
837            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
838            dtpMatrix, dspMatrix and dppMatrix conversions.
839    
840    
841    2006-08-23  Douglas Bates  <bates@R-project.org>
842    
843            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
844            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
845            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
846            dgeMatrix_crossprod (may need to do this in other places).
847            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
848            generic and method for dsCMatrix.  Use CHOLMOD for chol().
849    
850    2006-08-22  Douglas Bates  <bates@R-project.org>
851    
852            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
853            types of classed Matrices, matrices or numeric or logical vectors.
854            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
855            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
856            to Mutils.h (as an inline) and change name to Matrix_check_class;
857            fixes in as_cholmod_factor and chm_factor_to_SEXP.
858            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
859            dsCMatrix_matrix_solve.  Comment out vestigial functions.
860            * src/Csparse.c: use diag_P and uplo_P macros.
861    
862    2006-08-21  Douglas Bates  <bates@R-project.org>
863    
864            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
865            valgrind.
866            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
867            inverses.
868            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
869            -Wall warnings.
870            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
871            Use dup_mMatrix_as_dgeMatrix.
872    
873    2006-08-20  Douglas Bates  <bates@R-project.org>
874    
875            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
876            * tests/sparseQR.R: Added
877            * man/sparseQR-class.Rd: Document methods for qr.* generics
878            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
879    
880    2006-08-19  Douglas Bates  <bates@R-project.org>
881    
882            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
883            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
884            and qr.fitted.
885            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
886            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
887    
888    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
889    
890            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
891            the base version has no "..." argument.
892    
893            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
894    
895            * R/Matrix.R: define and
896            * NAMESPACE: export as.numeric() and as.logical() methods.
897                    Let's hope these do not badly slow down something...
898            Finally export the zapsmall() method.
899    
900    2006-08-17  Douglas Bates  <bates@R-project.org>
901    
902            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
903            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
904            * src/dtCMatrix.c :Remove code that is no longer used
905            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
906    
907    2006-08-14  Douglas Bates  <bates@R-project.org>
908    
909            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
910            Csparse_to_logical and Csparse_symmetric_to_general.
911            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
912            coercion methods between CsparseMatrix and TsparseMatrix.
913    
914    2006-08-14  Douglas Bates  <bates@R-project.org>
915    
916            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
917            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
918            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
919            possible.
920    
921    2006-08-12  Douglas Bates  <bates@R-project.org>
922    
923            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
924              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
925              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
926              generalize conversions between TsparseMatrix, CsparseMatrix,
927              denseMatrix and matrix.  Preserve triangularity property and
928              propagate Dimnames in the easy cases.
929    
930    2006-08-10  Douglas Bates  <bates@R-project.org>
931    
932            * src/lmer.c: adjust checks in glmer_init for S4SXP
933            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
934            before S4SXP but for the wrong reasons.
935    
936    2006-08-08  Douglas Bates  <bates@R-project.org>
937    
938            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
939            Later modified to return the upper triangle only.
940            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
941    
942    2006-08-07  Douglas Bates  <bates@R-project.org>
943    
944            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
945            R-level conversion to a sparse symmetric class.
946            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
947            Remove conversion to sparse symmetric classes (now done in C code).
948    
949    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
950    
951            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
952            * man/band.Rd:  adapt the \dontshow{} unit test.
953    
954    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
955    
956            * DESCRIPTION (Version): 0.995-14  for CRAN
957    
958            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
959    
960            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
961            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
962    
963            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
964            * R/Tsparse.R (tril, triu, band): methods
965            * R/dgRMatrix.R (tril, ...):    ditto
966            * man/band.Rd:                  ditto
967    
968    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
969    
970            * R/Matrix.R (head, tail): directly use utils:::head.matrix
971                    to be up-to-date automatically.
972    
973    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
974    
975            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
976    
977            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
978            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
979            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
980            such that the S4 objects are always created by the current version
981            of R and 'Matrix' class definitions.
982    
983    2006-08-01  Douglas Bates  <bates@R-project.org>
984    
985            * R/lmer.R (LMEoptimize method), tests/lmer.R,
986            inst/external/test3comp.rda: Added warnings for convergence on
987            boundary and test cases.
988    
989            * src/lmer.c (mer_postVar): Modified to return the variances that
990            are marginal to the fixed effects, not conditional on them (which
991            is what the bVar slot contents represent).
992    
993    2006-07-31  Douglas Bates  <bates@R-project.org>
994    
995            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
996            function which calls the C function mer_hat_trace2.
997    
998            * man/ranef.Rd: Include description of "postVar" argument and
999            producing a caterpillar plot.
1000    
1001    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1002    
1003            * NAMESPACE:    change  "correlation" to "corMatrix"
1004            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1005            * R/dpoMatrix.R: ditto
1006            * R/lmer.R:      ditto
1007    
1008    2006-07-28  Douglas Bates  <bates@R-project.org>
1009    
1010            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1011            RZXinv slot's contents into a separate internal function that can
1012            be used in mer_hat_trace.
1013    
1014    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1015    
1016            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1017            via new smart
1018            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1019            utility functions.
1020    
1021    
1022    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1023    
1024            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1025            matrices when appropriate; band() even symmetric ones.
1026            (replCmat): extend to potentially all "CsparseMatrix"
1027            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1028            allow subassignment for special sparse matrices.
1029    
1030            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1031    
1032            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1033            argument; in glmer_*(): print only if(verbose).
1034    
1035            speed-optimize a few places by moving REAL(.) out of loops.
1036    
1037            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1038    
1039    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1040    
1041            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1042                    since that wrongly triggers also for M[ logi , ]
1043    
1044            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1045            a symmetric matrix that results in a non-symmetric one.
1046            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1047    
1048            * R/dMatrix.R: make round(M) work as round(M, 0)
1049    
1050            * R/dgTMatrix.R (image): coordinate system and axis now use
1051            1-based indices, not 0-based ones.
1052    
1053            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1054            * tests/indexing.R: test it.
1055    
1056            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1057            * man/isSymmetric-methods.Rd: and document it.
1058    
1059            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1060            * man/SparseM-conv.Rd: docu them
1061    
1062            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1063                    for 'SparseM' conversions
1064    
1065    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1066    
1067            * R/Matrix.R (head): added head() and tail() methods.
1068    
1069    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1070    
1071            * DESCRIPTION (Version): 0.995-12 released to CRAN
1072    
1073    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1074    
1075            * tests/simple.R: add check for correct dsT -> dgT coercion;
1076                    add check for correct printing of symmetric sparse matrices.
1077    
1078            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1079            for sparse symmetric matrices.
1080    
1081            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1082            diagonal twice.
1083    
1084    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1085    
1086            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1087            being applied to the x slot (detected by Brian Ripley).
1088    
1089  2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1090    
1091          * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.          * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
# Line 38  Line 1126 
1126    
1127  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
1128    
1129            * DESCRIPTION (Version): 0.995-11 released to CRAN
1130    
1131          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1132          the output from mcmcsamp.          the output from mcmcsamp.
1133    
# Line 88  Line 1178 
1178    
1179          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1180          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
1181          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1182    
1183    
1184  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 211  Line 1301 
1301          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1302          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1303          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1304          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1305    
1306  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1307    
# Line 415  Line 1505 
1505  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1506    
1507          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1508          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1509          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1510    
1511  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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