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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1897, Fri Jun 15 18:22:25 2007 UTC
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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>
1010    
1011            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1012              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1013              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1014              generalize conversions between TsparseMatrix, CsparseMatrix,
1015              denseMatrix and matrix.  Preserve triangularity property and
1016              propagate Dimnames in the easy cases.
1017    
1018    2006-08-10  Douglas Bates  <bates@R-project.org>
1019    
1020            * src/lmer.c: adjust checks in glmer_init for S4SXP
1021            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1022            before S4SXP but for the wrong reasons.
1023    
1024    2006-08-08  Douglas Bates  <bates@R-project.org>
1025    
1026            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1027            Later modified to return the upper triangle only.
1028            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1029    
1030    2006-08-07  Douglas Bates  <bates@R-project.org>
1031    
1032            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1033            R-level conversion to a sparse symmetric class.
1034            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1035            Remove conversion to sparse symmetric classes (now done in C code).
1036    
1037    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1038    
1039            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1040            * man/band.Rd:  adapt the \dontshow{} unit test.
1041    
1042    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1043    
1044            * DESCRIPTION (Version): 0.995-14  for CRAN
1045    
1046            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1047    
1048            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1049            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1050    
1051            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1052            * R/Tsparse.R (tril, triu, band): methods
1053            * R/dgRMatrix.R (tril, ...):    ditto
1054            * man/band.Rd:                  ditto
1055    
1056    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1057    
1058            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1059                    to be up-to-date automatically.
1060    
1061    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1062    
1063            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1064    
1065            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1066            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1067            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1068            such that the S4 objects are always created by the current version
1069            of R and 'Matrix' class definitions.
1070    
1071    2006-08-01  Douglas Bates  <bates@R-project.org>
1072    
1073            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1074            inst/external/test3comp.rda: Added warnings for convergence on
1075            boundary and test cases.
1076    
1077            * src/lmer.c (mer_postVar): Modified to return the variances that
1078            are marginal to the fixed effects, not conditional on them (which
1079            is what the bVar slot contents represent).
1080    
1081    2006-07-31  Douglas Bates  <bates@R-project.org>
1082    
1083            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1084            function which calls the C function mer_hat_trace2.
1085    
1086            * man/ranef.Rd: Include description of "postVar" argument and
1087            producing a caterpillar plot.
1088    
1089    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1090    
1091            * NAMESPACE:    change  "correlation" to "corMatrix"
1092            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1093            * R/dpoMatrix.R: ditto
1094            * R/lmer.R:      ditto
1095    
1096    2006-07-28  Douglas Bates  <bates@R-project.org>
1097    
1098            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1099            RZXinv slot's contents into a separate internal function that can
1100            be used in mer_hat_trace.
1101    
1102    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1103    
1104            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1105            via new smart
1106            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1107            utility functions.
1108    
1109    
1110    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1111    
1112            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1113            matrices when appropriate; band() even symmetric ones.
1114            (replCmat): extend to potentially all "CsparseMatrix"
1115            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1116            allow subassignment for special sparse matrices.
1117    
1118            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1119    
1120            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1121            argument; in glmer_*(): print only if(verbose).
1122    
1123            speed-optimize a few places by moving REAL(.) out of loops.
1124    
1125            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1126    
1127    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1128    
1129            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1130                    since that wrongly triggers also for M[ logi , ]
1131    
1132            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1133            a symmetric matrix that results in a non-symmetric one.
1134            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1135    
1136            * R/dMatrix.R: make round(M) work as round(M, 0)
1137    
1138            * R/dgTMatrix.R (image): coordinate system and axis now use
1139            1-based indices, not 0-based ones.
1140    
1141            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1142            * tests/indexing.R: test it.
1143    
1144            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1145            * man/isSymmetric-methods.Rd: and document it.
1146    
1147            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1148            * man/SparseM-conv.Rd: docu them
1149    
1150            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1151                    for 'SparseM' conversions
1152    
1153    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1154    
1155            * R/Matrix.R (head): added head() and tail() methods.
1156    
1157    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1158    
1159            * DESCRIPTION (Version): 0.995-12 released to CRAN
1160    
1161    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1162    
1163            * tests/simple.R: add check for correct dsT -> dgT coercion;
1164                    add check for correct printing of symmetric sparse matrices.
1165    
1166            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1167            for sparse symmetric matrices.
1168    
1169            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1170            diagonal twice.
1171    
1172    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1173    
1174            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1175            being applied to the x slot (detected by Brian Ripley).
1176    
1177    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1178    
1179            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1180    
1181            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1182    
1183    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1184    
1185            * src/lgCMatrix.c (lgCMatrix_diag): new function
1186            * R/lgCMatrix.R (diag): for new method
1187    
1188            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1189                 ==> construction of illegal "*gTMatrix" via new() should
1190                 now be much less easy:
1191            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1192    
1193            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1194                    directly.
1195            * man/Matrix.Rd: documents it.
1196    
1197    2006-07-06  Douglas Bates  <bates@R-project.org>
1198    
1199            * src/pedigree.c (pedigree_inbreeding): Correction in
1200            initialization.  This function is not currently being used and is
1201            not fully tested.
1202    
1203            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1204            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1205            objects.  Modified validity check on pedigree objects to account
1206            for nonparallel patterns of missingness of parents.
1207    
1208            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1209            class.
1210    
1211    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1212    
1213            * R/pMatrix.R: coercion pMatrix -> Tsparse
1214    
1215    2006-06-12  Douglas Bates  <bates@R-project.org>
1216    
1217            * DESCRIPTION (Version): 0.995-11 released to CRAN
1218    
1219            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1220            the output from mcmcsamp.
1221    
1222  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
1223    
1224          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
1225            of the hat matrix.
1226    
1227  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1228    
1229          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1230          classes.          classes.
1231            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1232    
1233  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1234    
# Line 43  Line 1266 
1266    
1267          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1268          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.
1269          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1270    
1271    
1272  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 1389 
1389          * 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)
1390          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1391          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1392          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1393    
1394  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1395    
# Line 370  Line 1593 
1593  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1594    
1595          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1596          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1597          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1598    
1599  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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