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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1886, Thu Jun 7 09:03:40 2007 UTC
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1    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
4            of colSums(*, sparseResult = TRUE)
5    
6    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
9            'na.rm = FALSE' as "everywhere" else in R.
10    
11    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
12    
13            * [r4421] src/CSparse_install.sh: Modify for new organization of
14              CSparse package
15            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
16              SuiteSparse
17            * [r4426] src/Makefile: add ./UFconfig to the include path for
18              compilation
19            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
20            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
21              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
22    
23    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
26            * R/sparseMatrix.R (prSpMatrix): now gives a message about
27            suppressed column names.
28    
29    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
30    
31            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
32              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
33              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
34              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
35              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
36              Remove warnings after change to const char* CHAR
37    
38    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
39    
40            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
41              type of M_cholmod_ssmult
42    
43    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
44    
45            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
46              src/init.c: Yet another cholmod export - cholmod_ssmult
47    
48    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * NAMESPACE: exported drop0(), since
51            * man/drop0.Rd: I have seen several cases, I really wanted to use
52            it, so our users may want too.
53    
54    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * man/colSums.Rd: separately document colSums() etc, since these
57            have the extra argument 'sparseResult'.
58    
59    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
62            * man/spMatrix.Rd: docu., including examples
63    
64            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
65            in order to make colMeans() etc fast *and* correct.
66            * R/sparseVector.R (replSPvec): "[<-" functionality for
67            sparseVectors; tested in
68            * tests/simple.R:
69    
70    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
73            (very) sparse Matrices; output similar to Matlab's print().
74    
75    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
76    
77            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
78            0-based, indices (Jose Quesada <quesada@gmail.com>).
79    
80    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
81    
82            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
83    
84    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/Auxiliaries.R (sparsapply): new utility, much faster than
87            tapply1() for large sparse matrices.
88    
89    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/Matrix.R (dim<-): reshape now via sparseVector.
92    
93            * R/sparseVector.R: methods and function for
94            * R/AllClass.R: new "sparseVector" class and daughters.
95            * NAMESPACE: export new classes
96    
97    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * DESCRIPTION (Version): 0.99875-1
100            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
101    
102    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
105            indexing
106            * tests/indexing.R: test set for that.
107    
108    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
111            entries.
112            * tests/indexing.R(out): add regression test for it
113    
114    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
117            name for "!" method definitions.
118    
119    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/Tsparse.R (intI): new utility, used for "[" :
122                    Cleanup up there, and fixes for duplicated indices - more TODO!
123    
124            * tests/indexing.R(out): more tests
125    
126    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
127    
128            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
129            code that is now part of the R Lapack library.
130    
131            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
132            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
133    
134    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
137    
138    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
141            up with extraneous names '0'...'<n-1>'
142    
143    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/dgTMatrix.R (mat2dgT): care about NAs
146    
147    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/kronecker.R: triangularity preserving methods
150    
151    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/kronecker.R: new file collecting kronecker() methods in one
154                    place.  Goal: become much faster!
155    
156    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
159            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
160            can be much faster.
161    
162            * tests/matprod.R: add regression tests for these (upper & lower).
163    
164    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/Matrix.R (diff): method for our Matrices.
167    
168            * R/sparseMatrix.R (isDiagonal): check dim()!
169    
170    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/Matrix.R (dim<-): new method for "reshape()" built on a
173            proposal from Tamas Papp.
174    
175    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
178    
179            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
180            rather define and export  cBind() and rBind() only.
181            --> useRs *must* change code that used to have cbind()/rbind() !!
182    
183            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
184            * R/bind.Rout.save: ditto
185    
186    2007-02-16  Douglas Bates  <bates@r-project.org>
187    
188            * DESCRIPTION (Date, Version): 0.9975-11 with new date
189            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
190            const modifier on declaration of the array 'valid'
191    
192    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
193    
194            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
195    
196    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
199    
200            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
201            * tests/simple.R: test the above and some of these coercions:
202    
203            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
204                    be careful to avoid infinite recursion, using new coercions in
205            * R/ngCMatrix.R and nsC... and ntC...
206            * R/lsparseMatrix.R: ditto
207    
208            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
209    
210            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
211            * R/Rsparse.R: reactivate .Call()s
212    
213            * tests/Class+Meth.R: a bit more on actual classes
214    
215    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
216    
217            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
218    
219    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * DESCRIPTION (Version): 0.9975-10 to upload
222    
223            * tests/Class+Meth.R (tstMatrixClass): require coercions to
224            specific classes less unconditionally.
225    
226            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
227    
228            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
229    
230            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
231            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
232            R_to_CMatrix segfaults on one platform.
233            Eliminate most coercion method to *specific* classes, and replace
234            with virtual classes coercions.
235    
236    
237    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
238    
239            * src/init.c: export the CHM...._validate() placeholders, since
240            they *are* called.
241    
242            * tests/Class+Meth.R (classCanCoerce): and starting to test
243            all as(<from>, <to>)
244    
245    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
248            * tests/indexing.R: tested now
249            * tests/indexing.Rout.save: updated
250    
251            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
252            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
253            appropriate.
254    
255            * NAMESPACE: export a trivial
256            * R/Matrix.R: drop() Matrix-method
257    
258            * R/AllClass.R: moved all prototypes to virtual super classes.
259    
260            * R/Rsparse.R: many more coercions to have less exceptions in
261            * tests/Class+Meth.R:
262    
263            * R/Ops.R (Compare): tweak for case with NA
264            * tests/simpl.R: hence another 'FIXME' eliminated
265    
266    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
269            objects.
270    
271            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
272              and more of "!", "&", "|", all, any; coercions
273    
274            * R/Rsparse.R: many coercions (which enable quite a few other
275            methods), thanks to enhancements in
276            * src/dgCMatrix.c (R_to_CMatrix): new, and
277            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
278            symmetric & triangular and ..RMatrix objects.
279    
280            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
281            renamed file from src/dsTMatrix.c;
282            now dealing with symmetric and triangular Tsparse coercions, both
283            to dense and general.
284    
285    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
288    
289            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
290            where sensible when the <numeric> is of length > 1.
291    
292    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/Matrix.R ([<-): for M[] <- value: fix length
295    
296    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
299            * R/ndenseMatrix.R: new coercions n* -> l*
300    
301    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
304    
305            * R/Ops.R ("Logic"): and other "Ops", many updates
306    
307    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * src/Mutils.h (SET_DimNames): new utility
310    
311            * R/Auxiliaries.R (nnzero): improved and now exported via
312    
313            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
314    
315    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/diagMatrix.R (!): fix typo.
318    
319    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Auxiliaries.R (as_Csparse): and quite a few others:
322                    allow to pass class definition --> speedup
323            * R/sparseMatrix.R: apply the above
324    
325            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
326    
327            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
328            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
329            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
330    
331            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
332    
333            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
334            and use it for "sparse*" as well, since it's faster than the
335            as_Csparse(.) way.
336    
337    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
340    
341    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
344            as method for   M[ ij ] <- v
345            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
346    
347            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
348            FALSE answer
349    
350            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
351            * tests/indexing.R: test it, and some of the above
352    
353    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/Auxiliaries.R (is_duplicatedT): new utility
356    
357    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
358    
359            * src/init.c (R_init_Matrix): export cholmod_scale
360    
361    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
364            base::as.matrix to (x, ...)
365    
366    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
369            file; start using "Logic", hence
370    
371            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
372            * NAMESPACE: import and export "Logic"
373    
374    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
377            only needed previously to R version 2.5.0.
378    
379    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
382    
383            * R/Tsparse.R (replTmat): fix subassignment of triangular
384            * R/Csparse.R (replCmat): ditto
385            * tests/indexing.R: more tests, incl the above fix
386    
387    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/Auxiliaries.R (drop0): extend for non CSparse
390            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
391    
392            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
393                    use uplo correctly (!); other places: use uplo_P() macro
394    
395            * R/Csparse.R (replCmat): call diagU2N() when needed
396            * R/Tsparse.R (replTmat): ditto
397    
398            * src/dtCMatrix.c (tCMatrix_validate): new
399            * src/dtTMatrix.c (tTMatrix_validate): new, used in
400            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
401    
402            * R/diagMatrix.R (replDiag): to use in [<-
403    
404    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
407                    also more general diagU2N().
408    
409    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
412            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
413    
414    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * tests/bind.R: a few more cases
417            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
418    
419            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
420            * R/ddenseMatrix.R (cbind2/rbind2)
421            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
422            * tests/indexing.R
423            * tests/indexing.Rout.save: updated
424    
425    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
428            * tests/indexing.R
429    
430    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
433            align with proper position of "0", i.e., right for integers.
434            argument 'align' by default is "fancy".
435    
436    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
439            * R/Csparse.R: and fix "Compare" for more cases.
440            * tests/Class+Meth.R: test some of these (m == m, m != m)
441    
442    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/lsparseMatrix.R: all() and any() methods
445            * R/ldenseMatrix.R:      ditto
446            * NAMESPACE, R/Matrix.R: ditto
447    
448            * man/all-methods.Rd: document them minimally
449    
450            * tests/simple.R: add a few examples for these
451    
452    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/Tsparse.R ([): fix long standing typo in symmetric case
455            * man/dsCMatrix-class.Rd: add example exhibiting the above case
456    
457    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
458    
459            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
460            to LL before converting to a sparse matrix. (The LDL form can be
461            converted to a sparse matrix but it is implicitly a unit
462            triangular matrix and a diagonal matrix overwritten on the diagonal.)
463    
464    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
465    
466            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
467    
468    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
469    
470            * DESCRIPTION (Version): updated -> release 0.9975-7
471            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
472    
473    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
474    
475            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
476    
477    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
478    
479            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
480            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
481            is exactly singular.
482    
483    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
484    
485            * DESCRIPTION (Date): updated -> release 0.9975-6
486    
487    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
490            now returns symmetric.
491    
492            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
493    
494            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
495            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
496    
497            * R/Auxiliaries.R (.type.kind): added
498    
499    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
502            running src/CSparse_install.sh
503    
504            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
505    
506    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
509            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
510    
511            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
512    
513            * tests/Class+Meth.R (tstMatrixClass): now assure
514            the (important in method programming) property :
515    
516                    ###>>  Every "Matrix" is either
517                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
518    
519                    (where "*" stands for "Matrix")
520    
521            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
522    
523            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
524            * tests/validObj.R: checks for "comparison"
525    
526            * R/sparseMatrix.R ([): improved indexing for sparse;
527                    trying to keep <symmetric>[ n, n] symmmetric
528    
529            * tests/indexing.R: indexing for logical sparse now ok
530    
531    
532    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * src/Tsparse.c: use xTsparse_validate() , and hence remove
535    
536            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
537    
538    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
539    
540            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
541    
542            * tests/simple.R: validObject() checking the above.
543    
544            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
545            replacing both dgCMatrix_validate and lgCM*.
546    
547            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
548            fix dimnames setting in other places.
549            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
550    
551    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
554    
555            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
556            symmetry test, via
557            * R/Auxiliaries.R (.as.dgC.0.factors):
558    
559    2006-11-01  Douglas Bates  <bates@r-project.org>
560    
561            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
562            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
563            <CsparseMatrix>) added
564    
565    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * tests/matprod.R: add a variation of Harri's example
568    
569            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
570            recursive infinitely.
571    
572            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
573    
574            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
575    
576    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
579            matrix if possible; test m+m == 2*m; now test dgRMatrix.
580            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
581            satisfy the above test.
582    
583    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
586    
587            * R/dgCMatrix.R: solve(a, b="missing") based on
588            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
589            RHS = NULL.
590    
591            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
592            add more (needed) [t]crossprod() methods.
593    
594            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
595    
596            * R/Auxiliaries.R (as_CspClass): cleanup
597            (drop0): internal utility for "Csparse_drop(*, 0)"
598            (.bail.out.2): encourage active feedback
599    
600    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * R/dMatrix.R(Compare): new(), then slots [no validity check]
603    
604            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
605            non-valid or 'sorted' case).
606    
607            * R/dsparseMatrix.R: add "chol" method.
608            * R/ddenseMatrix.R: ditto
609    
610            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
611            * NAMESPACE (Ops)
612            * R/diagMatrix.R (diag2T): simple utility used "higher level"
613            coercion; deprecating direct lower level coercions.
614    
615            * R/*.R (seq): use seq_len() and seq_along() where possible.
616    
617    
618    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * DESCRIPTION (Version): 0.9975-5 ready for release
621    
622    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
623    
624            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
625    
626    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * R/AllClass.R (corMatrix): add 'validity' check;
629                    comment out unused "LDL" class definition
630            * NAMESPACE: mention, but do not export "LDL" class
631            * R/corMatrix.R: new (simple), needed for R-devel with
632            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
633              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
634    
635    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
636    
637            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
638            use Rprintf and R's error handling.
639    
640    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
643            * tests/matprod.R: add tests for the bug fixed.
644    
645    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
646    
647            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
648            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
649    
650    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
651    
652            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
653    
654    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
655    
656            * DESCRIPTION (Version): 0.9975-3
657    
658            * R/diagMatrix.R (bdiag): new function constructing block diagonal
659            (sparse) matrices.
660            * man/bdiag.Rd: docu + examples
661    
662            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
663    
664            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
665            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
666    
667            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
668            that result is sparse or diagonal (and not dense).
669    
670            * man/Subassign-methods.Rd: fix examples
671    
672            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
673            should always return a sparse (and not sometimes a diagonal) matrix.
674    
675    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
678    
679    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
680    
681            * DESCRIPTION (Version): 0.9975-2
682    
683            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
684    
685    2006-10-02  Douglas Bates  <bates@R-project.org>
686    
687            * tests/dg_Matrix.R: Simplify test taking into account new code.
688    
689    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
690    
691            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
692    
693            * R/lsTMatrix.R: new files w/ missing methods
694            * R/nsTMatrix.R:  "  'for completeness'
695    
696            * tests/Class+Meth.R: a bit less 'not.ok.classes'
697    
698            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
699    
700    
701    2006-09-28  Douglas Bates  <bates@R-project.org>
702    
703            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
704            included.
705    
706            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
707            Export C-callable functions used in Zt_create in lme4.
708    
709    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * DESCRIPTION (Version): 0.9975-1
712    
713            * tests/simple.R: less checks fail; using NA, found that our
714                    kronecker() is not base-compatible with NA's.
715    
716            * R/dMatrix.R: "Compare" method now implemented for all cases
717    
718            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
719    
720            * man/dtpMatrix-class.Rd: mention length of 'x' slot
721    
722            * src/dtpMatrix.c (dtpMatrix_validate): fix check
723            * src/dspMatrix.c (dspMatrix_validate): ditto
724    
725            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
726              including coercion to [nl]tTMatrix.
727    
728            * R/diagMatrix.R (show): print a header line as for other classes.
729    
730    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * src/Makefile.win (SUBDIRS): fix typo
733    
734    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
735    
736            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
737    
738    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
739    
740            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
741            symmetric and y missing in R code using %*% (cholmod_aat doesn't
742            accept a symmetric matrix).
743            * tests/group-methods.R: Uncomment test of crossprod applied to
744            lsCMatrix objects.
745    
746    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * R/AllClass.R (symmetricMatrix): add validity method (available
749            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
750    
751            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
752    
753            * tests/indexing.Rout.save:
754            * tests/indexing.R: additions, mainly for 'lsparse'
755    
756            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
757            case.
758    
759            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
760    
761    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
764                    as 'N' (1-letter - Ok?)
765    
766            * tests/group-methods.R: add test for logical + NAs
767    
768            * R/dMatrix.R ("Compare"): fix to work with NA's
769    
770            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
771    
772            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
773                    which is implemented.
774    
775    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * src/chm_common.c: coerce logical <-> double instead of
778            typecasting;  needed for "l" matrix handling in cholmod.
779    
780            * tests/other-pkgs.R (graph): small extension in "graph" checks.
781    
782            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
783            (Tsp2grNEL): other fixes needed
784    
785    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
788                    Matrices, since "lMatrix", also "lsparseM" can have NA
789            * R/ndenseMatrix.R, etc: new source files
790            * man/nsparseMatrix-classes.Rd, etc: new help files
791            * tests/: adaptions
792            * src/chm_common.c (chm_dense_to_SEXP): and others:
793                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
794            * src/Csparse.c, etc: ditto
795    
796    2006-09-11  Douglas Bates  <bates@R-project.org>
797    
798            * src/Mutils.[ch],init.c inst/include/*.h: Move the
799            alloc_d**Matrix functions to the lme4 package.
800    
801    2006-09-09  Douglas Bates  <bates@R-project.org>
802    
803            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
804            fixed
805    
806    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
807    
808            * R/lMatrix.R: new
809    
810            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
811    
812            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
813            * man/tcrossprod.Rd: ditto
814    
815    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
816    
817            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
818            for exported functions
819            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
820            Remove partitioning algorithms for sparse matrix reordering.  The
821            copyright on the Metis code was problematic and the methods were
822            rarely used.
823            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
824            operations are now done entirely in CHOLMOD code.
825    
826    2006-09-06  Douglas Bates  <bates@R-project.org>
827    
828            * src/Mutils.h: Remove functions that are no longer used.
829    
830    2006-09-04  Douglas Bates  <bates@R-project.org>
831    
832            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
833            * src/DEPS.mkf: update
834    
835    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
836    
837            * created branches/Matrix-for-R-2.3.x;  on trunk: do
838            * DESCRIPTION (Version): 0.9975-0
839            (Depends): R (>= 2.4.0)
840    
841    2006-09-01  Douglas Bates  <bates@R-project.org>
842    
843            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
844    
845    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
846    
847            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
848            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
849    
850            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
851    
852    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
853    
854            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
855            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
856            * R/dsparseMatrix.R: ditto
857            * R/Csparse.R: ditto
858    
859    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * R/dMatrix.R (Compare): improve availability of "<", etc
862            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
863    
864    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
865    
866            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
867            of a 0-index which was used as 1-index (..hmm)
868    
869            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
870    
871            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
872            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
873            (.is.diagonal): ditto
874    
875            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
876    
877            * R/Matrix.R (Matrix): also work for NA data
878    
879    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
880    
881            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
882            in all cases.
883    
884    2006-08-27  Douglas Bates  <bates@R-project.org>
885    
886            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
887            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
888    
889    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
892            subclasses of "ddenseMatrix"
893            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
894            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
895            instead of half dozen specialized ones.
896    
897    2006-08-25  Douglas Bates  <bates@R-project.org>
898    
899            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
900            <tillard@cirad.fr> - ordering standard errors to match effects.
901    
902    2006-08-24  Douglas Bates  <bates@R-project.org>
903    
904            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
905            on R_ldl.
906            * R/lCholCMatrix.R,
907            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
908            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
909            * many files in ./R and ./src: Use more general version of
910            dup_mMatrix_as_dgeMatrix to simplify method definitions.
911            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
912            dtpMatrix, dspMatrix and dppMatrix conversions.
913    
914    
915    2006-08-23  Douglas Bates  <bates@R-project.org>
916    
917            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
918            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
919            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
920            dgeMatrix_crossprod (may need to do this in other places).
921            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
922            generic and method for dsCMatrix.  Use CHOLMOD for chol().
923    
924    2006-08-22  Douglas Bates  <bates@R-project.org>
925    
926            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
927            types of classed Matrices, matrices or numeric or logical vectors.
928            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
929            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
930            to Mutils.h (as an inline) and change name to Matrix_check_class;
931            fixes in as_cholmod_factor and chm_factor_to_SEXP.
932            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
933            dsCMatrix_matrix_solve.  Comment out vestigial functions.
934            * src/Csparse.c: use diag_P and uplo_P macros.
935    
936    2006-08-21  Douglas Bates  <bates@R-project.org>
937    
938            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
939            valgrind.
940            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
941            inverses.
942            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
943            -Wall warnings.
944            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
945            Use dup_mMatrix_as_dgeMatrix.
946    
947    2006-08-20  Douglas Bates  <bates@R-project.org>
948    
949            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
950            * tests/sparseQR.R: Added
951            * man/sparseQR-class.Rd: Document methods for qr.* generics
952            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
953    
954    2006-08-19  Douglas Bates  <bates@R-project.org>
955    
956            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
957            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
958            and qr.fitted.
959            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
960            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
961    
962    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
963    
964            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
965            the base version has no "..." argument.
966    
967            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
968    
969            * R/Matrix.R: define and
970            * NAMESPACE: export as.numeric() and as.logical() methods.
971                    Let's hope these do not badly slow down something...
972            Finally export the zapsmall() method.
973    
974    2006-08-17  Douglas Bates  <bates@R-project.org>
975    
976            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
977            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
978            * src/dtCMatrix.c :Remove code that is no longer used
979            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
980    
981    2006-08-14  Douglas Bates  <bates@R-project.org>
982    
983            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
984            Csparse_to_logical and Csparse_symmetric_to_general.
985            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
986            coercion methods between CsparseMatrix and TsparseMatrix.
987    
988    2006-08-14  Douglas Bates  <bates@R-project.org>
989    
990            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
991            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
992            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
993            possible.
994    
995    2006-08-12  Douglas Bates  <bates@R-project.org>
996    
997            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
998              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
999              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1000              generalize conversions between TsparseMatrix, CsparseMatrix,
1001              denseMatrix and matrix.  Preserve triangularity property and
1002              propagate Dimnames in the easy cases.
1003    
1004    2006-08-10  Douglas Bates  <bates@R-project.org>
1005    
1006            * src/lmer.c: adjust checks in glmer_init for S4SXP
1007            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1008            before S4SXP but for the wrong reasons.
1009    
1010    2006-08-08  Douglas Bates  <bates@R-project.org>
1011    
1012            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1013            Later modified to return the upper triangle only.
1014            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1015    
1016    2006-08-07  Douglas Bates  <bates@R-project.org>
1017    
1018            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1019            R-level conversion to a sparse symmetric class.
1020            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1021            Remove conversion to sparse symmetric classes (now done in C code).
1022    
1023    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1024    
1025            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1026            * man/band.Rd:  adapt the \dontshow{} unit test.
1027    
1028    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1029    
1030            * DESCRIPTION (Version): 0.995-14  for CRAN
1031    
1032            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1033    
1034            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1035            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1036    
1037            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1038            * R/Tsparse.R (tril, triu, band): methods
1039            * R/dgRMatrix.R (tril, ...):    ditto
1040            * man/band.Rd:                  ditto
1041    
1042    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1043    
1044            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1045                    to be up-to-date automatically.
1046    
1047    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1048    
1049            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1050    
1051            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1052            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1053            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1054            such that the S4 objects are always created by the current version
1055            of R and 'Matrix' class definitions.
1056    
1057    2006-08-01  Douglas Bates  <bates@R-project.org>
1058    
1059            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1060            inst/external/test3comp.rda: Added warnings for convergence on
1061            boundary and test cases.
1062    
1063            * src/lmer.c (mer_postVar): Modified to return the variances that
1064            are marginal to the fixed effects, not conditional on them (which
1065            is what the bVar slot contents represent).
1066    
1067    2006-07-31  Douglas Bates  <bates@R-project.org>
1068    
1069            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1070            function which calls the C function mer_hat_trace2.
1071    
1072            * man/ranef.Rd: Include description of "postVar" argument and
1073            producing a caterpillar plot.
1074    
1075    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1076    
1077            * NAMESPACE:    change  "correlation" to "corMatrix"
1078            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1079            * R/dpoMatrix.R: ditto
1080            * R/lmer.R:      ditto
1081    
1082    2006-07-28  Douglas Bates  <bates@R-project.org>
1083    
1084            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1085            RZXinv slot's contents into a separate internal function that can
1086            be used in mer_hat_trace.
1087    
1088    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1089    
1090            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1091            via new smart
1092            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1093            utility functions.
1094    
1095    
1096    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1097    
1098            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1099            matrices when appropriate; band() even symmetric ones.
1100            (replCmat): extend to potentially all "CsparseMatrix"
1101            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1102            allow subassignment for special sparse matrices.
1103    
1104            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1105    
1106            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1107            argument; in glmer_*(): print only if(verbose).
1108    
1109            speed-optimize a few places by moving REAL(.) out of loops.
1110    
1111            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1112    
1113    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1114    
1115            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1116                    since that wrongly triggers also for M[ logi , ]
1117    
1118            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1119            a symmetric matrix that results in a non-symmetric one.
1120            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1121    
1122            * R/dMatrix.R: make round(M) work as round(M, 0)
1123    
1124            * R/dgTMatrix.R (image): coordinate system and axis now use
1125            1-based indices, not 0-based ones.
1126    
1127            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1128            * tests/indexing.R: test it.
1129    
1130            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1131            * man/isSymmetric-methods.Rd: and document it.
1132    
1133            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1134            * man/SparseM-conv.Rd: docu them
1135    
1136            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1137                    for 'SparseM' conversions
1138    
1139    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1140    
1141            * R/Matrix.R (head): added head() and tail() methods.
1142    
1143    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1144    
1145            * DESCRIPTION (Version): 0.995-12 released to CRAN
1146    
1147    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1148    
1149            * tests/simple.R: add check for correct dsT -> dgT coercion;
1150                    add check for correct printing of symmetric sparse matrices.
1151    
1152            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1153            for sparse symmetric matrices.
1154    
1155            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1156            diagonal twice.
1157    
1158    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1159    
1160            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1161            being applied to the x slot (detected by Brian Ripley).
1162    
1163    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1164    
1165            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1166    
1167            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1168    
1169    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1170    
1171            * src/lgCMatrix.c (lgCMatrix_diag): new function
1172            * R/lgCMatrix.R (diag): for new method
1173    
1174            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1175                 ==> construction of illegal "*gTMatrix" via new() should
1176                 now be much less easy:
1177            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1178    
1179            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1180                    directly.
1181            * man/Matrix.Rd: documents it.
1182    
1183    2006-07-06  Douglas Bates  <bates@R-project.org>
1184    
1185            * src/pedigree.c (pedigree_inbreeding): Correction in
1186            initialization.  This function is not currently being used and is
1187            not fully tested.
1188    
1189            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1190            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1191            objects.  Modified validity check on pedigree objects to account
1192            for nonparallel patterns of missingness of parents.
1193    
1194            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1195            class.
1196    
1197    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1198    
1199            * R/pMatrix.R: coercion pMatrix -> Tsparse
1200    
1201    2006-06-12  Douglas Bates  <bates@R-project.org>
1202    
1203            * DESCRIPTION (Version): 0.995-11 released to CRAN
1204    
1205            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1206            the output from mcmcsamp.
1207    
1208  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
1209    
1210          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
1211            of the hat matrix.
1212    
1213  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1214    
1215          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1216          classes.          classes.
1217            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1218    
1219  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1220    
# Line 43  Line 1252 
1252    
1253          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1254          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.
1255          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1256    
1257    
1258  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 1375 
1375          * 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)
1376          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1377          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1378          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1379    
1380  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1381    
# Line 370  Line 1579 
1579  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1580    
1581          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1582          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1583          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1584    
1585  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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