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revision 1283, Sat May 27 19:51:01 2006 UTC revision 1968, Sat Jul 7 22:49:12 2007 UTC
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1    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dgCMatrix.c (compressed_to_TMatrix):
4    
5    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * src/Csparse.c (Rsparse_validate): new, to have some validity
8            checking for RsparseMatrix
9            * src/dgCMatrix.c (xRMatrix_validate): ditto
10            * src/dtCMatrix.c (tRMatrix_validate): ditto
11    
12    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
13    
14            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
15              lgRMatrix
16            * [r4568] DESCRIPTION: Prepare for bug-fix release
17            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
18              for declaration of cholmod_symmetry
19    
20    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
23            release.
24    
25    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
26    
27            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
28              functions - no longer used
29            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
30              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
31              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
32              Alloca
33    
34    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
35    
36            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
37              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
38              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
39              src/t_gCMatrix_colSums.c: more R_CheckStack()s
40    
41    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
42    
43            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
44              the required amount of memory then call M_numeric_as_chm_dense.
45            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
46              (like Calloc but calling alloca)
47    
48    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
51            and extended with more sophisticated 'col.names' option.
52            * NAMESPACE: export  printSparseMatrix()
53            * man/printSpMatrix.Rd: document, incl. examples
54    
55    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
56    
57            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
58              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
59              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
60    
61    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * DESCRIPTION (Version): 0.99875-4
64    
65            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
66            some dimnames perservation.
67    
68            * R/dsTMatrix.R (t-method): keep dimnames
69            * R/dtTMatrix.R:  ditto
70    
71            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
72            and ncol(.) < 10
73    
74            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
75            from Mutils.h
76    
77            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
78            e.g. in as(<ngCMatrix>, "matrix")
79    
80    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
81    
82            * [r4529] .: Create a branch for the API changes from the 0.99875
83              series to the 0.999375 series
84            * [r4530] DESCRIPTION, inst/include/Matrix.h,
85              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
86              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
87              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
88              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
89              as_cholmod_x functions
90    
91    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
92    
93            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
94              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
95              to Comparisons
96    
97    >>>>>>> .merge-right.r4561
98    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * DESCRIPTION (Version): 0.99875-3 ready to be released.
101    
102            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
103    
104            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
105            that should also work in a future version of R.
106    
107    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
110    
111            * R/sparseVector.R: more *sparseVector coercions, notably for
112            non - double ones.
113    
114    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
117              notably the new ones building on the new .Call(.)s:
118    
119            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
120            all 4 of [dlin]gCMatrix_colSums().
121    
122    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
123    
124            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
125            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
126              result
127    
128    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/kronecker.R: fix typo (could lead to inf.recursion)
131            * test/simple.R: testing that
132    
133            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
134            method as well (which can have arguments, show() can't).
135    
136    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
137    
138            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
139              added dgCMatrix_colSums for [col,row][Sums,Means]
140    
141    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
142    
143            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
144              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
145              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
146            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
147              class
148            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
149              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
150              row names to store the levels - duh!  Added an example.
151    
152    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * src/Csparse.c (Csparse_validate): check for *repeated* entries
155            thanks to example from Christian Buchta; with a test here:
156            * tests/simple.R:
157    
158    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
161            of colSums(*, sparseResult = TRUE)
162    
163    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
166            'na.rm = FALSE' as "everywhere" else in R.
167    
168    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
169    
170            * [r4421] src/CSparse_install.sh: Modify for new organization of
171              CSparse package
172            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
173              SuiteSparse
174            * [r4426] src/Makefile: add ./UFconfig to the include path for
175              compilation
176            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
177            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
178              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
179    
180    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
183            * R/sparseMatrix.R (prSpMatrix): now gives a message about
184            suppressed column names.
185    
186    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
187    
188            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
189              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
190              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
191              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
192              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
193              Remove warnings after change to const char* CHAR
194    
195    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
196    
197            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
198              type of M_cholmod_ssmult
199    
200    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
201    
202            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
203              src/init.c: Yet another cholmod export - cholmod_ssmult
204    
205    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * NAMESPACE: exported drop0(), since
208            * man/drop0.Rd: I have seen several cases, I really wanted to use
209            it, so our users may want too.
210    
211    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * man/colSums.Rd: separately document colSums() etc, since these
214            have the extra argument 'sparseResult'.
215    
216    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
219            * man/spMatrix.Rd: docu., including examples
220    
221            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
222            in order to make colMeans() etc fast *and* correct.
223            * R/sparseVector.R (replSPvec): "[<-" functionality for
224            sparseVectors; tested in
225            * tests/simple.R:
226    
227    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
230            (very) sparse Matrices; output similar to Matlab's print().
231    
232    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
233    
234            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
235            0-based, indices (Jose Quesada <quesada@gmail.com>).
236    
237    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
238    
239            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
240    
241    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/Auxiliaries.R (sparsapply): new utility, much faster than
244            tapply1() for large sparse matrices.
245    
246    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Matrix.R (dim<-): reshape now via sparseVector.
249    
250            * R/sparseVector.R: methods and function for
251            * R/AllClass.R: new "sparseVector" class and daughters.
252            * NAMESPACE: export new classes
253    
254    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * DESCRIPTION (Version): 0.99875-1
257            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
258    
259    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
262            indexing
263            * tests/indexing.R: test set for that.
264    
265    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
268            entries.
269            * tests/indexing.R(out): add regression test for it
270    
271    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
274            name for "!" method definitions.
275    
276    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/Tsparse.R (intI): new utility, used for "[" :
279                    Cleanup up there, and fixes for duplicated indices - more TODO!
280    
281            * tests/indexing.R(out): more tests
282    
283    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
284    
285            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
286            code that is now part of the R Lapack library.
287    
288            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
289            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
290    
291    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
294    
295    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
298            up with extraneous names '0'...'<n-1>'
299    
300    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dgTMatrix.R (mat2dgT): care about NAs
303    
304    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/kronecker.R: triangularity preserving methods
307    
308    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/kronecker.R: new file collecting kronecker() methods in one
311                    place.  Goal: become much faster!
312    
313    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
316            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
317            can be much faster.
318    
319            * tests/matprod.R: add regression tests for these (upper & lower).
320    
321    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * R/Matrix.R (diff): method for our Matrices.
324    
325            * R/sparseMatrix.R (isDiagonal): check dim()!
326    
327    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * R/Matrix.R (dim<-): new method for "reshape()" built on a
330            proposal from Tamas Papp.
331    
332    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
335    
336            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
337            rather define and export  cBind() and rBind() only.
338            --> useRs *must* change code that used to have cbind()/rbind() !!
339    
340            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
341            * R/bind.Rout.save: ditto
342    
343    2007-02-16  Douglas Bates  <bates@r-project.org>
344    
345            * DESCRIPTION (Date, Version): 0.9975-11 with new date
346            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
347            const modifier on declaration of the array 'valid'
348    
349    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
350    
351            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
352    
353    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
356    
357            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
358            * tests/simple.R: test the above and some of these coercions:
359    
360            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
361                    be careful to avoid infinite recursion, using new coercions in
362            * R/ngCMatrix.R and nsC... and ntC...
363            * R/lsparseMatrix.R: ditto
364    
365            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
366    
367            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
368            * R/Rsparse.R: reactivate .Call()s
369    
370            * tests/Class+Meth.R: a bit more on actual classes
371    
372    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
373    
374            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
375    
376    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * DESCRIPTION (Version): 0.9975-10 to upload
379    
380            * tests/Class+Meth.R (tstMatrixClass): require coercions to
381            specific classes less unconditionally.
382    
383            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
384    
385            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
386    
387            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
388            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
389            R_to_CMatrix segfaults on one platform.
390            Eliminate most coercion method to *specific* classes, and replace
391            with virtual classes coercions.
392    
393    
394    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
395    
396            * src/init.c: export the CHM...._validate() placeholders, since
397            they *are* called.
398    
399            * tests/Class+Meth.R (classCanCoerce): and starting to test
400            all as(<from>, <to>)
401    
402    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
405            * tests/indexing.R: tested now
406            * tests/indexing.Rout.save: updated
407    
408            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
409            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
410            appropriate.
411    
412            * NAMESPACE: export a trivial
413            * R/Matrix.R: drop() Matrix-method
414    
415            * R/AllClass.R: moved all prototypes to virtual super classes.
416    
417            * R/Rsparse.R: many more coercions to have less exceptions in
418            * tests/Class+Meth.R:
419    
420            * R/Ops.R (Compare): tweak for case with NA
421            * tests/simpl.R: hence another 'FIXME' eliminated
422    
423    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
426            objects.
427    
428            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
429              and more of "!", "&", "|", all, any; coercions
430    
431            * R/Rsparse.R: many coercions (which enable quite a few other
432            methods), thanks to enhancements in
433            * src/dgCMatrix.c (R_to_CMatrix): new, and
434            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
435            symmetric & triangular and ..RMatrix objects.
436    
437            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
438            renamed file from src/dsTMatrix.c;
439            now dealing with symmetric and triangular Tsparse coercions, both
440            to dense and general.
441    
442    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
445    
446            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
447            where sensible when the <numeric> is of length > 1.
448    
449    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/Matrix.R ([<-): for M[] <- value: fix length
452    
453    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
456            * R/ndenseMatrix.R: new coercions n* -> l*
457    
458    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
461    
462            * R/Ops.R ("Logic"): and other "Ops", many updates
463    
464    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * src/Mutils.h (SET_DimNames): new utility
467    
468            * R/Auxiliaries.R (nnzero): improved and now exported via
469    
470            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
471    
472    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/diagMatrix.R (!): fix typo.
475    
476    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/Auxiliaries.R (as_Csparse): and quite a few others:
479                    allow to pass class definition --> speedup
480            * R/sparseMatrix.R: apply the above
481    
482            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
483    
484            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
485            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
486            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
487    
488            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
489    
490            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
491            and use it for "sparse*" as well, since it's faster than the
492            as_Csparse(.) way.
493    
494    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
497    
498    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
501            as method for   M[ ij ] <- v
502            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
503    
504            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
505            FALSE answer
506    
507            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
508            * tests/indexing.R: test it, and some of the above
509    
510    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
511    
512            * R/Auxiliaries.R (is_duplicatedT): new utility
513    
514    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
515    
516            * src/init.c (R_init_Matrix): export cholmod_scale
517    
518    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
521            base::as.matrix to (x, ...)
522    
523    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
526            file; start using "Logic", hence
527    
528            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
529            * NAMESPACE: import and export "Logic"
530    
531    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
534            only needed previously to R version 2.5.0.
535    
536    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
539    
540            * R/Tsparse.R (replTmat): fix subassignment of triangular
541            * R/Csparse.R (replCmat): ditto
542            * tests/indexing.R: more tests, incl the above fix
543    
544    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * R/Auxiliaries.R (drop0): extend for non CSparse
547            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
548    
549            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
550                    use uplo correctly (!); other places: use uplo_P() macro
551    
552            * R/Csparse.R (replCmat): call diagU2N() when needed
553            * R/Tsparse.R (replTmat): ditto
554    
555            * src/dtCMatrix.c (tCMatrix_validate): new
556            * src/dtTMatrix.c (tTMatrix_validate): new, used in
557            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
558    
559            * R/diagMatrix.R (replDiag): to use in [<-
560    
561    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
564                    also more general diagU2N().
565    
566    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
569            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
570    
571    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * tests/bind.R: a few more cases
574            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
575    
576            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
577            * R/ddenseMatrix.R (cbind2/rbind2)
578            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
579            * tests/indexing.R
580            * tests/indexing.Rout.save: updated
581    
582    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
585            * tests/indexing.R
586    
587    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
588    
589            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
590            align with proper position of "0", i.e., right for integers.
591            argument 'align' by default is "fancy".
592    
593    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
596            * R/Csparse.R: and fix "Compare" for more cases.
597            * tests/Class+Meth.R: test some of these (m == m, m != m)
598    
599    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * R/lsparseMatrix.R: all() and any() methods
602            * R/ldenseMatrix.R:      ditto
603            * NAMESPACE, R/Matrix.R: ditto
604    
605            * man/all-methods.Rd: document them minimally
606    
607            * tests/simple.R: add a few examples for these
608    
609    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/Tsparse.R ([): fix long standing typo in symmetric case
612            * man/dsCMatrix-class.Rd: add example exhibiting the above case
613    
614    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
615    
616            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
617            to LL before converting to a sparse matrix. (The LDL form can be
618            converted to a sparse matrix but it is implicitly a unit
619            triangular matrix and a diagonal matrix overwritten on the diagonal.)
620    
621    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
622    
623            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
624    
625    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
626    
627            * DESCRIPTION (Version): updated -> release 0.9975-7
628            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
629    
630    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
633    
634    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
635    
636            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
637            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
638            is exactly singular.
639    
640    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * DESCRIPTION (Date): updated -> release 0.9975-6
643    
644    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
647            now returns symmetric.
648    
649            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
650    
651            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
652            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
653    
654            * R/Auxiliaries.R (.type.kind): added
655    
656    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
659            running src/CSparse_install.sh
660    
661            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
662    
663    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
666            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
667    
668            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
669    
670            * tests/Class+Meth.R (tstMatrixClass): now assure
671            the (important in method programming) property :
672    
673                    ###>>  Every "Matrix" is either
674                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
675    
676                    (where "*" stands for "Matrix")
677    
678            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
679    
680            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
681            * tests/validObj.R: checks for "comparison"
682    
683            * R/sparseMatrix.R ([): improved indexing for sparse;
684                    trying to keep <symmetric>[ n, n] symmmetric
685    
686            * tests/indexing.R: indexing for logical sparse now ok
687    
688    
689    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
690    
691            * src/Tsparse.c: use xTsparse_validate() , and hence remove
692    
693            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
694    
695    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
698    
699            * tests/simple.R: validObject() checking the above.
700    
701            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
702            replacing both dgCMatrix_validate and lgCM*.
703    
704            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
705            fix dimnames setting in other places.
706            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
707    
708    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
711    
712            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
713            symmetry test, via
714            * R/Auxiliaries.R (.as.dgC.0.factors):
715    
716    2006-11-01  Douglas Bates  <bates@r-project.org>
717    
718            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
719            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
720            <CsparseMatrix>) added
721    
722    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * tests/matprod.R: add a variation of Harri's example
725    
726            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
727            recursive infinitely.
728    
729            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
730    
731            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
732    
733    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
736            matrix if possible; test m+m == 2*m; now test dgRMatrix.
737            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
738            satisfy the above test.
739    
740    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
741    
742            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
743    
744            * R/dgCMatrix.R: solve(a, b="missing") based on
745            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
746            RHS = NULL.
747    
748            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
749            add more (needed) [t]crossprod() methods.
750    
751            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
752    
753            * R/Auxiliaries.R (as_CspClass): cleanup
754            (drop0): internal utility for "Csparse_drop(*, 0)"
755            (.bail.out.2): encourage active feedback
756    
757    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/dMatrix.R(Compare): new(), then slots [no validity check]
760    
761            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
762            non-valid or 'sorted' case).
763    
764            * R/dsparseMatrix.R: add "chol" method.
765            * R/ddenseMatrix.R: ditto
766    
767            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
768            * NAMESPACE (Ops)
769            * R/diagMatrix.R (diag2T): simple utility used "higher level"
770            coercion; deprecating direct lower level coercions.
771    
772            * R/*.R (seq): use seq_len() and seq_along() where possible.
773    
774    
775    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * DESCRIPTION (Version): 0.9975-5 ready for release
778    
779    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
780    
781            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
782    
783    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * R/AllClass.R (corMatrix): add 'validity' check;
786                    comment out unused "LDL" class definition
787            * NAMESPACE: mention, but do not export "LDL" class
788            * R/corMatrix.R: new (simple), needed for R-devel with
789            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
790              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
791    
792    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
793    
794            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
795            use Rprintf and R's error handling.
796    
797    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
800            * tests/matprod.R: add tests for the bug fixed.
801    
802    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
803    
804            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
805            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
806    
807    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
808    
809            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
810    
811    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
812    
813            * DESCRIPTION (Version): 0.9975-3
814    
815            * R/diagMatrix.R (bdiag): new function constructing block diagonal
816            (sparse) matrices.
817            * man/bdiag.Rd: docu + examples
818    
819            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
820    
821            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
822            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
823    
824            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
825            that result is sparse or diagonal (and not dense).
826    
827            * man/Subassign-methods.Rd: fix examples
828    
829            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
830            should always return a sparse (and not sometimes a diagonal) matrix.
831    
832    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
835    
836    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
837    
838            * DESCRIPTION (Version): 0.9975-2
839    
840            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
841    
842    2006-10-02  Douglas Bates  <bates@R-project.org>
843    
844            * tests/dg_Matrix.R: Simplify test taking into account new code.
845    
846    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
849    
850            * R/lsTMatrix.R: new files w/ missing methods
851            * R/nsTMatrix.R:  "  'for completeness'
852    
853            * tests/Class+Meth.R: a bit less 'not.ok.classes'
854    
855            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
856    
857    
858    2006-09-28  Douglas Bates  <bates@R-project.org>
859    
860            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
861            included.
862    
863            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
864            Export C-callable functions used in Zt_create in lme4.
865    
866    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * DESCRIPTION (Version): 0.9975-1
869    
870            * tests/simple.R: less checks fail; using NA, found that our
871                    kronecker() is not base-compatible with NA's.
872    
873            * R/dMatrix.R: "Compare" method now implemented for all cases
874    
875            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
876    
877            * man/dtpMatrix-class.Rd: mention length of 'x' slot
878    
879            * src/dtpMatrix.c (dtpMatrix_validate): fix check
880            * src/dspMatrix.c (dspMatrix_validate): ditto
881    
882            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
883              including coercion to [nl]tTMatrix.
884    
885            * R/diagMatrix.R (show): print a header line as for other classes.
886    
887    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
888    
889            * src/Makefile.win (SUBDIRS): fix typo
890    
891    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
894    
895    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
896    
897            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
898            symmetric and y missing in R code using %*% (cholmod_aat doesn't
899            accept a symmetric matrix).
900            * tests/group-methods.R: Uncomment test of crossprod applied to
901            lsCMatrix objects.
902    
903    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
904    
905            * R/AllClass.R (symmetricMatrix): add validity method (available
906            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
907    
908            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
909    
910            * tests/indexing.Rout.save:
911            * tests/indexing.R: additions, mainly for 'lsparse'
912    
913            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
914            case.
915    
916            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
917    
918    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
921                    as 'N' (1-letter - Ok?)
922    
923            * tests/group-methods.R: add test for logical + NAs
924    
925            * R/dMatrix.R ("Compare"): fix to work with NA's
926    
927            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
928    
929            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
930                    which is implemented.
931    
932    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
933    
934            * src/chm_common.c: coerce logical <-> double instead of
935            typecasting;  needed for "l" matrix handling in cholmod.
936    
937            * tests/other-pkgs.R (graph): small extension in "graph" checks.
938    
939            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
940            (Tsp2grNEL): other fixes needed
941    
942    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
943    
944            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
945                    Matrices, since "lMatrix", also "lsparseM" can have NA
946            * R/ndenseMatrix.R, etc: new source files
947            * man/nsparseMatrix-classes.Rd, etc: new help files
948            * tests/: adaptions
949            * src/chm_common.c (chm_dense_to_SEXP): and others:
950                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
951            * src/Csparse.c, etc: ditto
952    
953    2006-09-11  Douglas Bates  <bates@R-project.org>
954    
955            * src/Mutils.[ch],init.c inst/include/*.h: Move the
956            alloc_d**Matrix functions to the lme4 package.
957    
958    2006-09-09  Douglas Bates  <bates@R-project.org>
959    
960            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
961            fixed
962    
963    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * R/lMatrix.R: new
966    
967            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
968    
969            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
970            * man/tcrossprod.Rd: ditto
971    
972    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
973    
974            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
975            for exported functions
976            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
977            Remove partitioning algorithms for sparse matrix reordering.  The
978            copyright on the Metis code was problematic and the methods were
979            rarely used.
980            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
981            operations are now done entirely in CHOLMOD code.
982    
983    2006-09-06  Douglas Bates  <bates@R-project.org>
984    
985            * src/Mutils.h: Remove functions that are no longer used.
986    
987    2006-09-04  Douglas Bates  <bates@R-project.org>
988    
989            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
990            * src/DEPS.mkf: update
991    
992    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
993    
994            * created branches/Matrix-for-R-2.3.x;  on trunk: do
995            * DESCRIPTION (Version): 0.9975-0
996            (Depends): R (>= 2.4.0)
997    
998    2006-09-01  Douglas Bates  <bates@R-project.org>
999    
1000            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1001    
1002    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1003    
1004            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1005            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1006    
1007            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1008    
1009    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1010    
1011            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1012            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1013            * R/dsparseMatrix.R: ditto
1014            * R/Csparse.R: ditto
1015    
1016    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1017    
1018            * R/dMatrix.R (Compare): improve availability of "<", etc
1019            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1020    
1021    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1024            of a 0-index which was used as 1-index (..hmm)
1025    
1026            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1027    
1028            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1029            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1030            (.is.diagonal): ditto
1031    
1032            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1033    
1034            * R/Matrix.R (Matrix): also work for NA data
1035    
1036    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1037    
1038            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1039            in all cases.
1040    
1041    2006-08-27  Douglas Bates  <bates@R-project.org>
1042    
1043            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1044            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1045    
1046    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1047    
1048            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1049            subclasses of "ddenseMatrix"
1050            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1051            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1052            instead of half dozen specialized ones.
1053    
1054    2006-08-25  Douglas Bates  <bates@R-project.org>
1055    
1056            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1057            <tillard@cirad.fr> - ordering standard errors to match effects.
1058    
1059    2006-08-24  Douglas Bates  <bates@R-project.org>
1060    
1061            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1062            on R_ldl.
1063            * R/lCholCMatrix.R,
1064            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1065            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1066            * many files in ./R and ./src: Use more general version of
1067            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1068            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1069            dtpMatrix, dspMatrix and dppMatrix conversions.
1070    
1071    
1072    2006-08-23  Douglas Bates  <bates@R-project.org>
1073    
1074            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1075            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1076            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1077            dgeMatrix_crossprod (may need to do this in other places).
1078            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1079            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1080    
1081    2006-08-22  Douglas Bates  <bates@R-project.org>
1082    
1083            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1084            types of classed Matrices, matrices or numeric or logical vectors.
1085            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1086            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1087            to Mutils.h (as an inline) and change name to Matrix_check_class;
1088            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1089            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1090            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1091            * src/Csparse.c: use diag_P and uplo_P macros.
1092    
1093    2006-08-21  Douglas Bates  <bates@R-project.org>
1094    
1095            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1096            valgrind.
1097            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1098            inverses.
1099            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1100            -Wall warnings.
1101            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1102            Use dup_mMatrix_as_dgeMatrix.
1103    
1104    2006-08-20  Douglas Bates  <bates@R-project.org>
1105    
1106            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1107            * tests/sparseQR.R: Added
1108            * man/sparseQR-class.Rd: Document methods for qr.* generics
1109            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1110    
1111    2006-08-19  Douglas Bates  <bates@R-project.org>
1112    
1113            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1114            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1115            and qr.fitted.
1116            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1117            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1118    
1119    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1120    
1121            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1122            the base version has no "..." argument.
1123    
1124            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1125    
1126            * R/Matrix.R: define and
1127            * NAMESPACE: export as.numeric() and as.logical() methods.
1128                    Let's hope these do not badly slow down something...
1129            Finally export the zapsmall() method.
1130    
1131    2006-08-17  Douglas Bates  <bates@R-project.org>
1132    
1133            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1134            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1135            * src/dtCMatrix.c :Remove code that is no longer used
1136            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1137    
1138    2006-08-14  Douglas Bates  <bates@R-project.org>
1139    
1140            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1141            Csparse_to_logical and Csparse_symmetric_to_general.
1142            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1143            coercion methods between CsparseMatrix and TsparseMatrix.
1144    
1145    2006-08-14  Douglas Bates  <bates@R-project.org>
1146    
1147            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1148            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1149            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1150            possible.
1151    
1152    2006-08-12  Douglas Bates  <bates@R-project.org>
1153    
1154            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1155              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1156              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1157              generalize conversions between TsparseMatrix, CsparseMatrix,
1158              denseMatrix and matrix.  Preserve triangularity property and
1159              propagate Dimnames in the easy cases.
1160    
1161    2006-08-10  Douglas Bates  <bates@R-project.org>
1162    
1163            * src/lmer.c: adjust checks in glmer_init for S4SXP
1164            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1165            before S4SXP but for the wrong reasons.
1166    
1167    2006-08-08  Douglas Bates  <bates@R-project.org>
1168    
1169            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1170            Later modified to return the upper triangle only.
1171            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1172    
1173    2006-08-07  Douglas Bates  <bates@R-project.org>
1174    
1175            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1176            R-level conversion to a sparse symmetric class.
1177            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1178            Remove conversion to sparse symmetric classes (now done in C code).
1179    
1180    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1181    
1182            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1183            * man/band.Rd:  adapt the \dontshow{} unit test.
1184    
1185    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1186    
1187            * DESCRIPTION (Version): 0.995-14  for CRAN
1188    
1189            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1190    
1191            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1192            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1193    
1194            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1195            * R/Tsparse.R (tril, triu, band): methods
1196            * R/dgRMatrix.R (tril, ...):    ditto
1197            * man/band.Rd:                  ditto
1198    
1199    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1200    
1201            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1202                    to be up-to-date automatically.
1203    
1204    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1205    
1206            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1207    
1208            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1209            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1210            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1211            such that the S4 objects are always created by the current version
1212            of R and 'Matrix' class definitions.
1213    
1214    2006-08-01  Douglas Bates  <bates@R-project.org>
1215    
1216            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1217            inst/external/test3comp.rda: Added warnings for convergence on
1218            boundary and test cases.
1219    
1220            * src/lmer.c (mer_postVar): Modified to return the variances that
1221            are marginal to the fixed effects, not conditional on them (which
1222            is what the bVar slot contents represent).
1223    
1224    2006-07-31  Douglas Bates  <bates@R-project.org>
1225    
1226            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1227            function which calls the C function mer_hat_trace2.
1228    
1229            * man/ranef.Rd: Include description of "postVar" argument and
1230            producing a caterpillar plot.
1231    
1232    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1233    
1234            * NAMESPACE:    change  "correlation" to "corMatrix"
1235            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1236            * R/dpoMatrix.R: ditto
1237            * R/lmer.R:      ditto
1238    
1239    2006-07-28  Douglas Bates  <bates@R-project.org>
1240    
1241            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1242            RZXinv slot's contents into a separate internal function that can
1243            be used in mer_hat_trace.
1244    
1245    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1246    
1247            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1248            via new smart
1249            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1250            utility functions.
1251    
1252    
1253    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1254    
1255            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1256            matrices when appropriate; band() even symmetric ones.
1257            (replCmat): extend to potentially all "CsparseMatrix"
1258            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1259            allow subassignment for special sparse matrices.
1260    
1261            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1262    
1263            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1264            argument; in glmer_*(): print only if(verbose).
1265    
1266            speed-optimize a few places by moving REAL(.) out of loops.
1267    
1268            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1269    
1270    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1271    
1272            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1273                    since that wrongly triggers also for M[ logi , ]
1274    
1275            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1276            a symmetric matrix that results in a non-symmetric one.
1277            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1278    
1279            * R/dMatrix.R: make round(M) work as round(M, 0)
1280    
1281            * R/dgTMatrix.R (image): coordinate system and axis now use
1282            1-based indices, not 0-based ones.
1283    
1284            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1285            * tests/indexing.R: test it.
1286    
1287            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1288            * man/isSymmetric-methods.Rd: and document it.
1289    
1290            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1291            * man/SparseM-conv.Rd: docu them
1292    
1293            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1294                    for 'SparseM' conversions
1295    
1296    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1297    
1298            * R/Matrix.R (head): added head() and tail() methods.
1299    
1300    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1301    
1302            * DESCRIPTION (Version): 0.995-12 released to CRAN
1303    
1304    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1305    
1306            * tests/simple.R: add check for correct dsT -> dgT coercion;
1307                    add check for correct printing of symmetric sparse matrices.
1308    
1309            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1310            for sparse symmetric matrices.
1311    
1312            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1313            diagonal twice.
1314    
1315    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1316    
1317            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1318            being applied to the x slot (detected by Brian Ripley).
1319    
1320    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1321    
1322            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1323    
1324            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1325    
1326    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1327    
1328            * src/lgCMatrix.c (lgCMatrix_diag): new function
1329            * R/lgCMatrix.R (diag): for new method
1330    
1331            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1332                 ==> construction of illegal "*gTMatrix" via new() should
1333                 now be much less easy:
1334            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1335    
1336            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1337                    directly.
1338            * man/Matrix.Rd: documents it.
1339    
1340    2006-07-06  Douglas Bates  <bates@R-project.org>
1341    
1342            * src/pedigree.c (pedigree_inbreeding): Correction in
1343            initialization.  This function is not currently being used and is
1344            not fully tested.
1345    
1346            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1347            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1348            objects.  Modified validity check on pedigree objects to account
1349            for nonparallel patterns of missingness of parents.
1350    
1351            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1352            class.
1353    
1354    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1355    
1356            * R/pMatrix.R: coercion pMatrix -> Tsparse
1357    
1358    2006-06-12  Douglas Bates  <bates@R-project.org>
1359    
1360            * DESCRIPTION (Version): 0.995-11 released to CRAN
1361    
1362            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1363            the output from mcmcsamp.
1364    
1365    2006-06-10  Douglas Bates  <bates@R-project.org>
1366    
1367            * R/lmer.R (simulestimate): added C code for calculating the trace
1368            of the hat matrix.
1369    
1370    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1371    
1372            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1373            classes.
1374            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1375    
1376    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1377    
1378            * R/dgTMatrix.R (colSums): etc. All four of
1379            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1380            all "Matrices".
1381    
1382    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1383    
1384            * R/lmer.R (panel.ci): Add a reference line at zero and a
1385            background grid to the qqmath plot of ranef.lmer.
1386    
1387    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1388    
1389            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1390            grouping factors to be specified in the formula as (1|foo/bar).
1391    
1392    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1393    
1394            * R/lmer.R (findbars and others): Change check of is.numeric to
1395            !is.language to resolve the bug reported by Jacob Wegelin.
1396    
1397            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1398            code to evaluate inbreeding coefficients without calculating T,
1399            based on code in Sargolzaei and Iwaisaki's paper.
1400    
1401  2006-05-27  Douglas Bates  <bates@stat.wisc.edu>  2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1402    
1403          * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local          * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
# Line 9  Line 1409 
1409    
1410          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1411          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.
1412          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1413    
1414    
1415  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 132  Line 1532 
1532          * 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)
1533          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1534          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1535          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1536    
1537  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1538    
# Line 336  Line 1736 
1736  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1737    
1738          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1739          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1740          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1741    
1742  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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