SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

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

revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 2069, Sun Sep 23 17:35:17 2007 UTC
# Line 1  Line 1 
1    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4778] R/AllGeneric.R: Check R version before defining generics for
4              primitives
5    
6    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
9            * tests/indexing.R: add new regression for the above cases.
10    
11    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * src/Mutils.h (__sun): clause for alloca.h on Solaris
14    
15    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * DESCRIPTION (Date, Version): 0.999375-2
18    
19    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/HBMM.R (readMM): make work for pattern matrices as well
22    
23    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
24    
25            * [r4730] src/Mutils.h: declare alloca
26            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
27              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
28              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
29              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
30              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
31              methods; switch writeMM to use CHOLMOD code; repair readMM
32    
33    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
36            Oehlschlaegel's ... result type still to be discussed!
37    
38    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * man/image-methods.Rd: new, combining all image() methods
41    
42    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
45            to work via dgC...
46    
47            * R/Matrix.R (Matrix): special treatment for "table" (S3)
48    
49    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * R/dgTMatrix.R (image): change defaults to
52                    aspect = "iso", colorkey = FALSE
53    
54    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
57            must copy its *expanded* x slot before LAPACK call.
58    
59            * tests/matprod.R: test the last days' changes.
60    
61    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
62    
63            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
64              as well as in sources
65            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
66              Lapack call
67    
68    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
71                    ("Matrix", "matrix") which is needed in some cases.
72            Ditto for solve().
73    
74            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
75            infinite recursion in dispatch for some cases.
76    
77    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
78    
79            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
80              so pointers match
81    
82    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * DESCRIPTION (Date): set ready for release -- 0.999375-1
85    
86    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
87    
88            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
89              src/chm_common.c, src/chm_common.h: Change API for
90              numeric_as_chm_dense and N_AS_CHM_DN
91    
92    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
95            * tests/matprod.R: regr.test for it
96    
97    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
100            * tests/group-methods.R: and regression-test it
101    
102    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
103    
104            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
105              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
106              triplet_to_sparse, documentation, use typedefs
107    
108    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * man/dpoMatrix-class.Rd: added 'corMatrix' example
111    
112            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
113            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
114            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
115    
116            * R/lsparseMatrix.R: bug fix in "all" method
117            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
118    
119            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
120            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
121                    + matrix |-> nMatrix coercion
122            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
123            * man/pMatrix-class.Rd: ditto
124    
125            * R/Matrix.R (Summary): method for non-dMatrix
126    
127            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
128            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
129                    test all Summary methods.
130    
131    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
134    
135    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
138    
139            * R/pMatrix.R (t?crossprod): methods for pMatrix
140    
141    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
142    
143            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
144    
145    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
146    
147            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
148              trying to fix a subtle bug - which has been somewhere else.
149    
150    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
151    
152            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
153              solve the bug
154    
155    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * src/dgCMatrix.c (compressed_to_TMatrix):
158    
159    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * src/Csparse.c (Rsparse_validate): new, to have some validity
162            checking for RsparseMatrix
163            * src/dgCMatrix.c (xRMatrix_validate): ditto
164            * src/dtCMatrix.c (tRMatrix_validate): ditto
165    
166    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
167    
168            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
169              lgRMatrix
170            * [r4568] DESCRIPTION: Prepare for bug-fix release
171            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
172              for declaration of cholmod_symmetry
173    
174    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
177            release.
178    
179    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
180    
181            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
182              functions - no longer used
183            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
184              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
185              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
186              Alloca
187    
188    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
189    
190            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
191              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
192              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
193              src/t_gCMatrix_colSums.c: more R_CheckStack()s
194    
195    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
196    
197            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
198              the required amount of memory then call M_numeric_as_chm_dense.
199            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
200              (like Calloc but calling alloca)
201    
202    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
205            and extended with more sophisticated 'col.names' option.
206            * NAMESPACE: export  printSparseMatrix()
207            * man/printSpMatrix.Rd: document, incl. examples
208    
209    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
210    
211            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
212              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
213              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
214    
215    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * DESCRIPTION (Version): 0.99875-4
218    
219            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
220            some dimnames perservation.
221    
222            * R/dsTMatrix.R (t-method): keep dimnames
223            * R/dtTMatrix.R:  ditto
224    
225            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
226            and ncol(.) < 10
227    
228            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
229            from Mutils.h
230    
231            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
232            e.g. in as(<ngCMatrix>, "matrix")
233    
234    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
235    
236            * [r4529] .: Create a branch for the API changes from the 0.99875
237              series to the 0.999375 series
238            * [r4530] DESCRIPTION, inst/include/Matrix.h,
239              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
240              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
241              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
242              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
243              as_cholmod_x functions
244    
245    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
246    
247            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
248              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
249              to Comparisons
250    
251    >>>>>>> .merge-right.r4561
252    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * DESCRIPTION (Version): 0.99875-3 ready to be released.
255    
256            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
257    
258            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
259            that should also work in a future version of R.
260    
261    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
264    
265            * R/sparseVector.R: more *sparseVector coercions, notably for
266            non - double ones.
267    
268    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
271              notably the new ones building on the new .Call(.)s:
272    
273            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
274            all 4 of [dlin]gCMatrix_colSums().
275    
276    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
277    
278            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
279            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
280              result
281    
282    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/kronecker.R: fix typo (could lead to inf.recursion)
285            * test/simple.R: testing that
286    
287            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
288            method as well (which can have arguments, show() can't).
289    
290    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
291    
292            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
293              added dgCMatrix_colSums for [col,row][Sums,Means]
294    
295    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
296    
297            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
298              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
299              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
300            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
301              class
302            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
303              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
304              row names to store the levels - duh!  Added an example.
305    
306    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * src/Csparse.c (Csparse_validate): check for *repeated* entries
309            thanks to example from Christian Buchta; with a test here:
310            * tests/simple.R:
311    
312    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
315            of colSums(*, sparseResult = TRUE)
316    
317    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
320            'na.rm = FALSE' as "everywhere" else in R.
321    
322    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
323    
324            * [r4421] src/CSparse_install.sh: Modify for new organization of
325              CSparse package
326            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
327              SuiteSparse
328            * [r4426] src/Makefile: add ./UFconfig to the include path for
329              compilation
330            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
331            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
332              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
333    
334    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
337            * R/sparseMatrix.R (prSpMatrix): now gives a message about
338            suppressed column names.
339    
340    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
341    
342            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
343              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
344              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
345              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
346              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
347              Remove warnings after change to const char* CHAR
348    
349    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
350    
351            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
352              type of M_cholmod_ssmult
353    
354    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
355    
356            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
357              src/init.c: Yet another cholmod export - cholmod_ssmult
358    
359    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * NAMESPACE: exported drop0(), since
362            * man/drop0.Rd: I have seen several cases, I really wanted to use
363            it, so our users may want too.
364    
365    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * man/colSums.Rd: separately document colSums() etc, since these
368            have the extra argument 'sparseResult'.
369    
370    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
373            * man/spMatrix.Rd: docu., including examples
374    
375            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
376            in order to make colMeans() etc fast *and* correct.
377            * R/sparseVector.R (replSPvec): "[<-" functionality for
378            sparseVectors; tested in
379            * tests/simple.R:
380    
381    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
384            (very) sparse Matrices; output similar to Matlab's print().
385    
386    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
387    
388            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
389            0-based, indices (Jose Quesada <quesada@gmail.com>).
390    
391    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
392    
393            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
394    
395    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/Auxiliaries.R (sparsapply): new utility, much faster than
398            tapply1() for large sparse matrices.
399    
400    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/Matrix.R (dim<-): reshape now via sparseVector.
403    
404            * R/sparseVector.R: methods and function for
405            * R/AllClass.R: new "sparseVector" class and daughters.
406            * NAMESPACE: export new classes
407    
408    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * DESCRIPTION (Version): 0.99875-1
411            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
412    
413    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
416            indexing
417            * tests/indexing.R: test set for that.
418    
419    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
422            entries.
423            * tests/indexing.R(out): add regression test for it
424    
425    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
428            name for "!" method definitions.
429    
430    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * R/Tsparse.R (intI): new utility, used for "[" :
433                    Cleanup up there, and fixes for duplicated indices - more TODO!
434    
435            * tests/indexing.R(out): more tests
436    
437    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
438    
439            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
440            code that is now part of the R Lapack library.
441    
442            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
443            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
444    
445    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
448    
449    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
452            up with extraneous names '0'...'<n-1>'
453    
454    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
455    
456            * R/dgTMatrix.R (mat2dgT): care about NAs
457    
458    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/kronecker.R: triangularity preserving methods
461    
462    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/kronecker.R: new file collecting kronecker() methods in one
465                    place.  Goal: become much faster!
466    
467    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
470            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
471            can be much faster.
472    
473            * tests/matprod.R: add regression tests for these (upper & lower).
474    
475    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/Matrix.R (diff): method for our Matrices.
478    
479            * R/sparseMatrix.R (isDiagonal): check dim()!
480    
481    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * R/Matrix.R (dim<-): new method for "reshape()" built on a
484            proposal from Tamas Papp.
485    
486    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
489    
490            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
491            rather define and export  cBind() and rBind() only.
492            --> useRs *must* change code that used to have cbind()/rbind() !!
493    
494            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
495            * R/bind.Rout.save: ditto
496    
497    2007-02-16  Douglas Bates  <bates@r-project.org>
498    
499            * DESCRIPTION (Date, Version): 0.9975-11 with new date
500            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
501            const modifier on declaration of the array 'valid'
502    
503    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
504    
505            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
506    
507    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
510    
511            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
512            * tests/simple.R: test the above and some of these coercions:
513    
514            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
515                    be careful to avoid infinite recursion, using new coercions in
516            * R/ngCMatrix.R and nsC... and ntC...
517            * R/lsparseMatrix.R: ditto
518    
519            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
520    
521            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
522            * R/Rsparse.R: reactivate .Call()s
523    
524            * tests/Class+Meth.R: a bit more on actual classes
525    
526    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
527    
528            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
529    
530    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * DESCRIPTION (Version): 0.9975-10 to upload
533    
534            * tests/Class+Meth.R (tstMatrixClass): require coercions to
535            specific classes less unconditionally.
536    
537            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
538    
539            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
540    
541            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
542            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
543            R_to_CMatrix segfaults on one platform.
544            Eliminate most coercion method to *specific* classes, and replace
545            with virtual classes coercions.
546    
547    
548    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
549    
550            * src/init.c: export the CHM...._validate() placeholders, since
551            they *are* called.
552    
553            * tests/Class+Meth.R (classCanCoerce): and starting to test
554            all as(<from>, <to>)
555    
556    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
559            * tests/indexing.R: tested now
560            * tests/indexing.Rout.save: updated
561    
562            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
563            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
564            appropriate.
565    
566            * NAMESPACE: export a trivial
567            * R/Matrix.R: drop() Matrix-method
568    
569            * R/AllClass.R: moved all prototypes to virtual super classes.
570    
571            * R/Rsparse.R: many more coercions to have less exceptions in
572            * tests/Class+Meth.R:
573    
574            * R/Ops.R (Compare): tweak for case with NA
575            * tests/simpl.R: hence another 'FIXME' eliminated
576    
577    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
580            objects.
581    
582            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
583              and more of "!", "&", "|", all, any; coercions
584    
585            * R/Rsparse.R: many coercions (which enable quite a few other
586            methods), thanks to enhancements in
587            * src/dgCMatrix.c (R_to_CMatrix): new, and
588            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
589            symmetric & triangular and ..RMatrix objects.
590    
591            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
592            renamed file from src/dsTMatrix.c;
593            now dealing with symmetric and triangular Tsparse coercions, both
594            to dense and general.
595    
596    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
599    
600            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
601            where sensible when the <numeric> is of length > 1.
602    
603    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * R/Matrix.R ([<-): for M[] <- value: fix length
606    
607    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
610            * R/ndenseMatrix.R: new coercions n* -> l*
611    
612    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
615    
616            * R/Ops.R ("Logic"): and other "Ops", many updates
617    
618    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * src/Mutils.h (SET_DimNames): new utility
621    
622            * R/Auxiliaries.R (nnzero): improved and now exported via
623    
624            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
625    
626    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * R/diagMatrix.R (!): fix typo.
629    
630    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * R/Auxiliaries.R (as_Csparse): and quite a few others:
633                    allow to pass class definition --> speedup
634            * R/sparseMatrix.R: apply the above
635    
636            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
637    
638            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
639            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
640            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
641    
642            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
643    
644            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
645            and use it for "sparse*" as well, since it's faster than the
646            as_Csparse(.) way.
647    
648    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
651    
652    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
655            as method for   M[ ij ] <- v
656            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
657    
658            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
659            FALSE answer
660    
661            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
662            * tests/indexing.R: test it, and some of the above
663    
664    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
665    
666            * R/Auxiliaries.R (is_duplicatedT): new utility
667    
668    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
669    
670            * src/init.c (R_init_Matrix): export cholmod_scale
671    
672    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
675            base::as.matrix to (x, ...)
676    
677    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
678    
679            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
680            file; start using "Logic", hence
681    
682            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
683            * NAMESPACE: import and export "Logic"
684    
685    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
688            only needed previously to R version 2.5.0.
689    
690    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
693    
694            * R/Tsparse.R (replTmat): fix subassignment of triangular
695            * R/Csparse.R (replCmat): ditto
696            * tests/indexing.R: more tests, incl the above fix
697    
698    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * R/Auxiliaries.R (drop0): extend for non CSparse
701            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
702    
703            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
704                    use uplo correctly (!); other places: use uplo_P() macro
705    
706            * R/Csparse.R (replCmat): call diagU2N() when needed
707            * R/Tsparse.R (replTmat): ditto
708    
709            * src/dtCMatrix.c (tCMatrix_validate): new
710            * src/dtTMatrix.c (tTMatrix_validate): new, used in
711            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
712    
713            * R/diagMatrix.R (replDiag): to use in [<-
714    
715    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
718                    also more general diagU2N().
719    
720    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
723            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
724    
725    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * tests/bind.R: a few more cases
728            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
729    
730            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
731            * R/ddenseMatrix.R (cbind2/rbind2)
732            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
733            * tests/indexing.R
734            * tests/indexing.Rout.save: updated
735    
736    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
739            * tests/indexing.R
740    
741    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
744            align with proper position of "0", i.e., right for integers.
745            argument 'align' by default is "fancy".
746    
747    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
750            * R/Csparse.R: and fix "Compare" for more cases.
751            * tests/Class+Meth.R: test some of these (m == m, m != m)
752    
753    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * R/lsparseMatrix.R: all() and any() methods
756            * R/ldenseMatrix.R:      ditto
757            * NAMESPACE, R/Matrix.R: ditto
758    
759            * man/all-methods.Rd: document them minimally
760    
761            * tests/simple.R: add a few examples for these
762    
763    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * R/Tsparse.R ([): fix long standing typo in symmetric case
766            * man/dsCMatrix-class.Rd: add example exhibiting the above case
767    
768    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
769    
770            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
771            to LL before converting to a sparse matrix. (The LDL form can be
772            converted to a sparse matrix but it is implicitly a unit
773            triangular matrix and a diagonal matrix overwritten on the diagonal.)
774    
775    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
776    
777            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
778    
779    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
780    
781            * DESCRIPTION (Version): updated -> release 0.9975-7
782            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
783    
784    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
787    
788    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
789    
790            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
791            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
792            is exactly singular.
793    
794    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
795    
796            * DESCRIPTION (Date): updated -> release 0.9975-6
797    
798    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
801            now returns symmetric.
802    
803            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
804    
805            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
806            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
807    
808            * R/Auxiliaries.R (.type.kind): added
809    
810    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
813            running src/CSparse_install.sh
814    
815            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
816    
817    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
818    
819            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
820            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
821    
822            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
823    
824            * tests/Class+Meth.R (tstMatrixClass): now assure
825            the (important in method programming) property :
826    
827                    ###>>  Every "Matrix" is either
828                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
829    
830                    (where "*" stands for "Matrix")
831    
832            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
833    
834            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
835            * tests/validObj.R: checks for "comparison"
836    
837            * R/sparseMatrix.R ([): improved indexing for sparse;
838                    trying to keep <symmetric>[ n, n] symmmetric
839    
840            * tests/indexing.R: indexing for logical sparse now ok
841    
842    
843    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * src/Tsparse.c: use xTsparse_validate() , and hence remove
846    
847            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
848    
849    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
850    
851            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
852    
853            * tests/simple.R: validObject() checking the above.
854    
855            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
856            replacing both dgCMatrix_validate and lgCM*.
857    
858            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
859            fix dimnames setting in other places.
860            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
861    
862    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
863    
864            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
865    
866            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
867            symmetry test, via
868            * R/Auxiliaries.R (.as.dgC.0.factors):
869    
870    2006-11-01  Douglas Bates  <bates@r-project.org>
871    
872            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
873            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
874            <CsparseMatrix>) added
875    
876    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
877    
878            * tests/matprod.R: add a variation of Harri's example
879    
880            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
881            recursive infinitely.
882    
883            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
884    
885            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
886    
887    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
888    
889            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
890            matrix if possible; test m+m == 2*m; now test dgRMatrix.
891            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
892            satisfy the above test.
893    
894    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
895    
896            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
897    
898            * R/dgCMatrix.R: solve(a, b="missing") based on
899            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
900            RHS = NULL.
901    
902            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
903            add more (needed) [t]crossprod() methods.
904    
905            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
906    
907            * R/Auxiliaries.R (as_CspClass): cleanup
908            (drop0): internal utility for "Csparse_drop(*, 0)"
909            (.bail.out.2): encourage active feedback
910    
911    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
912    
913            * R/dMatrix.R(Compare): new(), then slots [no validity check]
914    
915            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
916            non-valid or 'sorted' case).
917    
918            * R/dsparseMatrix.R: add "chol" method.
919            * R/ddenseMatrix.R: ditto
920    
921            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
922            * NAMESPACE (Ops)
923            * R/diagMatrix.R (diag2T): simple utility used "higher level"
924            coercion; deprecating direct lower level coercions.
925    
926            * R/*.R (seq): use seq_len() and seq_along() where possible.
927    
928    
929    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * DESCRIPTION (Version): 0.9975-5 ready for release
932    
933    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
934    
935            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
936    
937    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
938    
939            * R/AllClass.R (corMatrix): add 'validity' check;
940                    comment out unused "LDL" class definition
941            * NAMESPACE: mention, but do not export "LDL" class
942            * R/corMatrix.R: new (simple), needed for R-devel with
943            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
944              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
945    
946    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
947    
948            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
949            use Rprintf and R's error handling.
950    
951    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
953            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
954            * tests/matprod.R: add tests for the bug fixed.
955    
956    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
957    
958            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
959            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
960    
961    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
962    
963            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
964    
965    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
966    
967            * DESCRIPTION (Version): 0.9975-3
968    
969            * R/diagMatrix.R (bdiag): new function constructing block diagonal
970            (sparse) matrices.
971            * man/bdiag.Rd: docu + examples
972    
973            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
974    
975            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
976            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
977    
978            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
979            that result is sparse or diagonal (and not dense).
980    
981            * man/Subassign-methods.Rd: fix examples
982    
983            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
984            should always return a sparse (and not sometimes a diagonal) matrix.
985    
986    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
989    
990    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
991    
992            * DESCRIPTION (Version): 0.9975-2
993    
994            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
995    
996    2006-10-02  Douglas Bates  <bates@R-project.org>
997    
998            * tests/dg_Matrix.R: Simplify test taking into account new code.
999    
1000    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1001    
1002            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1003    
1004            * R/lsTMatrix.R: new files w/ missing methods
1005            * R/nsTMatrix.R:  "  'for completeness'
1006    
1007            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1008    
1009            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1010    
1011    
1012    2006-09-28  Douglas Bates  <bates@R-project.org>
1013    
1014            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1015            included.
1016    
1017            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1018            Export C-callable functions used in Zt_create in lme4.
1019    
1020    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1021    
1022            * DESCRIPTION (Version): 0.9975-1
1023    
1024            * tests/simple.R: less checks fail; using NA, found that our
1025                    kronecker() is not base-compatible with NA's.
1026    
1027            * R/dMatrix.R: "Compare" method now implemented for all cases
1028    
1029            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1030    
1031            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1032    
1033            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1034            * src/dspMatrix.c (dspMatrix_validate): ditto
1035    
1036            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1037              including coercion to [nl]tTMatrix.
1038    
1039            * R/diagMatrix.R (show): print a header line as for other classes.
1040    
1041    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1042    
1043            * src/Makefile.win (SUBDIRS): fix typo
1044    
1045    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1046    
1047            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1048    
1049    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1050    
1051            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1052            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1053            accept a symmetric matrix).
1054            * tests/group-methods.R: Uncomment test of crossprod applied to
1055            lsCMatrix objects.
1056    
1057    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1058    
1059            * R/AllClass.R (symmetricMatrix): add validity method (available
1060            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1061    
1062            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1063    
1064            * tests/indexing.Rout.save:
1065            * tests/indexing.R: additions, mainly for 'lsparse'
1066    
1067            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1068            case.
1069    
1070            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1071    
1072    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1073    
1074            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1075                    as 'N' (1-letter - Ok?)
1076    
1077            * tests/group-methods.R: add test for logical + NAs
1078    
1079            * R/dMatrix.R ("Compare"): fix to work with NA's
1080    
1081            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1082    
1083            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1084                    which is implemented.
1085    
1086    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1087    
1088            * src/chm_common.c: coerce logical <-> double instead of
1089            typecasting;  needed for "l" matrix handling in cholmod.
1090    
1091            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1092    
1093            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1094            (Tsp2grNEL): other fixes needed
1095    
1096    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1097    
1098            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1099                    Matrices, since "lMatrix", also "lsparseM" can have NA
1100            * R/ndenseMatrix.R, etc: new source files
1101            * man/nsparseMatrix-classes.Rd, etc: new help files
1102            * tests/: adaptions
1103            * src/chm_common.c (chm_dense_to_SEXP): and others:
1104                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1105            * src/Csparse.c, etc: ditto
1106    
1107    2006-09-11  Douglas Bates  <bates@R-project.org>
1108    
1109            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1110            alloc_d**Matrix functions to the lme4 package.
1111    
1112    2006-09-09  Douglas Bates  <bates@R-project.org>
1113    
1114            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1115            fixed
1116    
1117    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1118    
1119            * R/lMatrix.R: new
1120    
1121            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1122    
1123            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1124            * man/tcrossprod.Rd: ditto
1125    
1126    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1127    
1128            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1129            for exported functions
1130            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1131            Remove partitioning algorithms for sparse matrix reordering.  The
1132            copyright on the Metis code was problematic and the methods were
1133            rarely used.
1134            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1135            operations are now done entirely in CHOLMOD code.
1136    
1137    2006-09-06  Douglas Bates  <bates@R-project.org>
1138    
1139            * src/Mutils.h: Remove functions that are no longer used.
1140    
1141    2006-09-04  Douglas Bates  <bates@R-project.org>
1142    
1143            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1144            * src/DEPS.mkf: update
1145    
1146    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1147    
1148            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1149            * DESCRIPTION (Version): 0.9975-0
1150            (Depends): R (>= 2.4.0)
1151    
1152    2006-09-01  Douglas Bates  <bates@R-project.org>
1153    
1154            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1155    
1156    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1157    
1158            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1159            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1160    
1161            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1162    
1163    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1164    
1165            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1166            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1167            * R/dsparseMatrix.R: ditto
1168            * R/Csparse.R: ditto
1169    
1170    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1171    
1172            * R/dMatrix.R (Compare): improve availability of "<", etc
1173            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1174    
1175    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1176    
1177            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1178            of a 0-index which was used as 1-index (..hmm)
1179    
1180            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1181    
1182            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1183            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1184            (.is.diagonal): ditto
1185    
1186            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1187    
1188            * R/Matrix.R (Matrix): also work for NA data
1189    
1190    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1191    
1192            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1193            in all cases.
1194    
1195    2006-08-27  Douglas Bates  <bates@R-project.org>
1196    
1197            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1198            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1199    
1200    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1201    
1202            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1203            subclasses of "ddenseMatrix"
1204            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1205            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1206            instead of half dozen specialized ones.
1207    
1208    2006-08-25  Douglas Bates  <bates@R-project.org>
1209    
1210            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1211            <tillard@cirad.fr> - ordering standard errors to match effects.
1212    
1213    2006-08-24  Douglas Bates  <bates@R-project.org>
1214    
1215            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1216            on R_ldl.
1217            * R/lCholCMatrix.R,
1218            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1219            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1220            * many files in ./R and ./src: Use more general version of
1221            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1222            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1223            dtpMatrix, dspMatrix and dppMatrix conversions.
1224    
1225    
1226    2006-08-23  Douglas Bates  <bates@R-project.org>
1227    
1228            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1229            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1230            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1231            dgeMatrix_crossprod (may need to do this in other places).
1232            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1233            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1234    
1235    2006-08-22  Douglas Bates  <bates@R-project.org>
1236    
1237            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1238            types of classed Matrices, matrices or numeric or logical vectors.
1239            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1240            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1241            to Mutils.h (as an inline) and change name to Matrix_check_class;
1242            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1243            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1244            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1245            * src/Csparse.c: use diag_P and uplo_P macros.
1246    
1247    2006-08-21  Douglas Bates  <bates@R-project.org>
1248    
1249            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1250            valgrind.
1251            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1252            inverses.
1253            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1254            -Wall warnings.
1255            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1256            Use dup_mMatrix_as_dgeMatrix.
1257    
1258    2006-08-20  Douglas Bates  <bates@R-project.org>
1259    
1260            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1261            * tests/sparseQR.R: Added
1262            * man/sparseQR-class.Rd: Document methods for qr.* generics
1263            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1264    
1265    2006-08-19  Douglas Bates  <bates@R-project.org>
1266    
1267            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1268            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1269            and qr.fitted.
1270            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1271            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1272    
1273    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1274    
1275            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1276            the base version has no "..." argument.
1277    
1278            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1279    
1280            * R/Matrix.R: define and
1281            * NAMESPACE: export as.numeric() and as.logical() methods.
1282                    Let's hope these do not badly slow down something...
1283            Finally export the zapsmall() method.
1284    
1285    2006-08-17  Douglas Bates  <bates@R-project.org>
1286    
1287            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1288            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1289            * src/dtCMatrix.c :Remove code that is no longer used
1290            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1291    
1292    2006-08-14  Douglas Bates  <bates@R-project.org>
1293    
1294            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1295            Csparse_to_logical and Csparse_symmetric_to_general.
1296            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1297            coercion methods between CsparseMatrix and TsparseMatrix.
1298    
1299    2006-08-14  Douglas Bates  <bates@R-project.org>
1300    
1301            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1302            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1303            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1304            possible.
1305    
1306  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
1307    
1308          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,

Legend:
Removed from v.1368  
changed lines
  Added in v.2069

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