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 1329, Fri Jul 21 06:47:06 2006 UTC revision 2062, Sat Sep 1 21:06:52 2007 UTC
# Line 1  Line 1 
1    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
4            * tests/indexing.R: add new regression for the above cases.
5    
6    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * src/Mutils.h (__sun): clause for alloca.h on Solaris
9    
10    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * DESCRIPTION (Date, Version): 0.999375-2
13    
14    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/HBMM.R (readMM): make work for pattern matrices as well
17    
18    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
19    
20            * [r4730] src/Mutils.h: declare alloca
21            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
22              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
23              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
24              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
25              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
26              methods; switch writeMM to use CHOLMOD code; repair readMM
27    
28    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
31            Oehlschlaegel's ... result type still to be discussed!
32    
33    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * man/image-methods.Rd: new, combining all image() methods
36    
37    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
40            to work via dgC...
41    
42            * R/Matrix.R (Matrix): special treatment for "table" (S3)
43    
44    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/dgTMatrix.R (image): change defaults to
47                    aspect = "iso", colorkey = FALSE
48    
49    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
52            must copy its *expanded* x slot before LAPACK call.
53    
54            * tests/matprod.R: test the last days' changes.
55    
56    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
57    
58            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
59              as well as in sources
60            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
61              Lapack call
62    
63    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
66                    ("Matrix", "matrix") which is needed in some cases.
67            Ditto for solve().
68    
69            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
70            infinite recursion in dispatch for some cases.
71    
72    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
73    
74            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
75              so pointers match
76    
77    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * DESCRIPTION (Date): set ready for release -- 0.999375-1
80    
81    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
82    
83            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
84              src/chm_common.c, src/chm_common.h: Change API for
85              numeric_as_chm_dense and N_AS_CHM_DN
86    
87    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
90            * tests/matprod.R: regr.test for it
91    
92    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
95            * tests/group-methods.R: and regression-test it
96    
97    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
98    
99            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
100              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
101              triplet_to_sparse, documentation, use typedefs
102    
103    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * man/dpoMatrix-class.Rd: added 'corMatrix' example
106    
107            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
108            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
109            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
110    
111            * R/lsparseMatrix.R: bug fix in "all" method
112            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
113    
114            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
115            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
116                    + matrix |-> nMatrix coercion
117            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
118            * man/pMatrix-class.Rd: ditto
119    
120            * R/Matrix.R (Summary): method for non-dMatrix
121    
122            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
123            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
124                    test all Summary methods.
125    
126    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
129    
130    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
133    
134            * R/pMatrix.R (t?crossprod): methods for pMatrix
135    
136    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
137    
138            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
139    
140    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
141    
142            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
143              trying to fix a subtle bug - which has been somewhere else.
144    
145    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
146    
147            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
148              solve the bug
149    
150    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * src/dgCMatrix.c (compressed_to_TMatrix):
153    
154    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * src/Csparse.c (Rsparse_validate): new, to have some validity
157            checking for RsparseMatrix
158            * src/dgCMatrix.c (xRMatrix_validate): ditto
159            * src/dtCMatrix.c (tRMatrix_validate): ditto
160    
161    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
162    
163            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
164              lgRMatrix
165            * [r4568] DESCRIPTION: Prepare for bug-fix release
166            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
167              for declaration of cholmod_symmetry
168    
169    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
172            release.
173    
174    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
175    
176            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
177              functions - no longer used
178            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
179              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
180              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
181              Alloca
182    
183    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
184    
185            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
186              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
187              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
188              src/t_gCMatrix_colSums.c: more R_CheckStack()s
189    
190    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
191    
192            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
193              the required amount of memory then call M_numeric_as_chm_dense.
194            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
195              (like Calloc but calling alloca)
196    
197    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
200            and extended with more sophisticated 'col.names' option.
201            * NAMESPACE: export  printSparseMatrix()
202            * man/printSpMatrix.Rd: document, incl. examples
203    
204    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
205    
206            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
207              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
208              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
209    
210    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * DESCRIPTION (Version): 0.99875-4
213    
214            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
215            some dimnames perservation.
216    
217            * R/dsTMatrix.R (t-method): keep dimnames
218            * R/dtTMatrix.R:  ditto
219    
220            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
221            and ncol(.) < 10
222    
223            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
224            from Mutils.h
225    
226            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
227            e.g. in as(<ngCMatrix>, "matrix")
228    
229    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
230    
231            * [r4529] .: Create a branch for the API changes from the 0.99875
232              series to the 0.999375 series
233            * [r4530] DESCRIPTION, inst/include/Matrix.h,
234              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
235              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
236              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
237              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
238              as_cholmod_x functions
239    
240    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
241    
242            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
243              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
244              to Comparisons
245    
246    >>>>>>> .merge-right.r4561
247    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * DESCRIPTION (Version): 0.99875-3 ready to be released.
250    
251            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
252    
253            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
254            that should also work in a future version of R.
255    
256    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
259    
260            * R/sparseVector.R: more *sparseVector coercions, notably for
261            non - double ones.
262    
263    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
266              notably the new ones building on the new .Call(.)s:
267    
268            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
269            all 4 of [dlin]gCMatrix_colSums().
270    
271    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
272    
273            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
274            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
275              result
276    
277    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/kronecker.R: fix typo (could lead to inf.recursion)
280            * test/simple.R: testing that
281    
282            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
283            method as well (which can have arguments, show() can't).
284    
285    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
286    
287            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
288              added dgCMatrix_colSums for [col,row][Sums,Means]
289    
290    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
291    
292            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
293              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
294              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
295            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
296              class
297            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
298              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
299              row names to store the levels - duh!  Added an example.
300    
301    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * src/Csparse.c (Csparse_validate): check for *repeated* entries
304            thanks to example from Christian Buchta; with a test here:
305            * tests/simple.R:
306    
307    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
310            of colSums(*, sparseResult = TRUE)
311    
312    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
315            'na.rm = FALSE' as "everywhere" else in R.
316    
317    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
318    
319            * [r4421] src/CSparse_install.sh: Modify for new organization of
320              CSparse package
321            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
322              SuiteSparse
323            * [r4426] src/Makefile: add ./UFconfig to the include path for
324              compilation
325            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
326            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
327              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
328    
329    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
332            * R/sparseMatrix.R (prSpMatrix): now gives a message about
333            suppressed column names.
334    
335    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
336    
337            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
338              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
339              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
340              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
341              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
342              Remove warnings after change to const char* CHAR
343    
344    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
345    
346            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
347              type of M_cholmod_ssmult
348    
349    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
350    
351            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
352              src/init.c: Yet another cholmod export - cholmod_ssmult
353    
354    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * NAMESPACE: exported drop0(), since
357            * man/drop0.Rd: I have seen several cases, I really wanted to use
358            it, so our users may want too.
359    
360    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * man/colSums.Rd: separately document colSums() etc, since these
363            have the extra argument 'sparseResult'.
364    
365    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
368            * man/spMatrix.Rd: docu., including examples
369    
370            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
371            in order to make colMeans() etc fast *and* correct.
372            * R/sparseVector.R (replSPvec): "[<-" functionality for
373            sparseVectors; tested in
374            * tests/simple.R:
375    
376    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
379            (very) sparse Matrices; output similar to Matlab's print().
380    
381    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
382    
383            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
384            0-based, indices (Jose Quesada <quesada@gmail.com>).
385    
386    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
387    
388            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
389    
390    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/Auxiliaries.R (sparsapply): new utility, much faster than
393            tapply1() for large sparse matrices.
394    
395    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/Matrix.R (dim<-): reshape now via sparseVector.
398    
399            * R/sparseVector.R: methods and function for
400            * R/AllClass.R: new "sparseVector" class and daughters.
401            * NAMESPACE: export new classes
402    
403    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * DESCRIPTION (Version): 0.99875-1
406            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
407    
408    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
411            indexing
412            * tests/indexing.R: test set for that.
413    
414    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
417            entries.
418            * tests/indexing.R(out): add regression test for it
419    
420    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
423            name for "!" method definitions.
424    
425    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/Tsparse.R (intI): new utility, used for "[" :
428                    Cleanup up there, and fixes for duplicated indices - more TODO!
429    
430            * tests/indexing.R(out): more tests
431    
432    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
433    
434            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
435            code that is now part of the R Lapack library.
436    
437            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
438            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
439    
440    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
443    
444    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
447            up with extraneous names '0'...'<n-1>'
448    
449    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/dgTMatrix.R (mat2dgT): care about NAs
452    
453    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * R/kronecker.R: triangularity preserving methods
456    
457    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/kronecker.R: new file collecting kronecker() methods in one
460                    place.  Goal: become much faster!
461    
462    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
465            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
466            can be much faster.
467    
468            * tests/matprod.R: add regression tests for these (upper & lower).
469    
470    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * R/Matrix.R (diff): method for our Matrices.
473    
474            * R/sparseMatrix.R (isDiagonal): check dim()!
475    
476    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/Matrix.R (dim<-): new method for "reshape()" built on a
479            proposal from Tamas Papp.
480    
481    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
484    
485            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
486            rather define and export  cBind() and rBind() only.
487            --> useRs *must* change code that used to have cbind()/rbind() !!
488    
489            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
490            * R/bind.Rout.save: ditto
491    
492    2007-02-16  Douglas Bates  <bates@r-project.org>
493    
494            * DESCRIPTION (Date, Version): 0.9975-11 with new date
495            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
496            const modifier on declaration of the array 'valid'
497    
498    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
499    
500            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
501    
502    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
505    
506            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
507            * tests/simple.R: test the above and some of these coercions:
508    
509            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
510                    be careful to avoid infinite recursion, using new coercions in
511            * R/ngCMatrix.R and nsC... and ntC...
512            * R/lsparseMatrix.R: ditto
513    
514            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
515    
516            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
517            * R/Rsparse.R: reactivate .Call()s
518    
519            * tests/Class+Meth.R: a bit more on actual classes
520    
521    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
522    
523            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
524    
525    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * DESCRIPTION (Version): 0.9975-10 to upload
528    
529            * tests/Class+Meth.R (tstMatrixClass): require coercions to
530            specific classes less unconditionally.
531    
532            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
533    
534            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
535    
536            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
537            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
538            R_to_CMatrix segfaults on one platform.
539            Eliminate most coercion method to *specific* classes, and replace
540            with virtual classes coercions.
541    
542    
543    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
544    
545            * src/init.c: export the CHM...._validate() placeholders, since
546            they *are* called.
547    
548            * tests/Class+Meth.R (classCanCoerce): and starting to test
549            all as(<from>, <to>)
550    
551    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
554            * tests/indexing.R: tested now
555            * tests/indexing.Rout.save: updated
556    
557            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
558            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
559            appropriate.
560    
561            * NAMESPACE: export a trivial
562            * R/Matrix.R: drop() Matrix-method
563    
564            * R/AllClass.R: moved all prototypes to virtual super classes.
565    
566            * R/Rsparse.R: many more coercions to have less exceptions in
567            * tests/Class+Meth.R:
568    
569            * R/Ops.R (Compare): tweak for case with NA
570            * tests/simpl.R: hence another 'FIXME' eliminated
571    
572    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
575            objects.
576    
577            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
578              and more of "!", "&", "|", all, any; coercions
579    
580            * R/Rsparse.R: many coercions (which enable quite a few other
581            methods), thanks to enhancements in
582            * src/dgCMatrix.c (R_to_CMatrix): new, and
583            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
584            symmetric & triangular and ..RMatrix objects.
585    
586            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
587            renamed file from src/dsTMatrix.c;
588            now dealing with symmetric and triangular Tsparse coercions, both
589            to dense and general.
590    
591    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
594    
595            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
596            where sensible when the <numeric> is of length > 1.
597    
598    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * R/Matrix.R ([<-): for M[] <- value: fix length
601    
602    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
605            * R/ndenseMatrix.R: new coercions n* -> l*
606    
607    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
610    
611            * R/Ops.R ("Logic"): and other "Ops", many updates
612    
613    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * src/Mutils.h (SET_DimNames): new utility
616    
617            * R/Auxiliaries.R (nnzero): improved and now exported via
618    
619            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
620    
621    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
622    
623            * R/diagMatrix.R (!): fix typo.
624    
625    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * R/Auxiliaries.R (as_Csparse): and quite a few others:
628                    allow to pass class definition --> speedup
629            * R/sparseMatrix.R: apply the above
630    
631            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
632    
633            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
634            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
635            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
636    
637            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
638    
639            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
640            and use it for "sparse*" as well, since it's faster than the
641            as_Csparse(.) way.
642    
643    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
646    
647    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
648    
649            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
650            as method for   M[ ij ] <- v
651            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
652    
653            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
654            FALSE answer
655    
656            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
657            * tests/indexing.R: test it, and some of the above
658    
659    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * R/Auxiliaries.R (is_duplicatedT): new utility
662    
663    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
664    
665            * src/init.c (R_init_Matrix): export cholmod_scale
666    
667    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
668    
669            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
670            base::as.matrix to (x, ...)
671    
672    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
675            file; start using "Logic", hence
676    
677            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
678            * NAMESPACE: import and export "Logic"
679    
680    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
681    
682            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
683            only needed previously to R version 2.5.0.
684    
685    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
688    
689            * R/Tsparse.R (replTmat): fix subassignment of triangular
690            * R/Csparse.R (replCmat): ditto
691            * tests/indexing.R: more tests, incl the above fix
692    
693    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * R/Auxiliaries.R (drop0): extend for non CSparse
696            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
697    
698            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
699                    use uplo correctly (!); other places: use uplo_P() macro
700    
701            * R/Csparse.R (replCmat): call diagU2N() when needed
702            * R/Tsparse.R (replTmat): ditto
703    
704            * src/dtCMatrix.c (tCMatrix_validate): new
705            * src/dtTMatrix.c (tTMatrix_validate): new, used in
706            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
707    
708            * R/diagMatrix.R (replDiag): to use in [<-
709    
710    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
713                    also more general diagU2N().
714    
715    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
718            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
719    
720    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * tests/bind.R: a few more cases
723            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
724    
725            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
726            * R/ddenseMatrix.R (cbind2/rbind2)
727            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
728            * tests/indexing.R
729            * tests/indexing.Rout.save: updated
730    
731    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
732    
733            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
734            * tests/indexing.R
735    
736    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
739            align with proper position of "0", i.e., right for integers.
740            argument 'align' by default is "fancy".
741    
742    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
745            * R/Csparse.R: and fix "Compare" for more cases.
746            * tests/Class+Meth.R: test some of these (m == m, m != m)
747    
748    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * R/lsparseMatrix.R: all() and any() methods
751            * R/ldenseMatrix.R:      ditto
752            * NAMESPACE, R/Matrix.R: ditto
753    
754            * man/all-methods.Rd: document them minimally
755    
756            * tests/simple.R: add a few examples for these
757    
758    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * R/Tsparse.R ([): fix long standing typo in symmetric case
761            * man/dsCMatrix-class.Rd: add example exhibiting the above case
762    
763    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
764    
765            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
766            to LL before converting to a sparse matrix. (The LDL form can be
767            converted to a sparse matrix but it is implicitly a unit
768            triangular matrix and a diagonal matrix overwritten on the diagonal.)
769    
770    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
771    
772            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
773    
774    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
775    
776            * DESCRIPTION (Version): updated -> release 0.9975-7
777            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
778    
779    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
780    
781            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
782    
783    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
784    
785            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
786            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
787            is exactly singular.
788    
789    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * DESCRIPTION (Date): updated -> release 0.9975-6
792    
793    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
794    
795            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
796            now returns symmetric.
797    
798            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
799    
800            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
801            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
802    
803            * R/Auxiliaries.R (.type.kind): added
804    
805    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
806    
807            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
808            running src/CSparse_install.sh
809    
810            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
811    
812    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
815            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
816    
817            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
818    
819            * tests/Class+Meth.R (tstMatrixClass): now assure
820            the (important in method programming) property :
821    
822                    ###>>  Every "Matrix" is either
823                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
824    
825                    (where "*" stands for "Matrix")
826    
827            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
828    
829            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
830            * tests/validObj.R: checks for "comparison"
831    
832            * R/sparseMatrix.R ([): improved indexing for sparse;
833                    trying to keep <symmetric>[ n, n] symmmetric
834    
835            * tests/indexing.R: indexing for logical sparse now ok
836    
837    
838    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * src/Tsparse.c: use xTsparse_validate() , and hence remove
841    
842            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
843    
844    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
845    
846            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
847    
848            * tests/simple.R: validObject() checking the above.
849    
850            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
851            replacing both dgCMatrix_validate and lgCM*.
852    
853            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
854            fix dimnames setting in other places.
855            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
856    
857    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
858    
859            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
860    
861            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
862            symmetry test, via
863            * R/Auxiliaries.R (.as.dgC.0.factors):
864    
865    2006-11-01  Douglas Bates  <bates@r-project.org>
866    
867            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
868            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
869            <CsparseMatrix>) added
870    
871    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
872    
873            * tests/matprod.R: add a variation of Harri's example
874    
875            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
876            recursive infinitely.
877    
878            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
879    
880            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
881    
882    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
883    
884            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
885            matrix if possible; test m+m == 2*m; now test dgRMatrix.
886            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
887            satisfy the above test.
888    
889    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
892    
893            * R/dgCMatrix.R: solve(a, b="missing") based on
894            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
895            RHS = NULL.
896    
897            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
898            add more (needed) [t]crossprod() methods.
899    
900            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
901    
902            * R/Auxiliaries.R (as_CspClass): cleanup
903            (drop0): internal utility for "Csparse_drop(*, 0)"
904            (.bail.out.2): encourage active feedback
905    
906    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
907    
908            * R/dMatrix.R(Compare): new(), then slots [no validity check]
909    
910            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
911            non-valid or 'sorted' case).
912    
913            * R/dsparseMatrix.R: add "chol" method.
914            * R/ddenseMatrix.R: ditto
915    
916            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
917            * NAMESPACE (Ops)
918            * R/diagMatrix.R (diag2T): simple utility used "higher level"
919            coercion; deprecating direct lower level coercions.
920    
921            * R/*.R (seq): use seq_len() and seq_along() where possible.
922    
923    
924    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * DESCRIPTION (Version): 0.9975-5 ready for release
927    
928    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
929    
930            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
931    
932    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
933    
934            * R/AllClass.R (corMatrix): add 'validity' check;
935                    comment out unused "LDL" class definition
936            * NAMESPACE: mention, but do not export "LDL" class
937            * R/corMatrix.R: new (simple), needed for R-devel with
938            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
939              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
940    
941    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
942    
943            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
944            use Rprintf and R's error handling.
945    
946    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
947    
948            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
949            * tests/matprod.R: add tests for the bug fixed.
950    
951    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
952    
953            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
954            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
955    
956    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
957    
958            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
959    
960    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
961    
962            * DESCRIPTION (Version): 0.9975-3
963    
964            * R/diagMatrix.R (bdiag): new function constructing block diagonal
965            (sparse) matrices.
966            * man/bdiag.Rd: docu + examples
967    
968            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
969    
970            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
971            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
972    
973            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
974            that result is sparse or diagonal (and not dense).
975    
976            * man/Subassign-methods.Rd: fix examples
977    
978            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
979            should always return a sparse (and not sometimes a diagonal) matrix.
980    
981    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
982    
983            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
984    
985    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
986    
987            * DESCRIPTION (Version): 0.9975-2
988    
989            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
990    
991    2006-10-02  Douglas Bates  <bates@R-project.org>
992    
993            * tests/dg_Matrix.R: Simplify test taking into account new code.
994    
995    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
998    
999            * R/lsTMatrix.R: new files w/ missing methods
1000            * R/nsTMatrix.R:  "  'for completeness'
1001    
1002            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1003    
1004            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1005    
1006    
1007    2006-09-28  Douglas Bates  <bates@R-project.org>
1008    
1009            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1010            included.
1011    
1012            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1013            Export C-callable functions used in Zt_create in lme4.
1014    
1015    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1016    
1017            * DESCRIPTION (Version): 0.9975-1
1018    
1019            * tests/simple.R: less checks fail; using NA, found that our
1020                    kronecker() is not base-compatible with NA's.
1021    
1022            * R/dMatrix.R: "Compare" method now implemented for all cases
1023    
1024            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1025    
1026            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1027    
1028            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1029            * src/dspMatrix.c (dspMatrix_validate): ditto
1030    
1031            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1032              including coercion to [nl]tTMatrix.
1033    
1034            * R/diagMatrix.R (show): print a header line as for other classes.
1035    
1036    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1037    
1038            * src/Makefile.win (SUBDIRS): fix typo
1039    
1040    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1041    
1042            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1043    
1044    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1045    
1046            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1047            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1048            accept a symmetric matrix).
1049            * tests/group-methods.R: Uncomment test of crossprod applied to
1050            lsCMatrix objects.
1051    
1052    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1053    
1054            * R/AllClass.R (symmetricMatrix): add validity method (available
1055            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1056    
1057            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1058    
1059            * tests/indexing.Rout.save:
1060            * tests/indexing.R: additions, mainly for 'lsparse'
1061    
1062            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1063            case.
1064    
1065            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1066    
1067    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1068    
1069            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1070                    as 'N' (1-letter - Ok?)
1071    
1072            * tests/group-methods.R: add test for logical + NAs
1073    
1074            * R/dMatrix.R ("Compare"): fix to work with NA's
1075    
1076            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1077    
1078            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1079                    which is implemented.
1080    
1081    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1082    
1083            * src/chm_common.c: coerce logical <-> double instead of
1084            typecasting;  needed for "l" matrix handling in cholmod.
1085    
1086            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1087    
1088            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1089            (Tsp2grNEL): other fixes needed
1090    
1091    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1092    
1093            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1094                    Matrices, since "lMatrix", also "lsparseM" can have NA
1095            * R/ndenseMatrix.R, etc: new source files
1096            * man/nsparseMatrix-classes.Rd, etc: new help files
1097            * tests/: adaptions
1098            * src/chm_common.c (chm_dense_to_SEXP): and others:
1099                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1100            * src/Csparse.c, etc: ditto
1101    
1102    2006-09-11  Douglas Bates  <bates@R-project.org>
1103    
1104            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1105            alloc_d**Matrix functions to the lme4 package.
1106    
1107    2006-09-09  Douglas Bates  <bates@R-project.org>
1108    
1109            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1110            fixed
1111    
1112    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1113    
1114            * R/lMatrix.R: new
1115    
1116            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1117    
1118            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1119            * man/tcrossprod.Rd: ditto
1120    
1121    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1122    
1123            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1124            for exported functions
1125            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1126            Remove partitioning algorithms for sparse matrix reordering.  The
1127            copyright on the Metis code was problematic and the methods were
1128            rarely used.
1129            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1130            operations are now done entirely in CHOLMOD code.
1131    
1132    2006-09-06  Douglas Bates  <bates@R-project.org>
1133    
1134            * src/Mutils.h: Remove functions that are no longer used.
1135    
1136    2006-09-04  Douglas Bates  <bates@R-project.org>
1137    
1138            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1139            * src/DEPS.mkf: update
1140    
1141    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1142    
1143            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1144            * DESCRIPTION (Version): 0.9975-0
1145            (Depends): R (>= 2.4.0)
1146    
1147    2006-09-01  Douglas Bates  <bates@R-project.org>
1148    
1149            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1150    
1151    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1152    
1153            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1154            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1155    
1156            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1157    
1158    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1159    
1160            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1161            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1162            * R/dsparseMatrix.R: ditto
1163            * R/Csparse.R: ditto
1164    
1165    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1166    
1167            * R/dMatrix.R (Compare): improve availability of "<", etc
1168            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1169    
1170    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1171    
1172            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1173            of a 0-index which was used as 1-index (..hmm)
1174    
1175            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1176    
1177            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1178            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1179            (.is.diagonal): ditto
1180    
1181            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1182    
1183            * R/Matrix.R (Matrix): also work for NA data
1184    
1185    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1186    
1187            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1188            in all cases.
1189    
1190    2006-08-27  Douglas Bates  <bates@R-project.org>
1191    
1192            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1193            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1194    
1195    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1196    
1197            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1198            subclasses of "ddenseMatrix"
1199            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1200            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1201            instead of half dozen specialized ones.
1202    
1203    2006-08-25  Douglas Bates  <bates@R-project.org>
1204    
1205            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1206            <tillard@cirad.fr> - ordering standard errors to match effects.
1207    
1208    2006-08-24  Douglas Bates  <bates@R-project.org>
1209    
1210            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1211            on R_ldl.
1212            * R/lCholCMatrix.R,
1213            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1214            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1215            * many files in ./R and ./src: Use more general version of
1216            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1217            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1218            dtpMatrix, dspMatrix and dppMatrix conversions.
1219    
1220    
1221    2006-08-23  Douglas Bates  <bates@R-project.org>
1222    
1223            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1224            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1225            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1226            dgeMatrix_crossprod (may need to do this in other places).
1227            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1228            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1229    
1230    2006-08-22  Douglas Bates  <bates@R-project.org>
1231    
1232            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1233            types of classed Matrices, matrices or numeric or logical vectors.
1234            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1235            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1236            to Mutils.h (as an inline) and change name to Matrix_check_class;
1237            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1238            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1239            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1240            * src/Csparse.c: use diag_P and uplo_P macros.
1241    
1242    2006-08-21  Douglas Bates  <bates@R-project.org>
1243    
1244            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1245            valgrind.
1246            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1247            inverses.
1248            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1249            -Wall warnings.
1250            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1251            Use dup_mMatrix_as_dgeMatrix.
1252    
1253    2006-08-20  Douglas Bates  <bates@R-project.org>
1254    
1255            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1256            * tests/sparseQR.R: Added
1257            * man/sparseQR-class.Rd: Document methods for qr.* generics
1258            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1259    
1260    2006-08-19  Douglas Bates  <bates@R-project.org>
1261    
1262            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1263            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1264            and qr.fitted.
1265            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1266            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1267    
1268    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1269    
1270            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1271            the base version has no "..." argument.
1272    
1273            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1274    
1275            * R/Matrix.R: define and
1276            * NAMESPACE: export as.numeric() and as.logical() methods.
1277                    Let's hope these do not badly slow down something...
1278            Finally export the zapsmall() method.
1279    
1280    2006-08-17  Douglas Bates  <bates@R-project.org>
1281    
1282            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1283            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1284            * src/dtCMatrix.c :Remove code that is no longer used
1285            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1286    
1287    2006-08-14  Douglas Bates  <bates@R-project.org>
1288    
1289            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1290            Csparse_to_logical and Csparse_symmetric_to_general.
1291            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1292            coercion methods between CsparseMatrix and TsparseMatrix.
1293    
1294    2006-08-14  Douglas Bates  <bates@R-project.org>
1295    
1296            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1297            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1298            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1299            possible.
1300    
1301    2006-08-12  Douglas Bates  <bates@R-project.org>
1302    
1303            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1304              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1305              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1306              generalize conversions between TsparseMatrix, CsparseMatrix,
1307              denseMatrix and matrix.  Preserve triangularity property and
1308              propagate Dimnames in the easy cases.
1309    
1310    2006-08-10  Douglas Bates  <bates@R-project.org>
1311    
1312            * src/lmer.c: adjust checks in glmer_init for S4SXP
1313            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1314            before S4SXP but for the wrong reasons.
1315    
1316    2006-08-08  Douglas Bates  <bates@R-project.org>
1317    
1318            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1319            Later modified to return the upper triangle only.
1320            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1321    
1322    2006-08-07  Douglas Bates  <bates@R-project.org>
1323    
1324            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1325            R-level conversion to a sparse symmetric class.
1326            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1327            Remove conversion to sparse symmetric classes (now done in C code).
1328    
1329    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1330    
1331            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1332            * man/band.Rd:  adapt the \dontshow{} unit test.
1333    
1334    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1335    
1336            * DESCRIPTION (Version): 0.995-14  for CRAN
1337    
1338            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1339    
1340            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1341            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1342    
1343            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1344            * R/Tsparse.R (tril, triu, band): methods
1345            * R/dgRMatrix.R (tril, ...):    ditto
1346            * man/band.Rd:                  ditto
1347    
1348    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1349    
1350            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1351                    to be up-to-date automatically.
1352    
1353    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1354    
1355            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1356    
1357            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1358            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1359            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1360            such that the S4 objects are always created by the current version
1361            of R and 'Matrix' class definitions.
1362    
1363    2006-08-01  Douglas Bates  <bates@R-project.org>
1364    
1365            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1366            inst/external/test3comp.rda: Added warnings for convergence on
1367            boundary and test cases.
1368    
1369            * src/lmer.c (mer_postVar): Modified to return the variances that
1370            are marginal to the fixed effects, not conditional on them (which
1371            is what the bVar slot contents represent).
1372    
1373    2006-07-31  Douglas Bates  <bates@R-project.org>
1374    
1375            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1376            function which calls the C function mer_hat_trace2.
1377    
1378            * man/ranef.Rd: Include description of "postVar" argument and
1379            producing a caterpillar plot.
1380    
1381    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1382    
1383            * NAMESPACE:    change  "correlation" to "corMatrix"
1384            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1385            * R/dpoMatrix.R: ditto
1386            * R/lmer.R:      ditto
1387    
1388    2006-07-28  Douglas Bates  <bates@R-project.org>
1389    
1390            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1391            RZXinv slot's contents into a separate internal function that can
1392            be used in mer_hat_trace.
1393    
1394    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1395    
1396            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1397            via new smart
1398            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1399            utility functions.
1400    
1401    
1402    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1403    
1404            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1405            matrices when appropriate; band() even symmetric ones.
1406            (replCmat): extend to potentially all "CsparseMatrix"
1407            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1408            allow subassignment for special sparse matrices.
1409    
1410            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1411    
1412            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1413            argument; in glmer_*(): print only if(verbose).
1414    
1415            speed-optimize a few places by moving REAL(.) out of loops.
1416    
1417            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1418    
1419  2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1420    
1421          * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),          * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
# Line 140  Line 1558 
1558    
1559          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1560          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.
1561          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1562    
1563    
1564  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 263  Line 1681 
1681          * 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)
1682          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
1683          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
1684          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
1685    
1686  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1687    
# Line 467  Line 1885 
1885  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1886    
1887          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1888          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1889          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1890    
1891  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

Legend:
Removed from v.1329  
changed lines
  Added in v.2062

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