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 388, Mon Dec 13 16:00:22 2004 UTC revision 2024, Thu Aug 2 07:22:44 2007 UTC
# Line 1  Line 1 
1  2004-12-13  Douglas Bates  <bates@bates1-home>  2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Date): set ready for release
4    
5    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
6    
7            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
8              src/chm_common.c, src/chm_common.h: Change API for
9              numeric_as_chm_dense and N_AS_CHM_DN
10    
11    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
14            * tests/matprod.R: regr.test for it
15    
16    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
19            * tests/group-methods.R: and regression-test it
20    
21    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
22    
23            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
24              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
25              triplet_to_sparse, documentation, use typedefs
26    
27    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * man/dpoMatrix-class.Rd: added 'corMatrix' example
30    
31            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
32            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
33            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
34    
35            * R/lsparseMatrix.R: bug fix in "all" method
36            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
37    
38            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
39            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
40                    + matrix |-> nMatrix coercion
41            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
42            * man/pMatrix-class.Rd: ditto
43    
44            * R/Matrix.R (Summary): method for non-dMatrix
45    
46            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
47            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
48                    test all Summary methods.
49    
50    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
53    
54    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
57    
58            * R/pMatrix.R (t?crossprod): methods for pMatrix
59    
60    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
61    
62            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
63    
64    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
65    
66            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
67              trying to fix a subtle bug - which has been somewhere else.
68    
69    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
70    
71            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
72              solve the bug
73    
74    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * src/dgCMatrix.c (compressed_to_TMatrix):
77    
78    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * src/Csparse.c (Rsparse_validate): new, to have some validity
81            checking for RsparseMatrix
82            * src/dgCMatrix.c (xRMatrix_validate): ditto
83            * src/dtCMatrix.c (tRMatrix_validate): ditto
84    
85    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
86    
87            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
88              lgRMatrix
89            * [r4568] DESCRIPTION: Prepare for bug-fix release
90            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
91              for declaration of cholmod_symmetry
92    
93    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
96            release.
97    
98    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
99    
100            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
101              functions - no longer used
102            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
103              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
104              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
105              Alloca
106    
107    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
108    
109            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
110              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
111              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
112              src/t_gCMatrix_colSums.c: more R_CheckStack()s
113    
114    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
115    
116            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
117              the required amount of memory then call M_numeric_as_chm_dense.
118            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
119              (like Calloc but calling alloca)
120    
121    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
124            and extended with more sophisticated 'col.names' option.
125            * NAMESPACE: export  printSparseMatrix()
126            * man/printSpMatrix.Rd: document, incl. examples
127    
128    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
129    
130            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
131              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
132              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
133    
134    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * DESCRIPTION (Version): 0.99875-4
137    
138            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
139            some dimnames perservation.
140    
141            * R/dsTMatrix.R (t-method): keep dimnames
142            * R/dtTMatrix.R:  ditto
143    
144            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
145            and ncol(.) < 10
146    
147            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
148            from Mutils.h
149    
150            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
151            e.g. in as(<ngCMatrix>, "matrix")
152    
153    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
154    
155            * [r4529] .: Create a branch for the API changes from the 0.99875
156              series to the 0.999375 series
157            * [r4530] DESCRIPTION, inst/include/Matrix.h,
158              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
159              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
160              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
161              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
162              as_cholmod_x functions
163    
164    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
165    
166            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
167              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
168              to Comparisons
169    
170    >>>>>>> .merge-right.r4561
171    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * DESCRIPTION (Version): 0.99875-3 ready to be released.
174    
175            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
176    
177            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
178            that should also work in a future version of R.
179    
180    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
183    
184            * R/sparseVector.R: more *sparseVector coercions, notably for
185            non - double ones.
186    
187    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
190              notably the new ones building on the new .Call(.)s:
191    
192            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
193            all 4 of [dlin]gCMatrix_colSums().
194    
195    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
196    
197            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
198            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
199              result
200    
201    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/kronecker.R: fix typo (could lead to inf.recursion)
204            * test/simple.R: testing that
205    
206            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
207            method as well (which can have arguments, show() can't).
208    
209    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
210    
211            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
212              added dgCMatrix_colSums for [col,row][Sums,Means]
213    
214    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
215    
216            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
217              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
218              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
219            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
220              class
221            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
222              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
223              row names to store the levels - duh!  Added an example.
224    
225    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * src/Csparse.c (Csparse_validate): check for *repeated* entries
228            thanks to example from Christian Buchta; with a test here:
229            * tests/simple.R:
230    
231    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
234            of colSums(*, sparseResult = TRUE)
235    
236    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
239            'na.rm = FALSE' as "everywhere" else in R.
240    
241    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
242    
243            * [r4421] src/CSparse_install.sh: Modify for new organization of
244              CSparse package
245            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
246              SuiteSparse
247            * [r4426] src/Makefile: add ./UFconfig to the include path for
248              compilation
249            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
250            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
251              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
252    
253    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
256            * R/sparseMatrix.R (prSpMatrix): now gives a message about
257            suppressed column names.
258    
259    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
260    
261            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
262              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
263              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
264              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
265              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
266              Remove warnings after change to const char* CHAR
267    
268    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
269    
270            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
271              type of M_cholmod_ssmult
272    
273    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
274    
275            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
276              src/init.c: Yet another cholmod export - cholmod_ssmult
277    
278    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * NAMESPACE: exported drop0(), since
281            * man/drop0.Rd: I have seen several cases, I really wanted to use
282            it, so our users may want too.
283    
284    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * man/colSums.Rd: separately document colSums() etc, since these
287            have the extra argument 'sparseResult'.
288    
289    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
292            * man/spMatrix.Rd: docu., including examples
293    
294            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
295            in order to make colMeans() etc fast *and* correct.
296            * R/sparseVector.R (replSPvec): "[<-" functionality for
297            sparseVectors; tested in
298            * tests/simple.R:
299    
300    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
303            (very) sparse Matrices; output similar to Matlab's print().
304    
305    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
306    
307            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
308            0-based, indices (Jose Quesada <quesada@gmail.com>).
309    
310    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
311    
312            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
313    
314    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/Auxiliaries.R (sparsapply): new utility, much faster than
317            tapply1() for large sparse matrices.
318    
319    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Matrix.R (dim<-): reshape now via sparseVector.
322    
323            * R/sparseVector.R: methods and function for
324            * R/AllClass.R: new "sparseVector" class and daughters.
325            * NAMESPACE: export new classes
326    
327    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * DESCRIPTION (Version): 0.99875-1
330            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
331    
332    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
335            indexing
336            * tests/indexing.R: test set for that.
337    
338    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
341            entries.
342            * tests/indexing.R(out): add regression test for it
343    
344    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
347            name for "!" method definitions.
348    
349    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/Tsparse.R (intI): new utility, used for "[" :
352                    Cleanup up there, and fixes for duplicated indices - more TODO!
353    
354            * tests/indexing.R(out): more tests
355    
356    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
357    
358            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
359            code that is now part of the R Lapack library.
360    
361            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
362            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
363    
364    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
367    
368    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
371            up with extraneous names '0'...'<n-1>'
372    
373    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/dgTMatrix.R (mat2dgT): care about NAs
376    
377    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/kronecker.R: triangularity preserving methods
380    
381    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/kronecker.R: new file collecting kronecker() methods in one
384                    place.  Goal: become much faster!
385    
386    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
389            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
390            can be much faster.
391    
392            * tests/matprod.R: add regression tests for these (upper & lower).
393    
394    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/Matrix.R (diff): method for our Matrices.
397    
398            * R/sparseMatrix.R (isDiagonal): check dim()!
399    
400    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/Matrix.R (dim<-): new method for "reshape()" built on a
403            proposal from Tamas Papp.
404    
405    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
408    
409            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
410            rather define and export  cBind() and rBind() only.
411            --> useRs *must* change code that used to have cbind()/rbind() !!
412    
413            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
414            * R/bind.Rout.save: ditto
415    
416    2007-02-16  Douglas Bates  <bates@r-project.org>
417    
418            * DESCRIPTION (Date, Version): 0.9975-11 with new date
419            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
420            const modifier on declaration of the array 'valid'
421    
422    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
423    
424            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
425    
426    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
429    
430            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
431            * tests/simple.R: test the above and some of these coercions:
432    
433            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
434                    be careful to avoid infinite recursion, using new coercions in
435            * R/ngCMatrix.R and nsC... and ntC...
436            * R/lsparseMatrix.R: ditto
437    
438            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
439    
440            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
441            * R/Rsparse.R: reactivate .Call()s
442    
443            * tests/Class+Meth.R: a bit more on actual classes
444    
445    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
446    
447            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
448    
449    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * DESCRIPTION (Version): 0.9975-10 to upload
452    
453            * tests/Class+Meth.R (tstMatrixClass): require coercions to
454            specific classes less unconditionally.
455    
456            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
457    
458            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
459    
460            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
461            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
462            R_to_CMatrix segfaults on one platform.
463            Eliminate most coercion method to *specific* classes, and replace
464            with virtual classes coercions.
465    
466    
467    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
468    
469            * src/init.c: export the CHM...._validate() placeholders, since
470            they *are* called.
471    
472            * tests/Class+Meth.R (classCanCoerce): and starting to test
473            all as(<from>, <to>)
474    
475    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
478            * tests/indexing.R: tested now
479            * tests/indexing.Rout.save: updated
480    
481            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
482            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
483            appropriate.
484    
485            * NAMESPACE: export a trivial
486            * R/Matrix.R: drop() Matrix-method
487    
488            * R/AllClass.R: moved all prototypes to virtual super classes.
489    
490            * R/Rsparse.R: many more coercions to have less exceptions in
491            * tests/Class+Meth.R:
492    
493            * R/Ops.R (Compare): tweak for case with NA
494            * tests/simpl.R: hence another 'FIXME' eliminated
495    
496    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
499            objects.
500    
501            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
502              and more of "!", "&", "|", all, any; coercions
503    
504            * R/Rsparse.R: many coercions (which enable quite a few other
505            methods), thanks to enhancements in
506            * src/dgCMatrix.c (R_to_CMatrix): new, and
507            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
508            symmetric & triangular and ..RMatrix objects.
509    
510            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
511            renamed file from src/dsTMatrix.c;
512            now dealing with symmetric and triangular Tsparse coercions, both
513            to dense and general.
514    
515    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
516    
517            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
518    
519            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
520            where sensible when the <numeric> is of length > 1.
521    
522    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
523    
524            * R/Matrix.R ([<-): for M[] <- value: fix length
525    
526    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
529            * R/ndenseMatrix.R: new coercions n* -> l*
530    
531    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
534    
535            * R/Ops.R ("Logic"): and other "Ops", many updates
536    
537    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * src/Mutils.h (SET_DimNames): new utility
540    
541            * R/Auxiliaries.R (nnzero): improved and now exported via
542    
543            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
544    
545    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * R/diagMatrix.R (!): fix typo.
548    
549    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/Auxiliaries.R (as_Csparse): and quite a few others:
552                    allow to pass class definition --> speedup
553            * R/sparseMatrix.R: apply the above
554    
555            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
556    
557            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
558            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
559            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
560    
561            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
562    
563            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
564            and use it for "sparse*" as well, since it's faster than the
565            as_Csparse(.) way.
566    
567    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
568    
569            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
570    
571    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
574            as method for   M[ ij ] <- v
575            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
576    
577            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
578            FALSE answer
579    
580            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
581            * tests/indexing.R: test it, and some of the above
582    
583    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * R/Auxiliaries.R (is_duplicatedT): new utility
586    
587    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
588    
589            * src/init.c (R_init_Matrix): export cholmod_scale
590    
591    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
594            base::as.matrix to (x, ...)
595    
596    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
599            file; start using "Logic", hence
600    
601            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
602            * NAMESPACE: import and export "Logic"
603    
604    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
605    
606            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
607            only needed previously to R version 2.5.0.
608    
609    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
612    
613            * R/Tsparse.R (replTmat): fix subassignment of triangular
614            * R/Csparse.R (replCmat): ditto
615            * tests/indexing.R: more tests, incl the above fix
616    
617    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * R/Auxiliaries.R (drop0): extend for non CSparse
620            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
621    
622            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
623                    use uplo correctly (!); other places: use uplo_P() macro
624    
625            * R/Csparse.R (replCmat): call diagU2N() when needed
626            * R/Tsparse.R (replTmat): ditto
627    
628            * src/dtCMatrix.c (tCMatrix_validate): new
629            * src/dtTMatrix.c (tTMatrix_validate): new, used in
630            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
631    
632            * R/diagMatrix.R (replDiag): to use in [<-
633    
634    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
637                    also more general diagU2N().
638    
639    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
642            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
643    
644    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * tests/bind.R: a few more cases
647            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
648    
649            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
650            * R/ddenseMatrix.R (cbind2/rbind2)
651            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
652            * tests/indexing.R
653            * tests/indexing.Rout.save: updated
654    
655    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
658            * tests/indexing.R
659    
660    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
663            align with proper position of "0", i.e., right for integers.
664            argument 'align' by default is "fancy".
665    
666    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
669            * R/Csparse.R: and fix "Compare" for more cases.
670            * tests/Class+Meth.R: test some of these (m == m, m != m)
671    
672    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/lsparseMatrix.R: all() and any() methods
675            * R/ldenseMatrix.R:      ditto
676            * NAMESPACE, R/Matrix.R: ditto
677    
678            * man/all-methods.Rd: document them minimally
679    
680            * tests/simple.R: add a few examples for these
681    
682    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * R/Tsparse.R ([): fix long standing typo in symmetric case
685            * man/dsCMatrix-class.Rd: add example exhibiting the above case
686    
687    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
688    
689            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
690            to LL before converting to a sparse matrix. (The LDL form can be
691            converted to a sparse matrix but it is implicitly a unit
692            triangular matrix and a diagonal matrix overwritten on the diagonal.)
693    
694    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
695    
696            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
697    
698    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
699    
700            * DESCRIPTION (Version): updated -> release 0.9975-7
701            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
702    
703    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
706    
707    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
708    
709            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
710            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
711            is exactly singular.
712    
713    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * DESCRIPTION (Date): updated -> release 0.9975-6
716    
717    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
720            now returns symmetric.
721    
722            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
723    
724            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
725            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
726    
727            * R/Auxiliaries.R (.type.kind): added
728    
729    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
732            running src/CSparse_install.sh
733    
734            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
735    
736    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
739            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
740    
741            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
742    
743            * tests/Class+Meth.R (tstMatrixClass): now assure
744            the (important in method programming) property :
745    
746                    ###>>  Every "Matrix" is either
747                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
748    
749                    (where "*" stands for "Matrix")
750    
751            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
752    
753            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
754            * tests/validObj.R: checks for "comparison"
755    
756            * R/sparseMatrix.R ([): improved indexing for sparse;
757                    trying to keep <symmetric>[ n, n] symmmetric
758    
759            * tests/indexing.R: indexing for logical sparse now ok
760    
761    
762    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * src/Tsparse.c: use xTsparse_validate() , and hence remove
765    
766            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
767    
768    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
770            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
771    
772            * tests/simple.R: validObject() checking the above.
773    
774            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
775            replacing both dgCMatrix_validate and lgCM*.
776    
777            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
778            fix dimnames setting in other places.
779            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
780    
781    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
782    
783            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
784    
785            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
786            symmetry test, via
787            * R/Auxiliaries.R (.as.dgC.0.factors):
788    
789    2006-11-01  Douglas Bates  <bates@r-project.org>
790    
791            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
792            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
793            <CsparseMatrix>) added
794    
795    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * tests/matprod.R: add a variation of Harri's example
798    
799            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
800            recursive infinitely.
801    
802            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
803    
804            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
805    
806    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
807    
808            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
809            matrix if possible; test m+m == 2*m; now test dgRMatrix.
810            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
811            satisfy the above test.
812    
813    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
814    
815            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
816    
817            * R/dgCMatrix.R: solve(a, b="missing") based on
818            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
819            RHS = NULL.
820    
821            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
822            add more (needed) [t]crossprod() methods.
823    
824            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
825    
826            * R/Auxiliaries.R (as_CspClass): cleanup
827            (drop0): internal utility for "Csparse_drop(*, 0)"
828            (.bail.out.2): encourage active feedback
829    
830    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
831    
832            * R/dMatrix.R(Compare): new(), then slots [no validity check]
833    
834            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
835            non-valid or 'sorted' case).
836    
837            * R/dsparseMatrix.R: add "chol" method.
838            * R/ddenseMatrix.R: ditto
839    
840            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
841            * NAMESPACE (Ops)
842            * R/diagMatrix.R (diag2T): simple utility used "higher level"
843            coercion; deprecating direct lower level coercions.
844    
845            * R/*.R (seq): use seq_len() and seq_along() where possible.
846    
847    
848    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
849    
850            * DESCRIPTION (Version): 0.9975-5 ready for release
851    
852    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
853    
854            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
855    
856    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
857    
858            * R/AllClass.R (corMatrix): add 'validity' check;
859                    comment out unused "LDL" class definition
860            * NAMESPACE: mention, but do not export "LDL" class
861            * R/corMatrix.R: new (simple), needed for R-devel with
862            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
863              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
864    
865    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
866    
867            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
868            use Rprintf and R's error handling.
869    
870    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
871    
872            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
873            * tests/matprod.R: add tests for the bug fixed.
874    
875    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
876    
877            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
878            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
879    
880    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
881    
882            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
883    
884    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
885    
886            * DESCRIPTION (Version): 0.9975-3
887    
888            * R/diagMatrix.R (bdiag): new function constructing block diagonal
889            (sparse) matrices.
890            * man/bdiag.Rd: docu + examples
891    
892            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
893    
894            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
895            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
896    
897            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
898            that result is sparse or diagonal (and not dense).
899    
900            * man/Subassign-methods.Rd: fix examples
901    
902            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
903            should always return a sparse (and not sometimes a diagonal) matrix.
904    
905    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
908    
909    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
910    
911            * DESCRIPTION (Version): 0.9975-2
912    
913            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
914    
915    2006-10-02  Douglas Bates  <bates@R-project.org>
916    
917            * tests/dg_Matrix.R: Simplify test taking into account new code.
918    
919    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
922    
923            * R/lsTMatrix.R: new files w/ missing methods
924            * R/nsTMatrix.R:  "  'for completeness'
925    
926            * tests/Class+Meth.R: a bit less 'not.ok.classes'
927    
928            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
929    
930    
931    2006-09-28  Douglas Bates  <bates@R-project.org>
932    
933            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
934            included.
935    
936            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
937            Export C-callable functions used in Zt_create in lme4.
938    
939    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
940    
941            * DESCRIPTION (Version): 0.9975-1
942    
943            * tests/simple.R: less checks fail; using NA, found that our
944                    kronecker() is not base-compatible with NA's.
945    
946            * R/dMatrix.R: "Compare" method now implemented for all cases
947    
948            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
949    
950            * man/dtpMatrix-class.Rd: mention length of 'x' slot
951    
952            * src/dtpMatrix.c (dtpMatrix_validate): fix check
953            * src/dspMatrix.c (dspMatrix_validate): ditto
954    
955            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
956              including coercion to [nl]tTMatrix.
957    
958            * R/diagMatrix.R (show): print a header line as for other classes.
959    
960    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
961    
962            * src/Makefile.win (SUBDIRS): fix typo
963    
964    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
965    
966            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
967    
968    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
969    
970            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
971            symmetric and y missing in R code using %*% (cholmod_aat doesn't
972            accept a symmetric matrix).
973            * tests/group-methods.R: Uncomment test of crossprod applied to
974            lsCMatrix objects.
975    
976    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
977    
978            * R/AllClass.R (symmetricMatrix): add validity method (available
979            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
980    
981            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
982    
983            * tests/indexing.Rout.save:
984            * tests/indexing.R: additions, mainly for 'lsparse'
985    
986            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
987            case.
988    
989            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
990    
991    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
992    
993            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
994                    as 'N' (1-letter - Ok?)
995    
996            * tests/group-methods.R: add test for logical + NAs
997    
998            * R/dMatrix.R ("Compare"): fix to work with NA's
999    
1000            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1001    
1002            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1003                    which is implemented.
1004    
1005    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1006    
1007            * src/chm_common.c: coerce logical <-> double instead of
1008            typecasting;  needed for "l" matrix handling in cholmod.
1009    
1010            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1011    
1012            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1013            (Tsp2grNEL): other fixes needed
1014    
1015    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1016    
1017            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1018                    Matrices, since "lMatrix", also "lsparseM" can have NA
1019            * R/ndenseMatrix.R, etc: new source files
1020            * man/nsparseMatrix-classes.Rd, etc: new help files
1021            * tests/: adaptions
1022            * src/chm_common.c (chm_dense_to_SEXP): and others:
1023                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1024            * src/Csparse.c, etc: ditto
1025    
1026    2006-09-11  Douglas Bates  <bates@R-project.org>
1027    
1028            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1029            alloc_d**Matrix functions to the lme4 package.
1030    
1031    2006-09-09  Douglas Bates  <bates@R-project.org>
1032    
1033            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1034            fixed
1035    
1036    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1037    
1038            * R/lMatrix.R: new
1039    
1040            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1041    
1042            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1043            * man/tcrossprod.Rd: ditto
1044    
1045    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1046    
1047            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1048            for exported functions
1049            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1050            Remove partitioning algorithms for sparse matrix reordering.  The
1051            copyright on the Metis code was problematic and the methods were
1052            rarely used.
1053            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1054            operations are now done entirely in CHOLMOD code.
1055    
1056    2006-09-06  Douglas Bates  <bates@R-project.org>
1057    
1058            * src/Mutils.h: Remove functions that are no longer used.
1059    
1060    2006-09-04  Douglas Bates  <bates@R-project.org>
1061    
1062            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1063            * src/DEPS.mkf: update
1064    
1065    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1066    
1067            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1068            * DESCRIPTION (Version): 0.9975-0
1069            (Depends): R (>= 2.4.0)
1070    
1071    2006-09-01  Douglas Bates  <bates@R-project.org>
1072    
1073            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1074    
1075    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1076    
1077            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1078            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1079    
1080            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1081    
1082    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1083    
1084            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1085            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1086            * R/dsparseMatrix.R: ditto
1087            * R/Csparse.R: ditto
1088    
1089    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1090    
1091            * R/dMatrix.R (Compare): improve availability of "<", etc
1092            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1093    
1094    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1095    
1096            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1097            of a 0-index which was used as 1-index (..hmm)
1098    
1099            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1100    
1101            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1102            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1103            (.is.diagonal): ditto
1104    
1105            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1106    
1107            * R/Matrix.R (Matrix): also work for NA data
1108    
1109    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1110    
1111            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1112            in all cases.
1113    
1114    2006-08-27  Douglas Bates  <bates@R-project.org>
1115    
1116            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1117            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1118    
1119    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1120    
1121            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1122            subclasses of "ddenseMatrix"
1123            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1124            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1125            instead of half dozen specialized ones.
1126    
1127    2006-08-25  Douglas Bates  <bates@R-project.org>
1128    
1129            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1130            <tillard@cirad.fr> - ordering standard errors to match effects.
1131    
1132    2006-08-24  Douglas Bates  <bates@R-project.org>
1133    
1134            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1135            on R_ldl.
1136            * R/lCholCMatrix.R,
1137            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1138            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1139            * many files in ./R and ./src: Use more general version of
1140            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1141            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1142            dtpMatrix, dspMatrix and dppMatrix conversions.
1143    
1144    
1145    2006-08-23  Douglas Bates  <bates@R-project.org>
1146    
1147            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1148            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1149            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1150            dgeMatrix_crossprod (may need to do this in other places).
1151            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1152            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1153    
1154    2006-08-22  Douglas Bates  <bates@R-project.org>
1155    
1156            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1157            types of classed Matrices, matrices or numeric or logical vectors.
1158            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1159            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1160            to Mutils.h (as an inline) and change name to Matrix_check_class;
1161            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1162            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1163            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1164            * src/Csparse.c: use diag_P and uplo_P macros.
1165    
1166    2006-08-21  Douglas Bates  <bates@R-project.org>
1167    
1168            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1169            valgrind.
1170            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1171            inverses.
1172            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1173            -Wall warnings.
1174            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1175            Use dup_mMatrix_as_dgeMatrix.
1176    
1177    2006-08-20  Douglas Bates  <bates@R-project.org>
1178    
1179            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1180            * tests/sparseQR.R: Added
1181            * man/sparseQR-class.Rd: Document methods for qr.* generics
1182            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1183    
1184    2006-08-19  Douglas Bates  <bates@R-project.org>
1185    
1186            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1187            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1188            and qr.fitted.
1189            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1190            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1191    
1192    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1193    
1194            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1195            the base version has no "..." argument.
1196    
1197            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1198    
1199            * R/Matrix.R: define and
1200            * NAMESPACE: export as.numeric() and as.logical() methods.
1201                    Let's hope these do not badly slow down something...
1202            Finally export the zapsmall() method.
1203    
1204    2006-08-17  Douglas Bates  <bates@R-project.org>
1205    
1206            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1207            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1208            * src/dtCMatrix.c :Remove code that is no longer used
1209            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1210    
1211    2006-08-14  Douglas Bates  <bates@R-project.org>
1212    
1213            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1214            Csparse_to_logical and Csparse_symmetric_to_general.
1215            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1216            coercion methods between CsparseMatrix and TsparseMatrix.
1217    
1218    2006-08-14  Douglas Bates  <bates@R-project.org>
1219    
1220            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1221            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1222            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1223            possible.
1224    
1225    2006-08-12  Douglas Bates  <bates@R-project.org>
1226    
1227            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1228              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1229              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1230              generalize conversions between TsparseMatrix, CsparseMatrix,
1231              denseMatrix and matrix.  Preserve triangularity property and
1232              propagate Dimnames in the easy cases.
1233    
1234    2006-08-10  Douglas Bates  <bates@R-project.org>
1235    
1236            * src/lmer.c: adjust checks in glmer_init for S4SXP
1237            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1238            before S4SXP but for the wrong reasons.
1239    
1240    2006-08-08  Douglas Bates  <bates@R-project.org>
1241    
1242            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1243            Later modified to return the upper triangle only.
1244            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1245    
1246    2006-08-07  Douglas Bates  <bates@R-project.org>
1247    
1248            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1249            R-level conversion to a sparse symmetric class.
1250            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1251            Remove conversion to sparse symmetric classes (now done in C code).
1252    
1253    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1254    
1255            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1256            * man/band.Rd:  adapt the \dontshow{} unit test.
1257    
1258    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1259    
1260            * DESCRIPTION (Version): 0.995-14  for CRAN
1261    
1262            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1263    
1264            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1265            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
1266    
1267            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1268            * R/Tsparse.R (tril, triu, band): methods
1269            * R/dgRMatrix.R (tril, ...):    ditto
1270            * man/band.Rd:                  ditto
1271    
1272    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1273    
1274            * R/Matrix.R (head, tail): directly use utils:::head.matrix
1275                    to be up-to-date automatically.
1276    
1277    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1278    
1279            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1280    
1281            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1282            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1283            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1284            such that the S4 objects are always created by the current version
1285            of R and 'Matrix' class definitions.
1286    
1287    2006-08-01  Douglas Bates  <bates@R-project.org>
1288    
1289            * R/lmer.R (LMEoptimize method), tests/lmer.R,
1290            inst/external/test3comp.rda: Added warnings for convergence on
1291            boundary and test cases.
1292    
1293            * src/lmer.c (mer_postVar): Modified to return the variances that
1294            are marginal to the fixed effects, not conditional on them (which
1295            is what the bVar slot contents represent).
1296    
1297    2006-07-31  Douglas Bates  <bates@R-project.org>
1298    
1299            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
1300            function which calls the C function mer_hat_trace2.
1301    
1302            * man/ranef.Rd: Include description of "postVar" argument and
1303            producing a caterpillar plot.
1304    
1305    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1306    
1307            * NAMESPACE:    change  "correlation" to "corMatrix"
1308            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1309            * R/dpoMatrix.R: ditto
1310            * R/lmer.R:      ditto
1311    
1312    2006-07-28  Douglas Bates  <bates@R-project.org>
1313    
1314            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1315            RZXinv slot's contents into a separate internal function that can
1316            be used in mer_hat_trace.
1317    
1318    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1319    
1320            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1321            via new smart
1322            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1323            utility functions.
1324    
1325    
1326    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1327    
1328            * R/Csparse.R (tril, triu, band): do return *triangular* classed
1329            matrices when appropriate; band() even symmetric ones.
1330            (replCmat): extend to potentially all "CsparseMatrix"
1331            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1332            allow subassignment for special sparse matrices.
1333    
1334            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
1335    
1336            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1337            argument; in glmer_*(): print only if(verbose).
1338    
1339            speed-optimize a few places by moving REAL(.) out of loops.
1340    
1341            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
1342    
1343    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1344    
1345            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1346                    since that wrongly triggers also for M[ logi , ]
1347    
1348            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1349            a symmetric matrix that results in a non-symmetric one.
1350            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1351    
1352            * R/dMatrix.R: make round(M) work as round(M, 0)
1353    
1354            * R/dgTMatrix.R (image): coordinate system and axis now use
1355            1-based indices, not 0-based ones.
1356    
1357            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1358            * tests/indexing.R: test it.
1359    
1360            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1361            * man/isSymmetric-methods.Rd: and document it.
1362    
1363            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1364            * man/SparseM-conv.Rd: docu them
1365    
1366            * tests/other-pkgs.R: renamed from tests/graph.R and add example
1367                    for 'SparseM' conversions
1368    
1369    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
1370    
1371            * R/Matrix.R (head): added head() and tail() methods.
1372    
1373    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1374    
1375            * DESCRIPTION (Version): 0.995-12 released to CRAN
1376    
1377    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1378    
1379            * tests/simple.R: add check for correct dsT -> dgT coercion;
1380                    add check for correct printing of symmetric sparse matrices.
1381    
1382            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1383            for sparse symmetric matrices.
1384    
1385            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1386            diagonal twice.
1387    
1388    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
1389    
1390            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1391            being applied to the x slot (detected by Brian Ripley).
1392    
1393    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1394    
1395            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1396    
1397            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1398    
1399    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1400    
1401            * src/lgCMatrix.c (lgCMatrix_diag): new function
1402            * R/lgCMatrix.R (diag): for new method
1403    
1404            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1405                 ==> construction of illegal "*gTMatrix" via new() should
1406                 now be much less easy:
1407            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1408    
1409            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1410                    directly.
1411            * man/Matrix.Rd: documents it.
1412    
1413    2006-07-06  Douglas Bates  <bates@R-project.org>
1414    
1415            * src/pedigree.c (pedigree_inbreeding): Correction in
1416            initialization.  This function is not currently being used and is
1417            not fully tested.
1418    
1419            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1420            Introduced the glmer class.  Added code for mcmcmsamp on glmer
1421            objects.  Modified validity check on pedigree objects to account
1422            for nonparallel patterns of missingness of parents.
1423    
1424            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1425            class.
1426    
1427    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1428    
1429            * R/pMatrix.R: coercion pMatrix -> Tsparse
1430    
1431    2006-06-12  Douglas Bates  <bates@R-project.org>
1432    
1433            * DESCRIPTION (Version): 0.995-11 released to CRAN
1434    
1435            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1436            the output from mcmcsamp.
1437    
1438    2006-06-10  Douglas Bates  <bates@R-project.org>
1439    
1440            * R/lmer.R (simulestimate): added C code for calculating the trace
1441            of the hat matrix.
1442    
1443    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1444    
1445            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1446            classes.
1447            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1448    
1449    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1450    
1451            * R/dgTMatrix.R (colSums): etc. All four of
1452            colSums(), rowSums(), colMeans(), rowMeans() now should work for
1453            all "Matrices".
1454    
1455    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
1456    
1457            * R/lmer.R (panel.ci): Add a reference line at zero and a
1458            background grid to the qqmath plot of ranef.lmer.
1459    
1460    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
1461    
1462            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1463            grouping factors to be specified in the formula as (1|foo/bar).
1464    
1465    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1466    
1467            * R/lmer.R (findbars and others): Change check of is.numeric to
1468            !is.language to resolve the bug reported by Jacob Wegelin.
1469    
1470            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1471            code to evaluate inbreeding coefficients without calculating T,
1472            based on code in Sargolzaei and Iwaisaki's paper.
1473    
1474    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
1475    
1476            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1477            generic and mer methods for isNested and denomDF. This denomDF was
1478            an attempt to emulate that in lme but I don't think that makes
1479            sense.  Use the trace of the hat matrix instead.
1480    
1481    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1482    
1483            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1484            the C code depending on a slot structure that's no longer valid.
1485            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1486    
1487    
1488    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
1489    
1490            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1491            of lowerTriMatrix generic and methods to tril (also upper to triu)
1492            and added a general band extractor.
1493    
1494    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
1495    
1496            * R/pedigree.R (pedigree): Replace sire and dam values outside the
1497            allowable range with NAs. Added a corresponding check in the
1498            validity check for the pedigree class.
1499    
1500            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1501            crossprod methods now inherits from symmetricMatrix.
1502    
1503    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
1504    
1505            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1506            generics lowerTriMatrix and upperTriMatrix along with methods for
1507            the Csparse virtual class.  Also added a C function Csparse_band
1508            that implements these methods by calling cholmod_band.
1509    
1510    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1511    
1512            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1513            erased when it was NULL.  This led to invalid subselections!
1514    
1515    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
1516    
1517            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1518            in method for "t" so as not to lose the unit diagonal property.
1519    
1520    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
1521    
1522            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1523            and methods.  This is now an option to the ranef method for the
1524            mer class.
1525    
1526            * src/cs_utils.c: Ensure that the nz component is -1 for a
1527            compressed column-oriented matrix.  Minor formatting cleanup.
1528    
1529            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1530            objects.
1531    
1532    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1533    
1534            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1535            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1536    
1537    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
1538    
1539            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1540            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1541    
1542            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1543            for the dtCMatrix class.
1544    
1545    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
1546    
1547            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1548            and methods for it.
1549    
1550    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1551    
1552            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
1553            arguments, such that M %*% 1:6 now works
1554            * Tests/matprod.R: test the above
1555    
1556    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
1557    
1558            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1559            the ranef.lmer class.
1560    
1561            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1562            methods to extract the posterior variances from the bVar slot.
1563    
1564    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1565    
1566            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
1567            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1568    
1569            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1570            * tests/simple: (extended)
1571    
1572            * R/sparseMatrix.R (isTriangular): now using much improved
1573            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1574    
1575    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
1576    
1577            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1578            (problem report from Franklin Parlamis).  This should be done
1579            generally.
1580    
1581    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
1582    
1583            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1584            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
1585            update the plot methods.
1586    
1587    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
1588    
1589            * R/lmer.R (resid and ranef methods):  Added methods for the
1590            "residuals" and "resid" generic but only for linear mixed model
1591            fits.  Changed the ranef method to return a list of data frames so
1592            that the plot methods now work.
1593    
1594    2006-03-16  Douglas Bates  <bates@bates2>
1595    
1596            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1597            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1598    
1599            * DESCRIPTION (Date): New release
1600    
1601    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1602    
1603            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
1604    
1605            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1606            * man/KNex.Rd: and other help files
1607            * tests/*.R: several ones needed adaption
1608            * inst/doc/Comparisons.Rnw: ditto
1609    
1610    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1611    
1612            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1613    
1614            * tests/indexing.R: tests for new [<- methods for sparse matrices.
1615    
1616    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
1617    
1618            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1619    
1620            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1621    
1622    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1623    
1624            * R/dMatrix.R: enable things like  M [ M < 10 ]
1625            * R/dgeMatrix.R: implement it
1626    
1627    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1628    
1629            * R/AllClass.R: define "summary.mer" and "*.lmer"
1630            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1631            * R/lmer.R (show): now works with summary()
1632    
1633    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1634    
1635            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
1636            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1637                    support the above
1638    
1639    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
1640    
1641            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1642            Use glmFit$prior.weights for weights in a glmm.
1643            Allow an option usePQL = FALSE to skip the PQL steps for the
1644            Laplace method (and, in time, the AGQ method).
1645    
1646            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1647            into a separate function internal_mer_Xfactor to be able to call
1648            it from internal_bhat.
1649    
1650    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1651    
1652            * tests/Class+Meth.R (tstMatrixClass): function for much better
1653            testing; now again of all actual classes.
1654    
1655            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1656                    use macros and define make_d_matrix_* and make_i_matrix_*
1657                    where _i_ is for the ldense routines:
1658    
1659            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1660            * src/ldense.c (lsyMatrix_as_lgeMatrix):
1661    
1662            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1663    
1664    
1665    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1666    
1667            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1668                    many different kinds of matrices.
1669            * R/*.R: quite a few new methods were needed for R CMD check with
1670                    new Matrix().  Very good for users playing around.
1671    
1672    
1673    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1674    
1675            * src/dgeMatrix.c (dMatrix_validate): new
1676            * src/Mutils.c (dense_nonpacked_validate): new
1677    
1678            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1679    
1680    
1681    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
1682    
1683            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1684    
1685    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
1686    
1687            * DESCRIPTION (Version): 0.99-6 released to CRAN
1688    
1689            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1690            segfault in cases with multiple non-nested grouping factors.
1691    
1692    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1693    
1694            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1695                    (Depends): also on 'utils'
1696    
1697            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1698            * R/diagMatrix.R (Diagonal): constructor and methods for
1699            diagonal matrices
1700    
1701            * R/ltTMatrix.R: new "minimal methods"
1702    
1703    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1704    
1705            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1706            all methods (and help files).
1707    
1708    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1709    
1710            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1711                    for case (dimn.  op  no_dimn.)
1712    
1713    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
1714    
1715            * DESCRIPTION (Version): 0.99-2  released to CRAN
1716    
1717    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
1718    
1719            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1720            by Julian Faraway.
1721    
1722    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1723    
1724            * R/Auxiliaries.R (try_as): new utility
1725            * R/sparseMatrix.R: use try_as() in coercion to original class
1726    
1727    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1728    
1729            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1730    
1731    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1732    
1733            * R/Auxiliaries.R (dimNamesCheck): added
1734    
1735            * R/Matrix.R (as.array), (as.vector): new
1736    
1737    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1738    
1739            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1740                    default.
1741            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1742                    "pMatrix" now contains "sparseMatrix"
1743    
1744    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1745    
1746            * tests/Class+Meth.R: new tests; t(t(m)) == m
1747    
1748            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1749    
1750            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1751            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1752    
1753            * R/dspMatrix.R: typo in "t" method
1754    
1755    2005-09-18  Douglas Bates  <bates@wisc.edu>
1756    
1757            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1758            * R/Tsparse.R: instead of R/gTMatrix.R
1759            * R/Csparse.R: new
1760            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1761            * src/Tsparse.c: new; many trivial methods calling cholmod_()
1762            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1763                            via cholmod
1764    
1765    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1766    
1767            * R/Auxiliaries.R (non0ind): new function using new C code
1768            * src/dgCMatrix.c (compressed_non_0_ij): new utility
1769    
1770    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
1771    
1772            * src/chm_common.h: header file required by all C sources that
1773            call CHOLMOD functions.  It defines a cholmod_common structure
1774            called 'c' whose address is passed as the last argument to
1775            (virtually) every CHOLMOD function.
1776    
1777            * src/Pattern.c: Simple example of the use of CHOLMOD.
1778    
1779            * src/init.c: initialize and finalize the cholmod_common structure.
1780    
1781            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1782            LDL and CCOLAMD from the U. of Florida sparse matrix library.
1783    
1784    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1785    
1786            * inst/test-tools.R: new file collecting the utility functions used
1787                    in ./tests/*.R
1788    
1789            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1790            * R/Matrix.R (cbind2): methods for NULL and missing
1791    
1792    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1793    
1794            * R/AllClass.R: new "index" class for "[" and "[<-":
1795                    First cut at "symmetricMatrix" and "triangularMatrix"
1796            * R/gTMatrix.R (.ind.prep): new function;
1797                    Logical and character indexing now work too.
1798            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1799            * tests/indexing.R: new, including *.Rout.save
1800            * tests/dgTMatrix.R: new
1801    
1802    2005-08-29  Douglas Bates  <bates@wisc.edu>
1803    
1804            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1805            indicator pos not being updated.  Also enforced upper triangular
1806            for symmetric case.  Need to coerce edges component of elements of
1807            edge list - grr! (Why don't they define their classes cleanly?)
1808    
1809    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1810    
1811            * R/Matrix.R:  added first "[<-" methods; not yet functional
1812            * R/denseMatrix.R: ditto
1813            * man/Subassign-methods.Rd: new help file for these
1814    
1815    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1816    
1817            * DESCRIPTION (Version): 0.98-6
1818    
1819            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1820            matrices.
1821    
1822    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1823    
1824            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1825                    as( <logical>, "matrix")
1826    
1827            * R/pMatrix.R: coercion to "lgTMatrix"
1828    
1829            * R/gTMatrix.R: new virtual class to define "[" methods for.
1830            * man/gTMatrix-class.Rd:
1831            * General slight re-organization of where "[" methods are defined.
1832              more to come.
1833    
1834    2005-08-18  Douglas Bates  <bates@wisc.edu>
1835    
1836            * DESCRIPTION (Version): 0.98-5  released to CRAN
1837    
1838            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1839            * .....
1840    
1841    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1842    
1843            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1844            or glmer objects.
1845    
1846    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1847    
1848            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1849    
1850    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1851    
1852            * R/HBMM.R: finish re-writing R-only code.
1853    
1854    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1855    
1856            * man/externalFormats.Rd: move documentation for writeHB and
1857            writeMM here.
1858    
1859            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1860            (suggested by Paul Roecker).
1861    
1862            * tests/validObj.R (assertError): Comment out test that is failing
1863            after recent changes in r-devel.
1864    
1865    
1866    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1867    
1868            * R/AllClass.R: intermediate virtual class "denseMatrix"
1869            * man/denseMatrix-class.Rd
1870            * NAMESPACE: export it, and also export
1871            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1872    
1873    2005-08-10  Douglas Bates  <bates@wisc.edu>
1874    
1875            * DESCRIPTION (Version): 0.98-3 to CRAN
1876    
1877            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1878            matrix_solve code (which was really, really wrong).
1879    
1880    2005-08-07  Douglas Bates  <bates@wisc.edu>
1881    
1882            * DESCRIPTION (Version): 0.98-2
1883    
1884            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1885    
1886            * R/lmer.R (abbrvNms): new
1887            * R/lmer.R (mcmcsamp): allow transformed parameters
1888            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1889            for the Harwell-Boeing and the MatrixMarket formats.
1890    
1891    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1892    
1893            * man/dtrMatrix-class.Rd: add examples
1894            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1895    
1896            * TODO: note the dtpMatrix (docu) bug
1897    
1898            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1899            in order to ensure that new as.matrix() is used by old functions,
1900            e.g., svd(), qr(), eigen(), dist(),..;
1901                  apply(), also matplot() or pairs().
1902    
1903    
1904    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1905    
1906            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1907              add comments about 'control' / lmerControl() arguments
1908    
1909    2005-07-27  Douglas Bates  <bates@wisc.edu>
1910    
1911            * man/sleepstudy.Rd: Added the sleep data set.
1912            * DESCRIPTION (Version): 0.98-1  released to CRAN
1913    
1914    2005-07-12  Douglas Bates  <bates@wisc.edu>
1915            * man/sleepstudy.Rd: Added the sleep data set.
1916    
1917            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1918            .Call calls that were producing spurious output.
1919    
1920    2005-07-05  Douglas Bates  <bates@wisc.edu>
1921    
1922            * R/lmer.R (lmer): stored updated variance component estimates in
1923            mer object for the generalized model.  (Bug reported by Renaud
1924            Lancelot).
1925    
1926    2005-07-03  Douglas Bates  <bates@wisc.edu>
1927    
1928            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1929            unidimensional case.
1930    
1931    2005-06-08  Douglas Bates  <bates@wisc.edu>
1932    
1933            * DESCRIPTION (Version): 0.96-1
1934    
1935            * moved  lmer-class' R and C code moved from lme4 to here
1936    
1937    2005-06-04  Douglas Bates  <bates@wisc.edu>
1938    
1939            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1940            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1941    
1942    2005-06-02  Douglas Bates  <bates@wisc.edu>
1943    
1944            * src/Makefile.win: Forgot to update this when Makefile changed.
1945    
1946    2005-05-11  Douglas Bates  <bates@wisc.edu>
1947    
1948            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1949            bug reported by Kurt Hornik and Michael Hahsler.
1950    
1951    2005-05-10  Douglas Bates  <bates@wisc.edu>
1952    
1953            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1954            logical sparse matrices.  These will also be used in the symbolic
1955            analysis for lmer objects.
1956    
1957            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1958            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1959    
1960    2005-05-06  Douglas Bates  <bates@wisc.edu>
1961    
1962            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1963            colMeans, colSums, rowMeans and rowSums.
1964    
1965    2005-04-18  Douglas Bates  <bates@wisc.edu>
1966    
1967            * src/lgCMatrix.[ch]: code for _validate method and stub for
1968            multiplication operation.
1969    
1970            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1971            to dgetrs.
1972    
1973            * src/init.c: Fix cut-and-paste error in definition of
1974            dgeMatrix_matrix_solve
1975    
1976            * src/{many files}: Tighten code by using ALLOC_SLOT.
1977    
1978    2005-04-15  Douglas Bates  <bates@wisc.edu>
1979    
1980            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1981    
1982            * DESCRIPTION: Eliminate import of stats.
1983    
1984    
1985    2005-04-06  Douglas Bates  <bates@wisc.edu>
1986    
1987            * R/AllClass.R : add logical sparse matrix classes
1988    
1989    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1990    
1991            * R/dgTMatrix.R: add "[" method for triplet matrices
1992            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1993    
1994    2005-03-31  Douglas Bates  <bates@wisc.edu>
1995    
1996            * DESCRIPTION (Version): release 0.95-5 to CRAN
1997    
1998            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1999            * R/sparseMatrix.R: %*%, crossprod()
2000            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
2001            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
2002            * src/lmer.c (lmer_fitted): fix thinko
2003    
2004    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2005    
2006            * R/AllClass.R: add two virtual sparse classes ``on top''
2007    
2008    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
2009    
2010            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
2011                    correspondingly fix examples and tests/ since new()
2012                    doesn't work for virtual classes.
2013    
2014    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2015    
2016            * R/Matrix.R (as.matrix): method and one for unname()
2017            * tests/dpoMatrix.R: tests should now be less platform dependent;
2018              also run for R 2.1.0; using as.matrix()
2019    
2020    2005-03-15  Douglas Bates  <bates@wisc.edu>
2021    
2022            * R/pMatrix.R: "pMatrix" class added
2023            * ....
2024    
2025    2005-03-14  Douglas Bates  <bates@wisc.edu>
2026    
2027            * R/dtpMatrix.R: Add unpack method and an example.
2028    
2029            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
2030            of general symmetric matrices and associated S4 methods.
2031    
2032    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
2033            +
2034    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2035    
2036            * R/dgeMatrix.R (setAs): and many other files: more coercion,
2037              crossprod() and "%*%" methods added; tests, too.
2038            * tests/matprod.R: new, for testing these
2039    
2040    2005-03-03  Douglas Bates  <bates@wisc.edu>
2041    
2042            * src/lmer.c (lmer_fitted): Added.
2043    
2044    2005-03-02  Douglas Bates  <bates@wisc.edu>
2045    
2046            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2047    
2048    2005-02-28  Douglas Bates  <bates@wisc.edu>
2049    
2050            * src/*.c,po/,inst/po: Internationalization and localization of
2051            the package.
2052    
2053            * src/ldl.[ch]: Removed these as their contents are referenced in the
2054            R_ldl.c file.
2055    
2056            * src/flame.[ch]: Removed these source files.
2057    
2058            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
2059    
2060            * src/LU.[ch],src/init.c: absorb in factorizations
2061    
2062            * src/Mutils.h: prepare for internationalization
2063    
2064            * src/cblas.h: move the enum definitions to Mutils.h and remove
2065            this file
2066    
2067    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2068    
2069            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
2070    
2071            * R/dtrMatrix.R: fix t() method
2072    
2073            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2074            * NAMESPACE: export them (and import generics from "methods")
2075            * tests/group-methods.R : and test them.
2076    
2077            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2078            border case
2079    
2080    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
2081    
2082            * DESCRIPTION (Version): 0.95-2  released to CRAN
2083    
2084            * src/dgBCMatrix.c:
2085            * src/lmer.c: many changes
2086            * ...
2087    
2088    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
2089    
2090            * R/Matrix.R: add more sophisticated show() method.
2091    
2092    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
2093    
2094            * */* : almost complete reorganization of classes.
2095    
2096    2005-01-26  Douglas Bates  <bates@wisc.edu>
2097    
2098            * R/AllGeneric.R: Added matrix exponential generic expm and a method
2099            for the geMatrix class.
2100    
2101    2005-01-24  Douglas Bates  <bates@wisc.edu>
2102    
2103            * src/Makefile (clean): Remove *.a and *.so
2104    
2105            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2106    
2107    2005-01-23  Douglas Bates  <bates@wisc.edu>
2108    
2109            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
2110            had an effect in cases with more than 2 grouping factors.
2111    
2112    2005-01-03  Douglas Bates  <bates@wisc.edu>
2113    
2114            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2115    
2116    2004-12-23  Douglas Bates  <bates@wisc.edu>
2117    
2118            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2119            and R_useDynamicSymbols (suggested by B.D.Ripley).
2120    
2121    2004-12-14  Douglas Bates  <bates@wisc.edu>
2122    
2123            * R/sscMatrix.R: Add determinant methods
2124    
2125            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2126            for tripletMatrix to matrix.
2127    
2128    2004-12-13  Douglas Bates  <bates@wisc.edu>
2129    
2130            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2131            no longer used.
2132    
2133          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
2134          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 2137 
2137          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
2138          Fixes part but not all of #15.          Fixes part but not all of #15.
2139    
2140  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
2141    
2142          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2143          scalar grouping factors corrected.          scalar grouping factors corrected.
2144    
2145  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
2146    
2147          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
2148    
2149  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
2150    
2151          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
2152          .h file can be included.          .h file can be included.
2153    
2154  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
2155    
2156          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2157          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
2158    
2159          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
2160    
2161  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
2162    
2163          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
2164    
2165  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
2166    
2167          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
2168    
2169  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
2170    
2171          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2172    
2173  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
2174    
2175          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2176    
2177  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
2178    
2179          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
2180          routines.          routines.
2181    
2182  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
2183    
2184          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2185    
2186  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
2187    
2188          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2189    

Legend:
Removed from v.388  
changed lines
  Added in v.2024

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