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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1200, Mon Jan 23 16:01:20 2006 UTC
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1  2004-11-16  Douglas Bates  <bates@bates1-home>  2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/Class+Meth.R (tstMatrixClass): function for much better
4            testing; now again of all actual classes.
5    
6            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
7                    use macros and define make_d_matrix_* and make_i_matrix_*
8                    where _i_ is for the ldense routines:
9    
10            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
11            * src/ldense.c (lsyMatrix_as_lgeMatrix):
12    
13            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
14    
15    
16    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
19                    many different kinds of matrices.
20            * R/*.R: quite a few new methods were needed for R CMD check with
21                    new Matrix().  Very good for users playing around.
22    
23    
24    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * src/dgeMatrix.c (dMatrix_validate): new
27            * src/Mutils.c (dense_nonpacked_validate): new
28    
29            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
30    
31    
32    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
33    
34            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
35    
36    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
37    
38            * DESCRIPTION (Version): 0.99-6 released to CRAN
39    
40            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
41            segfault in cases with multiple non-nested grouping factors.
42    
43    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
46                    (Depends): also on 'utils'
47    
48            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
49            * R/diagMatrix.R (Diagonal): constructor and methods for
50            diagonal matrices
51    
52            * R/ltTMatrix.R: new "minimal methods"
53    
54    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
57            all methods (and help files).
58    
59    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
62                    for case (dimn.  op  no_dimn.)
63    
64    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * DESCRIPTION (Version): 0.99-2  released to CRAN
67    
68    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
69    
70            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
71            by Julian Faraway.
72    
73    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Auxiliaries.R (try_as): new utility
76            * R/sparseMatrix.R: use try_as() in coercion to original class
77    
78    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
81    
82    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/Auxiliaries.R (dimNamesCheck): added
85    
86            * R/Matrix.R (as.array), (as.vector): new
87    
88    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
91                    default.
92            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
93                    "pMatrix" now contains "sparseMatrix"
94    
95    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * tests/Class+Meth.R: new tests; t(t(m)) == m
98    
99            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
100    
101            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
102            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
103    
104            * R/dspMatrix.R: typo in "t" method
105    
106    2005-09-18  Douglas Bates  <bates@wisc.edu>
107    
108            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
109            * R/Tsparse.R: instead of R/gTMatrix.R
110            * R/Csparse.R: new
111            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
112            * src/Tsparse.c: new; many trivial methods calling cholmod_()
113            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
114                            via cholmod
115    
116    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Auxiliaries.R (non0ind): new function using new C code
119            * src/dgCMatrix.c (compressed_non_0_ij): new utility
120    
121    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
122    
123            * src/chm_common.h: header file required by all C sources that
124            call CHOLMOD functions.  It defines a cholmod_common structure
125            called 'c' whose address is passed as the last argument to
126            (virtually) every CHOLMOD function.
127    
128            * src/Pattern.c: Simple example of the use of CHOLMOD.
129    
130            * src/init.c: initialize and finalize the cholmod_common structure.
131    
132            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
133            LDL and CCOLAMD from the U. of Florida sparse matrix library.
134    
135    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * inst/test-tools.R: new file collecting the utility functions used
138                    in ./tests/*.R
139    
140            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
141            * R/Matrix.R (cbind2): methods for NULL and missing
142    
143    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/AllClass.R: new "index" class for "[" and "[<-":
146                    First cut at "symmetricMatrix" and "triangularMatrix"
147            * R/gTMatrix.R (.ind.prep): new function;
148                    Logical and character indexing now work too.
149            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
150            * tests/indexing.R: new, including *.Rout.save
151            * tests/dgTMatrix.R: new
152    
153    2005-08-29  Douglas Bates  <bates@wisc.edu>
154    
155            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
156            indicator pos not being updated.  Also enforced upper triangular
157            for symmetric case.  Need to coerce edges component of elements of
158            edge list - grr! (Why don't they define their classes cleanly?)
159    
160    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/Matrix.R:  added first "[<-" methods; not yet functional
163            * R/denseMatrix.R: dito
164            * man/Subassign-methods.Rd: new help file for these
165    
166    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * DESCRIPTION (Version): 0.98-6
169    
170            * R/denseMatrix.R: new file for "[" fallback methods for all dense
171            matrices.
172    
173    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
176                    as( <logical>, "matrix")
177    
178            * R/pMatrix.R: coercion to "lgTMatrix"
179    
180            * R/gTMatrix.R: new virtual class to define "[" methods for.
181            * man/gTMatrix-class.Rd:
182            * General slight re-organization of where "[" methods are defined.
183              more to come.
184    
185    2005-08-18  Douglas Bates  <bates@wisc.edu>
186    
187            * DESCRIPTION (Version): 0.98-5  released to CRAN
188    
189            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
190            * .....
191    
192    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
193    
194            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
195            or glmer objects.
196    
197    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
200    
201    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
202    
203            * R/HBMM.R: finish re-writing R-only code.
204    
205    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
206    
207            * man/externalFormats.Rd: move documentation for writeHB and
208            writeMM here.
209    
210            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
211            (suggested by Paul Roecker).
212    
213            * tests/validObj.R (assertError): Comment out test that is failing
214            after recent changes in r-devel.
215    
216    
217    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/AllClass.R: intermediate virtual class "denseMatrix"
220            * man/denseMatrix-class.Rd
221            * NAMESPACE: export it, and also export
222            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
223    
224    2005-08-10  Douglas Bates  <bates@wisc.edu>
225    
226            * DESCRIPTION (Version): 0.98-3 to CRAN
227    
228            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
229            matrix_solve code (which was really, really wrong).
230    
231    2005-08-07  Douglas Bates  <bates@wisc.edu>
232    
233            * DESCRIPTION (Version): 0.98-2
234    
235            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
236    
237            * R/lmer.R (abbrvNms): new
238            * R/lmer.R (mcmcsamp): allow transformed parameters
239            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
240            for the Harwell-Boeing and the MatrixMarket formats.
241    
242    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * man/dtrMatrix-class.Rd: add examples
245            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
246    
247            * TODO: note the dtpMatrix (docu) bug
248    
249            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
250            in order to ensure that new as.matrix() is used by old functions,
251            e.g., svd(), qr(), eigen(), dist(),..;
252                  apply(), also matplot() or pairs().
253    
254    
255    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
258              add comments about 'control' / lmerControl() arguments
259    
260    2005-07-27  Douglas Bates  <bates@wisc.edu>
261    
262            * man/sleepstudy.Rd: Added the sleep data set.
263            * DESCRIPTION (Version): 0.98-1  released to CRAN
264    
265    2005-07-12  Douglas Bates  <bates@wisc.edu>
266            * man/sleepstudy.Rd: Added the sleep data set.
267    
268            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
269            .Call calls that were producing spurious output.
270    
271    2005-07-05  Douglas Bates  <bates@wisc.edu>
272    
273            * R/lmer.R (lmer): stored updated variance component estimates in
274            mer object for the generalized model.  (Bug reported by Renaud
275            Lancelot).
276    
277    2005-07-03  Douglas Bates  <bates@wisc.edu>
278    
279            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
280            unidimensional case.
281    
282    2005-06-08  Douglas Bates  <bates@wisc.edu>
283    
284            * DESCRIPTION (Version): 0.96-1
285    
286            * moved  lmer-class' R and C code moved from lme4 to here
287    
288    2005-06-04  Douglas Bates  <bates@wisc.edu>
289    
290            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
291            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
292    
293    2005-06-02  Douglas Bates  <bates@wisc.edu>
294    
295            * src/Makefile.win: Forgot to update this when Makefile changed.
296    
297    2005-05-11  Douglas Bates  <bates@wisc.edu>
298    
299            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
300            bug reported by Kurt Hornik and Michael Hahsler.
301    
302    2005-05-10  Douglas Bates  <bates@wisc.edu>
303    
304            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
305            logical sparse matrices.  These will also be used in the symbolic
306            analysis for lmer objects.
307    
308            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
309            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
310    
311    2005-05-06  Douglas Bates  <bates@wisc.edu>
312    
313            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
314            colMeans, colSums, rowMeans and rowSums.
315    
316    2005-04-18  Douglas Bates  <bates@wisc.edu>
317    
318            * src/lgCMatrix.[ch]: code for _validate method and stub for
319            multiplication operation.
320    
321            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
322            to dgetrs.
323    
324            * src/init.c: Fix cut-and-paste error in definition of
325            dgeMatrix_matrix_solve
326    
327            * src/{many files}: Tighten code by using ALLOC_SLOT.
328    
329    2005-04-15  Douglas Bates  <bates@wisc.edu>
330    
331            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
332    
333            * DESCRIPTION: Eliminate import of stats.
334    
335    
336    2005-04-06  Douglas Bates  <bates@wisc.edu>
337    
338            * R/AllClass.R : add logical sparse matrix classes
339    
340    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/dgTMatrix.R: add "[" method for triplet matrices
343            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
344    
345    2005-03-31  Douglas Bates  <bates@wisc.edu>
346    
347            * DESCRIPTION (Version): release 0.95-5 to CRAN
348    
349            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
350            * R/sparseMatrix.R: %*%, crossprod()
351            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
352            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
353            * src/lmer.c (lmer_fitted): fix thinko
354    
355    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/AllClass.R: add two virtual sparse classes ``on top''
358    
359    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
362                    correspondingly fix examples and tests/ since new()
363                    doesn't work for virtual classes.
364    
365    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * R/Matrix.R (as.matrix): method and one for unname()
368            * tests/dpoMatrix.R: tests should now be less platform dependent;
369              also run for R 2.1.0; using as.matrix()
370    
371    2005-03-15  Douglas Bates  <bates@wisc.edu>
372    
373            * R/pMatrix.R: "pMatrix" class added
374            * ....
375    
376    2005-03-14  Douglas Bates  <bates@wisc.edu>
377    
378            * R/dtpMatrix.R: Add unpack method and an example.
379    
380            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
381            of general symmetric matrices and associated S4 methods.
382    
383    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
384            +
385    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/dgeMatrix.R (setAs): and many other files: more coercion,
388              crossprod() and "%*%" methods added; tests, too.
389            * tests/matprod.R: new, for testing these
390    
391    2005-03-03  Douglas Bates  <bates@wisc.edu>
392    
393            * src/lmer.c (lmer_fitted): Added.
394    
395    2005-03-02  Douglas Bates  <bates@wisc.edu>
396    
397            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
398    
399    2005-02-28  Douglas Bates  <bates@wisc.edu>
400    
401            * src/*.c,po/,inst/po: Internationalization and localization of
402            the package.
403    
404            * src/ldl.[ch]: Removed these as their contents are referenced in the
405            R_ldl.c file.
406    
407            * src/flame.[ch]: Removed these source files.
408    
409            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
410    
411            * src/LU.[ch],src/init.c: absorb in factorizations
412    
413            * src/Mutils.h: prepare for internationalization
414    
415            * src/cblas.h: move the enum definitions to Mutils.h and remove
416            this file
417    
418    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
421    
422            * R/dtrMatrix.R: fix t() method
423    
424            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
425            * NAMESPACE: export them (and import generics from "methods")
426            * tests/group-methods.R : and test them.
427    
428            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
429            border case
430    
431    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
432    
433            * DESCRIPTION (Version): 0.95-2  released to CRAN
434    
435            * src/dgBCMatrix.c:
436            * src/lmer.c: many changes
437            * ...
438    
439    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/Matrix.R: add more sophisticated show() method.
442    
443    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
444    
445            * */* : almost complete reorganization of classes.
446    
447    2005-01-26  Douglas Bates  <bates@wisc.edu>
448    
449            * R/AllGeneric.R: Added matrix exponential generic expm and a method
450            for the geMatrix class.
451    
452    2005-01-24  Douglas Bates  <bates@wisc.edu>
453    
454            * src/Makefile (clean): Remove *.a and *.so
455    
456            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
457    
458    2005-01-23  Douglas Bates  <bates@wisc.edu>
459    
460            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
461            had an effect in cases with more than 2 grouping factors.
462    
463    2005-01-03  Douglas Bates  <bates@wisc.edu>
464    
465            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
466    
467    2004-12-23  Douglas Bates  <bates@wisc.edu>
468    
469            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
470            and R_useDynamicSymbols (suggested by B.D.Ripley).
471    
472    2004-12-14  Douglas Bates  <bates@wisc.edu>
473    
474            * R/sscMatrix.R: Add determinant methods
475    
476            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
477            for tripletMatrix to matrix.
478    
479    2004-12-13  Douglas Bates  <bates@wisc.edu>
480    
481            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
482            no longer used.
483    
484            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
485            with dynamic allocation of scratch arrays.
486    
487            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
488            for multivariate random effects with multiple grouping factors.
489            Fixes part but not all of #15.
490    
491    2004-12-03  Douglas Bates  <bates@wisc.edu>
492    
493            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
494            scalar grouping factors corrected.
495    
496    2004-11-29  Douglas Bates  <bates@wisc.edu>
497    
498            * src/bCrosstab.c: remove diag_update which is no longer used
499    
500    2004-11-16  Douglas Bates  <bates@wisc.edu>
501    
502          * 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
503          .h file can be included.          .h file can be included.
504    
505  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
506    
507          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
508          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
509    
510          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
511    
512  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
513    
514          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
515    
516  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
517    
518          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
519    
520  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
521    
522          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
523    
524  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
525    
526          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
527    
528  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
529    
530          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
531          routines.          routines.
532    
533  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
534    
535          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
536    
537  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
538    
539          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
540    

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