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revision 726, Thu May 12 14:59:04 2005 UTC revision 1127, Tue Jan 10 18:11:23 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * DESCRIPTION (Version): 0.99-6 released to CRAN
4    
5            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
6            segfault in cases with multiple non-nested grouping factors.
7    
8    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
11                    (Depends): also on 'utils'
12    
13            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
14            * R/diagMatrix.R (Diagonal): constructor and methods for
15            diagonal matrices
16    
17            * R/ltTMatrix.R: new "minimal methods"
18    
19    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
22            all methods (and help files).
23    
24    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
27                    for case (dimn.  op  no_dimn.)
28    
29    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
30    
31            * DESCRIPTION (Version): 0.99-2  released to CRAN
32    
33    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
34    
35            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
36            by Julian Faraway.
37    
38    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/Auxiliaries.R (try_as): new utility
41            * R/sparseMatrix.R: use try_as() in coercion to original class
42    
43    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
46    
47    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/Auxiliaries.R (dimNamesCheck): added
50    
51            * R/Matrix.R (as.array), (as.vector): new
52    
53    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
56                    default.
57            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
58                    "pMatrix" now contains "sparseMatrix"
59    
60    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * tests/Class+Meth.R: new tests; t(t(m)) == m
63    
64            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
65    
66            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
67            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
68    
69            * R/dspMatrix.R: typo in "t" method
70    
71    2005-09-18  Douglas Bates  <bates@wisc.edu>
72    
73            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
74            * R/Tsparse.R: instead of R/gTMatrix.R
75            * R/Csparse.R: new
76            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
77            * src/Tsparse.c: new; many trivial methods calling cholmod_()
78            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
79                            via cholmod
80    
81    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/Auxiliaries.R (non0ind): new function using new C code
84            * src/dgCMatrix.c (compressed_non_0_ij): new utility
85    
86    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
87    
88            * src/chm_common.h: header file required by all C sources that
89            call CHOLMOD functions.  It defines a cholmod_common structure
90            called 'c' whose address is passed as the last argument to
91            (virtually) every CHOLMOD function.
92    
93            * src/Pattern.c: Simple example of the use of CHOLMOD.
94    
95            * src/init.c: initialize and finalize the cholmod_common structure.
96    
97            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
98            LDL and CCOLAMD from the U. of Florida sparse matrix library.
99    
100    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * inst/test-tools.R: new file collecting the utility functions used
103                    in ./tests/*.R
104    
105            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
106            * R/Matrix.R (cbind2): methods for NULL and missing
107    
108    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/AllClass.R: new "index" class for "[" and "[<-":
111                    First cut at "symmetricMatrix" and "triangularMatrix"
112            * R/gTMatrix.R (.ind.prep): new function;
113                    Logical and character indexing now work too.
114            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
115            * tests/indexing.R: new, including *.Rout.save
116            * tests/dgTMatrix.R: new
117    
118    2005-08-29  Douglas Bates  <bates@wisc.edu>
119    
120            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
121            indicator pos not being updated.  Also enforced upper triangular
122            for symmetric case.  Need to coerce edges component of elements of
123            edge list - grr! (Why don't they define their classes cleanly?)
124    
125    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/Matrix.R:  added first "[<-" methods; not yet functional
128            * R/denseMatrix.R: dito
129            * man/Subassign-methods.Rd: new help file for these
130    
131    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * DESCRIPTION (Version): 0.98-6
134    
135            * R/denseMatrix.R: new file for "[" fallback methods for all dense
136            matrices.
137    
138    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
141                    as( <logical>, "matrix")
142    
143            * R/pMatrix.R: coercion to "lgTMatrix"
144    
145            * R/gTMatrix.R: new virtual class to define "[" methods for.
146            * man/gTMatrix-class.Rd:
147            * General slight re-organization of where "[" methods are defined.
148              more to come.
149    
150    2005-08-18  Douglas Bates  <bates@wisc.edu>
151    
152            * DESCRIPTION (Version): 0.98-5  released to CRAN
153    
154            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
155            * .....
156    
157    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
158    
159            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
160            or glmer objects.
161    
162    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
165    
166    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
167    
168            * R/HBMM.R: finish re-writing R-only code.
169    
170    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
171    
172            * man/externalFormats.Rd: move documentation for writeHB and
173            writeMM here.
174    
175            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
176            (suggested by Paul Roecker).
177    
178            * tests/validObj.R (assertError): Comment out test that is failing
179            after recent changes in r-devel.
180    
181    
182    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/AllClass.R: intermediate virtual class "denseMatrix"
185            * man/denseMatrix-class.Rd
186            * NAMESPACE: export it, and also export
187            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
188    
189    2005-08-10  Douglas Bates  <bates@wisc.edu>
190    
191            * DESCRIPTION (Version): 0.98-3 to CRAN
192    
193            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
194            matrix_solve code (which was really, really wrong).
195    
196    2005-08-07  Douglas Bates  <bates@wisc.edu>
197    
198            * DESCRIPTION (Version): 0.98-2
199    
200            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
201    
202            * R/lmer.R (abbrvNms): new
203            * R/lmer.R (mcmcsamp): allow transformed parameters
204            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
205            for the Harwell-Boeing and the MatrixMarket formats.
206    
207    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * man/dtrMatrix-class.Rd: add examples
210            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
211    
212            * TODO: note the dtpMatrix (docu) bug
213    
214            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
215            in order to ensure that new as.matrix() is used by old functions,
216            e.g., svd(), qr(), eigen(), dist(),..;
217                  apply(), also matplot() or pairs().
218    
219    
220    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
223              add comments about 'control' / lmerControl() arguments
224    
225    2005-07-27  Douglas Bates  <bates@wisc.edu>
226    
227            * man/sleepstudy.Rd: Added the sleep data set.
228            * DESCRIPTION (Version): 0.98-1  released to CRAN
229    
230    2005-07-12  Douglas Bates  <bates@wisc.edu>
231            * man/sleepstudy.Rd: Added the sleep data set.
232    
233            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
234            .Call calls that were producing spurious output.
235    
236    2005-07-05  Douglas Bates  <bates@wisc.edu>
237    
238            * R/lmer.R (lmer): stored updated variance component estimates in
239            mer object for the generalized model.  (Bug reported by Renaud
240            Lancelot).
241    
242    2005-07-03  Douglas Bates  <bates@wisc.edu>
243    
244            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
245            unidimensional case.
246    
247    2005-06-08  Douglas Bates  <bates@wisc.edu>
248    
249            * DESCRIPTION (Version): 0.96-1
250    
251            * moved  lmer-class' R and C code moved from lme4 to here
252    
253    2005-06-04  Douglas Bates  <bates@wisc.edu>
254    
255            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
256            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
257    
258    2005-06-02  Douglas Bates  <bates@wisc.edu>
259    
260            * src/Makefile.win: Forgot to update this when Makefile changed.
261    
262    2005-05-11  Douglas Bates  <bates@wisc.edu>
263    
264          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
265          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
266    
267  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
268    
269          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
270          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 273 
273          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
274          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
275    
276  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
277    
278          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
279          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
280    
281  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
282    
283          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
284          multiplication operation.          multiplication operation.
# Line 30  Line 291 
291    
292          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
293    
294  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
295    
296          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
297    
298          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
299    
300    
301  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
302    
303          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
304    
# Line 46  Line 307 
307          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
308          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
309    
310  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
311    
312          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
313    
# Line 72  Line 333 
333          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
334            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
335    
336  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
337    
338          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
339          * ....          * ....
340    
341  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
342    
343          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
344    
# Line 92  Line 353 
353            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
354          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
355    
356  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
357    
358          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
359    
360  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
361    
362          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
363    
364  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
365    
366          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
367          the package.          the package.
# Line 148  Line 409 
409    
410          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
411    
412  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
413    
414          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
415          for the geMatrix class.          for the geMatrix class.
416    
417  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
418    
419          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
420    
421          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
422    
423  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
424    
425          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
426          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
427    
428  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
429    
430          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
431    
432  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
433    
434          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
435          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
436    
437  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
438    
439          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
440    
441          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
442          for tripletMatrix to matrix.          for tripletMatrix to matrix.
443    
444  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
445    
446          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
447          no longer used.          no longer used.
# Line 192  Line 453 
453          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
454          Fixes part but not all of #15.          Fixes part but not all of #15.
455    
456  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
457    
458          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
459          scalar grouping factors corrected.          scalar grouping factors corrected.
460    
461  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
462    
463          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
464    
465  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
466    
467          * 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
468          .h file can be included.          .h file can be included.
469    
470  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
471    
472          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
473          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
474    
475          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
476    
477  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
478    
479          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
480    
481  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
482    
483          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
484    
485  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
486    
487          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
488    
489  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
490    
491          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
492    
493  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
494    
495          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
496          routines.          routines.
497    
498  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
499    
500          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
501    
502  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
503    
504          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
505    

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