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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1165, Sat Jan 14 23:41:55 2006 UTC
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1  2004-11-16  Douglas Bates  <bates@bates1-home>  2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dgeMatrix.c (dMatrix_validate): new
4            * src/Mutils.c (dense_nonpacked_validate): new
5    
6            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
7    
8    
9    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
10    
11            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
12    
13    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
14    
15            * DESCRIPTION (Version): 0.99-6 released to CRAN
16    
17            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
18            segfault in cases with multiple non-nested grouping factors.
19    
20    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
23                    (Depends): also on 'utils'
24    
25            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
26            * R/diagMatrix.R (Diagonal): constructor and methods for
27            diagonal matrices
28    
29            * R/ltTMatrix.R: new "minimal methods"
30    
31    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
34            all methods (and help files).
35    
36    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
39                    for case (dimn.  op  no_dimn.)
40    
41    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
42    
43            * DESCRIPTION (Version): 0.99-2  released to CRAN
44    
45    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
46    
47            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
48            by Julian Faraway.
49    
50    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Auxiliaries.R (try_as): new utility
53            * R/sparseMatrix.R: use try_as() in coercion to original class
54    
55    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
58    
59    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/Auxiliaries.R (dimNamesCheck): added
62    
63            * R/Matrix.R (as.array), (as.vector): new
64    
65    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
68                    default.
69            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
70                    "pMatrix" now contains "sparseMatrix"
71    
72    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * tests/Class+Meth.R: new tests; t(t(m)) == m
75    
76            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
77    
78            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
79            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
80    
81            * R/dspMatrix.R: typo in "t" method
82    
83    2005-09-18  Douglas Bates  <bates@wisc.edu>
84    
85            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
86            * R/Tsparse.R: instead of R/gTMatrix.R
87            * R/Csparse.R: new
88            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
89            * src/Tsparse.c: new; many trivial methods calling cholmod_()
90            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
91                            via cholmod
92    
93    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/Auxiliaries.R (non0ind): new function using new C code
96            * src/dgCMatrix.c (compressed_non_0_ij): new utility
97    
98    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
99    
100            * src/chm_common.h: header file required by all C sources that
101            call CHOLMOD functions.  It defines a cholmod_common structure
102            called 'c' whose address is passed as the last argument to
103            (virtually) every CHOLMOD function.
104    
105            * src/Pattern.c: Simple example of the use of CHOLMOD.
106    
107            * src/init.c: initialize and finalize the cholmod_common structure.
108    
109            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
110            LDL and CCOLAMD from the U. of Florida sparse matrix library.
111    
112    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * inst/test-tools.R: new file collecting the utility functions used
115                    in ./tests/*.R
116    
117            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
118            * R/Matrix.R (cbind2): methods for NULL and missing
119    
120    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * R/AllClass.R: new "index" class for "[" and "[<-":
123                    First cut at "symmetricMatrix" and "triangularMatrix"
124            * R/gTMatrix.R (.ind.prep): new function;
125                    Logical and character indexing now work too.
126            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
127            * tests/indexing.R: new, including *.Rout.save
128            * tests/dgTMatrix.R: new
129    
130    2005-08-29  Douglas Bates  <bates@wisc.edu>
131    
132            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
133            indicator pos not being updated.  Also enforced upper triangular
134            for symmetric case.  Need to coerce edges component of elements of
135            edge list - grr! (Why don't they define their classes cleanly?)
136    
137    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/Matrix.R:  added first "[<-" methods; not yet functional
140            * R/denseMatrix.R: dito
141            * man/Subassign-methods.Rd: new help file for these
142    
143    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * DESCRIPTION (Version): 0.98-6
146    
147            * R/denseMatrix.R: new file for "[" fallback methods for all dense
148            matrices.
149    
150    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
153                    as( <logical>, "matrix")
154    
155            * R/pMatrix.R: coercion to "lgTMatrix"
156    
157            * R/gTMatrix.R: new virtual class to define "[" methods for.
158            * man/gTMatrix-class.Rd:
159            * General slight re-organization of where "[" methods are defined.
160              more to come.
161    
162    2005-08-18  Douglas Bates  <bates@wisc.edu>
163    
164            * DESCRIPTION (Version): 0.98-5  released to CRAN
165    
166            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
167            * .....
168    
169    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
170    
171            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
172            or glmer objects.
173    
174    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
177    
178    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
179    
180            * R/HBMM.R: finish re-writing R-only code.
181    
182    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
183    
184            * man/externalFormats.Rd: move documentation for writeHB and
185            writeMM here.
186    
187            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
188            (suggested by Paul Roecker).
189    
190            * tests/validObj.R (assertError): Comment out test that is failing
191            after recent changes in r-devel.
192    
193    
194    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/AllClass.R: intermediate virtual class "denseMatrix"
197            * man/denseMatrix-class.Rd
198            * NAMESPACE: export it, and also export
199            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
200    
201    2005-08-10  Douglas Bates  <bates@wisc.edu>
202    
203            * DESCRIPTION (Version): 0.98-3 to CRAN
204    
205            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
206            matrix_solve code (which was really, really wrong).
207    
208    2005-08-07  Douglas Bates  <bates@wisc.edu>
209    
210            * DESCRIPTION (Version): 0.98-2
211    
212            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
213    
214            * R/lmer.R (abbrvNms): new
215            * R/lmer.R (mcmcsamp): allow transformed parameters
216            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
217            for the Harwell-Boeing and the MatrixMarket formats.
218    
219    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * man/dtrMatrix-class.Rd: add examples
222            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
223    
224            * TODO: note the dtpMatrix (docu) bug
225    
226            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
227            in order to ensure that new as.matrix() is used by old functions,
228            e.g., svd(), qr(), eigen(), dist(),..;
229                  apply(), also matplot() or pairs().
230    
231    
232    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
235              add comments about 'control' / lmerControl() arguments
236    
237    2005-07-27  Douglas Bates  <bates@wisc.edu>
238    
239            * man/sleepstudy.Rd: Added the sleep data set.
240            * DESCRIPTION (Version): 0.98-1  released to CRAN
241    
242    2005-07-12  Douglas Bates  <bates@wisc.edu>
243            * man/sleepstudy.Rd: Added the sleep data set.
244    
245            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
246            .Call calls that were producing spurious output.
247    
248    2005-07-05  Douglas Bates  <bates@wisc.edu>
249    
250            * R/lmer.R (lmer): stored updated variance component estimates in
251            mer object for the generalized model.  (Bug reported by Renaud
252            Lancelot).
253    
254    2005-07-03  Douglas Bates  <bates@wisc.edu>
255    
256            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
257            unidimensional case.
258    
259    2005-06-08  Douglas Bates  <bates@wisc.edu>
260    
261            * DESCRIPTION (Version): 0.96-1
262    
263            * moved  lmer-class' R and C code moved from lme4 to here
264    
265    2005-06-04  Douglas Bates  <bates@wisc.edu>
266    
267            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
268            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
269    
270    2005-06-02  Douglas Bates  <bates@wisc.edu>
271    
272            * src/Makefile.win: Forgot to update this when Makefile changed.
273    
274    2005-05-11  Douglas Bates  <bates@wisc.edu>
275    
276            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
277            bug reported by Kurt Hornik and Michael Hahsler.
278    
279    2005-05-10  Douglas Bates  <bates@wisc.edu>
280    
281            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
282            logical sparse matrices.  These will also be used in the symbolic
283            analysis for lmer objects.
284    
285            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
286            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
287    
288    2005-05-06  Douglas Bates  <bates@wisc.edu>
289    
290            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
291            colMeans, colSums, rowMeans and rowSums.
292    
293    2005-04-18  Douglas Bates  <bates@wisc.edu>
294    
295            * src/lgCMatrix.[ch]: code for _validate method and stub for
296            multiplication operation.
297    
298            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
299            to dgetrs.
300    
301            * src/init.c: Fix cut-and-paste error in definition of
302            dgeMatrix_matrix_solve
303    
304            * src/{many files}: Tighten code by using ALLOC_SLOT.
305    
306    2005-04-15  Douglas Bates  <bates@wisc.edu>
307    
308            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
309    
310            * DESCRIPTION: Eliminate import of stats.
311    
312    
313    2005-04-06  Douglas Bates  <bates@wisc.edu>
314    
315            * R/AllClass.R : add logical sparse matrix classes
316    
317    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/dgTMatrix.R: add "[" method for triplet matrices
320            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
321    
322    2005-03-31  Douglas Bates  <bates@wisc.edu>
323    
324            * DESCRIPTION (Version): release 0.95-5 to CRAN
325    
326            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
327            * R/sparseMatrix.R: %*%, crossprod()
328            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
329            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
330            * src/lmer.c (lmer_fitted): fix thinko
331    
332    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/AllClass.R: add two virtual sparse classes ``on top''
335    
336    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
339                    correspondingly fix examples and tests/ since new()
340                    doesn't work for virtual classes.
341    
342    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/Matrix.R (as.matrix): method and one for unname()
345            * tests/dpoMatrix.R: tests should now be less platform dependent;
346              also run for R 2.1.0; using as.matrix()
347    
348    2005-03-15  Douglas Bates  <bates@wisc.edu>
349    
350            * R/pMatrix.R: "pMatrix" class added
351            * ....
352    
353    2005-03-14  Douglas Bates  <bates@wisc.edu>
354    
355            * R/dtpMatrix.R: Add unpack method and an example.
356    
357            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
358            of general symmetric matrices and associated S4 methods.
359    
360    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
361            +
362    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/dgeMatrix.R (setAs): and many other files: more coercion,
365              crossprod() and "%*%" methods added; tests, too.
366            * tests/matprod.R: new, for testing these
367    
368    2005-03-03  Douglas Bates  <bates@wisc.edu>
369    
370            * src/lmer.c (lmer_fitted): Added.
371    
372    2005-03-02  Douglas Bates  <bates@wisc.edu>
373    
374            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
375    
376    2005-02-28  Douglas Bates  <bates@wisc.edu>
377    
378            * src/*.c,po/,inst/po: Internationalization and localization of
379            the package.
380    
381            * src/ldl.[ch]: Removed these as their contents are referenced in the
382            R_ldl.c file.
383    
384            * src/flame.[ch]: Removed these source files.
385    
386            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
387    
388            * src/LU.[ch],src/init.c: absorb in factorizations
389    
390            * src/Mutils.h: prepare for internationalization
391    
392            * src/cblas.h: move the enum definitions to Mutils.h and remove
393            this file
394    
395    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
398    
399            * R/dtrMatrix.R: fix t() method
400    
401            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
402            * NAMESPACE: export them (and import generics from "methods")
403            * tests/group-methods.R : and test them.
404    
405            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
406            border case
407    
408    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
409    
410            * DESCRIPTION (Version): 0.95-2  released to CRAN
411    
412            * src/dgBCMatrix.c:
413            * src/lmer.c: many changes
414            * ...
415    
416    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * R/Matrix.R: add more sophisticated show() method.
419    
420    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
421    
422            * */* : almost complete reorganization of classes.
423    
424    2005-01-26  Douglas Bates  <bates@wisc.edu>
425    
426            * R/AllGeneric.R: Added matrix exponential generic expm and a method
427            for the geMatrix class.
428    
429    2005-01-24  Douglas Bates  <bates@wisc.edu>
430    
431            * src/Makefile (clean): Remove *.a and *.so
432    
433            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
434    
435    2005-01-23  Douglas Bates  <bates@wisc.edu>
436    
437            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
438            had an effect in cases with more than 2 grouping factors.
439    
440    2005-01-03  Douglas Bates  <bates@wisc.edu>
441    
442            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
443    
444    2004-12-23  Douglas Bates  <bates@wisc.edu>
445    
446            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
447            and R_useDynamicSymbols (suggested by B.D.Ripley).
448    
449    2004-12-14  Douglas Bates  <bates@wisc.edu>
450    
451            * R/sscMatrix.R: Add determinant methods
452    
453            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
454            for tripletMatrix to matrix.
455    
456    2004-12-13  Douglas Bates  <bates@wisc.edu>
457    
458            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
459            no longer used.
460    
461            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
462            with dynamic allocation of scratch arrays.
463    
464            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
465            for multivariate random effects with multiple grouping factors.
466            Fixes part but not all of #15.
467    
468    2004-12-03  Douglas Bates  <bates@wisc.edu>
469    
470            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
471            scalar grouping factors corrected.
472    
473    2004-11-29  Douglas Bates  <bates@wisc.edu>
474    
475            * src/bCrosstab.c: remove diag_update which is no longer used
476    
477    2004-11-16  Douglas Bates  <bates@wisc.edu>
478    
479          * 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
480          .h file can be included.          .h file can be included.
481    
482  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
483    
484          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
485          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
486    
487          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
488    
489  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
490    
491          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
492    
493  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
494    
495          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
496    
497  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
498    
499          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
500    
501  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
502    
503          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
504    
505  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
506    
507          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
508          routines.          routines.
509    
510  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
511    
512          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
513    
514  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
515    
516          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
517    

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