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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1119, Sat Jan 7 19:52:37 2006 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2006-01-07  Douglas Bates  <bates@bates4.stat.wisc.edu>
2    
3            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
4            segfault in cases with multiple non-nested grouping factors.
5    
6    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
9                    (Depends): also on 'utils'
10    
11            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
12            * R/diagMatrix.R (Diagonal): constructor and methods for
13            diagonal matrices
14    
15            * R/ltTMatrix.R: new "minimal methods"
16    
17    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
20            all methods (and help files).
21    
22    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
25                    for case (dimn.  op  no_dimn.)
26    
27    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
28    
29            * DESCRIPTION (Version): 0.99-2  released to CRAN
30    
31    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
32    
33            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
34            by Julian Faraway.
35    
36    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/Auxiliaries.R (try_as): new utility
39            * R/sparseMatrix.R: use try_as() in coercion to original class
40    
41    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
44    
45    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/Auxiliaries.R (dimNamesCheck): added
48    
49            * R/Matrix.R (as.array), (as.vector): new
50    
51    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
54                    default.
55            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
56                    "pMatrix" now contains "sparseMatrix"
57    
58    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * tests/Class+Meth.R: new tests; t(t(m)) == m
61    
62            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
63    
64            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
65            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
66    
67            * R/dspMatrix.R: typo in "t" method
68    
69    2005-09-18  Douglas Bates  <bates@wisc.edu>
70    
71            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
72            * R/Tsparse.R: instead of R/gTMatrix.R
73            * R/Csparse.R: new
74            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
75            * src/Tsparse.c: new; many trivial methods calling cholmod_()
76            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
77                            via cholmod
78    
79    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/Auxiliaries.R (non0ind): new function using new C code
82            * src/dgCMatrix.c (compressed_non_0_ij): new utility
83    
84    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
85    
86            * src/chm_common.h: header file required by all C sources that
87            call CHOLMOD functions.  It defines a cholmod_common structure
88            called 'c' whose address is passed as the last argument to
89            (virtually) every CHOLMOD function.
90    
91            * src/Pattern.c: Simple example of the use of CHOLMOD.
92    
93            * src/init.c: initialize and finalize the cholmod_common structure.
94    
95            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
96            LDL and CCOLAMD from the U. of Florida sparse matrix library.
97    
98    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * inst/test-tools.R: new file collecting the utility functions used
101                    in ./tests/*.R
102    
103            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
104            * R/Matrix.R (cbind2): methods for NULL and missing
105    
106    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/AllClass.R: new "index" class for "[" and "[<-":
109                    First cut at "symmetricMatrix" and "triangularMatrix"
110            * R/gTMatrix.R (.ind.prep): new function;
111                    Logical and character indexing now work too.
112            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
113            * tests/indexing.R: new, including *.Rout.save
114            * tests/dgTMatrix.R: new
115    
116    2005-08-29  Douglas Bates  <bates@wisc.edu>
117    
118            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
119            indicator pos not being updated.  Also enforced upper triangular
120            for symmetric case.  Need to coerce edges component of elements of
121            edge list - grr! (Why don't they define their classes cleanly?)
122    
123    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/Matrix.R:  added first "[<-" methods; not yet functional
126            * R/denseMatrix.R: dito
127            * man/Subassign-methods.Rd: new help file for these
128    
129    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * DESCRIPTION (Version): 0.98-6
132    
133            * R/denseMatrix.R: new file for "[" fallback methods for all dense
134            matrices.
135    
136    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
139                    as( <logical>, "matrix")
140    
141            * R/pMatrix.R: coercion to "lgTMatrix"
142    
143            * R/gTMatrix.R: new virtual class to define "[" methods for.
144            * man/gTMatrix-class.Rd:
145            * General slight re-organization of where "[" methods are defined.
146              more to come.
147    
148    2005-08-18  Douglas Bates  <bates@wisc.edu>
149    
150            * DESCRIPTION (Version): 0.98-5  released to CRAN
151    
152            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
153            * .....
154    
155    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
156    
157            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
158            or glmer objects.
159    
160    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
163    
164    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
165    
166            * R/HBMM.R: finish re-writing R-only code.
167    
168    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
169    
170            * man/externalFormats.Rd: move documentation for writeHB and
171            writeMM here.
172    
173            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
174            (suggested by Paul Roecker).
175    
176            * tests/validObj.R (assertError): Comment out test that is failing
177            after recent changes in r-devel.
178    
179    
180    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/AllClass.R: intermediate virtual class "denseMatrix"
183            * man/denseMatrix-class.Rd
184            * NAMESPACE: export it, and also export
185            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
186    
187    2005-08-10  Douglas Bates  <bates@wisc.edu>
188    
189            * DESCRIPTION (Version): 0.98-3 to CRAN
190    
191            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
192            matrix_solve code (which was really, really wrong).
193    
194    2005-08-07  Douglas Bates  <bates@wisc.edu>
195    
196            * DESCRIPTION (Version): 0.98-2
197    
198            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
199    
200            * R/lmer.R (abbrvNms): new
201            * R/lmer.R (mcmcsamp): allow transformed parameters
202            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
203            for the Harwell-Boeing and the MatrixMarket formats.
204    
205    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * man/dtrMatrix-class.Rd: add examples
208            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
209    
210            * TODO: note the dtpMatrix (docu) bug
211    
212            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
213            in order to ensure that new as.matrix() is used by old functions,
214            e.g., svd(), qr(), eigen(), dist(),..;
215                  apply(), also matplot() or pairs().
216    
217    
218    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
221              add comments about 'control' / lmerControl() arguments
222    
223    2005-07-27  Douglas Bates  <bates@wisc.edu>
224    
225            * man/sleepstudy.Rd: Added the sleep data set.
226            * DESCRIPTION (Version): 0.98-1  released to CRAN
227    
228    2005-07-12  Douglas Bates  <bates@wisc.edu>
229            * man/sleepstudy.Rd: Added the sleep data set.
230    
231            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
232            .Call calls that were producing spurious output.
233    
234    2005-07-05  Douglas Bates  <bates@wisc.edu>
235    
236            * R/lmer.R (lmer): stored updated variance component estimates in
237            mer object for the generalized model.  (Bug reported by Renaud
238            Lancelot).
239    
240    2005-07-03  Douglas Bates  <bates@wisc.edu>
241    
242            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
243            unidimensional case.
244    
245    2005-06-08  Douglas Bates  <bates@wisc.edu>
246    
247            * DESCRIPTION (Version): 0.96-1
248    
249            * moved  lmer-class' R and C code moved from lme4 to here
250    
251    2005-06-04  Douglas Bates  <bates@wisc.edu>
252    
253            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
254            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
255    
256    2005-06-02  Douglas Bates  <bates@wisc.edu>
257    
258            * src/Makefile.win: Forgot to update this when Makefile changed.
259    
260    2005-05-11  Douglas Bates  <bates@wisc.edu>
261    
262            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
263            bug reported by Kurt Hornik and Michael Hahsler.
264    
265    2005-05-10  Douglas Bates  <bates@wisc.edu>
266    
267            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
268            logical sparse matrices.  These will also be used in the symbolic
269            analysis for lmer objects.
270    
271            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
272            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
273    
274    2005-05-06  Douglas Bates  <bates@wisc.edu>
275    
276            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
277            colMeans, colSums, rowMeans and rowSums.
278    
279    2005-04-18  Douglas Bates  <bates@wisc.edu>
280    
281            * src/lgCMatrix.[ch]: code for _validate method and stub for
282            multiplication operation.
283    
284            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
285            to dgetrs.
286    
287            * src/init.c: Fix cut-and-paste error in definition of
288            dgeMatrix_matrix_solve
289    
290            * src/{many files}: Tighten code by using ALLOC_SLOT.
291    
292    2005-04-15  Douglas Bates  <bates@wisc.edu>
293    
294            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
295    
296            * DESCRIPTION: Eliminate import of stats.
297    
298    
299    2005-04-06  Douglas Bates  <bates@wisc.edu>
300    
301            * R/AllClass.R : add logical sparse matrix classes
302    
303    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/dgTMatrix.R: add "[" method for triplet matrices
306            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
307    
308    2005-03-31  Douglas Bates  <bates@wisc.edu>
309    
310            * DESCRIPTION (Version): release 0.95-5 to CRAN
311    
312            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
313            * R/sparseMatrix.R: %*%, crossprod()
314            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
315            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
316            * src/lmer.c (lmer_fitted): fix thinko
317    
318    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/AllClass.R: add two virtual sparse classes ``on top''
321    
322    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
325                    correspondingly fix examples and tests/ since new()
326                    doesn't work for virtual classes.
327    
328    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Matrix.R (as.matrix): method and one for unname()
331            * tests/dpoMatrix.R: tests should now be less platform dependent;
332              also run for R 2.1.0; using as.matrix()
333    
334    2005-03-15  Douglas Bates  <bates@wisc.edu>
335    
336            * R/pMatrix.R: "pMatrix" class added
337            * ....
338    
339    2005-03-14  Douglas Bates  <bates@wisc.edu>
340    
341            * R/dtpMatrix.R: Add unpack method and an example.
342    
343            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
344            of general symmetric matrices and associated S4 methods.
345    
346    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
347            +
348    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/dgeMatrix.R (setAs): and many other files: more coercion,
351              crossprod() and "%*%" methods added; tests, too.
352            * tests/matprod.R: new, for testing these
353    
354    2005-03-03  Douglas Bates  <bates@wisc.edu>
355    
356            * src/lmer.c (lmer_fitted): Added.
357    
358    2005-03-02  Douglas Bates  <bates@wisc.edu>
359    
360            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
361    
362    2005-02-28  Douglas Bates  <bates@wisc.edu>
363    
364            * src/*.c,po/,inst/po: Internationalization and localization of
365            the package.
366    
367            * src/ldl.[ch]: Removed these as their contents are referenced in the
368            R_ldl.c file.
369    
370            * src/flame.[ch]: Removed these source files.
371    
372            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
373    
374            * src/LU.[ch],src/init.c: absorb in factorizations
375    
376            * src/Mutils.h: prepare for internationalization
377    
378            * src/cblas.h: move the enum definitions to Mutils.h and remove
379            this file
380    
381    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
384    
385            * R/dtrMatrix.R: fix t() method
386    
387            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
388            * NAMESPACE: export them (and import generics from "methods")
389            * tests/group-methods.R : and test them.
390    
391            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
392            border case
393    
394    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
395    
396            * DESCRIPTION (Version): 0.95-2  released to CRAN
397    
398            * src/dgBCMatrix.c:
399            * src/lmer.c: many changes
400            * ...
401    
402    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * R/Matrix.R: add more sophisticated show() method.
405    
406    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
407    
408            * */* : almost complete reorganization of classes.
409    
410    2005-01-26  Douglas Bates  <bates@wisc.edu>
411    
412            * R/AllGeneric.R: Added matrix exponential generic expm and a method
413            for the geMatrix class.
414    
415    2005-01-24  Douglas Bates  <bates@wisc.edu>
416    
417            * src/Makefile (clean): Remove *.a and *.so
418    
419            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
420    
421    2005-01-23  Douglas Bates  <bates@wisc.edu>
422    
423            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
424            had an effect in cases with more than 2 grouping factors.
425    
426    2005-01-03  Douglas Bates  <bates@wisc.edu>
427    
428            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
429    
430    2004-12-23  Douglas Bates  <bates@wisc.edu>
431    
432            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
433            and R_useDynamicSymbols (suggested by B.D.Ripley).
434    
435    2004-12-14  Douglas Bates  <bates@wisc.edu>
436    
437          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
438    
439          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
440          for tripletMatrix to matrix.          for tripletMatrix to matrix.
441    
442  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
443    
444          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
445          no longer used.          no longer used.
# Line 17  Line 451 
451          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
452          Fixes part but not all of #15.          Fixes part but not all of #15.
453    
454  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
455    
456          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
457          scalar grouping factors corrected.          scalar grouping factors corrected.
458    
459  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
460    
461          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
462    
463  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
464    
465          * 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
466          .h file can be included.          .h file can be included.
467    
468  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
469    
470          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
471          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
472    
473          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
474    
475  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
476    
477          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
478    
479  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
480    
481          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
482    
483  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
484    
485          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
486    
487  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
488    
489          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
490    
491  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
492    
493          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
494          routines.          routines.
495    
496  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
497    
498          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
499    
500  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
501    
502          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
503    

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