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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1174, Mon Jan 16 20:03:48 2006 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
4                    many different kinds of matrices.
5            * R/*.R: quite a few new methods were needed for R CMD check with
6                    new Matrix().  Very good for users playing around.
7    
8    
9    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * src/dgeMatrix.c (dMatrix_validate): new
12            * src/Mutils.c (dense_nonpacked_validate): new
13    
14            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
15    
16    
17    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
18    
19            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
20    
21    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
22    
23            * DESCRIPTION (Version): 0.99-6 released to CRAN
24    
25            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
26            segfault in cases with multiple non-nested grouping factors.
27    
28    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
31                    (Depends): also on 'utils'
32    
33            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
34            * R/diagMatrix.R (Diagonal): constructor and methods for
35            diagonal matrices
36    
37            * R/ltTMatrix.R: new "minimal methods"
38    
39    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
42            all methods (and help files).
43    
44    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
47                    for case (dimn.  op  no_dimn.)
48    
49    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
50    
51            * DESCRIPTION (Version): 0.99-2  released to CRAN
52    
53    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
54    
55            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
56            by Julian Faraway.
57    
58    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Auxiliaries.R (try_as): new utility
61            * R/sparseMatrix.R: use try_as() in coercion to original class
62    
63    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
66    
67    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Auxiliaries.R (dimNamesCheck): added
70    
71            * R/Matrix.R (as.array), (as.vector): new
72    
73    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
76                    default.
77            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
78                    "pMatrix" now contains "sparseMatrix"
79    
80    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * tests/Class+Meth.R: new tests; t(t(m)) == m
83    
84            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
85    
86            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
87            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
88    
89            * R/dspMatrix.R: typo in "t" method
90    
91    2005-09-18  Douglas Bates  <bates@wisc.edu>
92    
93            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
94            * R/Tsparse.R: instead of R/gTMatrix.R
95            * R/Csparse.R: new
96            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
97            * src/Tsparse.c: new; many trivial methods calling cholmod_()
98            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
99                            via cholmod
100    
101    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/Auxiliaries.R (non0ind): new function using new C code
104            * src/dgCMatrix.c (compressed_non_0_ij): new utility
105    
106    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
107    
108            * src/chm_common.h: header file required by all C sources that
109            call CHOLMOD functions.  It defines a cholmod_common structure
110            called 'c' whose address is passed as the last argument to
111            (virtually) every CHOLMOD function.
112    
113            * src/Pattern.c: Simple example of the use of CHOLMOD.
114    
115            * src/init.c: initialize and finalize the cholmod_common structure.
116    
117            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
118            LDL and CCOLAMD from the U. of Florida sparse matrix library.
119    
120    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * inst/test-tools.R: new file collecting the utility functions used
123                    in ./tests/*.R
124    
125            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
126            * R/Matrix.R (cbind2): methods for NULL and missing
127    
128    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/AllClass.R: new "index" class for "[" and "[<-":
131                    First cut at "symmetricMatrix" and "triangularMatrix"
132            * R/gTMatrix.R (.ind.prep): new function;
133                    Logical and character indexing now work too.
134            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
135            * tests/indexing.R: new, including *.Rout.save
136            * tests/dgTMatrix.R: new
137    
138    2005-08-29  Douglas Bates  <bates@wisc.edu>
139    
140            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
141            indicator pos not being updated.  Also enforced upper triangular
142            for symmetric case.  Need to coerce edges component of elements of
143            edge list - grr! (Why don't they define their classes cleanly?)
144    
145    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/Matrix.R:  added first "[<-" methods; not yet functional
148            * R/denseMatrix.R: dito
149            * man/Subassign-methods.Rd: new help file for these
150    
151    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * DESCRIPTION (Version): 0.98-6
154    
155            * R/denseMatrix.R: new file for "[" fallback methods for all dense
156            matrices.
157    
158    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
161                    as( <logical>, "matrix")
162    
163            * R/pMatrix.R: coercion to "lgTMatrix"
164    
165            * R/gTMatrix.R: new virtual class to define "[" methods for.
166            * man/gTMatrix-class.Rd:
167            * General slight re-organization of where "[" methods are defined.
168              more to come.
169    
170    2005-08-18  Douglas Bates  <bates@wisc.edu>
171    
172            * DESCRIPTION (Version): 0.98-5  released to CRAN
173    
174            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
175            * .....
176    
177    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
178    
179            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
180            or glmer objects.
181    
182    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
185    
186    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
187    
188            * R/HBMM.R: finish re-writing R-only code.
189    
190    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
191    
192            * man/externalFormats.Rd: move documentation for writeHB and
193            writeMM here.
194    
195            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
196            (suggested by Paul Roecker).
197    
198            * tests/validObj.R (assertError): Comment out test that is failing
199            after recent changes in r-devel.
200    
201    
202    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/AllClass.R: intermediate virtual class "denseMatrix"
205            * man/denseMatrix-class.Rd
206            * NAMESPACE: export it, and also export
207            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
208    
209    2005-08-10  Douglas Bates  <bates@wisc.edu>
210    
211            * DESCRIPTION (Version): 0.98-3 to CRAN
212    
213            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
214            matrix_solve code (which was really, really wrong).
215    
216    2005-08-07  Douglas Bates  <bates@wisc.edu>
217    
218            * DESCRIPTION (Version): 0.98-2
219    
220            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
221    
222            * R/lmer.R (abbrvNms): new
223            * R/lmer.R (mcmcsamp): allow transformed parameters
224            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
225            for the Harwell-Boeing and the MatrixMarket formats.
226    
227    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * man/dtrMatrix-class.Rd: add examples
230            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
231    
232            * TODO: note the dtpMatrix (docu) bug
233    
234            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
235            in order to ensure that new as.matrix() is used by old functions,
236            e.g., svd(), qr(), eigen(), dist(),..;
237                  apply(), also matplot() or pairs().
238    
239    
240    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
243              add comments about 'control' / lmerControl() arguments
244    
245    2005-07-27  Douglas Bates  <bates@wisc.edu>
246    
247            * man/sleepstudy.Rd: Added the sleep data set.
248            * DESCRIPTION (Version): 0.98-1  released to CRAN
249    
250    2005-07-12  Douglas Bates  <bates@wisc.edu>
251            * man/sleepstudy.Rd: Added the sleep data set.
252    
253            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
254            .Call calls that were producing spurious output.
255    
256    2005-07-05  Douglas Bates  <bates@wisc.edu>
257    
258            * R/lmer.R (lmer): stored updated variance component estimates in
259            mer object for the generalized model.  (Bug reported by Renaud
260            Lancelot).
261    
262    2005-07-03  Douglas Bates  <bates@wisc.edu>
263    
264            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
265            unidimensional case.
266    
267    2005-06-08  Douglas Bates  <bates@wisc.edu>
268    
269            * DESCRIPTION (Version): 0.96-1
270    
271            * moved  lmer-class' R and C code moved from lme4 to here
272    
273    2005-06-04  Douglas Bates  <bates@wisc.edu>
274    
275            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
276            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
277    
278    2005-06-02  Douglas Bates  <bates@wisc.edu>
279    
280            * src/Makefile.win: Forgot to update this when Makefile changed.
281    
282    2005-05-11  Douglas Bates  <bates@wisc.edu>
283    
284            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
285            bug reported by Kurt Hornik and Michael Hahsler.
286    
287    2005-05-10  Douglas Bates  <bates@wisc.edu>
288    
289            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
290            logical sparse matrices.  These will also be used in the symbolic
291            analysis for lmer objects.
292    
293            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
294            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
295    
296    2005-05-06  Douglas Bates  <bates@wisc.edu>
297    
298            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
299            colMeans, colSums, rowMeans and rowSums.
300    
301    2005-04-18  Douglas Bates  <bates@wisc.edu>
302    
303            * src/lgCMatrix.[ch]: code for _validate method and stub for
304            multiplication operation.
305    
306            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
307            to dgetrs.
308    
309            * src/init.c: Fix cut-and-paste error in definition of
310            dgeMatrix_matrix_solve
311    
312            * src/{many files}: Tighten code by using ALLOC_SLOT.
313    
314    2005-04-15  Douglas Bates  <bates@wisc.edu>
315    
316            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
317    
318            * DESCRIPTION: Eliminate import of stats.
319    
320    
321    2005-04-06  Douglas Bates  <bates@wisc.edu>
322    
323            * R/AllClass.R : add logical sparse matrix classes
324    
325    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/dgTMatrix.R: add "[" method for triplet matrices
328            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
329    
330    2005-03-31  Douglas Bates  <bates@wisc.edu>
331    
332            * DESCRIPTION (Version): release 0.95-5 to CRAN
333    
334            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
335            * R/sparseMatrix.R: %*%, crossprod()
336            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
337            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
338            * src/lmer.c (lmer_fitted): fix thinko
339    
340    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/AllClass.R: add two virtual sparse classes ``on top''
343    
344    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
347                    correspondingly fix examples and tests/ since new()
348                    doesn't work for virtual classes.
349    
350    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/Matrix.R (as.matrix): method and one for unname()
353            * tests/dpoMatrix.R: tests should now be less platform dependent;
354              also run for R 2.1.0; using as.matrix()
355    
356    2005-03-15  Douglas Bates  <bates@wisc.edu>
357    
358            * R/pMatrix.R: "pMatrix" class added
359            * ....
360    
361    2005-03-14  Douglas Bates  <bates@wisc.edu>
362    
363            * R/dtpMatrix.R: Add unpack method and an example.
364    
365            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
366            of general symmetric matrices and associated S4 methods.
367    
368    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
369            +
370    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/dgeMatrix.R (setAs): and many other files: more coercion,
373              crossprod() and "%*%" methods added; tests, too.
374            * tests/matprod.R: new, for testing these
375    
376    2005-03-03  Douglas Bates  <bates@wisc.edu>
377    
378            * src/lmer.c (lmer_fitted): Added.
379    
380    2005-03-02  Douglas Bates  <bates@wisc.edu>
381    
382            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
383    
384    2005-02-28  Douglas Bates  <bates@wisc.edu>
385    
386            * src/*.c,po/,inst/po: Internationalization and localization of
387            the package.
388    
389            * src/ldl.[ch]: Removed these as their contents are referenced in the
390            R_ldl.c file.
391    
392            * src/flame.[ch]: Removed these source files.
393    
394            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
395    
396            * src/LU.[ch],src/init.c: absorb in factorizations
397    
398            * src/Mutils.h: prepare for internationalization
399    
400            * src/cblas.h: move the enum definitions to Mutils.h and remove
401            this file
402    
403    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
406    
407            * R/dtrMatrix.R: fix t() method
408    
409            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
410            * NAMESPACE: export them (and import generics from "methods")
411            * tests/group-methods.R : and test them.
412    
413            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
414            border case
415    
416    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
417    
418            * DESCRIPTION (Version): 0.95-2  released to CRAN
419    
420            * src/dgBCMatrix.c:
421            * src/lmer.c: many changes
422            * ...
423    
424    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/Matrix.R: add more sophisticated show() method.
427    
428    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
429    
430            * */* : almost complete reorganization of classes.
431    
432    2005-01-26  Douglas Bates  <bates@wisc.edu>
433    
434            * R/AllGeneric.R: Added matrix exponential generic expm and a method
435            for the geMatrix class.
436    
437    2005-01-24  Douglas Bates  <bates@wisc.edu>
438    
439            * src/Makefile (clean): Remove *.a and *.so
440    
441            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
442    
443    2005-01-23  Douglas Bates  <bates@wisc.edu>
444    
445            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
446            had an effect in cases with more than 2 grouping factors.
447    
448    2005-01-03  Douglas Bates  <bates@wisc.edu>
449    
450            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
451    
452    2004-12-23  Douglas Bates  <bates@wisc.edu>
453    
454            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
455            and R_useDynamicSymbols (suggested by B.D.Ripley).
456    
457    2004-12-14  Douglas Bates  <bates@wisc.edu>
458    
459          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
460    
461          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
462          for tripletMatrix to matrix.          for tripletMatrix to matrix.
463    
464  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
465    
466          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
467          no longer used.          no longer used.
# Line 17  Line 473 
473          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
474          Fixes part but not all of #15.          Fixes part but not all of #15.
475    
476  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
477    
478          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
479          scalar grouping factors corrected.          scalar grouping factors corrected.
480    
481  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
482    
483          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
484    
485  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
486    
487          * 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
488          .h file can be included.          .h file can be included.
489    
490  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
491    
492          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
493          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
494    
495          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
496    
497  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
498    
499          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
500    
501  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
502    
503          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
504    
505  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
506    
507          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
508    
509  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
510    
511          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
512    
513  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
514    
515          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
516          routines.          routines.
517    
518  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
519    
520          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
521    
522  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
523    
524          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
525    

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