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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 976, Fri Oct 7 20:18:29 2005 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Auxiliaries.R (try_as): new utility
4            * R/sparseMatrix.R: use try_as() in coercion to original class
5    
6    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
9    
10    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Auxiliaries.R (dimNamesCheck): added
13    
14            * R/Matrix.R (as.array), (as.vector): new
15    
16    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
19                    default.
20            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
21                    "pMatrix" now contains "sparseMatrix"
22    
23    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * tests/Class+Meth.R: new tests; t(t(m)) == m
26    
27            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
28    
29            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
30            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
31    
32            * R/dspMatrix.R: typo in "t" method
33    
34    2005-09-18  Douglas Bates  <bates@wisc.edu>
35    
36            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
37            * R/Tsparse.R: instead of R/gTMatrix.R
38            * R/Csparse.R: new
39            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
40            * src/Tsparse.c: new; many trivial methods calling cholmod_()
41            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
42                            via cholmod
43    
44    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/Auxiliaries.R (non0ind): new function using new C code
47            * src/dgCMatrix.c (compressed_non_0_ij): new utility
48    
49    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
50    
51            * src/chm_common.h: header file required by all C sources that
52            call CHOLMOD functions.  It defines a cholmod_common structure
53            called 'c' whose address is passed as the last argument to
54            (virtually) every CHOLMOD function.
55    
56            * src/Pattern.c: Simple example of the use of CHOLMOD.
57    
58            * src/init.c: initialize and finalize the cholmod_common structure.
59    
60            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
61            LDL and CCOLAMD from the U. of Florida sparse matrix library.
62    
63    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * inst/test-tools.R: new file collecting the utility functions used
66                    in ./tests/*.R
67    
68            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
69            * R/Matrix.R (cbind2): methods for NULL and missing
70    
71    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/AllClass.R: new "index" class for "[" and "[<-":
74                    First cut at "symmetricMatrix" and "triangularMatrix"
75            * R/gTMatrix.R (.ind.prep): new function;
76                    Logical and character indexing now work too.
77            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
78            * tests/indexing.R: new, including *.Rout.save
79            * tests/dgTMatrix.R: new
80    
81    2005-08-29  Douglas Bates  <bates@wisc.edu>
82    
83            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
84            indicator pos not being updated.  Also enforced upper triangular
85            for symmetric case.  Need to coerce edges component of elements of
86            edge list - grr! (Why don't they define their classes cleanly?)
87    
88    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/Matrix.R:  added first "[<-" methods; not yet functional
91            * R/denseMatrix.R: dito
92            * man/Subassign-methods.Rd: new help file for these
93    
94    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * DESCRIPTION (Version): 0.98-6
97    
98            * R/denseMatrix.R: new file for "[" fallback methods for all dense
99            matrices.
100    
101    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
104                    as( <logical>, "matrix")
105    
106            * R/pMatrix.R: coercion to "lgTMatrix"
107    
108            * R/gTMatrix.R: new virtual class to define "[" methods for.
109            * man/gTMatrix-class.Rd:
110            * General slight re-organization of where "[" methods are defined.
111              more to come.
112    
113    2005-08-18  Douglas Bates  <bates@wisc.edu>
114    
115            * DESCRIPTION (Version): 0.98-5  released to CRAN
116    
117            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
118            * .....
119    
120    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
121    
122            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
123            or glmer objects.
124    
125    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
128    
129    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
130    
131            * R/HBMM.R: finish re-writing R-only code.
132    
133    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
134    
135            * man/externalFormats.Rd: move documentation for writeHB and
136            writeMM here.
137    
138            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
139            (suggested by Paul Roecker).
140    
141            * tests/validObj.R (assertError): Comment out test that is failing
142            after recent changes in r-devel.
143    
144    
145    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/AllClass.R: intermediate virtual class "denseMatrix"
148            * man/denseMatrix-class.Rd
149            * NAMESPACE: export it, and also export
150            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
151    
152    2005-08-10  Douglas Bates  <bates@wisc.edu>
153    
154            * DESCRIPTION (Version): 0.98-3 to CRAN
155    
156            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
157            matrix_solve code (which was really, really wrong).
158    
159    2005-08-07  Douglas Bates  <bates@wisc.edu>
160    
161            * DESCRIPTION (Version): 0.98-2
162    
163            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
164    
165            * R/lmer.R (abbrvNms): new
166            * R/lmer.R (mcmcsamp): allow transformed parameters
167            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
168            for the Harwell-Boeing and the MatrixMarket formats.
169    
170    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * man/dtrMatrix-class.Rd: add examples
173            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
174    
175            * TODO: note the dtpMatrix (docu) bug
176    
177            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
178            in order to ensure that new as.matrix() is used by old functions,
179            e.g., svd(), qr(), eigen(), dist(),..;
180                  apply(), also matplot() or pairs().
181    
182    
183    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
186              add comments about 'control' / lmerControl() arguments
187    
188    2005-07-27  Douglas Bates  <bates@wisc.edu>
189    
190            * man/sleepstudy.Rd: Added the sleep data set.
191            * DESCRIPTION (Version): 0.98-1  released to CRAN
192    
193    2005-07-12  Douglas Bates  <bates@wisc.edu>
194            * man/sleepstudy.Rd: Added the sleep data set.
195    
196            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
197            .Call calls that were producing spurious output.
198    
199    2005-07-05  Douglas Bates  <bates@wisc.edu>
200    
201            * R/lmer.R (lmer): stored updated variance component estimates in
202            mer object for the generalized model.  (Bug reported by Renaud
203            Lancelot).
204    
205    2005-07-03  Douglas Bates  <bates@wisc.edu>
206    
207            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
208            unidimensional case.
209    
210    2005-06-08  Douglas Bates  <bates@wisc.edu>
211    
212            * DESCRIPTION (Version): 0.96-1
213    
214            * moved  lmer-class' R and C code moved from lme4 to here
215    
216    2005-06-04  Douglas Bates  <bates@wisc.edu>
217    
218            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
219            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
220    
221    2005-06-02  Douglas Bates  <bates@wisc.edu>
222    
223            * src/Makefile.win: Forgot to update this when Makefile changed.
224    
225    2005-05-11  Douglas Bates  <bates@wisc.edu>
226    
227            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
228            bug reported by Kurt Hornik and Michael Hahsler.
229    
230    2005-05-10  Douglas Bates  <bates@wisc.edu>
231    
232            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
233            logical sparse matrices.  These will also be used in the symbolic
234            analysis for lmer objects.
235    
236            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
237            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
238    
239    2005-05-06  Douglas Bates  <bates@wisc.edu>
240    
241            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
242            colMeans, colSums, rowMeans and rowSums.
243    
244    2005-04-18  Douglas Bates  <bates@wisc.edu>
245    
246            * src/lgCMatrix.[ch]: code for _validate method and stub for
247            multiplication operation.
248    
249            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
250            to dgetrs.
251    
252            * src/init.c: Fix cut-and-paste error in definition of
253            dgeMatrix_matrix_solve
254    
255            * src/{many files}: Tighten code by using ALLOC_SLOT.
256    
257    2005-04-15  Douglas Bates  <bates@wisc.edu>
258    
259            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
260    
261            * DESCRIPTION: Eliminate import of stats.
262    
263    
264    2005-04-06  Douglas Bates  <bates@wisc.edu>
265    
266            * R/AllClass.R : add logical sparse matrix classes
267    
268    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/dgTMatrix.R: add "[" method for triplet matrices
271            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
272    
273    2005-03-31  Douglas Bates  <bates@wisc.edu>
274    
275            * DESCRIPTION (Version): release 0.95-5 to CRAN
276    
277            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
278            * R/sparseMatrix.R: %*%, crossprod()
279            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
280            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
281            * src/lmer.c (lmer_fitted): fix thinko
282    
283    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/AllClass.R: add two virtual sparse classes ``on top''
286    
287    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
290                    correspondingly fix examples and tests/ since new()
291                    doesn't work for virtual classes.
292    
293    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/Matrix.R (as.matrix): method and one for unname()
296            * tests/dpoMatrix.R: tests should now be less platform dependent;
297              also run for R 2.1.0; using as.matrix()
298    
299    2005-03-15  Douglas Bates  <bates@wisc.edu>
300    
301            * R/pMatrix.R: "pMatrix" class added
302            * ....
303    
304    2005-03-14  Douglas Bates  <bates@wisc.edu>
305    
306            * R/dtpMatrix.R: Add unpack method and an example.
307    
308            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
309            of general symmetric matrices and associated S4 methods.
310    
311    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
312            +
313    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/dgeMatrix.R (setAs): and many other files: more coercion,
316              crossprod() and "%*%" methods added; tests, too.
317            * tests/matprod.R: new, for testing these
318    
319    2005-03-03  Douglas Bates  <bates@wisc.edu>
320    
321            * src/lmer.c (lmer_fitted): Added.
322    
323    2005-03-02  Douglas Bates  <bates@wisc.edu>
324    
325            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
326    
327    2005-02-28  Douglas Bates  <bates@wisc.edu>
328    
329            * src/*.c,po/,inst/po: Internationalization and localization of
330            the package.
331    
332            * src/ldl.[ch]: Removed these as their contents are referenced in the
333            R_ldl.c file.
334    
335            * src/flame.[ch]: Removed these source files.
336    
337            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
338    
339            * src/LU.[ch],src/init.c: absorb in factorizations
340    
341            * src/Mutils.h: prepare for internationalization
342    
343            * src/cblas.h: move the enum definitions to Mutils.h and remove
344            this file
345    
346    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
349    
350            * R/dtrMatrix.R: fix t() method
351    
352            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
353            * NAMESPACE: export them (and import generics from "methods")
354            * tests/group-methods.R : and test them.
355    
356            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
357            border case
358    
359    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
360    
361            * DESCRIPTION (Version): 0.95-2  released to CRAN
362    
363            * src/dgBCMatrix.c:
364            * src/lmer.c: many changes
365            * ...
366    
367    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/Matrix.R: add more sophisticated show() method.
370    
371    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
372    
373            * */* : almost complete reorganization of classes.
374    
375    2005-01-26  Douglas Bates  <bates@wisc.edu>
376    
377            * R/AllGeneric.R: Added matrix exponential generic expm and a method
378            for the geMatrix class.
379    
380    2005-01-24  Douglas Bates  <bates@wisc.edu>
381    
382            * src/Makefile (clean): Remove *.a and *.so
383    
384            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
385    
386    2005-01-23  Douglas Bates  <bates@wisc.edu>
387    
388            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
389            had an effect in cases with more than 2 grouping factors.
390    
391    2005-01-03  Douglas Bates  <bates@wisc.edu>
392    
393            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
394    
395    2004-12-23  Douglas Bates  <bates@wisc.edu>
396    
397            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
398            and R_useDynamicSymbols (suggested by B.D.Ripley).
399    
400    2004-12-14  Douglas Bates  <bates@wisc.edu>
401    
402            * R/sscMatrix.R: Add determinant methods
403    
404            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
405            for tripletMatrix to matrix.
406    
407    2004-12-13  Douglas Bates  <bates@wisc.edu>
408    
409            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
410            no longer used.
411    
412          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
413          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 416 
416          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
417          Fixes part but not all of #15.          Fixes part but not all of #15.
418    
419  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
420    
421          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
422          scalar grouping factors corrected.          scalar grouping factors corrected.
423    
424  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
425    
426          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
427    
428  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
429    
430          * 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
431          .h file can be included.          .h file can be included.
432    
433  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
434    
435          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
436          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
437    
438          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
439    
440  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
441    
442          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
443    
444  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
445    
446          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
447    
448  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
449    
450          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
451    
452  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
453    
454          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
455    
456  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
457    
458          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
459          routines.          routines.
460    
461  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
462    
463          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
464    
465  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
466    
467          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
468    

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