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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 956, Fri Sep 30 17:28:00 2005 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
4    
5    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Auxiliaries.R (dimNamesCheck): added
8    
9            * R/Matrix.R (as.array), (as.vector): new
10    
11    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
14                    default.
15            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
16                    "pMatrix" now contains "sparseMatrix"
17    
18    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * tests/Class+Meth.R: new tests; t(t(m)) == m
21    
22            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
23    
24            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
25            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
26    
27            * R/dspMatrix.R: typo in "t" method
28    
29    2005-09-18  Douglas Bates  <bates@wisc.edu>
30    
31            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
32            * R/Tsparse.R: instead of R/gTMatrix.R
33            * R/Csparse.R: new
34            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
35            * src/Tsparse.c: new; many trivial methods calling cholmod_()
36            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
37                            via cholmod
38    
39    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Auxiliaries.R (non0ind): new function using new C code
42            * src/dgCMatrix.c (compressed_non_0_ij): new utility
43    
44    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
45    
46            * src/chm_common.h: header file required by all C sources that
47            call CHOLMOD functions.  It defines a cholmod_common structure
48            called 'c' whose address is passed as the last argument to
49            (virtually) every CHOLMOD function.
50    
51            * src/Pattern.c: Simple example of the use of CHOLMOD.
52    
53            * src/init.c: initialize and finalize the cholmod_common structure.
54    
55            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
56            LDL and CCOLAMD from the U. of Florida sparse matrix library.
57    
58    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * inst/test-tools.R: new file collecting the utility functions used
61                    in ./tests/*.R
62    
63            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
64            * R/Matrix.R (cbind2): methods for NULL and missing
65    
66    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/AllClass.R: new "index" class for "[" and "[<-":
69                    First cut at "symmetricMatrix" and "triangularMatrix"
70            * R/gTMatrix.R (.ind.prep): new function;
71                    Logical and character indexing now work too.
72            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
73            * tests/indexing.R: new, including *.Rout.save
74            * tests/dgTMatrix.R: new
75    
76    2005-08-29  Douglas Bates  <bates@wisc.edu>
77    
78            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
79            indicator pos not being updated.  Also enforced upper triangular
80            for symmetric case.  Need to coerce edges component of elements of
81            edge list - grr! (Why don't they define their classes cleanly?)
82    
83    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/Matrix.R:  added first "[<-" methods; not yet functional
86            * R/denseMatrix.R: dito
87            * man/Subassign-methods.Rd: new help file for these
88    
89    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * DESCRIPTION (Version): 0.98-6
92    
93            * R/denseMatrix.R: new file for "[" fallback methods for all dense
94            matrices.
95    
96    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
99                    as( <logical>, "matrix")
100    
101            * R/pMatrix.R: coercion to "lgTMatrix"
102    
103            * R/gTMatrix.R: new virtual class to define "[" methods for.
104            * man/gTMatrix-class.Rd:
105            * General slight re-organization of where "[" methods are defined.
106              more to come.
107    
108    2005-08-18  Douglas Bates  <bates@wisc.edu>
109    
110            * DESCRIPTION (Version): 0.98-5  released to CRAN
111    
112            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
113            * .....
114    
115    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
116    
117            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
118            or glmer objects.
119    
120    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
123    
124    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
125    
126            * R/HBMM.R: finish re-writing R-only code.
127    
128    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
129    
130            * man/externalFormats.Rd: move documentation for writeHB and
131            writeMM here.
132    
133            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
134            (suggested by Paul Roecker).
135    
136            * tests/validObj.R (assertError): Comment out test that is failing
137            after recent changes in r-devel.
138    
139    
140    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/AllClass.R: intermediate virtual class "denseMatrix"
143            * man/denseMatrix-class.Rd
144            * NAMESPACE: export it, and also export
145            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
146    
147    2005-08-10  Douglas Bates  <bates@wisc.edu>
148    
149            * DESCRIPTION (Version): 0.98-3 to CRAN
150    
151            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
152            matrix_solve code (which was really, really wrong).
153    
154    2005-08-07  Douglas Bates  <bates@wisc.edu>
155    
156            * DESCRIPTION (Version): 0.98-2
157    
158            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
159    
160            * R/lmer.R (abbrvNms): new
161            * R/lmer.R (mcmcsamp): allow transformed parameters
162            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
163            for the Harwell-Boeing and the MatrixMarket formats.
164    
165    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * man/dtrMatrix-class.Rd: add examples
168            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
169    
170            * TODO: note the dtpMatrix (docu) bug
171    
172            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
173            in order to ensure that new as.matrix() is used by old functions,
174            e.g., svd(), qr(), eigen(), dist(),..;
175                  apply(), also matplot() or pairs().
176    
177    
178    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
181              add comments about 'control' / lmerControl() arguments
182    
183    2005-07-27  Douglas Bates  <bates@wisc.edu>
184    
185            * man/sleepstudy.Rd: Added the sleep data set.
186            * DESCRIPTION (Version): 0.98-1  released to CRAN
187    
188    2005-07-12  Douglas Bates  <bates@wisc.edu>
189            * man/sleepstudy.Rd: Added the sleep data set.
190    
191            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
192            .Call calls that were producing spurious output.
193    
194    2005-07-05  Douglas Bates  <bates@wisc.edu>
195    
196            * R/lmer.R (lmer): stored updated variance component estimates in
197            mer object for the generalized model.  (Bug reported by Renaud
198            Lancelot).
199    
200    2005-07-03  Douglas Bates  <bates@wisc.edu>
201    
202            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
203            unidimensional case.
204    
205    2005-06-08  Douglas Bates  <bates@wisc.edu>
206    
207            * DESCRIPTION (Version): 0.96-1
208    
209            * moved  lmer-class' R and C code moved from lme4 to here
210    
211    2005-06-04  Douglas Bates  <bates@wisc.edu>
212    
213            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
214            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
215    
216    2005-06-02  Douglas Bates  <bates@wisc.edu>
217    
218            * src/Makefile.win: Forgot to update this when Makefile changed.
219    
220    2005-05-11  Douglas Bates  <bates@wisc.edu>
221    
222            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
223            bug reported by Kurt Hornik and Michael Hahsler.
224    
225    2005-05-10  Douglas Bates  <bates@wisc.edu>
226    
227            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
228            logical sparse matrices.  These will also be used in the symbolic
229            analysis for lmer objects.
230    
231            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
232            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
233    
234    2005-05-06  Douglas Bates  <bates@wisc.edu>
235    
236            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
237            colMeans, colSums, rowMeans and rowSums.
238    
239    2005-04-18  Douglas Bates  <bates@wisc.edu>
240    
241            * src/lgCMatrix.[ch]: code for _validate method and stub for
242            multiplication operation.
243    
244            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
245            to dgetrs.
246    
247            * src/init.c: Fix cut-and-paste error in definition of
248            dgeMatrix_matrix_solve
249    
250            * src/{many files}: Tighten code by using ALLOC_SLOT.
251    
252    2005-04-15  Douglas Bates  <bates@wisc.edu>
253    
254            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
255    
256            * DESCRIPTION: Eliminate import of stats.
257    
258    
259    2005-04-06  Douglas Bates  <bates@wisc.edu>
260    
261            * R/AllClass.R : add logical sparse matrix classes
262    
263    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/dgTMatrix.R: add "[" method for triplet matrices
266            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
267    
268    2005-03-31  Douglas Bates  <bates@wisc.edu>
269    
270            * DESCRIPTION (Version): release 0.95-5 to CRAN
271    
272            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
273            * R/sparseMatrix.R: %*%, crossprod()
274            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
275            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
276            * src/lmer.c (lmer_fitted): fix thinko
277    
278    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/AllClass.R: add two virtual sparse classes ``on top''
281    
282    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
285                    correspondingly fix examples and tests/ since new()
286                    doesn't work for virtual classes.
287    
288    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/Matrix.R (as.matrix): method and one for unname()
291            * tests/dpoMatrix.R: tests should now be less platform dependent;
292              also run for R 2.1.0; using as.matrix()
293    
294    2005-03-15  Douglas Bates  <bates@wisc.edu>
295    
296            * R/pMatrix.R: "pMatrix" class added
297            * ....
298    
299    2005-03-14  Douglas Bates  <bates@wisc.edu>
300    
301            * R/dtpMatrix.R: Add unpack method and an example.
302    
303            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
304            of general symmetric matrices and associated S4 methods.
305    
306    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
307            +
308    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/dgeMatrix.R (setAs): and many other files: more coercion,
311              crossprod() and "%*%" methods added; tests, too.
312            * tests/matprod.R: new, for testing these
313    
314    2005-03-03  Douglas Bates  <bates@wisc.edu>
315    
316            * src/lmer.c (lmer_fitted): Added.
317    
318    2005-03-02  Douglas Bates  <bates@wisc.edu>
319    
320            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
321    
322    2005-02-28  Douglas Bates  <bates@wisc.edu>
323    
324            * src/*.c,po/,inst/po: Internationalization and localization of
325            the package.
326    
327            * src/ldl.[ch]: Removed these as their contents are referenced in the
328            R_ldl.c file.
329    
330            * src/flame.[ch]: Removed these source files.
331    
332            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
333    
334            * src/LU.[ch],src/init.c: absorb in factorizations
335    
336            * src/Mutils.h: prepare for internationalization
337    
338            * src/cblas.h: move the enum definitions to Mutils.h and remove
339            this file
340    
341    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
344    
345            * R/dtrMatrix.R: fix t() method
346    
347            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
348            * NAMESPACE: export them (and import generics from "methods")
349            * tests/group-methods.R : and test them.
350    
351            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
352            border case
353    
354    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
355    
356            * DESCRIPTION (Version): 0.95-2  released to CRAN
357    
358            * src/dgBCMatrix.c:
359            * src/lmer.c: many changes
360            * ...
361    
362    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/Matrix.R: add more sophisticated show() method.
365    
366    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
367    
368            * */* : almost complete reorganization of classes.
369    
370    2005-01-26  Douglas Bates  <bates@wisc.edu>
371    
372            * R/AllGeneric.R: Added matrix exponential generic expm and a method
373            for the geMatrix class.
374    
375    2005-01-24  Douglas Bates  <bates@wisc.edu>
376    
377            * src/Makefile (clean): Remove *.a and *.so
378    
379            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
380    
381    2005-01-23  Douglas Bates  <bates@wisc.edu>
382    
383            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
384            had an effect in cases with more than 2 grouping factors.
385    
386    2005-01-03  Douglas Bates  <bates@wisc.edu>
387    
388            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
389    
390    2004-12-23  Douglas Bates  <bates@wisc.edu>
391    
392            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
393            and R_useDynamicSymbols (suggested by B.D.Ripley).
394    
395    2004-12-14  Douglas Bates  <bates@wisc.edu>
396    
397          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
398    
399          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
400          for tripletMatrix to matrix.          for tripletMatrix to matrix.
401    
402  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
403    
404          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
405          no longer used.          no longer used.
# Line 17  Line 411 
411          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
412          Fixes part but not all of #15.          Fixes part but not all of #15.
413    
414  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
415    
416          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
417          scalar grouping factors corrected.          scalar grouping factors corrected.
418    
419  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
420    
421          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
422    
423  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
424    
425          * 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
426          .h file can be included.          .h file can be included.
427    
428  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
429    
430          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
431          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
432    
433          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
434    
435  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
436    
437          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
438    
439  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
440    
441          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
442    
443  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
444    
445          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
446    
447  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
448    
449          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
450    
451  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
452    
453          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
454          routines.          routines.
455    
456  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
457    
458          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
459    
460  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
461    
462          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
463    

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