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revision 579, Sun Feb 27 00:04:16 2005 UTC revision 954, Wed Sep 28 19:34:31 2005 UTC
# Line 1  Line 1 
1    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
4            default.
5    
6    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * tests/Class+Meth.R: new tests; t(t(m)) == m
9    
10            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
11    
12            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
13            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
14    
15            * R/dspMatrix.R: typo in "t" method
16    
17    2005-09-18  Douglas Bates  <bates@wisc.edu>
18    
19            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
20            * R/Tsparse.R: instead of R/gTMatrix.R
21            * R/Csparse.R: new
22            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
23            * src/Tsparse.c: new; many trivial methods calling cholmod_()
24            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
25                            via cholmod
26    
27    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Auxiliaries.R (non0ind): new function using new C code
30            * src/dgCMatrix.c (compressed_non_0_ij): new utility
31    
32    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
33    
34            * src/chm_common.h: header file required by all C sources that
35            call CHOLMOD functions.  It defines a cholmod_common structure
36            called 'c' whose address is passed as the last argument to
37            (virtually) every CHOLMOD function.
38    
39            * src/Pattern.c: Simple example of the use of CHOLMOD.
40    
41            * src/init.c: initialize and finalize the cholmod_common structure.
42    
43            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
44            LDL and CCOLAMD from the U. of Florida sparse matrix library.
45    
46    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * inst/test-tools.R: new file collecting the utility functions used
49                    in ./tests/*.R
50    
51            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
52            * R/Matrix.R (cbind2): methods for NULL and missing
53    
54    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/AllClass.R: new "index" class for "[" and "[<-":
57                    First cut at "symmetricMatrix" and "triangularMatrix"
58            * R/gTMatrix.R (.ind.prep): new function;
59                    Logical and character indexing now work too.
60            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
61            * tests/indexing.R: new, including *.Rout.save
62            * tests/dgTMatrix.R: new
63    
64    2005-08-29  Douglas Bates  <bates@wisc.edu>
65    
66            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
67            indicator pos not being updated.  Also enforced upper triangular
68            for symmetric case.  Need to coerce edges component of elements of
69            edge list - grr! (Why don't they define their classes cleanly?)
70    
71    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/Matrix.R:  added first "[<-" methods; not yet functional
74            * R/denseMatrix.R: dito
75            * man/Subassign-methods.Rd: new help file for these
76    
77    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * DESCRIPTION (Version): 0.98-6
80    
81            * R/denseMatrix.R: new file for "[" fallback methods for all dense
82            matrices.
83    
84    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
87                    as( <logical>, "matrix")
88    
89            * R/pMatrix.R: coercion to "lgTMatrix"
90    
91            * R/gTMatrix.R: new virtual class to define "[" methods for.
92            * man/gTMatrix-class.Rd:
93            * General slight re-organization of where "[" methods are defined.
94              more to come.
95    
96    2005-08-18  Douglas Bates  <bates@wisc.edu>
97    
98            * DESCRIPTION (Version): 0.98-5  released to CRAN
99    
100            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
101            * .....
102    
103    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
104    
105            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
106            or glmer objects.
107    
108    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
111    
112    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
113    
114            * R/HBMM.R: finish re-writing R-only code.
115    
116    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
117    
118            * man/externalFormats.Rd: move documentation for writeHB and
119            writeMM here.
120    
121            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
122            (suggested by Paul Roecker).
123    
124            * tests/validObj.R (assertError): Comment out test that is failing
125            after recent changes in r-devel.
126    
127    
128    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/AllClass.R: intermediate virtual class "denseMatrix"
131            * man/denseMatrix-class.Rd
132            * NAMESPACE: export it, and also export
133            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
134    
135    2005-08-10  Douglas Bates  <bates@wisc.edu>
136    
137            * DESCRIPTION (Version): 0.98-3 to CRAN
138    
139            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
140            matrix_solve code (which was really, really wrong).
141    
142    2005-08-07  Douglas Bates  <bates@wisc.edu>
143    
144            * DESCRIPTION (Version): 0.98-2
145    
146            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
147    
148            * R/lmer.R (abbrvNms): new
149            * R/lmer.R (mcmcsamp): allow transformed parameters
150            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
151            for the Harwell-Boeing and the MatrixMarket formats.
152    
153    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * man/dtrMatrix-class.Rd: add examples
156            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
157    
158            * TODO: note the dtpMatrix (docu) bug
159    
160            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
161            in order to ensure that new as.matrix() is used by old functions,
162            e.g., svd(), qr(), eigen(), dist(),..;
163                  apply(), also matplot() or pairs().
164    
165    
166    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
169              add comments about 'control' / lmerControl() arguments
170    
171    2005-07-27  Douglas Bates  <bates@wisc.edu>
172    
173            * man/sleepstudy.Rd: Added the sleep data set.
174            * DESCRIPTION (Version): 0.98-1  released to CRAN
175    
176    2005-07-12  Douglas Bates  <bates@wisc.edu>
177            * man/sleepstudy.Rd: Added the sleep data set.
178    
179            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
180            .Call calls that were producing spurious output.
181    
182    2005-07-05  Douglas Bates  <bates@wisc.edu>
183    
184            * R/lmer.R (lmer): stored updated variance component estimates in
185            mer object for the generalized model.  (Bug reported by Renaud
186            Lancelot).
187    
188    2005-07-03  Douglas Bates  <bates@wisc.edu>
189    
190            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
191            unidimensional case.
192    
193    2005-06-08  Douglas Bates  <bates@wisc.edu>
194    
195            * DESCRIPTION (Version): 0.96-1
196    
197            * moved  lmer-class' R and C code moved from lme4 to here
198    
199    2005-06-04  Douglas Bates  <bates@wisc.edu>
200    
201            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
202            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
203    
204    2005-06-02  Douglas Bates  <bates@wisc.edu>
205    
206            * src/Makefile.win: Forgot to update this when Makefile changed.
207    
208    2005-05-11  Douglas Bates  <bates@wisc.edu>
209    
210            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
211            bug reported by Kurt Hornik and Michael Hahsler.
212    
213    2005-05-10  Douglas Bates  <bates@wisc.edu>
214    
215            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
216            logical sparse matrices.  These will also be used in the symbolic
217            analysis for lmer objects.
218    
219            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
220            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
221    
222    2005-05-06  Douglas Bates  <bates@wisc.edu>
223    
224            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
225            colMeans, colSums, rowMeans and rowSums.
226    
227    2005-04-18  Douglas Bates  <bates@wisc.edu>
228    
229            * src/lgCMatrix.[ch]: code for _validate method and stub for
230            multiplication operation.
231    
232            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
233            to dgetrs.
234    
235            * src/init.c: Fix cut-and-paste error in definition of
236            dgeMatrix_matrix_solve
237    
238            * src/{many files}: Tighten code by using ALLOC_SLOT.
239    
240    2005-04-15  Douglas Bates  <bates@wisc.edu>
241    
242            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
243    
244            * DESCRIPTION: Eliminate import of stats.
245    
246    
247    2005-04-06  Douglas Bates  <bates@wisc.edu>
248    
249            * R/AllClass.R : add logical sparse matrix classes
250    
251    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/dgTMatrix.R: add "[" method for triplet matrices
254            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
255    
256    2005-03-31  Douglas Bates  <bates@wisc.edu>
257    
258            * DESCRIPTION (Version): release 0.95-5 to CRAN
259    
260            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
261            * R/sparseMatrix.R: %*%, crossprod()
262            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
263            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
264            * src/lmer.c (lmer_fitted): fix thinko
265    
266    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * R/AllClass.R: add two virtual sparse classes ``on top''
269    
270    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
273                    correspondingly fix examples and tests/ since new()
274                    doesn't work for virtual classes.
275    
276    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/Matrix.R (as.matrix): method and one for unname()
279            * tests/dpoMatrix.R: tests should now be less platform dependent;
280              also run for R 2.1.0; using as.matrix()
281    
282    2005-03-15  Douglas Bates  <bates@wisc.edu>
283    
284            * R/pMatrix.R: "pMatrix" class added
285            * ....
286    
287    2005-03-14  Douglas Bates  <bates@wisc.edu>
288    
289            * R/dtpMatrix.R: Add unpack method and an example.
290    
291            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
292            of general symmetric matrices and associated S4 methods.
293    
294    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
295            +
296    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/dgeMatrix.R (setAs): and many other files: more coercion,
299              crossprod() and "%*%" methods added; tests, too.
300            * tests/matprod.R: new, for testing these
301    
302    2005-03-03  Douglas Bates  <bates@wisc.edu>
303    
304            * src/lmer.c (lmer_fitted): Added.
305    
306    2005-03-02  Douglas Bates  <bates@wisc.edu>
307    
308            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
309    
310    2005-02-28  Douglas Bates  <bates@wisc.edu>
311    
312            * src/*.c,po/,inst/po: Internationalization and localization of
313            the package.
314    
315            * src/ldl.[ch]: Removed these as their contents are referenced in the
316            R_ldl.c file.
317    
318            * src/flame.[ch]: Removed these source files.
319    
320            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
321    
322            * src/LU.[ch],src/init.c: absorb in factorizations
323    
324            * src/Mutils.h: prepare for internationalization
325    
326            * src/cblas.h: move the enum definitions to Mutils.h and remove
327            this file
328    
329  2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331          * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods          * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
# Line 27  Line 355 
355    
356          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
357    
358  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
359    
360          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
361          for the geMatrix class.          for the geMatrix class.
362    
363  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
364    
365          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
366    
367          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
368    
369  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
370    
371          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
372          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
373    
374  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
375    
376          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
377    
378  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
379    
380          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
381          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
382    
383  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
384    
385          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
386    
387          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
388          for tripletMatrix to matrix.          for tripletMatrix to matrix.
389    
390  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
391    
392          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
393          no longer used.          no longer used.
# Line 71  Line 399 
399          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
400          Fixes part but not all of #15.          Fixes part but not all of #15.
401    
402  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
403    
404          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
405          scalar grouping factors corrected.          scalar grouping factors corrected.
406    
407  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
408    
409          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
410    
411  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
412    
413          * 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
414          .h file can be included.          .h file can be included.
415    
416  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
417    
418          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
419          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
420    
421          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
422    
423  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
424    
425          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
426    
427  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
428    
429          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
430    
431  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
432    
433          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
434    
435  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
436    
437          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
438    
439  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
440    
441          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
442          routines.          routines.
443    
444  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
445    
446          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
447    
448  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
449    
450          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
451    

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