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revision 820, Wed Jul 27 23:07:04 2005 UTC revision 954, Wed Sep 28 19:34:31 2005 UTC
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1  2005-07-27  Douglas Bates  <bates@localhost.localdomain>  2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3          * man/sleep.Rd: Added the sleep data set.          * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
4            default.
5    
6  2005-07-12  Douglas Bates  <bates@localhost.localdomain>  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          * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
180          .Call calls that were producing spurious output.          .Call calls that were producing spurious output.
181    
182  2005-07-05  Douglas Bates  <bates@bates1-home>  2005-07-05  Douglas Bates  <bates@wisc.edu>
183    
184          * R/lmer.R (lmer): stored updated variance component estimates in          * R/lmer.R (lmer): stored updated variance component estimates in
185          mer object for the generalized model.  (Bug reported by Renaud          mer object for the generalized model.  (Bug reported by Renaud
186          Lancelot).          Lancelot).
187    
188  2005-07-03  Douglas Bates  <bates@bates1-home>  2005-07-03  Douglas Bates  <bates@wisc.edu>
189    
190          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,          * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
191          unidimensional case.          unidimensional case.
192    
193  2005-06-08  Douglas Bates  <bates@bates1-home>  2005-06-08  Douglas Bates  <bates@wisc.edu>
194    
195          * DESCRIPTION (Version): 0.96-1          * DESCRIPTION (Version): 0.96-1
196    
197          * moved  lmer-class' R and C code moved from lme4 to here          * moved  lmer-class' R and C code moved from lme4 to here
198    
199  2005-06-04  Douglas Bates  <bates@bates1-home>  2005-06-04  Douglas Bates  <bates@wisc.edu>
200    
201          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments          * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
202          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)          (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
203    
204  2005-06-02  Douglas Bates  <bates@bates1-home>  2005-06-02  Douglas Bates  <bates@wisc.edu>
205    
206          * src/Makefile.win: Forgot to update this when Makefile changed.          * src/Makefile.win: Forgot to update this when Makefile changed.
207    
208  2005-05-11  Douglas Bates  <bates@bates1-home>  2005-05-11  Douglas Bates  <bates@wisc.edu>
209    
210          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
211          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
212    
213  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
214    
215          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
216          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 47  Line 219 
219          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * 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          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
221    
222  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
223    
224          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
225          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
226    
227  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
228    
229          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
230          multiplication operation.          multiplication operation.
# Line 65  Line 237 
237    
238          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
239    
240  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
241    
242          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
243    
244          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
245    
246    
247  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
248    
249          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
250    
# Line 81  Line 253 
253          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
254          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
255    
256  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
257    
258          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
259    
# Line 107  Line 279 
279          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
280            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
281    
282  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
283    
284          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
285          * ....          * ....
286    
287  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
288    
289          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
290    
# Line 127  Line 299 
299            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
300          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
301    
302  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
303    
304          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
305    
306  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
307    
308          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
309    
310  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
311    
312          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
313          the package.          the package.
# Line 183  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 227  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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