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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 925, Mon Sep 19 19:01:31 2005 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2005-09-18  Douglas Bates  <bates@wisc.edu>
2    
3            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
4            * R/Tsparse.R: instead of R/gTMatrix.R
5            * R/Csparse.R: new
6            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
7            * src/Tsparse.c: new; many trivial methods calling cholmod_()
8            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
9                            via cholmod
10    
11    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/Auxiliaries.R (non0ind): new function using new C code
14            * src/dgCMatrix.c (compressed_non_0_ij): new utility
15    
16    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
17    
18            * src/chm_common.h: header file required by all C sources that
19            call CHOLMOD functions.  It defines a cholmod_common structure
20            called 'c' whose address is passed as the last argument to
21            (virtually) every CHOLMOD function.
22    
23            * src/Pattern.c: Simple example of the use of CHOLMOD.
24    
25            * src/init.c: initialize and finalize the cholmod_common structure.
26    
27            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
28            LDL and CCOLAMD from the U. of Florida sparse matrix library.
29    
30    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * inst/test-tools.R: new file collecting the utility functions used
33                    in ./tests/*.R
34    
35            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
36            * R/Matrix.R (cbind2): methods for NULL and missing
37    
38    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/AllClass.R: new "index" class for "[" and "[<-":
41                    First cut at "symmetricMatrix" and "triangularMatrix"
42            * R/gTMatrix.R (.ind.prep): new function;
43                    Logical and character indexing now work too.
44            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
45            * tests/indexing.R: new, including *.Rout.save
46            * tests/dgTMatrix.R: new
47    
48    2005-08-29  Douglas Bates  <bates@wisc.edu>
49    
50            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
51            indicator pos not being updated.  Also enforced upper triangular
52            for symmetric case.  Need to coerce edges component of elements of
53            edge list - grr! (Why don't they define their classes cleanly?)
54    
55    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/Matrix.R:  added first "[<-" methods; not yet functional
58            * R/denseMatrix.R: dito
59            * man/Subassign-methods.Rd: new help file for these
60    
61    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * DESCRIPTION (Version): 0.98-6
64    
65            * R/denseMatrix.R: new file for "[" fallback methods for all dense
66            matrices.
67    
68    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
71                    as( <logical>, "matrix")
72    
73            * R/pMatrix.R: coercion to "lgTMatrix"
74    
75            * R/gTMatrix.R: new virtual class to define "[" methods for.
76            * man/gTMatrix-class.Rd:
77            * General slight re-organization of where "[" methods are defined.
78              more to come.
79    
80    2005-08-18  Douglas Bates  <bates@wisc.edu>
81    
82            * DESCRIPTION (Version): 0.98-5  released to CRAN
83    
84            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
85            * .....
86    
87    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
88    
89            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
90            or glmer objects.
91    
92    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
95    
96    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
97    
98            * R/HBMM.R: finish re-writing R-only code.
99    
100    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
101    
102            * man/externalFormats.Rd: move documentation for writeHB and
103            writeMM here.
104    
105            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
106            (suggested by Paul Roecker).
107    
108            * tests/validObj.R (assertError): Comment out test that is failing
109            after recent changes in r-devel.
110    
111    
112    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/AllClass.R: intermediate virtual class "denseMatrix"
115            * man/denseMatrix-class.Rd
116            * NAMESPACE: export it, and also export
117            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
118    
119    2005-08-10  Douglas Bates  <bates@wisc.edu>
120    
121            * DESCRIPTION (Version): 0.98-3 to CRAN
122    
123            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
124            matrix_solve code (which was really, really wrong).
125    
126    2005-08-07  Douglas Bates  <bates@wisc.edu>
127    
128            * DESCRIPTION (Version): 0.98-2
129    
130            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
131    
132            * R/lmer.R (abbrvNms): new
133            * R/lmer.R (mcmcsamp): allow transformed parameters
134            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
135            for the Harwell-Boeing and the MatrixMarket formats.
136    
137    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * man/dtrMatrix-class.Rd: add examples
140            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
141    
142            * TODO: note the dtpMatrix (docu) bug
143    
144            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
145            in order to ensure that new as.matrix() is used by old functions,
146            e.g., svd(), qr(), eigen(), dist(),..;
147                  apply(), also matplot() or pairs().
148    
149    
150    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
153              add comments about 'control' / lmerControl() arguments
154    
155    2005-07-27  Douglas Bates  <bates@wisc.edu>
156    
157            * man/sleepstudy.Rd: Added the sleep data set.
158            * DESCRIPTION (Version): 0.98-1  released to CRAN
159    
160    2005-07-12  Douglas Bates  <bates@wisc.edu>
161            * man/sleepstudy.Rd: Added the sleep data set.
162    
163            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
164            .Call calls that were producing spurious output.
165    
166    2005-07-05  Douglas Bates  <bates@wisc.edu>
167    
168            * R/lmer.R (lmer): stored updated variance component estimates in
169            mer object for the generalized model.  (Bug reported by Renaud
170            Lancelot).
171    
172    2005-07-03  Douglas Bates  <bates@wisc.edu>
173    
174            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
175            unidimensional case.
176    
177    2005-06-08  Douglas Bates  <bates@wisc.edu>
178    
179            * DESCRIPTION (Version): 0.96-1
180    
181            * moved  lmer-class' R and C code moved from lme4 to here
182    
183    2005-06-04  Douglas Bates  <bates@wisc.edu>
184    
185            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
186            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
187    
188    2005-06-02  Douglas Bates  <bates@wisc.edu>
189    
190            * src/Makefile.win: Forgot to update this when Makefile changed.
191    
192    2005-05-11  Douglas Bates  <bates@wisc.edu>
193    
194            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
195            bug reported by Kurt Hornik and Michael Hahsler.
196    
197    2005-05-10  Douglas Bates  <bates@wisc.edu>
198    
199            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
200            logical sparse matrices.  These will also be used in the symbolic
201            analysis for lmer objects.
202    
203            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
204            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
205    
206    2005-05-06  Douglas Bates  <bates@wisc.edu>
207    
208            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
209            colMeans, colSums, rowMeans and rowSums.
210    
211    2005-04-18  Douglas Bates  <bates@wisc.edu>
212    
213            * src/lgCMatrix.[ch]: code for _validate method and stub for
214            multiplication operation.
215    
216            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
217            to dgetrs.
218    
219            * src/init.c: Fix cut-and-paste error in definition of
220            dgeMatrix_matrix_solve
221    
222            * src/{many files}: Tighten code by using ALLOC_SLOT.
223    
224    2005-04-15  Douglas Bates  <bates@wisc.edu>
225    
226            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
227    
228            * DESCRIPTION: Eliminate import of stats.
229    
230    
231    2005-04-06  Douglas Bates  <bates@wisc.edu>
232    
233            * R/AllClass.R : add logical sparse matrix classes
234    
235    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/dgTMatrix.R: add "[" method for triplet matrices
238            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
239    
240    2005-03-31  Douglas Bates  <bates@wisc.edu>
241    
242            * DESCRIPTION (Version): release 0.95-5 to CRAN
243    
244            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
245            * R/sparseMatrix.R: %*%, crossprod()
246            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
247            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
248            * src/lmer.c (lmer_fitted): fix thinko
249    
250    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * R/AllClass.R: add two virtual sparse classes ``on top''
253    
254    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
257                    correspondingly fix examples and tests/ since new()
258                    doesn't work for virtual classes.
259    
260    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/Matrix.R (as.matrix): method and one for unname()
263            * tests/dpoMatrix.R: tests should now be less platform dependent;
264              also run for R 2.1.0; using as.matrix()
265    
266    2005-03-15  Douglas Bates  <bates@wisc.edu>
267    
268            * R/pMatrix.R: "pMatrix" class added
269            * ....
270    
271    2005-03-14  Douglas Bates  <bates@wisc.edu>
272    
273            * R/dtpMatrix.R: Add unpack method and an example.
274    
275            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
276            of general symmetric matrices and associated S4 methods.
277    
278    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
279            +
280    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/dgeMatrix.R (setAs): and many other files: more coercion,
283              crossprod() and "%*%" methods added; tests, too.
284            * tests/matprod.R: new, for testing these
285    
286    2005-03-03  Douglas Bates  <bates@wisc.edu>
287    
288            * src/lmer.c (lmer_fitted): Added.
289    
290    2005-03-02  Douglas Bates  <bates@wisc.edu>
291    
292            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
293    
294    2005-02-28  Douglas Bates  <bates@wisc.edu>
295    
296            * src/*.c,po/,inst/po: Internationalization and localization of
297            the package.
298    
299            * src/ldl.[ch]: Removed these as their contents are referenced in the
300            R_ldl.c file.
301    
302            * src/flame.[ch]: Removed these source files.
303    
304            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
305    
306            * src/LU.[ch],src/init.c: absorb in factorizations
307    
308            * src/Mutils.h: prepare for internationalization
309    
310            * src/cblas.h: move the enum definitions to Mutils.h and remove
311            this file
312    
313    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
316    
317            * R/dtrMatrix.R: fix t() method
318    
319            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
320            * NAMESPACE: export them (and import generics from "methods")
321            * tests/group-methods.R : and test them.
322    
323            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
324            border case
325    
326    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
327    
328            * DESCRIPTION (Version): 0.95-2  released to CRAN
329    
330            * src/dgBCMatrix.c:
331            * src/lmer.c: many changes
332            * ...
333    
334    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/Matrix.R: add more sophisticated show() method.
337    
338    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
339    
340            * */* : almost complete reorganization of classes.
341    
342    2005-01-26  Douglas Bates  <bates@wisc.edu>
343    
344            * R/AllGeneric.R: Added matrix exponential generic expm and a method
345            for the geMatrix class.
346    
347    2005-01-24  Douglas Bates  <bates@wisc.edu>
348    
349            * src/Makefile (clean): Remove *.a and *.so
350    
351            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
352    
353    2005-01-23  Douglas Bates  <bates@wisc.edu>
354    
355            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
356            had an effect in cases with more than 2 grouping factors.
357    
358    2005-01-03  Douglas Bates  <bates@wisc.edu>
359    
360            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
361    
362    2004-12-23  Douglas Bates  <bates@wisc.edu>
363    
364            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
365            and R_useDynamicSymbols (suggested by B.D.Ripley).
366    
367    2004-12-14  Douglas Bates  <bates@wisc.edu>
368    
369            * R/sscMatrix.R: Add determinant methods
370    
371            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
372            for tripletMatrix to matrix.
373    
374    2004-12-13  Douglas Bates  <bates@wisc.edu>
375    
376            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
377            no longer used.
378    
379          * 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
380          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 383 
383          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
384          Fixes part but not all of #15.          Fixes part but not all of #15.
385    
386  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
387    
388          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
389          scalar grouping factors corrected.          scalar grouping factors corrected.
390    
391  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
392    
393          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
394    
395  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
396    
397          * 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
398          .h file can be included.          .h file can be included.
399    
400  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
401    
402          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
403          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
404    
405          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
406    
407  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
408    
409          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
410    
411  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
412    
413          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
414    
415  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
416    
417          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
418    
419  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
420    
421          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
422    
423  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
424    
425          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
426          routines.          routines.
427    
428  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
429    
430          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
431    
432  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
433    
434          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
435    

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