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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 948, Wed Sep 28 08:57:56 2005 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/Class+Meth.R: new tests; t(t(m)) == m
4    
5            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
6    
7            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
8            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
9    
10            * R/dspMatrix.R: typo in "t" method
11    
12    2005-09-18  Douglas Bates  <bates@wisc.edu>
13    
14            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
15            * R/Tsparse.R: instead of R/gTMatrix.R
16            * R/Csparse.R: new
17            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
18            * src/Tsparse.c: new; many trivial methods calling cholmod_()
19            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
20                            via cholmod
21    
22    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/Auxiliaries.R (non0ind): new function using new C code
25            * src/dgCMatrix.c (compressed_non_0_ij): new utility
26    
27    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
28    
29            * src/chm_common.h: header file required by all C sources that
30            call CHOLMOD functions.  It defines a cholmod_common structure
31            called 'c' whose address is passed as the last argument to
32            (virtually) every CHOLMOD function.
33    
34            * src/Pattern.c: Simple example of the use of CHOLMOD.
35    
36            * src/init.c: initialize and finalize the cholmod_common structure.
37    
38            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
39            LDL and CCOLAMD from the U. of Florida sparse matrix library.
40    
41    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * inst/test-tools.R: new file collecting the utility functions used
44                    in ./tests/*.R
45    
46            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
47            * R/Matrix.R (cbind2): methods for NULL and missing
48    
49    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * R/AllClass.R: new "index" class for "[" and "[<-":
52                    First cut at "symmetricMatrix" and "triangularMatrix"
53            * R/gTMatrix.R (.ind.prep): new function;
54                    Logical and character indexing now work too.
55            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
56            * tests/indexing.R: new, including *.Rout.save
57            * tests/dgTMatrix.R: new
58    
59    2005-08-29  Douglas Bates  <bates@wisc.edu>
60    
61            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
62            indicator pos not being updated.  Also enforced upper triangular
63            for symmetric case.  Need to coerce edges component of elements of
64            edge list - grr! (Why don't they define their classes cleanly?)
65    
66    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/Matrix.R:  added first "[<-" methods; not yet functional
69            * R/denseMatrix.R: dito
70            * man/Subassign-methods.Rd: new help file for these
71    
72    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * DESCRIPTION (Version): 0.98-6
75    
76            * R/denseMatrix.R: new file for "[" fallback methods for all dense
77            matrices.
78    
79    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
82                    as( <logical>, "matrix")
83    
84            * R/pMatrix.R: coercion to "lgTMatrix"
85    
86            * R/gTMatrix.R: new virtual class to define "[" methods for.
87            * man/gTMatrix-class.Rd:
88            * General slight re-organization of where "[" methods are defined.
89              more to come.
90    
91    2005-08-18  Douglas Bates  <bates@wisc.edu>
92    
93            * DESCRIPTION (Version): 0.98-5  released to CRAN
94    
95            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
96            * .....
97    
98    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
99    
100            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
101            or glmer objects.
102    
103    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
106    
107    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
108    
109            * R/HBMM.R: finish re-writing R-only code.
110    
111    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
112    
113            * man/externalFormats.Rd: move documentation for writeHB and
114            writeMM here.
115    
116            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
117            (suggested by Paul Roecker).
118    
119            * tests/validObj.R (assertError): Comment out test that is failing
120            after recent changes in r-devel.
121    
122    
123    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/AllClass.R: intermediate virtual class "denseMatrix"
126            * man/denseMatrix-class.Rd
127            * NAMESPACE: export it, and also export
128            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
129    
130    2005-08-10  Douglas Bates  <bates@wisc.edu>
131    
132            * DESCRIPTION (Version): 0.98-3 to CRAN
133    
134            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
135            matrix_solve code (which was really, really wrong).
136    
137    2005-08-07  Douglas Bates  <bates@wisc.edu>
138    
139            * DESCRIPTION (Version): 0.98-2
140    
141            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
142    
143            * R/lmer.R (abbrvNms): new
144            * R/lmer.R (mcmcsamp): allow transformed parameters
145            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
146            for the Harwell-Boeing and the MatrixMarket formats.
147    
148    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * man/dtrMatrix-class.Rd: add examples
151            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
152    
153            * TODO: note the dtpMatrix (docu) bug
154    
155            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
156            in order to ensure that new as.matrix() is used by old functions,
157            e.g., svd(), qr(), eigen(), dist(),..;
158                  apply(), also matplot() or pairs().
159    
160    
161    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
164              add comments about 'control' / lmerControl() arguments
165    
166    2005-07-27  Douglas Bates  <bates@wisc.edu>
167    
168            * man/sleepstudy.Rd: Added the sleep data set.
169            * DESCRIPTION (Version): 0.98-1  released to CRAN
170    
171    2005-07-12  Douglas Bates  <bates@wisc.edu>
172            * man/sleepstudy.Rd: Added the sleep data set.
173    
174            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
175            .Call calls that were producing spurious output.
176    
177    2005-07-05  Douglas Bates  <bates@wisc.edu>
178    
179            * R/lmer.R (lmer): stored updated variance component estimates in
180            mer object for the generalized model.  (Bug reported by Renaud
181            Lancelot).
182    
183    2005-07-03  Douglas Bates  <bates@wisc.edu>
184    
185            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
186            unidimensional case.
187    
188    2005-06-08  Douglas Bates  <bates@wisc.edu>
189    
190            * DESCRIPTION (Version): 0.96-1
191    
192            * moved  lmer-class' R and C code moved from lme4 to here
193    
194    2005-06-04  Douglas Bates  <bates@wisc.edu>
195    
196            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
197            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
198    
199    2005-06-02  Douglas Bates  <bates@wisc.edu>
200    
201            * src/Makefile.win: Forgot to update this when Makefile changed.
202    
203    2005-05-11  Douglas Bates  <bates@wisc.edu>
204    
205            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
206            bug reported by Kurt Hornik and Michael Hahsler.
207    
208    2005-05-10  Douglas Bates  <bates@wisc.edu>
209    
210            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
211            logical sparse matrices.  These will also be used in the symbolic
212            analysis for lmer objects.
213    
214            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
215            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
216    
217    2005-05-06  Douglas Bates  <bates@wisc.edu>
218    
219            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
220            colMeans, colSums, rowMeans and rowSums.
221    
222    2005-04-18  Douglas Bates  <bates@wisc.edu>
223    
224            * src/lgCMatrix.[ch]: code for _validate method and stub for
225            multiplication operation.
226    
227            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
228            to dgetrs.
229    
230            * src/init.c: Fix cut-and-paste error in definition of
231            dgeMatrix_matrix_solve
232    
233            * src/{many files}: Tighten code by using ALLOC_SLOT.
234    
235    2005-04-15  Douglas Bates  <bates@wisc.edu>
236    
237            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
238    
239            * DESCRIPTION: Eliminate import of stats.
240    
241    
242    2005-04-06  Douglas Bates  <bates@wisc.edu>
243    
244            * R/AllClass.R : add logical sparse matrix classes
245    
246    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/dgTMatrix.R: add "[" method for triplet matrices
249            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
250    
251    2005-03-31  Douglas Bates  <bates@wisc.edu>
252    
253            * DESCRIPTION (Version): release 0.95-5 to CRAN
254    
255            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
256            * R/sparseMatrix.R: %*%, crossprod()
257            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
258            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
259            * src/lmer.c (lmer_fitted): fix thinko
260    
261    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/AllClass.R: add two virtual sparse classes ``on top''
264    
265    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
268                    correspondingly fix examples and tests/ since new()
269                    doesn't work for virtual classes.
270    
271    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/Matrix.R (as.matrix): method and one for unname()
274            * tests/dpoMatrix.R: tests should now be less platform dependent;
275              also run for R 2.1.0; using as.matrix()
276    
277    2005-03-15  Douglas Bates  <bates@wisc.edu>
278    
279            * R/pMatrix.R: "pMatrix" class added
280            * ....
281    
282    2005-03-14  Douglas Bates  <bates@wisc.edu>
283    
284            * R/dtpMatrix.R: Add unpack method and an example.
285    
286            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
287            of general symmetric matrices and associated S4 methods.
288    
289    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
290            +
291    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/dgeMatrix.R (setAs): and many other files: more coercion,
294              crossprod() and "%*%" methods added; tests, too.
295            * tests/matprod.R: new, for testing these
296    
297    2005-03-03  Douglas Bates  <bates@wisc.edu>
298    
299            * src/lmer.c (lmer_fitted): Added.
300    
301    2005-03-02  Douglas Bates  <bates@wisc.edu>
302    
303            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
304    
305    2005-02-28  Douglas Bates  <bates@wisc.edu>
306    
307            * src/*.c,po/,inst/po: Internationalization and localization of
308            the package.
309    
310            * src/ldl.[ch]: Removed these as their contents are referenced in the
311            R_ldl.c file.
312    
313            * src/flame.[ch]: Removed these source files.
314    
315            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
316    
317            * src/LU.[ch],src/init.c: absorb in factorizations
318    
319            * src/Mutils.h: prepare for internationalization
320    
321            * src/cblas.h: move the enum definitions to Mutils.h and remove
322            this file
323    
324    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
327    
328            * R/dtrMatrix.R: fix t() method
329    
330            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
331            * NAMESPACE: export them (and import generics from "methods")
332            * tests/group-methods.R : and test them.
333    
334            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
335            border case
336    
337    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
338    
339            * DESCRIPTION (Version): 0.95-2  released to CRAN
340    
341            * src/dgBCMatrix.c:
342            * src/lmer.c: many changes
343            * ...
344    
345    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/Matrix.R: add more sophisticated show() method.
348    
349    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
350    
351            * */* : almost complete reorganization of classes.
352    
353    2005-01-26  Douglas Bates  <bates@wisc.edu>
354    
355            * R/AllGeneric.R: Added matrix exponential generic expm and a method
356            for the geMatrix class.
357    
358    2005-01-24  Douglas Bates  <bates@wisc.edu>
359    
360            * src/Makefile (clean): Remove *.a and *.so
361    
362            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
363    
364    2005-01-23  Douglas Bates  <bates@wisc.edu>
365    
366            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
367            had an effect in cases with more than 2 grouping factors.
368    
369    2005-01-03  Douglas Bates  <bates@wisc.edu>
370    
371            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
372    
373    2004-12-23  Douglas Bates  <bates@wisc.edu>
374    
375            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
376            and R_useDynamicSymbols (suggested by B.D.Ripley).
377    
378    2004-12-14  Douglas Bates  <bates@wisc.edu>
379    
380          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
381    
382          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
383          for tripletMatrix to matrix.          for tripletMatrix to matrix.
384    
385  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
386    
387          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
388          no longer used.          no longer used.
# Line 17  Line 394 
394          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
395          Fixes part but not all of #15.          Fixes part but not all of #15.
396    
397  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
398    
399          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
400          scalar grouping factors corrected.          scalar grouping factors corrected.
401    
402  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
403    
404          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
405    
406  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
407    
408          * 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
409          .h file can be included.          .h file can be included.
410    
411  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
412    
413          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
414          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
415    
416          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
417    
418  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
419    
420          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
421    
422  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
423    
424          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
425    
426  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
427    
428          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
429    
430  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
431    
432          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
433    
434  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
435    
436          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
437          routines.          routines.
438    
439  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
440    
441          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
442    
443  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
444    
445          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
446    

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