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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 854, Tue Aug 16 18:05:01 2005 UTC
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1  2004-11-16  Douglas Bates  <bates@bates1-home>  2005-08-15  Douglas Bates  <bates@localhost.localdomain>
2    
3            * man/externalFormats.Rd: move documentation for writeHB and
4            writeMM here.
5    
6            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
7            (suggested by Paul Roecker).
8    
9            * tests/validObj.R (assertError): Comment out test that is failing
10            after recent changes in r-devel.
11    
12    
13    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/AllClass.R: intermediate virtual class "denseMatrix"
16            * man/denseMatrix-class.Rd
17            * NAMESPACE: export it, and also export
18            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
19    
20    2005-08-10  Douglas Bates  <bates@wisc.edu>
21    
22            * DESCRIPTION (Version): 0.98-3 to CRAN
23    
24            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
25            matrix_solve code (which was really, really wrong).
26    
27    2005-08-07  Douglas Bates  <bates@wisc.edu>
28    
29            * DESCRIPTION (Version): 0.98-2
30    
31            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
32    
33            * R/lmer.R (abbrvNms): new
34            * R/lmer.R (mcmcsamp): allow transformed parameters
35            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
36            for the Harwell-Boeing and the MatrixMarket formats.
37    
38    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * man/dtrMatrix-class.Rd: add examples
41            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
42    
43            * TODO: note the dtpMatrix (docu) bug
44    
45            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
46            in order to ensure that new as.matrix() is used by old functions,
47            e.g., svd(), qr(), eigen(), dist(),..;
48                  apply(), also matplot() or pairs().
49    
50    
51    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
54              add comments about 'control' / lmerControl() arguments
55    
56    2005-07-27  Douglas Bates  <bates@wisc.edu>
57    
58            * man/sleepstudy.Rd: Added the sleep data set.
59            * DESCRIPTION (Version): 0.98-1  released to CRAN
60    
61    2005-07-12  Douglas Bates  <bates@wisc.edu>
62            * man/sleepstudy.Rd: Added the sleep data set.
63    
64            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
65            .Call calls that were producing spurious output.
66    
67    2005-07-05  Douglas Bates  <bates@wisc.edu>
68    
69            * R/lmer.R (lmer): stored updated variance component estimates in
70            mer object for the generalized model.  (Bug reported by Renaud
71            Lancelot).
72    
73    2005-07-03  Douglas Bates  <bates@wisc.edu>
74    
75            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
76            unidimensional case.
77    
78    2005-06-08  Douglas Bates  <bates@wisc.edu>
79    
80            * DESCRIPTION (Version): 0.96-1
81    
82            * moved  lmer-class' R and C code moved from lme4 to here
83    
84    2005-06-04  Douglas Bates  <bates@wisc.edu>
85    
86            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
87            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
88    
89    2005-06-02  Douglas Bates  <bates@wisc.edu>
90    
91            * src/Makefile.win: Forgot to update this when Makefile changed.
92    
93    2005-05-11  Douglas Bates  <bates@wisc.edu>
94    
95            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
96            bug reported by Kurt Hornik and Michael Hahsler.
97    
98    2005-05-10  Douglas Bates  <bates@wisc.edu>
99    
100            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
101            logical sparse matrices.  These will also be used in the symbolic
102            analysis for lmer objects.
103    
104            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
105            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
106    
107    2005-05-06  Douglas Bates  <bates@wisc.edu>
108    
109            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
110            colMeans, colSums, rowMeans and rowSums.
111    
112    2005-04-18  Douglas Bates  <bates@wisc.edu>
113    
114            * src/lgCMatrix.[ch]: code for _validate method and stub for
115            multiplication operation.
116    
117            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
118            to dgetrs.
119    
120            * src/init.c: Fix cut-and-paste error in definition of
121            dgeMatrix_matrix_solve
122    
123            * src/{many files}: Tighten code by using ALLOC_SLOT.
124    
125    2005-04-15  Douglas Bates  <bates@wisc.edu>
126    
127            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
128    
129            * DESCRIPTION: Eliminate import of stats.
130    
131    
132    2005-04-06  Douglas Bates  <bates@wisc.edu>
133    
134            * R/AllClass.R : add logical sparse matrix classes
135    
136    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/dgTMatrix.R: add "[" method for triplet matrices
139            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
140    
141    2005-03-31  Douglas Bates  <bates@wisc.edu>
142    
143            * DESCRIPTION (Version): release 0.95-5 to CRAN
144    
145            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
146            * R/sparseMatrix.R: %*%, crossprod()
147            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
148            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
149            * src/lmer.c (lmer_fitted): fix thinko
150    
151    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/AllClass.R: add two virtual sparse classes ``on top''
154    
155    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
158                    correspondingly fix examples and tests/ since new()
159                    doesn't work for virtual classes.
160    
161    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/Matrix.R (as.matrix): method and one for unname()
164            * tests/dpoMatrix.R: tests should now be less platform dependent;
165              also run for R 2.1.0; using as.matrix()
166    
167    2005-03-15  Douglas Bates  <bates@wisc.edu>
168    
169            * R/pMatrix.R: "pMatrix" class added
170            * ....
171    
172    2005-03-14  Douglas Bates  <bates@wisc.edu>
173    
174            * R/dtpMatrix.R: Add unpack method and an example.
175    
176            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
177            of general symmetric matrices and associated S4 methods.
178    
179    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
180            +
181    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/dgeMatrix.R (setAs): and many other files: more coercion,
184              crossprod() and "%*%" methods added; tests, too.
185            * tests/matprod.R: new, for testing these
186    
187    2005-03-03  Douglas Bates  <bates@wisc.edu>
188    
189            * src/lmer.c (lmer_fitted): Added.
190    
191    2005-03-02  Douglas Bates  <bates@wisc.edu>
192    
193            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
194    
195    2005-02-28  Douglas Bates  <bates@wisc.edu>
196    
197            * src/*.c,po/,inst/po: Internationalization and localization of
198            the package.
199    
200            * src/ldl.[ch]: Removed these as their contents are referenced in the
201            R_ldl.c file.
202    
203            * src/flame.[ch]: Removed these source files.
204    
205            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
206    
207            * src/LU.[ch],src/init.c: absorb in factorizations
208    
209            * src/Mutils.h: prepare for internationalization
210    
211            * src/cblas.h: move the enum definitions to Mutils.h and remove
212            this file
213    
214    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
217    
218            * R/dtrMatrix.R: fix t() method
219    
220            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
221            * NAMESPACE: export them (and import generics from "methods")
222            * tests/group-methods.R : and test them.
223    
224            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
225            border case
226    
227    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
228    
229            * DESCRIPTION (Version): 0.95-2  released to CRAN
230    
231            * src/dgBCMatrix.c:
232            * src/lmer.c: many changes
233            * ...
234    
235    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Matrix.R: add more sophisticated show() method.
238    
239    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
240    
241            * */* : almost complete reorganization of classes.
242    
243    2005-01-26  Douglas Bates  <bates@wisc.edu>
244    
245            * R/AllGeneric.R: Added matrix exponential generic expm and a method
246            for the geMatrix class.
247    
248    2005-01-24  Douglas Bates  <bates@wisc.edu>
249    
250            * src/Makefile (clean): Remove *.a and *.so
251    
252            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
253    
254    2005-01-23  Douglas Bates  <bates@wisc.edu>
255    
256            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
257            had an effect in cases with more than 2 grouping factors.
258    
259    2005-01-03  Douglas Bates  <bates@wisc.edu>
260    
261            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
262    
263    2004-12-23  Douglas Bates  <bates@wisc.edu>
264    
265            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
266            and R_useDynamicSymbols (suggested by B.D.Ripley).
267    
268    2004-12-14  Douglas Bates  <bates@wisc.edu>
269    
270            * R/sscMatrix.R: Add determinant methods
271    
272            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
273            for tripletMatrix to matrix.
274    
275    2004-12-13  Douglas Bates  <bates@wisc.edu>
276    
277            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
278            no longer used.
279    
280            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
281            with dynamic allocation of scratch arrays.
282    
283            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
284            for multivariate random effects with multiple grouping factors.
285            Fixes part but not all of #15.
286    
287    2004-12-03  Douglas Bates  <bates@wisc.edu>
288    
289            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
290            scalar grouping factors corrected.
291    
292    2004-11-29  Douglas Bates  <bates@wisc.edu>
293    
294            * src/bCrosstab.c: remove diag_update which is no longer used
295    
296    2004-11-16  Douglas Bates  <bates@wisc.edu>
297    
298          * 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
299          .h file can be included.          .h file can be included.
300    
301  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
302    
303          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
304          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
305    
306          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
307    
308  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
309    
310          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
311    
312  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
313    
314          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
315    
316  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
317    
318          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
319    
320  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
321    
322          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
323    
324  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
325    
326          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
327          routines.          routines.
328    
329  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
330    
331          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
332    
333  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
334    
335          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
336    

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