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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 886, Wed Aug 31 17:49:47 2005 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R: new "index" class for "[" and "[<-":
4                    First cut at "symmetricMatrix" and "triangularMatrix"
5            * R/gTMatrix.R (.ind.prep): new function;
6                    Logical and character indexing now work too.
7            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
8            * tests/indexing.R: new, including *.Rout.save
9            * tests/dgTMatrix.R: new
10    
11    2005-08-29  Douglas Bates  <bates@wisc.edu>
12    
13            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
14            indicator pos not being updated.  Also enforced upper triangular
15            for symmetric case.  Need to coerce edges component of elements of
16            edge list - grr! (Why don't they define their classes cleanly?)
17    
18    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/Matrix.R:  added first "[<-" methods; not yet functional
21            * R/denseMatrix.R: dito
22            * man/Subassign-methods.Rd: new help file for these
23    
24    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * DESCRIPTION (Version): 0.98-6
27    
28            * R/denseMatrix.R: new file for "[" fallback methods for all dense
29            matrices.
30    
31    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
34                    as( <logical>, "matrix")
35    
36            * R/pMatrix.R: coercion to "lgTMatrix"
37    
38            * R/gTMatrix.R: new virtual class to define "[" methods for.
39            * man/gTMatrix-class.Rd:
40            * General slight re-organization of where "[" methods are defined.
41              more to come.
42    
43    2005-08-18  Douglas Bates  <bates@wisc.edu>
44    
45            * DESCRIPTION (Version): 0.98-5  released to CRAN
46    
47            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
48            * .....
49    
50    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
51    
52            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
53            or glmer objects.
54    
55    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
58    
59    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
60    
61            * R/HBMM.R: finish re-writing R-only code.
62    
63    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
64    
65            * man/externalFormats.Rd: move documentation for writeHB and
66            writeMM here.
67    
68            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
69            (suggested by Paul Roecker).
70    
71            * tests/validObj.R (assertError): Comment out test that is failing
72            after recent changes in r-devel.
73    
74    
75    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/AllClass.R: intermediate virtual class "denseMatrix"
78            * man/denseMatrix-class.Rd
79            * NAMESPACE: export it, and also export
80            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
81    
82    2005-08-10  Douglas Bates  <bates@wisc.edu>
83    
84            * DESCRIPTION (Version): 0.98-3 to CRAN
85    
86            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
87            matrix_solve code (which was really, really wrong).
88    
89    2005-08-07  Douglas Bates  <bates@wisc.edu>
90    
91            * DESCRIPTION (Version): 0.98-2
92    
93            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
94    
95            * R/lmer.R (abbrvNms): new
96            * R/lmer.R (mcmcsamp): allow transformed parameters
97            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
98            for the Harwell-Boeing and the MatrixMarket formats.
99    
100    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * man/dtrMatrix-class.Rd: add examples
103            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
104    
105            * TODO: note the dtpMatrix (docu) bug
106    
107            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
108            in order to ensure that new as.matrix() is used by old functions,
109            e.g., svd(), qr(), eigen(), dist(),..;
110                  apply(), also matplot() or pairs().
111    
112    
113    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
116              add comments about 'control' / lmerControl() arguments
117    
118    2005-07-27  Douglas Bates  <bates@wisc.edu>
119    
120            * man/sleepstudy.Rd: Added the sleep data set.
121            * DESCRIPTION (Version): 0.98-1  released to CRAN
122    
123    2005-07-12  Douglas Bates  <bates@wisc.edu>
124            * man/sleepstudy.Rd: Added the sleep data set.
125    
126            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
127            .Call calls that were producing spurious output.
128    
129    2005-07-05  Douglas Bates  <bates@wisc.edu>
130    
131            * R/lmer.R (lmer): stored updated variance component estimates in
132            mer object for the generalized model.  (Bug reported by Renaud
133            Lancelot).
134    
135    2005-07-03  Douglas Bates  <bates@wisc.edu>
136    
137            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
138            unidimensional case.
139    
140    2005-06-08  Douglas Bates  <bates@wisc.edu>
141    
142            * DESCRIPTION (Version): 0.96-1
143    
144            * moved  lmer-class' R and C code moved from lme4 to here
145    
146    2005-06-04  Douglas Bates  <bates@wisc.edu>
147    
148            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
149            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
150    
151    2005-06-02  Douglas Bates  <bates@wisc.edu>
152    
153            * src/Makefile.win: Forgot to update this when Makefile changed.
154    
155    2005-05-11  Douglas Bates  <bates@wisc.edu>
156    
157            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
158            bug reported by Kurt Hornik and Michael Hahsler.
159    
160    2005-05-10  Douglas Bates  <bates@wisc.edu>
161    
162            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
163            logical sparse matrices.  These will also be used in the symbolic
164            analysis for lmer objects.
165    
166            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
167            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
168    
169    2005-05-06  Douglas Bates  <bates@wisc.edu>
170    
171            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
172            colMeans, colSums, rowMeans and rowSums.
173    
174    2005-04-18  Douglas Bates  <bates@wisc.edu>
175    
176            * src/lgCMatrix.[ch]: code for _validate method and stub for
177            multiplication operation.
178    
179            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
180            to dgetrs.
181    
182            * src/init.c: Fix cut-and-paste error in definition of
183            dgeMatrix_matrix_solve
184    
185            * src/{many files}: Tighten code by using ALLOC_SLOT.
186    
187    2005-04-15  Douglas Bates  <bates@wisc.edu>
188    
189            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
190    
191            * DESCRIPTION: Eliminate import of stats.
192    
193    
194    2005-04-06  Douglas Bates  <bates@wisc.edu>
195    
196            * R/AllClass.R : add logical sparse matrix classes
197    
198    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/dgTMatrix.R: add "[" method for triplet matrices
201            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
202    
203    2005-03-31  Douglas Bates  <bates@wisc.edu>
204    
205            * DESCRIPTION (Version): release 0.95-5 to CRAN
206    
207            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
208            * R/sparseMatrix.R: %*%, crossprod()
209            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
210            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
211            * src/lmer.c (lmer_fitted): fix thinko
212    
213    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/AllClass.R: add two virtual sparse classes ``on top''
216    
217    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
220                    correspondingly fix examples and tests/ since new()
221                    doesn't work for virtual classes.
222    
223    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/Matrix.R (as.matrix): method and one for unname()
226            * tests/dpoMatrix.R: tests should now be less platform dependent;
227              also run for R 2.1.0; using as.matrix()
228    
229    2005-03-15  Douglas Bates  <bates@wisc.edu>
230    
231            * R/pMatrix.R: "pMatrix" class added
232            * ....
233    
234    2005-03-14  Douglas Bates  <bates@wisc.edu>
235    
236            * R/dtpMatrix.R: Add unpack method and an example.
237    
238            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
239            of general symmetric matrices and associated S4 methods.
240    
241    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
242            +
243    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/dgeMatrix.R (setAs): and many other files: more coercion,
246              crossprod() and "%*%" methods added; tests, too.
247            * tests/matprod.R: new, for testing these
248    
249    2005-03-03  Douglas Bates  <bates@wisc.edu>
250    
251            * src/lmer.c (lmer_fitted): Added.
252    
253    2005-03-02  Douglas Bates  <bates@wisc.edu>
254    
255            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
256    
257    2005-02-28  Douglas Bates  <bates@wisc.edu>
258    
259            * src/*.c,po/,inst/po: Internationalization and localization of
260            the package.
261    
262            * src/ldl.[ch]: Removed these as their contents are referenced in the
263            R_ldl.c file.
264    
265            * src/flame.[ch]: Removed these source files.
266    
267            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
268    
269            * src/LU.[ch],src/init.c: absorb in factorizations
270    
271            * src/Mutils.h: prepare for internationalization
272    
273            * src/cblas.h: move the enum definitions to Mutils.h and remove
274            this file
275    
276    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
279    
280            * R/dtrMatrix.R: fix t() method
281    
282            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
283            * NAMESPACE: export them (and import generics from "methods")
284            * tests/group-methods.R : and test them.
285    
286            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
287            border case
288    
289    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
290    
291            * DESCRIPTION (Version): 0.95-2  released to CRAN
292    
293            * src/dgBCMatrix.c:
294            * src/lmer.c: many changes
295            * ...
296    
297    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/Matrix.R: add more sophisticated show() method.
300    
301    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
302    
303            * */* : almost complete reorganization of classes.
304    
305    2005-01-26  Douglas Bates  <bates@wisc.edu>
306    
307            * R/AllGeneric.R: Added matrix exponential generic expm and a method
308            for the geMatrix class.
309    
310    2005-01-24  Douglas Bates  <bates@wisc.edu>
311    
312            * src/Makefile (clean): Remove *.a and *.so
313    
314            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
315    
316    2005-01-23  Douglas Bates  <bates@wisc.edu>
317    
318            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
319            had an effect in cases with more than 2 grouping factors.
320    
321    2005-01-03  Douglas Bates  <bates@wisc.edu>
322    
323            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
324    
325    2004-12-23  Douglas Bates  <bates@wisc.edu>
326    
327            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
328            and R_useDynamicSymbols (suggested by B.D.Ripley).
329    
330    2004-12-14  Douglas Bates  <bates@wisc.edu>
331    
332          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
333    
334          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
335          for tripletMatrix to matrix.          for tripletMatrix to matrix.
336    
337  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
338    
339          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
340          no longer used.          no longer used.
# Line 17  Line 346 
346          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
347          Fixes part but not all of #15.          Fixes part but not all of #15.
348    
349  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
350    
351          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
352          scalar grouping factors corrected.          scalar grouping factors corrected.
353    
354  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
355    
356          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
357    
358  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
359    
360          * 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
361          .h file can be included.          .h file can be included.
362    
363  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
364    
365          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
366          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
367    
368          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
369    
370  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
371    
372          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
373    
374  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
375    
376          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
377    
378  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
379    
380          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
381    
382  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
383    
384          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
385    
386  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
387    
388          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
389          routines.          routines.
390    
391  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
392    
393          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
394    
395  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
396    
397          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
398    

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