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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 917, Thu Sep 15 18:03:55 2005 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2005-09-15  Douglas Bates  <bates@localhost.localdomain>
2    
3            * src/chm_common.h: header file required by all C sources that
4            call CHOLMOD functions.  It defines a cholmod_common structure
5            called 'c' whose address is passed as the last argument to
6            (virtually) every CHOLMOD function.
7    
8            * src/Pattern.c: Simple example of the use of CHOLMOD.
9    
10            * src/init.c: initialize and finalize the cholmod_common structure.
11    
12            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
13            LDL and CCOLAMD from the U. of Florida sparse matrix library.
14    
15    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * inst/test-tools.R: new file collecting the utility functions used
18                    in ./tests/*.R
19    
20            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
21            * R/Matrix.R (cbind2): methods for NULL and missing
22    
23    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/AllClass.R: new "index" class for "[" and "[<-":
26                    First cut at "symmetricMatrix" and "triangularMatrix"
27            * R/gTMatrix.R (.ind.prep): new function;
28                    Logical and character indexing now work too.
29            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
30            * tests/indexing.R: new, including *.Rout.save
31            * tests/dgTMatrix.R: new
32    
33    2005-08-29  Douglas Bates  <bates@wisc.edu>
34    
35            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
36            indicator pos not being updated.  Also enforced upper triangular
37            for symmetric case.  Need to coerce edges component of elements of
38            edge list - grr! (Why don't they define their classes cleanly?)
39    
40    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/Matrix.R:  added first "[<-" methods; not yet functional
43            * R/denseMatrix.R: dito
44            * man/Subassign-methods.Rd: new help file for these
45    
46    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * DESCRIPTION (Version): 0.98-6
49    
50            * R/denseMatrix.R: new file for "[" fallback methods for all dense
51            matrices.
52    
53    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
56                    as( <logical>, "matrix")
57    
58            * R/pMatrix.R: coercion to "lgTMatrix"
59    
60            * R/gTMatrix.R: new virtual class to define "[" methods for.
61            * man/gTMatrix-class.Rd:
62            * General slight re-organization of where "[" methods are defined.
63              more to come.
64    
65    2005-08-18  Douglas Bates  <bates@wisc.edu>
66    
67            * DESCRIPTION (Version): 0.98-5  released to CRAN
68    
69            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
70            * .....
71    
72    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
73    
74            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
75            or glmer objects.
76    
77    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
80    
81    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
82    
83            * R/HBMM.R: finish re-writing R-only code.
84    
85    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
86    
87            * man/externalFormats.Rd: move documentation for writeHB and
88            writeMM here.
89    
90            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
91            (suggested by Paul Roecker).
92    
93            * tests/validObj.R (assertError): Comment out test that is failing
94            after recent changes in r-devel.
95    
96    
97    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/AllClass.R: intermediate virtual class "denseMatrix"
100            * man/denseMatrix-class.Rd
101            * NAMESPACE: export it, and also export
102            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
103    
104    2005-08-10  Douglas Bates  <bates@wisc.edu>
105    
106            * DESCRIPTION (Version): 0.98-3 to CRAN
107    
108            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
109            matrix_solve code (which was really, really wrong).
110    
111    2005-08-07  Douglas Bates  <bates@wisc.edu>
112    
113            * DESCRIPTION (Version): 0.98-2
114    
115            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
116    
117            * R/lmer.R (abbrvNms): new
118            * R/lmer.R (mcmcsamp): allow transformed parameters
119            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
120            for the Harwell-Boeing and the MatrixMarket formats.
121    
122    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * man/dtrMatrix-class.Rd: add examples
125            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
126    
127            * TODO: note the dtpMatrix (docu) bug
128    
129            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
130            in order to ensure that new as.matrix() is used by old functions,
131            e.g., svd(), qr(), eigen(), dist(),..;
132                  apply(), also matplot() or pairs().
133    
134    
135    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
138              add comments about 'control' / lmerControl() arguments
139    
140    2005-07-27  Douglas Bates  <bates@wisc.edu>
141    
142            * man/sleepstudy.Rd: Added the sleep data set.
143            * DESCRIPTION (Version): 0.98-1  released to CRAN
144    
145    2005-07-12  Douglas Bates  <bates@wisc.edu>
146            * man/sleepstudy.Rd: Added the sleep data set.
147    
148            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
149            .Call calls that were producing spurious output.
150    
151    2005-07-05  Douglas Bates  <bates@wisc.edu>
152    
153            * R/lmer.R (lmer): stored updated variance component estimates in
154            mer object for the generalized model.  (Bug reported by Renaud
155            Lancelot).
156    
157    2005-07-03  Douglas Bates  <bates@wisc.edu>
158    
159            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
160            unidimensional case.
161    
162    2005-06-08  Douglas Bates  <bates@wisc.edu>
163    
164            * DESCRIPTION (Version): 0.96-1
165    
166            * moved  lmer-class' R and C code moved from lme4 to here
167    
168    2005-06-04  Douglas Bates  <bates@wisc.edu>
169    
170            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
171            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
172    
173    2005-06-02  Douglas Bates  <bates@wisc.edu>
174    
175            * src/Makefile.win: Forgot to update this when Makefile changed.
176    
177    2005-05-11  Douglas Bates  <bates@wisc.edu>
178    
179            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
180            bug reported by Kurt Hornik and Michael Hahsler.
181    
182    2005-05-10  Douglas Bates  <bates@wisc.edu>
183    
184            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
185            logical sparse matrices.  These will also be used in the symbolic
186            analysis for lmer objects.
187    
188            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
189            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
190    
191    2005-05-06  Douglas Bates  <bates@wisc.edu>
192    
193            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
194            colMeans, colSums, rowMeans and rowSums.
195    
196    2005-04-18  Douglas Bates  <bates@wisc.edu>
197    
198            * src/lgCMatrix.[ch]: code for _validate method and stub for
199            multiplication operation.
200    
201            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
202            to dgetrs.
203    
204            * src/init.c: Fix cut-and-paste error in definition of
205            dgeMatrix_matrix_solve
206    
207            * src/{many files}: Tighten code by using ALLOC_SLOT.
208    
209    2005-04-15  Douglas Bates  <bates@wisc.edu>
210    
211            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
212    
213            * DESCRIPTION: Eliminate import of stats.
214    
215    
216    2005-04-06  Douglas Bates  <bates@wisc.edu>
217    
218            * R/AllClass.R : add logical sparse matrix classes
219    
220    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/dgTMatrix.R: add "[" method for triplet matrices
223            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
224    
225    2005-03-31  Douglas Bates  <bates@wisc.edu>
226    
227            * DESCRIPTION (Version): release 0.95-5 to CRAN
228    
229            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
230            * R/sparseMatrix.R: %*%, crossprod()
231            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
232            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
233            * src/lmer.c (lmer_fitted): fix thinko
234    
235    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/AllClass.R: add two virtual sparse classes ``on top''
238    
239    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
242                    correspondingly fix examples and tests/ since new()
243                    doesn't work for virtual classes.
244    
245    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Matrix.R (as.matrix): method and one for unname()
248            * tests/dpoMatrix.R: tests should now be less platform dependent;
249              also run for R 2.1.0; using as.matrix()
250    
251    2005-03-15  Douglas Bates  <bates@wisc.edu>
252    
253            * R/pMatrix.R: "pMatrix" class added
254            * ....
255    
256    2005-03-14  Douglas Bates  <bates@wisc.edu>
257    
258            * R/dtpMatrix.R: Add unpack method and an example.
259    
260            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
261            of general symmetric matrices and associated S4 methods.
262    
263    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
264            +
265    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/dgeMatrix.R (setAs): and many other files: more coercion,
268              crossprod() and "%*%" methods added; tests, too.
269            * tests/matprod.R: new, for testing these
270    
271    2005-03-03  Douglas Bates  <bates@wisc.edu>
272    
273            * src/lmer.c (lmer_fitted): Added.
274    
275    2005-03-02  Douglas Bates  <bates@wisc.edu>
276    
277            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
278    
279    2005-02-28  Douglas Bates  <bates@wisc.edu>
280    
281            * src/*.c,po/,inst/po: Internationalization and localization of
282            the package.
283    
284            * src/ldl.[ch]: Removed these as their contents are referenced in the
285            R_ldl.c file.
286    
287            * src/flame.[ch]: Removed these source files.
288    
289            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
290    
291            * src/LU.[ch],src/init.c: absorb in factorizations
292    
293            * src/Mutils.h: prepare for internationalization
294    
295            * src/cblas.h: move the enum definitions to Mutils.h and remove
296            this file
297    
298    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
301    
302            * R/dtrMatrix.R: fix t() method
303    
304            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
305            * NAMESPACE: export them (and import generics from "methods")
306            * tests/group-methods.R : and test them.
307    
308            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
309            border case
310    
311    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
312    
313            * DESCRIPTION (Version): 0.95-2  released to CRAN
314    
315            * src/dgBCMatrix.c:
316            * src/lmer.c: many changes
317            * ...
318    
319    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Matrix.R: add more sophisticated show() method.
322    
323    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
324    
325            * */* : almost complete reorganization of classes.
326    
327    2005-01-26  Douglas Bates  <bates@wisc.edu>
328    
329            * R/AllGeneric.R: Added matrix exponential generic expm and a method
330            for the geMatrix class.
331    
332    2005-01-24  Douglas Bates  <bates@wisc.edu>
333    
334            * src/Makefile (clean): Remove *.a and *.so
335    
336            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
337    
338    2005-01-23  Douglas Bates  <bates@wisc.edu>
339    
340            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
341            had an effect in cases with more than 2 grouping factors.
342    
343    2005-01-03  Douglas Bates  <bates@wisc.edu>
344    
345            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
346    
347    2004-12-23  Douglas Bates  <bates@wisc.edu>
348    
349            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
350            and R_useDynamicSymbols (suggested by B.D.Ripley).
351    
352    2004-12-14  Douglas Bates  <bates@wisc.edu>
353    
354            * R/sscMatrix.R: Add determinant methods
355    
356            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
357            for tripletMatrix to matrix.
358    
359    2004-12-13  Douglas Bates  <bates@wisc.edu>
360    
361            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
362            no longer used.
363    
364          * 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
365          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 368 
368          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
369          Fixes part but not all of #15.          Fixes part but not all of #15.
370    
371  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
372    
373          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
374          scalar grouping factors corrected.          scalar grouping factors corrected.
375    
376  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
377    
378          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
379    
380  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
381    
382          * 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
383          .h file can be included.          .h file can be included.
384    
385  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
386    
387          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
388          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
389    
390          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
391    
392  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
393    
394          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
395    
396  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
397    
398          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
399    
400  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
401    
402          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
403    
404  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
405    
406          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
407    
408  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
409    
410          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
411          routines.          routines.
412    
413  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
414    
415          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
416    
417  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
418    
419          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
420    

Legend:
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