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revision 229, Tue Jun 15 21:37:15 2004 UTC revision 1109, Tue Jan 3 16:42:31 2006 UTC
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1  2004-06-15  Douglas Bates  <bates@bates7>  2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
4                    (Depends): also on 'utils'
5    
6            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
7            * R/diagMatrix.R (Diagonal): constructor and methods for
8            diagonal matrices
9    
10            * R/ltTMatrix.R: new "minimal methods"
11    
12    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
15            all methods (and help files).
16    
17    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
20                    for case (dimn.  op  no_dimn.)
21    
22    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
23    
24            * DESCRIPTION (Version): 0.99-2  released to CRAN
25    
26    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
29            by Julian Faraway.
30    
31    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Auxiliaries.R (try_as): new utility
34            * R/sparseMatrix.R: use try_as() in coercion to original class
35    
36    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
39    
40    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/Auxiliaries.R (dimNamesCheck): added
43    
44            * R/Matrix.R (as.array), (as.vector): new
45    
46    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
49                    default.
50            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
51                    "pMatrix" now contains "sparseMatrix"
52    
53    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * tests/Class+Meth.R: new tests; t(t(m)) == m
56    
57            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
58    
59            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
60            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
61    
62            * R/dspMatrix.R: typo in "t" method
63    
64    2005-09-18  Douglas Bates  <bates@wisc.edu>
65    
66            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
67            * R/Tsparse.R: instead of R/gTMatrix.R
68            * R/Csparse.R: new
69            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
70            * src/Tsparse.c: new; many trivial methods calling cholmod_()
71            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
72                            via cholmod
73    
74    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/Auxiliaries.R (non0ind): new function using new C code
77            * src/dgCMatrix.c (compressed_non_0_ij): new utility
78    
79    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
80    
81            * src/chm_common.h: header file required by all C sources that
82            call CHOLMOD functions.  It defines a cholmod_common structure
83            called 'c' whose address is passed as the last argument to
84            (virtually) every CHOLMOD function.
85    
86            * src/Pattern.c: Simple example of the use of CHOLMOD.
87    
88            * src/init.c: initialize and finalize the cholmod_common structure.
89    
90            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
91            LDL and CCOLAMD from the U. of Florida sparse matrix library.
92    
93    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * inst/test-tools.R: new file collecting the utility functions used
96                    in ./tests/*.R
97    
98            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
99            * R/Matrix.R (cbind2): methods for NULL and missing
100    
101    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/AllClass.R: new "index" class for "[" and "[<-":
104                    First cut at "symmetricMatrix" and "triangularMatrix"
105            * R/gTMatrix.R (.ind.prep): new function;
106                    Logical and character indexing now work too.
107            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
108            * tests/indexing.R: new, including *.Rout.save
109            * tests/dgTMatrix.R: new
110    
111    2005-08-29  Douglas Bates  <bates@wisc.edu>
112    
113            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
114            indicator pos not being updated.  Also enforced upper triangular
115            for symmetric case.  Need to coerce edges component of elements of
116            edge list - grr! (Why don't they define their classes cleanly?)
117    
118    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/Matrix.R:  added first "[<-" methods; not yet functional
121            * R/denseMatrix.R: dito
122            * man/Subassign-methods.Rd: new help file for these
123    
124    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * DESCRIPTION (Version): 0.98-6
127    
128            * R/denseMatrix.R: new file for "[" fallback methods for all dense
129            matrices.
130    
131    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
134                    as( <logical>, "matrix")
135    
136            * R/pMatrix.R: coercion to "lgTMatrix"
137    
138            * R/gTMatrix.R: new virtual class to define "[" methods for.
139            * man/gTMatrix-class.Rd:
140            * General slight re-organization of where "[" methods are defined.
141              more to come.
142    
143    2005-08-18  Douglas Bates  <bates@wisc.edu>
144    
145            * DESCRIPTION (Version): 0.98-5  released to CRAN
146    
147            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
148            * .....
149    
150    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
151    
152            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
153            or glmer objects.
154    
155    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
158    
159    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
160    
161            * R/HBMM.R: finish re-writing R-only code.
162    
163    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
164    
165            * man/externalFormats.Rd: move documentation for writeHB and
166            writeMM here.
167    
168            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
169            (suggested by Paul Roecker).
170    
171            * tests/validObj.R (assertError): Comment out test that is failing
172            after recent changes in r-devel.
173    
174    
175    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/AllClass.R: intermediate virtual class "denseMatrix"
178            * man/denseMatrix-class.Rd
179            * NAMESPACE: export it, and also export
180            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
181    
182    2005-08-10  Douglas Bates  <bates@wisc.edu>
183    
184            * DESCRIPTION (Version): 0.98-3 to CRAN
185    
186            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
187            matrix_solve code (which was really, really wrong).
188    
189    2005-08-07  Douglas Bates  <bates@wisc.edu>
190    
191            * DESCRIPTION (Version): 0.98-2
192    
193            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
194    
195            * R/lmer.R (abbrvNms): new
196            * R/lmer.R (mcmcsamp): allow transformed parameters
197            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
198            for the Harwell-Boeing and the MatrixMarket formats.
199    
200    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * man/dtrMatrix-class.Rd: add examples
203            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
204    
205            * TODO: note the dtpMatrix (docu) bug
206    
207            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
208            in order to ensure that new as.matrix() is used by old functions,
209            e.g., svd(), qr(), eigen(), dist(),..;
210                  apply(), also matplot() or pairs().
211    
212    
213    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
216              add comments about 'control' / lmerControl() arguments
217    
218    2005-07-27  Douglas Bates  <bates@wisc.edu>
219    
220            * man/sleepstudy.Rd: Added the sleep data set.
221            * DESCRIPTION (Version): 0.98-1  released to CRAN
222    
223    2005-07-12  Douglas Bates  <bates@wisc.edu>
224            * man/sleepstudy.Rd: Added the sleep data set.
225    
226            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
227            .Call calls that were producing spurious output.
228    
229    2005-07-05  Douglas Bates  <bates@wisc.edu>
230    
231            * R/lmer.R (lmer): stored updated variance component estimates in
232            mer object for the generalized model.  (Bug reported by Renaud
233            Lancelot).
234    
235    2005-07-03  Douglas Bates  <bates@wisc.edu>
236    
237            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
238            unidimensional case.
239    
240    2005-06-08  Douglas Bates  <bates@wisc.edu>
241    
242            * DESCRIPTION (Version): 0.96-1
243    
244            * moved  lmer-class' R and C code moved from lme4 to here
245    
246    2005-06-04  Douglas Bates  <bates@wisc.edu>
247    
248            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
249            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
250    
251    2005-06-02  Douglas Bates  <bates@wisc.edu>
252    
253            * src/Makefile.win: Forgot to update this when Makefile changed.
254    
255    2005-05-11  Douglas Bates  <bates@wisc.edu>
256    
257            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
258            bug reported by Kurt Hornik and Michael Hahsler.
259    
260    2005-05-10  Douglas Bates  <bates@wisc.edu>
261    
262            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
263            logical sparse matrices.  These will also be used in the symbolic
264            analysis for lmer objects.
265    
266            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
267            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
268    
269    2005-05-06  Douglas Bates  <bates@wisc.edu>
270    
271            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
272            colMeans, colSums, rowMeans and rowSums.
273    
274    2005-04-18  Douglas Bates  <bates@wisc.edu>
275    
276            * src/lgCMatrix.[ch]: code for _validate method and stub for
277            multiplication operation.
278    
279            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
280            to dgetrs.
281    
282            * src/init.c: Fix cut-and-paste error in definition of
283            dgeMatrix_matrix_solve
284    
285            * src/{many files}: Tighten code by using ALLOC_SLOT.
286    
287    2005-04-15  Douglas Bates  <bates@wisc.edu>
288    
289            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
290    
291            * DESCRIPTION: Eliminate import of stats.
292    
293    
294    2005-04-06  Douglas Bates  <bates@wisc.edu>
295    
296            * R/AllClass.R : add logical sparse matrix classes
297    
298    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/dgTMatrix.R: add "[" method for triplet matrices
301            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
302    
303    2005-03-31  Douglas Bates  <bates@wisc.edu>
304    
305            * DESCRIPTION (Version): release 0.95-5 to CRAN
306    
307            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
308            * R/sparseMatrix.R: %*%, crossprod()
309            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
310            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
311            * src/lmer.c (lmer_fitted): fix thinko
312    
313    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/AllClass.R: add two virtual sparse classes ``on top''
316    
317    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
320                    correspondingly fix examples and tests/ since new()
321                    doesn't work for virtual classes.
322    
323    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/Matrix.R (as.matrix): method and one for unname()
326            * tests/dpoMatrix.R: tests should now be less platform dependent;
327              also run for R 2.1.0; using as.matrix()
328    
329    2005-03-15  Douglas Bates  <bates@wisc.edu>
330    
331            * R/pMatrix.R: "pMatrix" class added
332            * ....
333    
334    2005-03-14  Douglas Bates  <bates@wisc.edu>
335    
336            * R/dtpMatrix.R: Add unpack method and an example.
337    
338            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
339            of general symmetric matrices and associated S4 methods.
340    
341    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
342            +
343    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/dgeMatrix.R (setAs): and many other files: more coercion,
346              crossprod() and "%*%" methods added; tests, too.
347            * tests/matprod.R: new, for testing these
348    
349    2005-03-03  Douglas Bates  <bates@wisc.edu>
350    
351            * src/lmer.c (lmer_fitted): Added.
352    
353    2005-03-02  Douglas Bates  <bates@wisc.edu>
354    
355            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
356    
357    2005-02-28  Douglas Bates  <bates@wisc.edu>
358    
359            * src/*.c,po/,inst/po: Internationalization and localization of
360            the package.
361    
362            * src/ldl.[ch]: Removed these as their contents are referenced in the
363            R_ldl.c file.
364    
365            * src/flame.[ch]: Removed these source files.
366    
367            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
368    
369            * src/LU.[ch],src/init.c: absorb in factorizations
370    
371            * src/Mutils.h: prepare for internationalization
372    
373            * src/cblas.h: move the enum definitions to Mutils.h and remove
374            this file
375    
376    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
379    
380            * R/dtrMatrix.R: fix t() method
381    
382            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
383            * NAMESPACE: export them (and import generics from "methods")
384            * tests/group-methods.R : and test them.
385    
386            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
387            border case
388    
389    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
390    
391            * DESCRIPTION (Version): 0.95-2  released to CRAN
392    
393            * src/dgBCMatrix.c:
394            * src/lmer.c: many changes
395            * ...
396    
397    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * R/Matrix.R: add more sophisticated show() method.
400    
401    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
402    
403            * */* : almost complete reorganization of classes.
404    
405    2005-01-26  Douglas Bates  <bates@wisc.edu>
406    
407            * R/AllGeneric.R: Added matrix exponential generic expm and a method
408            for the geMatrix class.
409    
410    2005-01-24  Douglas Bates  <bates@wisc.edu>
411    
412            * src/Makefile (clean): Remove *.a and *.so
413    
414            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
415    
416    2005-01-23  Douglas Bates  <bates@wisc.edu>
417    
418            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
419            had an effect in cases with more than 2 grouping factors.
420    
421    2005-01-03  Douglas Bates  <bates@wisc.edu>
422    
423            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
424    
425    2004-12-23  Douglas Bates  <bates@wisc.edu>
426    
427            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
428            and R_useDynamicSymbols (suggested by B.D.Ripley).
429    
430    2004-12-14  Douglas Bates  <bates@wisc.edu>
431    
432            * R/sscMatrix.R: Add determinant methods
433    
434            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
435            for tripletMatrix to matrix.
436    
437    2004-12-13  Douglas Bates  <bates@wisc.edu>
438    
439            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
440            no longer used.
441    
442            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
443            with dynamic allocation of scratch arrays.
444    
445            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
446            for multivariate random effects with multiple grouping factors.
447            Fixes part but not all of #15.
448    
449    2004-12-03  Douglas Bates  <bates@wisc.edu>
450    
451            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
452            scalar grouping factors corrected.
453    
454    2004-11-29  Douglas Bates  <bates@wisc.edu>
455    
456            * src/bCrosstab.c: remove diag_update which is no longer used
457    
458    2004-11-16  Douglas Bates  <bates@wisc.edu>
459    
460            * src/Metis_utils.c: Move metis.h include to C sources so that the
461            .h file can be included.
462    
463    2004-11-12  Douglas Bates  <bates@wisc.edu>
464    
465            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
466            Complete allocation of slots in NEW_OBJECT.
467    
468            * src/Mutils.h: Moved list of symbols to an include file
469    
470    2004-11-11  Douglas Bates  <bates@wisc.edu>
471    
472            * src/geMutils.c (Matrix_init): remove unused function
473    
474    2004-11-10  Douglas Bates  <bates@wisc.edu>
475    
476            * src/cscMatrix.c (csc_to_imagemat): removed unused function
477    
478    2004-11-05  Douglas Bates  <bates@wisc.edu>
479    
480            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
481    
482    2004-10-27  Douglas Bates  <bates@wisc.edu>
483    
484            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
485    
486    2004-10-04  Douglas Bates  <bates@wisc.edu>
487    
488            * src/init.c: Created R_init_Matrix and added registration of C
489            routines.
490    
491    2004-10-02  Douglas Bates  <bates@wisc.edu>
492    
493            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
494    
495    2004-06-15  Douglas Bates  <bates@wisc.edu>
496    
497          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
498    

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