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revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1091, Mon Dec 12 13:59:58 2005 UTC
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1  2004-12-13  Douglas Bates  <bates@bates1-home>  2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
4            all methods (and help files).
5    
6    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
9                    for case (dimn.  op  no_dimn.)
10    
11    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
12    
13            * DESCRIPTION (Version): 0.99-2  released to CRAN
14    
15    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
16    
17            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
18            by Julian Faraway.
19    
20    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Auxiliaries.R (try_as): new utility
23            * R/sparseMatrix.R: use try_as() in coercion to original class
24    
25    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
28    
29    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/Auxiliaries.R (dimNamesCheck): added
32    
33            * R/Matrix.R (as.array), (as.vector): new
34    
35    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
38                    default.
39            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
40                    "pMatrix" now contains "sparseMatrix"
41    
42    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * tests/Class+Meth.R: new tests; t(t(m)) == m
45    
46            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
47    
48            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
49            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
50    
51            * R/dspMatrix.R: typo in "t" method
52    
53    2005-09-18  Douglas Bates  <bates@wisc.edu>
54    
55            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
56            * R/Tsparse.R: instead of R/gTMatrix.R
57            * R/Csparse.R: new
58            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
59            * src/Tsparse.c: new; many trivial methods calling cholmod_()
60            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
61                            via cholmod
62    
63    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/Auxiliaries.R (non0ind): new function using new C code
66            * src/dgCMatrix.c (compressed_non_0_ij): new utility
67    
68    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
69    
70            * src/chm_common.h: header file required by all C sources that
71            call CHOLMOD functions.  It defines a cholmod_common structure
72            called 'c' whose address is passed as the last argument to
73            (virtually) every CHOLMOD function.
74    
75            * src/Pattern.c: Simple example of the use of CHOLMOD.
76    
77            * src/init.c: initialize and finalize the cholmod_common structure.
78    
79            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
80            LDL and CCOLAMD from the U. of Florida sparse matrix library.
81    
82    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * inst/test-tools.R: new file collecting the utility functions used
85                    in ./tests/*.R
86    
87            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
88            * R/Matrix.R (cbind2): methods for NULL and missing
89    
90    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/AllClass.R: new "index" class for "[" and "[<-":
93                    First cut at "symmetricMatrix" and "triangularMatrix"
94            * R/gTMatrix.R (.ind.prep): new function;
95                    Logical and character indexing now work too.
96            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
97            * tests/indexing.R: new, including *.Rout.save
98            * tests/dgTMatrix.R: new
99    
100    2005-08-29  Douglas Bates  <bates@wisc.edu>
101    
102            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
103            indicator pos not being updated.  Also enforced upper triangular
104            for symmetric case.  Need to coerce edges component of elements of
105            edge list - grr! (Why don't they define their classes cleanly?)
106    
107    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/Matrix.R:  added first "[<-" methods; not yet functional
110            * R/denseMatrix.R: dito
111            * man/Subassign-methods.Rd: new help file for these
112    
113    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * DESCRIPTION (Version): 0.98-6
116    
117            * R/denseMatrix.R: new file for "[" fallback methods for all dense
118            matrices.
119    
120    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
123                    as( <logical>, "matrix")
124    
125            * R/pMatrix.R: coercion to "lgTMatrix"
126    
127            * R/gTMatrix.R: new virtual class to define "[" methods for.
128            * man/gTMatrix-class.Rd:
129            * General slight re-organization of where "[" methods are defined.
130              more to come.
131    
132    2005-08-18  Douglas Bates  <bates@wisc.edu>
133    
134            * DESCRIPTION (Version): 0.98-5  released to CRAN
135    
136            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
137            * .....
138    
139    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
140    
141            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
142            or glmer objects.
143    
144    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
147    
148    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
149    
150            * R/HBMM.R: finish re-writing R-only code.
151    
152    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
153    
154            * man/externalFormats.Rd: move documentation for writeHB and
155            writeMM here.
156    
157            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
158            (suggested by Paul Roecker).
159    
160            * tests/validObj.R (assertError): Comment out test that is failing
161            after recent changes in r-devel.
162    
163    
164    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/AllClass.R: intermediate virtual class "denseMatrix"
167            * man/denseMatrix-class.Rd
168            * NAMESPACE: export it, and also export
169            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
170    
171    2005-08-10  Douglas Bates  <bates@wisc.edu>
172    
173            * DESCRIPTION (Version): 0.98-3 to CRAN
174    
175            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
176            matrix_solve code (which was really, really wrong).
177    
178    2005-08-07  Douglas Bates  <bates@wisc.edu>
179    
180            * DESCRIPTION (Version): 0.98-2
181    
182            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
183    
184            * R/lmer.R (abbrvNms): new
185            * R/lmer.R (mcmcsamp): allow transformed parameters
186            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
187            for the Harwell-Boeing and the MatrixMarket formats.
188    
189    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * man/dtrMatrix-class.Rd: add examples
192            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
193    
194            * TODO: note the dtpMatrix (docu) bug
195    
196            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
197            in order to ensure that new as.matrix() is used by old functions,
198            e.g., svd(), qr(), eigen(), dist(),..;
199                  apply(), also matplot() or pairs().
200    
201    
202    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
205              add comments about 'control' / lmerControl() arguments
206    
207    2005-07-27  Douglas Bates  <bates@wisc.edu>
208    
209            * man/sleepstudy.Rd: Added the sleep data set.
210            * DESCRIPTION (Version): 0.98-1  released to CRAN
211    
212    2005-07-12  Douglas Bates  <bates@wisc.edu>
213            * man/sleepstudy.Rd: Added the sleep data set.
214    
215            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
216            .Call calls that were producing spurious output.
217    
218    2005-07-05  Douglas Bates  <bates@wisc.edu>
219    
220            * R/lmer.R (lmer): stored updated variance component estimates in
221            mer object for the generalized model.  (Bug reported by Renaud
222            Lancelot).
223    
224    2005-07-03  Douglas Bates  <bates@wisc.edu>
225    
226            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
227            unidimensional case.
228    
229    2005-06-08  Douglas Bates  <bates@wisc.edu>
230    
231            * DESCRIPTION (Version): 0.96-1
232    
233            * moved  lmer-class' R and C code moved from lme4 to here
234    
235    2005-06-04  Douglas Bates  <bates@wisc.edu>
236    
237            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
238            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
239    
240    2005-06-02  Douglas Bates  <bates@wisc.edu>
241    
242            * src/Makefile.win: Forgot to update this when Makefile changed.
243    
244    2005-05-11  Douglas Bates  <bates@wisc.edu>
245    
246            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
247            bug reported by Kurt Hornik and Michael Hahsler.
248    
249    2005-05-10  Douglas Bates  <bates@wisc.edu>
250    
251            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
252            logical sparse matrices.  These will also be used in the symbolic
253            analysis for lmer objects.
254    
255            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
256            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
257    
258    2005-05-06  Douglas Bates  <bates@wisc.edu>
259    
260            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
261            colMeans, colSums, rowMeans and rowSums.
262    
263    2005-04-18  Douglas Bates  <bates@wisc.edu>
264    
265            * src/lgCMatrix.[ch]: code for _validate method and stub for
266            multiplication operation.
267    
268            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
269            to dgetrs.
270    
271            * src/init.c: Fix cut-and-paste error in definition of
272            dgeMatrix_matrix_solve
273    
274            * src/{many files}: Tighten code by using ALLOC_SLOT.
275    
276    2005-04-15  Douglas Bates  <bates@wisc.edu>
277    
278            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
279    
280            * DESCRIPTION: Eliminate import of stats.
281    
282    
283    2005-04-06  Douglas Bates  <bates@wisc.edu>
284    
285            * R/AllClass.R : add logical sparse matrix classes
286    
287    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/dgTMatrix.R: add "[" method for triplet matrices
290            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
291    
292    2005-03-31  Douglas Bates  <bates@wisc.edu>
293    
294            * DESCRIPTION (Version): release 0.95-5 to CRAN
295    
296            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
297            * R/sparseMatrix.R: %*%, crossprod()
298            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
299            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
300            * src/lmer.c (lmer_fitted): fix thinko
301    
302    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/AllClass.R: add two virtual sparse classes ``on top''
305    
306    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
309                    correspondingly fix examples and tests/ since new()
310                    doesn't work for virtual classes.
311    
312    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Matrix.R (as.matrix): method and one for unname()
315            * tests/dpoMatrix.R: tests should now be less platform dependent;
316              also run for R 2.1.0; using as.matrix()
317    
318    2005-03-15  Douglas Bates  <bates@wisc.edu>
319    
320            * R/pMatrix.R: "pMatrix" class added
321            * ....
322    
323    2005-03-14  Douglas Bates  <bates@wisc.edu>
324    
325            * R/dtpMatrix.R: Add unpack method and an example.
326    
327            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
328            of general symmetric matrices and associated S4 methods.
329    
330    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
331            +
332    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/dgeMatrix.R (setAs): and many other files: more coercion,
335              crossprod() and "%*%" methods added; tests, too.
336            * tests/matprod.R: new, for testing these
337    
338    2005-03-03  Douglas Bates  <bates@wisc.edu>
339    
340            * src/lmer.c (lmer_fitted): Added.
341    
342    2005-03-02  Douglas Bates  <bates@wisc.edu>
343    
344            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
345    
346    2005-02-28  Douglas Bates  <bates@wisc.edu>
347    
348            * src/*.c,po/,inst/po: Internationalization and localization of
349            the package.
350    
351            * src/ldl.[ch]: Removed these as their contents are referenced in the
352            R_ldl.c file.
353    
354            * src/flame.[ch]: Removed these source files.
355    
356            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
357    
358            * src/LU.[ch],src/init.c: absorb in factorizations
359    
360            * src/Mutils.h: prepare for internationalization
361    
362            * src/cblas.h: move the enum definitions to Mutils.h and remove
363            this file
364    
365    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
368    
369            * R/dtrMatrix.R: fix t() method
370    
371            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
372            * NAMESPACE: export them (and import generics from "methods")
373            * tests/group-methods.R : and test them.
374    
375            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
376            border case
377    
378    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
379    
380            * DESCRIPTION (Version): 0.95-2  released to CRAN
381    
382            * src/dgBCMatrix.c:
383            * src/lmer.c: many changes
384            * ...
385    
386    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/Matrix.R: add more sophisticated show() method.
389    
390    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
391    
392            * */* : almost complete reorganization of classes.
393    
394    2005-01-26  Douglas Bates  <bates@wisc.edu>
395    
396            * R/AllGeneric.R: Added matrix exponential generic expm and a method
397            for the geMatrix class.
398    
399    2005-01-24  Douglas Bates  <bates@wisc.edu>
400    
401            * src/Makefile (clean): Remove *.a and *.so
402    
403            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
404    
405    2005-01-23  Douglas Bates  <bates@wisc.edu>
406    
407            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
408            had an effect in cases with more than 2 grouping factors.
409    
410    2005-01-03  Douglas Bates  <bates@wisc.edu>
411    
412            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
413    
414    2004-12-23  Douglas Bates  <bates@wisc.edu>
415    
416            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
417            and R_useDynamicSymbols (suggested by B.D.Ripley).
418    
419    2004-12-14  Douglas Bates  <bates@wisc.edu>
420    
421            * R/sscMatrix.R: Add determinant methods
422    
423            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
424            for tripletMatrix to matrix.
425    
426    2004-12-13  Douglas Bates  <bates@wisc.edu>
427    
428            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
429            no longer used.
430    
431          * 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
432          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 435 
435          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
436          Fixes part but not all of #15.          Fixes part but not all of #15.
437    
438  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
439    
440          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
441          scalar grouping factors corrected.          scalar grouping factors corrected.
442    
443  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
444    
445          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
446    
447  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
448    
449          * 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
450          .h file can be included.          .h file can be included.
451    
452  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
453    
454          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
455          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
456    
457          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
458    
459  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
460    
461          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
462    
463  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
464    
465          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
466    
467  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
468    
469          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
470    
471  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
472    
473          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
474    
475  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
476    
477          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
478          routines.          routines.
479    
480  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
481    
482          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
483    
484  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
485    
486          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
487    

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