SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1084, Fri Dec 9 15:41:00 2005 UTC
# Line 1  Line 1 
1  2004-12-13  Douglas Bates  <bates@bates1-home>  2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
4                    for case (dimn.  op  no_dimn.)
5    
6    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * DESCRIPTION (Version): 0.99-2  released to CRAN
9    
10    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
11    
12            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
13            by Julian Faraway.
14    
15    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Auxiliaries.R (try_as): new utility
18            * R/sparseMatrix.R: use try_as() in coercion to original class
19    
20    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
23    
24    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/Auxiliaries.R (dimNamesCheck): added
27    
28            * R/Matrix.R (as.array), (as.vector): new
29    
30    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
33                    default.
34            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
35                    "pMatrix" now contains "sparseMatrix"
36    
37    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * tests/Class+Meth.R: new tests; t(t(m)) == m
40    
41            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
42    
43            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
44            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
45    
46            * R/dspMatrix.R: typo in "t" method
47    
48    2005-09-18  Douglas Bates  <bates@wisc.edu>
49    
50            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
51            * R/Tsparse.R: instead of R/gTMatrix.R
52            * R/Csparse.R: new
53            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
54            * src/Tsparse.c: new; many trivial methods calling cholmod_()
55            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
56                            via cholmod
57    
58    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Auxiliaries.R (non0ind): new function using new C code
61            * src/dgCMatrix.c (compressed_non_0_ij): new utility
62    
63    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
64    
65            * src/chm_common.h: header file required by all C sources that
66            call CHOLMOD functions.  It defines a cholmod_common structure
67            called 'c' whose address is passed as the last argument to
68            (virtually) every CHOLMOD function.
69    
70            * src/Pattern.c: Simple example of the use of CHOLMOD.
71    
72            * src/init.c: initialize and finalize the cholmod_common structure.
73    
74            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
75            LDL and CCOLAMD from the U. of Florida sparse matrix library.
76    
77    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * inst/test-tools.R: new file collecting the utility functions used
80                    in ./tests/*.R
81    
82            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
83            * R/Matrix.R (cbind2): methods for NULL and missing
84    
85    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/AllClass.R: new "index" class for "[" and "[<-":
88                    First cut at "symmetricMatrix" and "triangularMatrix"
89            * R/gTMatrix.R (.ind.prep): new function;
90                    Logical and character indexing now work too.
91            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
92            * tests/indexing.R: new, including *.Rout.save
93            * tests/dgTMatrix.R: new
94    
95    2005-08-29  Douglas Bates  <bates@wisc.edu>
96    
97            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
98            indicator pos not being updated.  Also enforced upper triangular
99            for symmetric case.  Need to coerce edges component of elements of
100            edge list - grr! (Why don't they define their classes cleanly?)
101    
102    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Matrix.R:  added first "[<-" methods; not yet functional
105            * R/denseMatrix.R: dito
106            * man/Subassign-methods.Rd: new help file for these
107    
108    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * DESCRIPTION (Version): 0.98-6
111    
112            * R/denseMatrix.R: new file for "[" fallback methods for all dense
113            matrices.
114    
115    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
118                    as( <logical>, "matrix")
119    
120            * R/pMatrix.R: coercion to "lgTMatrix"
121    
122            * R/gTMatrix.R: new virtual class to define "[" methods for.
123            * man/gTMatrix-class.Rd:
124            * General slight re-organization of where "[" methods are defined.
125              more to come.
126    
127    2005-08-18  Douglas Bates  <bates@wisc.edu>
128    
129            * DESCRIPTION (Version): 0.98-5  released to CRAN
130    
131            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
132            * .....
133    
134    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
135    
136            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
137            or glmer objects.
138    
139    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
142    
143    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
144    
145            * R/HBMM.R: finish re-writing R-only code.
146    
147    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
148    
149            * man/externalFormats.Rd: move documentation for writeHB and
150            writeMM here.
151    
152            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
153            (suggested by Paul Roecker).
154    
155            * tests/validObj.R (assertError): Comment out test that is failing
156            after recent changes in r-devel.
157    
158    
159    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/AllClass.R: intermediate virtual class "denseMatrix"
162            * man/denseMatrix-class.Rd
163            * NAMESPACE: export it, and also export
164            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
165    
166    2005-08-10  Douglas Bates  <bates@wisc.edu>
167    
168            * DESCRIPTION (Version): 0.98-3 to CRAN
169    
170            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
171            matrix_solve code (which was really, really wrong).
172    
173    2005-08-07  Douglas Bates  <bates@wisc.edu>
174    
175            * DESCRIPTION (Version): 0.98-2
176    
177            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
178    
179            * R/lmer.R (abbrvNms): new
180            * R/lmer.R (mcmcsamp): allow transformed parameters
181            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
182            for the Harwell-Boeing and the MatrixMarket formats.
183    
184    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * man/dtrMatrix-class.Rd: add examples
187            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
188    
189            * TODO: note the dtpMatrix (docu) bug
190    
191            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
192            in order to ensure that new as.matrix() is used by old functions,
193            e.g., svd(), qr(), eigen(), dist(),..;
194                  apply(), also matplot() or pairs().
195    
196    
197    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
200              add comments about 'control' / lmerControl() arguments
201    
202    2005-07-27  Douglas Bates  <bates@wisc.edu>
203    
204            * man/sleepstudy.Rd: Added the sleep data set.
205            * DESCRIPTION (Version): 0.98-1  released to CRAN
206    
207    2005-07-12  Douglas Bates  <bates@wisc.edu>
208            * man/sleepstudy.Rd: Added the sleep data set.
209    
210            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
211            .Call calls that were producing spurious output.
212    
213    2005-07-05  Douglas Bates  <bates@wisc.edu>
214    
215            * R/lmer.R (lmer): stored updated variance component estimates in
216            mer object for the generalized model.  (Bug reported by Renaud
217            Lancelot).
218    
219    2005-07-03  Douglas Bates  <bates@wisc.edu>
220    
221            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
222            unidimensional case.
223    
224    2005-06-08  Douglas Bates  <bates@wisc.edu>
225    
226            * DESCRIPTION (Version): 0.96-1
227    
228            * moved  lmer-class' R and C code moved from lme4 to here
229    
230    2005-06-04  Douglas Bates  <bates@wisc.edu>
231    
232            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
233            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
234    
235    2005-06-02  Douglas Bates  <bates@wisc.edu>
236    
237            * src/Makefile.win: Forgot to update this when Makefile changed.
238    
239    2005-05-11  Douglas Bates  <bates@wisc.edu>
240    
241            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
242            bug reported by Kurt Hornik and Michael Hahsler.
243    
244    2005-05-10  Douglas Bates  <bates@wisc.edu>
245    
246            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
247            logical sparse matrices.  These will also be used in the symbolic
248            analysis for lmer objects.
249    
250            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
251            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
252    
253    2005-05-06  Douglas Bates  <bates@wisc.edu>
254    
255            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
256            colMeans, colSums, rowMeans and rowSums.
257    
258    2005-04-18  Douglas Bates  <bates@wisc.edu>
259    
260            * src/lgCMatrix.[ch]: code for _validate method and stub for
261            multiplication operation.
262    
263            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
264            to dgetrs.
265    
266            * src/init.c: Fix cut-and-paste error in definition of
267            dgeMatrix_matrix_solve
268    
269            * src/{many files}: Tighten code by using ALLOC_SLOT.
270    
271    2005-04-15  Douglas Bates  <bates@wisc.edu>
272    
273            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
274    
275            * DESCRIPTION: Eliminate import of stats.
276    
277    
278    2005-04-06  Douglas Bates  <bates@wisc.edu>
279    
280            * R/AllClass.R : add logical sparse matrix classes
281    
282    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/dgTMatrix.R: add "[" method for triplet matrices
285            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
286    
287    2005-03-31  Douglas Bates  <bates@wisc.edu>
288    
289            * DESCRIPTION (Version): release 0.95-5 to CRAN
290    
291            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
292            * R/sparseMatrix.R: %*%, crossprod()
293            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
294            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
295            * src/lmer.c (lmer_fitted): fix thinko
296    
297    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/AllClass.R: add two virtual sparse classes ``on top''
300    
301    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
304                    correspondingly fix examples and tests/ since new()
305                    doesn't work for virtual classes.
306    
307    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/Matrix.R (as.matrix): method and one for unname()
310            * tests/dpoMatrix.R: tests should now be less platform dependent;
311              also run for R 2.1.0; using as.matrix()
312    
313    2005-03-15  Douglas Bates  <bates@wisc.edu>
314    
315            * R/pMatrix.R: "pMatrix" class added
316            * ....
317    
318    2005-03-14  Douglas Bates  <bates@wisc.edu>
319    
320            * R/dtpMatrix.R: Add unpack method and an example.
321    
322            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
323            of general symmetric matrices and associated S4 methods.
324    
325    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
326            +
327    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * R/dgeMatrix.R (setAs): and many other files: more coercion,
330              crossprod() and "%*%" methods added; tests, too.
331            * tests/matprod.R: new, for testing these
332    
333    2005-03-03  Douglas Bates  <bates@wisc.edu>
334    
335            * src/lmer.c (lmer_fitted): Added.
336    
337    2005-03-02  Douglas Bates  <bates@wisc.edu>
338    
339            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
340    
341    2005-02-28  Douglas Bates  <bates@wisc.edu>
342    
343            * src/*.c,po/,inst/po: Internationalization and localization of
344            the package.
345    
346            * src/ldl.[ch]: Removed these as their contents are referenced in the
347            R_ldl.c file.
348    
349            * src/flame.[ch]: Removed these source files.
350    
351            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
352    
353            * src/LU.[ch],src/init.c: absorb in factorizations
354    
355            * src/Mutils.h: prepare for internationalization
356    
357            * src/cblas.h: move the enum definitions to Mutils.h and remove
358            this file
359    
360    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
363    
364            * R/dtrMatrix.R: fix t() method
365    
366            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
367            * NAMESPACE: export them (and import generics from "methods")
368            * tests/group-methods.R : and test them.
369    
370            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
371            border case
372    
373    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
374    
375            * DESCRIPTION (Version): 0.95-2  released to CRAN
376    
377            * src/dgBCMatrix.c:
378            * src/lmer.c: many changes
379            * ...
380    
381    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/Matrix.R: add more sophisticated show() method.
384    
385    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
386    
387            * */* : almost complete reorganization of classes.
388    
389    2005-01-26  Douglas Bates  <bates@wisc.edu>
390    
391            * R/AllGeneric.R: Added matrix exponential generic expm and a method
392            for the geMatrix class.
393    
394    2005-01-24  Douglas Bates  <bates@wisc.edu>
395    
396            * src/Makefile (clean): Remove *.a and *.so
397    
398            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
399    
400    2005-01-23  Douglas Bates  <bates@wisc.edu>
401    
402            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
403            had an effect in cases with more than 2 grouping factors.
404    
405    2005-01-03  Douglas Bates  <bates@wisc.edu>
406    
407            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
408    
409    2004-12-23  Douglas Bates  <bates@wisc.edu>
410    
411            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
412            and R_useDynamicSymbols (suggested by B.D.Ripley).
413    
414    2004-12-14  Douglas Bates  <bates@wisc.edu>
415    
416            * R/sscMatrix.R: Add determinant methods
417    
418            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
419            for tripletMatrix to matrix.
420    
421    2004-12-13  Douglas Bates  <bates@wisc.edu>
422    
423            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
424            no longer used.
425    
426          * 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
427          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 430 
430          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
431          Fixes part but not all of #15.          Fixes part but not all of #15.
432    
433  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
434    
435          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
436          scalar grouping factors corrected.          scalar grouping factors corrected.
437    
438  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
439    
440          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
441    
442  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
443    
444          * 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
445          .h file can be included.          .h file can be included.
446    
447  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
448    
449          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
450          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
451    
452          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
453    
454  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
455    
456          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
457    
458  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
459    
460          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
461    
462  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
463    
464          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
465    
466  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
467    
468          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
469    
470  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
471    
472          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
473          routines.          routines.
474    
475  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
476    
477          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
478    
479  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
480    
481          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
482    

Legend:
Removed from v.388  
changed lines
  Added in v.1084

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge