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revision 229, Tue Jun 15 21:37:15 2004 UTC revision 988, Tue Oct 25 17:39:01 2005 UTC
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1  2004-06-15  Douglas Bates  <bates@bates7>  2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
4            by Julian Faraway.
5    
6    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/Auxiliaries.R (try_as): new utility
9            * R/sparseMatrix.R: use try_as() in coercion to original class
10    
11    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
14    
15    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Auxiliaries.R (dimNamesCheck): added
18    
19            * R/Matrix.R (as.array), (as.vector): new
20    
21    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
24                    default.
25            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
26                    "pMatrix" now contains "sparseMatrix"
27    
28    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * tests/Class+Meth.R: new tests; t(t(m)) == m
31    
32            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
33    
34            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
35            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
36    
37            * R/dspMatrix.R: typo in "t" method
38    
39    2005-09-18  Douglas Bates  <bates@wisc.edu>
40    
41            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
42            * R/Tsparse.R: instead of R/gTMatrix.R
43            * R/Csparse.R: new
44            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
45            * src/Tsparse.c: new; many trivial methods calling cholmod_()
46            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
47                            via cholmod
48    
49    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * R/Auxiliaries.R (non0ind): new function using new C code
52            * src/dgCMatrix.c (compressed_non_0_ij): new utility
53    
54    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
55    
56            * src/chm_common.h: header file required by all C sources that
57            call CHOLMOD functions.  It defines a cholmod_common structure
58            called 'c' whose address is passed as the last argument to
59            (virtually) every CHOLMOD function.
60    
61            * src/Pattern.c: Simple example of the use of CHOLMOD.
62    
63            * src/init.c: initialize and finalize the cholmod_common structure.
64    
65            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
66            LDL and CCOLAMD from the U. of Florida sparse matrix library.
67    
68    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * inst/test-tools.R: new file collecting the utility functions used
71                    in ./tests/*.R
72    
73            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
74            * R/Matrix.R (cbind2): methods for NULL and missing
75    
76    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/AllClass.R: new "index" class for "[" and "[<-":
79                    First cut at "symmetricMatrix" and "triangularMatrix"
80            * R/gTMatrix.R (.ind.prep): new function;
81                    Logical and character indexing now work too.
82            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
83            * tests/indexing.R: new, including *.Rout.save
84            * tests/dgTMatrix.R: new
85    
86    2005-08-29  Douglas Bates  <bates@wisc.edu>
87    
88            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
89            indicator pos not being updated.  Also enforced upper triangular
90            for symmetric case.  Need to coerce edges component of elements of
91            edge list - grr! (Why don't they define their classes cleanly?)
92    
93    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/Matrix.R:  added first "[<-" methods; not yet functional
96            * R/denseMatrix.R: dito
97            * man/Subassign-methods.Rd: new help file for these
98    
99    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * DESCRIPTION (Version): 0.98-6
102    
103            * R/denseMatrix.R: new file for "[" fallback methods for all dense
104            matrices.
105    
106    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
109                    as( <logical>, "matrix")
110    
111            * R/pMatrix.R: coercion to "lgTMatrix"
112    
113            * R/gTMatrix.R: new virtual class to define "[" methods for.
114            * man/gTMatrix-class.Rd:
115            * General slight re-organization of where "[" methods are defined.
116              more to come.
117    
118    2005-08-18  Douglas Bates  <bates@wisc.edu>
119    
120            * DESCRIPTION (Version): 0.98-5  released to CRAN
121    
122            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
123            * .....
124    
125    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
126    
127            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
128            or glmer objects.
129    
130    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
133    
134    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
135    
136            * R/HBMM.R: finish re-writing R-only code.
137    
138    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
139    
140            * man/externalFormats.Rd: move documentation for writeHB and
141            writeMM here.
142    
143            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
144            (suggested by Paul Roecker).
145    
146            * tests/validObj.R (assertError): Comment out test that is failing
147            after recent changes in r-devel.
148    
149    
150    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/AllClass.R: intermediate virtual class "denseMatrix"
153            * man/denseMatrix-class.Rd
154            * NAMESPACE: export it, and also export
155            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
156    
157    2005-08-10  Douglas Bates  <bates@wisc.edu>
158    
159            * DESCRIPTION (Version): 0.98-3 to CRAN
160    
161            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
162            matrix_solve code (which was really, really wrong).
163    
164    2005-08-07  Douglas Bates  <bates@wisc.edu>
165    
166            * DESCRIPTION (Version): 0.98-2
167    
168            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
169    
170            * R/lmer.R (abbrvNms): new
171            * R/lmer.R (mcmcsamp): allow transformed parameters
172            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
173            for the Harwell-Boeing and the MatrixMarket formats.
174    
175    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * man/dtrMatrix-class.Rd: add examples
178            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
179    
180            * TODO: note the dtpMatrix (docu) bug
181    
182            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
183            in order to ensure that new as.matrix() is used by old functions,
184            e.g., svd(), qr(), eigen(), dist(),..;
185                  apply(), also matplot() or pairs().
186    
187    
188    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
191              add comments about 'control' / lmerControl() arguments
192    
193    2005-07-27  Douglas Bates  <bates@wisc.edu>
194    
195            * man/sleepstudy.Rd: Added the sleep data set.
196            * DESCRIPTION (Version): 0.98-1  released to CRAN
197    
198    2005-07-12  Douglas Bates  <bates@wisc.edu>
199            * man/sleepstudy.Rd: Added the sleep data set.
200    
201            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
202            .Call calls that were producing spurious output.
203    
204    2005-07-05  Douglas Bates  <bates@wisc.edu>
205    
206            * R/lmer.R (lmer): stored updated variance component estimates in
207            mer object for the generalized model.  (Bug reported by Renaud
208            Lancelot).
209    
210    2005-07-03  Douglas Bates  <bates@wisc.edu>
211    
212            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
213            unidimensional case.
214    
215    2005-06-08  Douglas Bates  <bates@wisc.edu>
216    
217            * DESCRIPTION (Version): 0.96-1
218    
219            * moved  lmer-class' R and C code moved from lme4 to here
220    
221    2005-06-04  Douglas Bates  <bates@wisc.edu>
222    
223            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
224            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
225    
226    2005-06-02  Douglas Bates  <bates@wisc.edu>
227    
228            * src/Makefile.win: Forgot to update this when Makefile changed.
229    
230    2005-05-11  Douglas Bates  <bates@wisc.edu>
231    
232            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
233            bug reported by Kurt Hornik and Michael Hahsler.
234    
235    2005-05-10  Douglas Bates  <bates@wisc.edu>
236    
237            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
238            logical sparse matrices.  These will also be used in the symbolic
239            analysis for lmer objects.
240    
241            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
242            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
243    
244    2005-05-06  Douglas Bates  <bates@wisc.edu>
245    
246            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
247            colMeans, colSums, rowMeans and rowSums.
248    
249    2005-04-18  Douglas Bates  <bates@wisc.edu>
250    
251            * src/lgCMatrix.[ch]: code for _validate method and stub for
252            multiplication operation.
253    
254            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
255            to dgetrs.
256    
257            * src/init.c: Fix cut-and-paste error in definition of
258            dgeMatrix_matrix_solve
259    
260            * src/{many files}: Tighten code by using ALLOC_SLOT.
261    
262    2005-04-15  Douglas Bates  <bates@wisc.edu>
263    
264            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
265    
266            * DESCRIPTION: Eliminate import of stats.
267    
268    
269    2005-04-06  Douglas Bates  <bates@wisc.edu>
270    
271            * R/AllClass.R : add logical sparse matrix classes
272    
273    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/dgTMatrix.R: add "[" method for triplet matrices
276            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
277    
278    2005-03-31  Douglas Bates  <bates@wisc.edu>
279    
280            * DESCRIPTION (Version): release 0.95-5 to CRAN
281    
282            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
283            * R/sparseMatrix.R: %*%, crossprod()
284            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
285            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
286            * src/lmer.c (lmer_fitted): fix thinko
287    
288    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/AllClass.R: add two virtual sparse classes ``on top''
291    
292    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
295                    correspondingly fix examples and tests/ since new()
296                    doesn't work for virtual classes.
297    
298    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/Matrix.R (as.matrix): method and one for unname()
301            * tests/dpoMatrix.R: tests should now be less platform dependent;
302              also run for R 2.1.0; using as.matrix()
303    
304    2005-03-15  Douglas Bates  <bates@wisc.edu>
305    
306            * R/pMatrix.R: "pMatrix" class added
307            * ....
308    
309    2005-03-14  Douglas Bates  <bates@wisc.edu>
310    
311            * R/dtpMatrix.R: Add unpack method and an example.
312    
313            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
314            of general symmetric matrices and associated S4 methods.
315    
316    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
317            +
318    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/dgeMatrix.R (setAs): and many other files: more coercion,
321              crossprod() and "%*%" methods added; tests, too.
322            * tests/matprod.R: new, for testing these
323    
324    2005-03-03  Douglas Bates  <bates@wisc.edu>
325    
326            * src/lmer.c (lmer_fitted): Added.
327    
328    2005-03-02  Douglas Bates  <bates@wisc.edu>
329    
330            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
331    
332    2005-02-28  Douglas Bates  <bates@wisc.edu>
333    
334            * src/*.c,po/,inst/po: Internationalization and localization of
335            the package.
336    
337            * src/ldl.[ch]: Removed these as their contents are referenced in the
338            R_ldl.c file.
339    
340            * src/flame.[ch]: Removed these source files.
341    
342            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
343    
344            * src/LU.[ch],src/init.c: absorb in factorizations
345    
346            * src/Mutils.h: prepare for internationalization
347    
348            * src/cblas.h: move the enum definitions to Mutils.h and remove
349            this file
350    
351    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
354    
355            * R/dtrMatrix.R: fix t() method
356    
357            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
358            * NAMESPACE: export them (and import generics from "methods")
359            * tests/group-methods.R : and test them.
360    
361            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
362            border case
363    
364    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
365    
366            * DESCRIPTION (Version): 0.95-2  released to CRAN
367    
368            * src/dgBCMatrix.c:
369            * src/lmer.c: many changes
370            * ...
371    
372    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * R/Matrix.R: add more sophisticated show() method.
375    
376    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
377    
378            * */* : almost complete reorganization of classes.
379    
380    2005-01-26  Douglas Bates  <bates@wisc.edu>
381    
382            * R/AllGeneric.R: Added matrix exponential generic expm and a method
383            for the geMatrix class.
384    
385    2005-01-24  Douglas Bates  <bates@wisc.edu>
386    
387            * src/Makefile (clean): Remove *.a and *.so
388    
389            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
390    
391    2005-01-23  Douglas Bates  <bates@wisc.edu>
392    
393            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
394            had an effect in cases with more than 2 grouping factors.
395    
396    2005-01-03  Douglas Bates  <bates@wisc.edu>
397    
398            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
399    
400    2004-12-23  Douglas Bates  <bates@wisc.edu>
401    
402            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
403            and R_useDynamicSymbols (suggested by B.D.Ripley).
404    
405    2004-12-14  Douglas Bates  <bates@wisc.edu>
406    
407            * R/sscMatrix.R: Add determinant methods
408    
409            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
410            for tripletMatrix to matrix.
411    
412    2004-12-13  Douglas Bates  <bates@wisc.edu>
413    
414            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
415            no longer used.
416    
417            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
418            with dynamic allocation of scratch arrays.
419    
420            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
421            for multivariate random effects with multiple grouping factors.
422            Fixes part but not all of #15.
423    
424    2004-12-03  Douglas Bates  <bates@wisc.edu>
425    
426            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
427            scalar grouping factors corrected.
428    
429    2004-11-29  Douglas Bates  <bates@wisc.edu>
430    
431            * src/bCrosstab.c: remove diag_update which is no longer used
432    
433    2004-11-16  Douglas Bates  <bates@wisc.edu>
434    
435            * src/Metis_utils.c: Move metis.h include to C sources so that the
436            .h file can be included.
437    
438    2004-11-12  Douglas Bates  <bates@wisc.edu>
439    
440            * src/LU.c,geMatrix.c,trMatrix.c, etc.:
441            Complete allocation of slots in NEW_OBJECT.
442    
443            * src/Mutils.h: Moved list of symbols to an include file
444    
445    2004-11-11  Douglas Bates  <bates@wisc.edu>
446    
447            * src/geMutils.c (Matrix_init): remove unused function
448    
449    2004-11-10  Douglas Bates  <bates@wisc.edu>
450    
451            * src/cscMatrix.c (csc_to_imagemat): removed unused function
452    
453    2004-11-05  Douglas Bates  <bates@wisc.edu>
454    
455            * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
456    
457    2004-10-27  Douglas Bates  <bates@wisc.edu>
458    
459            * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
460    
461    2004-10-04  Douglas Bates  <bates@wisc.edu>
462    
463            * src/init.c: Created R_init_Matrix and added registration of C
464            routines.
465    
466    2004-10-02  Douglas Bates  <bates@wisc.edu>
467    
468            * R/tripletMatrix.R: Force a require(lattice) for the image methods.
469    
470    2004-06-15  Douglas Bates  <bates@wisc.edu>
471    
472          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
473    

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