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Annotation of /pkg/ChangeLog

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1 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
2 :    
3 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
4 :     * R/Tsparse.R: instead of R/gTMatrix.R
5 :     * R/Csparse.R: new
6 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
7 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
8 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
9 :     via cholmod
10 :    
11 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
12 :    
13 :     * R/Auxiliaries.R (non0ind): new function using new C code
14 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
15 :    
16 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
17 :    
18 :     * src/chm_common.h: header file required by all C sources that
19 :     call CHOLMOD functions. It defines a cholmod_common structure
20 :     called 'c' whose address is passed as the last argument to
21 :     (virtually) every CHOLMOD function.
22 :    
23 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
24 :    
25 :     * src/init.c: initialize and finalize the cholmod_common structure.
26 :    
27 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
28 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
29 :    
30 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
31 :    
32 :     * inst/test-tools.R: new file collecting the utility functions used
33 :     in ./tests/*.R
34 :    
35 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
36 :     * R/Matrix.R (cbind2): methods for NULL and missing
37 :    
38 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
39 :    
40 :     * R/AllClass.R: new "index" class for "[" and "[<-":
41 :     First cut at "symmetricMatrix" and "triangularMatrix"
42 :     * R/gTMatrix.R (.ind.prep): new function;
43 :     Logical and character indexing now work too.
44 :     * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
45 :     * tests/indexing.R: new, including *.Rout.save
46 :     * tests/dgTMatrix.R: new
47 :    
48 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
49 :    
50 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
51 :     indicator pos not being updated. Also enforced upper triangular
52 :     for symmetric case. Need to coerce edges component of elements of
53 :     edge list - grr! (Why don't they define their classes cleanly?)
54 :    
55 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
56 :    
57 :     * R/Matrix.R: added first "[<-" methods; not yet functional
58 :     * R/denseMatrix.R: dito
59 :     * man/Subassign-methods.Rd: new help file for these
60 :    
61 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
62 :    
63 :     * DESCRIPTION (Version): 0.98-6
64 :    
65 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
66 :     matrices.
67 :    
68 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
69 :    
70 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
71 :     as( <logical>, "matrix")
72 :    
73 :     * R/pMatrix.R: coercion to "lgTMatrix"
74 :    
75 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
76 :     * man/gTMatrix-class.Rd:
77 :     * General slight re-organization of where "[" methods are defined.
78 :     more to come.
79 :    
80 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
81 : maechler 868
82 : maechler 871 * DESCRIPTION (Version): 0.98-5 released to CRAN
83 :    
84 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
85 :     * .....
86 :    
87 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
88 :    
89 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
90 :     or glmer objects.
91 :    
92 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
93 :    
94 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
95 :    
96 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
97 :    
98 :     * R/HBMM.R: finish re-writing R-only code.
99 :    
100 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
101 :    
102 :     * man/externalFormats.Rd: move documentation for writeHB and
103 :     writeMM here.
104 :    
105 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
106 :     (suggested by Paul Roecker).
107 :    
108 :     * tests/validObj.R (assertError): Comment out test that is failing
109 :     after recent changes in r-devel.
110 :    
111 : maechler 860
112 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
113 :    
114 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
115 :     * man/denseMatrix-class.Rd
116 :     * NAMESPACE: export it, and also export
117 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
118 :    
119 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
120 :    
121 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
122 :    
123 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
124 :     matrix_solve code (which was really, really wrong).
125 :    
126 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
127 : maechler 834
128 :     * DESCRIPTION (Version): 0.98-2
129 :    
130 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
131 :    
132 :     * R/lmer.R (abbrvNms): new
133 :     * R/lmer.R (mcmcsamp): allow transformed parameters
134 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
135 :     for the Harwell-Boeing and the MatrixMarket formats.
136 : maechler 834
137 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
138 :    
139 :     * man/dtrMatrix-class.Rd: add examples
140 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
141 : maechler 834
142 :     * TODO: note the dtpMatrix (docu) bug
143 :    
144 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
145 :     in order to ensure that new as.matrix() is used by old functions,
146 :     e.g., svd(), qr(), eigen(), dist(),..;
147 :     apply(), also matplot() or pairs().
148 :    
149 :    
150 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
151 :    
152 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
153 :     add comments about 'control' / lmerControl() arguments
154 :    
155 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
156 : bates 820
157 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
158 : maechler 834 * DESCRIPTION (Version): 0.98-1 released to CRAN
159 : bates 820
160 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
161 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
162 :    
163 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
164 :     .Call calls that were producing spurious output.
165 :    
166 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
167 : bates 801
168 :     * R/lmer.R (lmer): stored updated variance component estimates in
169 :     mer object for the generalized model. (Bug reported by Renaud
170 :     Lancelot).
171 :    
172 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
173 : bates 794
174 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
175 :     unidimensional case.
176 :    
177 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
178 : maechler 791
179 :     * DESCRIPTION (Version): 0.96-1
180 :    
181 :     * moved lmer-class' R and C code moved from lme4 to here
182 :    
183 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
184 : bates 763
185 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
186 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
187 :    
188 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
189 : bates 763
190 :     * src/Makefile.win: Forgot to update this when Makefile changed.
191 :    
192 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
193 : bates 726
194 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
195 :     bug reported by Kurt Hornik and Michael Hahsler.
196 :    
197 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
198 : bates 725
199 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
200 :     logical sparse matrices. These will also be used in the symbolic
201 :     analysis for lmer objects.
202 :    
203 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
204 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
205 : maechler 791
206 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
207 : bates 714
208 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
209 :     colMeans, colSums, rowMeans and rowSums.
210 :    
211 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
212 : bates 692
213 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
214 :     multiplication operation.
215 :    
216 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
217 :     to dgetrs.
218 :    
219 :     * src/init.c: Fix cut-and-paste error in definition of
220 :     dgeMatrix_matrix_solve
221 :    
222 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
223 :    
224 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
225 : bates 692
226 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
227 :    
228 :     * DESCRIPTION: Eliminate import of stats.
229 :    
230 : maechler 791
231 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
232 : bates 692
233 :     * R/AllClass.R : add logical sparse matrix classes
234 :    
235 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
236 :    
237 :     * R/dgTMatrix.R: add "[" method for triplet matrices
238 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
239 :    
240 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
241 : maechler 687
242 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
243 :    
244 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
245 :     * R/sparseMatrix.R: %*%, crossprod()
246 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
247 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
248 :     * src/lmer.c (lmer_fitted): fix thinko
249 :    
250 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
251 :    
252 :     * R/AllClass.R: add two virtual sparse classes ``on top''
253 :    
254 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
255 :    
256 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
257 :     correspondingly fix examples and tests/ since new()
258 :     doesn't work for virtual classes.
259 :    
260 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
261 :    
262 :     * R/Matrix.R (as.matrix): method and one for unname()
263 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
264 :     also run for R 2.1.0; using as.matrix()
265 :    
266 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
267 : maechler 658
268 :     * R/pMatrix.R: "pMatrix" class added
269 :     * ....
270 :    
271 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
272 : bates 645
273 :     * R/dtpMatrix.R: Add unpack method and an example.
274 :    
275 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
276 :     of general symmetric matrices and associated S4 methods.
277 :    
278 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
279 :     +
280 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
281 :    
282 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
283 :     crossprod() and "%*%" methods added; tests, too.
284 :     * tests/matprod.R: new, for testing these
285 :    
286 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
287 : bates 599
288 :     * src/lmer.c (lmer_fitted): Added.
289 :    
290 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
291 : bates 596
292 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
293 :    
294 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
295 : bates 582
296 :     * src/*.c,po/,inst/po: Internationalization and localization of
297 :     the package.
298 :    
299 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
300 :     R_ldl.c file.
301 :    
302 :     * src/flame.[ch]: Removed these source files.
303 : maechler 658
304 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
305 :    
306 :     * src/LU.[ch],src/init.c: absorb in factorizations
307 :    
308 :     * src/Mutils.h: prepare for internationalization
309 :    
310 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
311 :     this file
312 :    
313 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
314 :    
315 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
316 :    
317 :     * R/dtrMatrix.R: fix t() method
318 :    
319 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
320 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
321 : maechler 578 * tests/group-methods.R : and test them.
322 :    
323 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
324 :     border case
325 :    
326 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
327 :    
328 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
329 : maechler 578
330 :     * src/dgBCMatrix.c:
331 :     * src/lmer.c: many changes
332 :     * ...
333 :    
334 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
335 :    
336 :     * R/Matrix.R: add more sophisticated show() method.
337 :    
338 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
339 :    
340 :     * */* : almost complete reorganization of classes.
341 :    
342 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
343 : bates 460
344 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
345 :     for the geMatrix class.
346 :    
347 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
348 : bates 460
349 :     * src/Makefile (clean): Remove *.a and *.so
350 :    
351 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
352 :    
353 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
354 : bates 460
355 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
356 : bates 460 had an effect in cases with more than 2 grouping factors.
357 :    
358 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
359 : bates 415
360 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
361 :    
362 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
363 : bates 410
364 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
365 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
366 :    
367 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
368 : bates 392
369 :     * R/sscMatrix.R: Add determinant methods
370 :    
371 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
372 :     for tripletMatrix to matrix.
373 :    
374 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
375 : bates 388
376 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
377 :     no longer used.
378 :    
379 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
380 :     with dynamic allocation of scratch arrays.
381 :    
382 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
383 :     for multivariate random effects with multiple grouping factors.
384 :     Fixes part but not all of #15.
385 :    
386 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
387 : bates 375
388 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
389 :     scalar grouping factors corrected.
390 :    
391 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
392 : bates 375
393 :     * src/bCrosstab.c: remove diag_update which is no longer used
394 :    
395 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
396 : bates 350
397 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
398 :     .h file can be included.
399 :    
400 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
401 : bates 342
402 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
403 : bates 342 Complete allocation of slots in NEW_OBJECT.
404 :    
405 :     * src/Mutils.h: Moved list of symbols to an include file
406 :    
407 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
408 : bates 342
409 :     * src/geMutils.c (Matrix_init): remove unused function
410 :    
411 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
412 : bates 342
413 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
414 :    
415 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
416 : bates 327
417 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
418 :    
419 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
420 : bates 303
421 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
422 :    
423 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
424 : bates 296
425 :     * src/init.c: Created R_init_Matrix and added registration of C
426 :     routines.
427 :    
428 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
429 : bates 283
430 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
431 :    
432 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
433 : bates 229
434 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
435 :    
436 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
437 :    
438 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
439 :    
440 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
441 :    
442 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
443 :     ssclme_update_mm
444 :    
445 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
446 :    
447 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
448 :     in the order of unconstrained and constrained parameters.
449 :     (ssclme_gradient): Added the gradients (not yet correct for
450 :     multidimensional, unconstrained case).
451 :    
452 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
453 :    
454 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
455 :    
456 :     * src/Makefile.win: Remove unneeded ranlib call
457 :    
458 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
459 :    
460 :     * DESCRIPTION (Version): New release
461 :    
462 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
463 :    
464 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
465 :    
466 :     * src/triplet_to_col.c: Create triplet_to_col as a native
467 : maechler 658 function, not the version from umfpack. There were problems with
468 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
469 :     only one umfpack routine being used so I moved it here.
470 :    
471 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
472 :    
473 :     * src/ssclme.c (ssclme_variances): New function.
474 :    
475 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
476 :    
477 :     * src/ssclme.c (ssclme_fitted): Added function.
478 :    
479 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
480 :    
481 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
482 :     store the dimnames in the XtX and bVar slots
483 :     (ssclme_update_mm): Change the dimensions of the bVar slot
484 :     components and the returned value from ssclme_ranef.
485 :    
486 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
487 :    
488 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
489 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
490 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
491 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
492 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
493 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
494 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
495 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
496 :     Moved the pdMat classes from the lme4 package.
497 :    
498 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
499 :    
500 :     * man/ssclme-class.Rd: Update definition and documentation of the
501 :     ssclme class to include the DIsqrt slot.
502 :    
503 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
504 :     (much faster using dsyrk, a level 3 BLAS routine).
505 :    
506 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
507 :    
508 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
509 :    
510 :     * tests/ssclme.R: Modify the test to account for the permutation
511 :     of the levels of the grouping factors.
512 :    
513 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
514 :    
515 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
516 :     directly into the ssclme class definition.
517 :    
518 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
519 :    
520 :     * DESCRIPTION (Date): New release
521 :    
522 :     * man/ssclme-class.Rd: new file.
523 :    
524 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
525 :     works and it's fast!
526 :    
527 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
528 :    
529 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
530 :    
531 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
532 :    
533 :     * DESCRIPTION (Date): New release
534 :    
535 :     * NAMESPACE: Don't export ssclme.
536 :    
537 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
538 :     school data.
539 :    
540 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
541 :    
542 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
543 :     keep track of the fixed-effects and the response. Counts also
544 :     gets an extra element, which is always one.
545 :    
546 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
547 :    
548 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
549 :    
550 :     * src/cscMatrix.c (csc_transpose): new function
551 :    
552 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
553 :     (csc_components_transpose): new function
554 :    
555 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
556 :    
557 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
558 :     triplets
559 :    
560 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
561 :    
562 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
563 :    
564 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
565 :     and all other .h files in src.
566 :    
567 :     * src/Makefile.win: This and other Makefile.win files contributed
568 :     by Brian Ripley.
569 :    
570 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
571 :    
572 :     * R/syMatrix.R: Added methods for "%*%".
573 :    
574 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
575 :     poMatrix object.
576 :    
577 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
578 :    
579 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
580 :    
581 :     2004-01-25 Douglas Bates <bates@bates2_home>
582 :    
583 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
584 :    
585 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
586 :     of nrow.
587 :    
588 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
589 :    
590 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
591 :     subdirectories.
592 :    
593 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
594 :    
595 :     * src/taucs.h: Accidently referred to global header files
596 :     instead of local files.
597 :    
598 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
599 :    
600 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
601 :     and methods and replaced all classes with S4 classes.
602 :    
603 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
604 :    
605 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
606 :    
607 :     * src/R_LapackPP.cc: Change method of calculating determinants
608 :    
609 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
610 :    
611 :     * DESCRIPTION (Version): removed empty data directory as requested
612 :     by CRAN maintainers. Changed version number and date.
613 :    
614 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
615 :    
616 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
617 :     under Windows.
618 :    
619 :     * Added configure.win and src/Makevars.win as requested by Brian
620 :     Ripley.
621 :    
622 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
623 :    
624 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
625 :     Hornik.
626 :    
627 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
628 :    
629 :     * configure.ac: Replaced configure.in with configure.ac
630 :     contributed by Kurt Hornik.
631 :    
632 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
633 :     version for R-1.5.0
634 :    
635 : maechler 512
636 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
637 :    
638 :     * man/eigen.Rd: Removed the .Alias in the example

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