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Annotation of /pkg/ChangeLog

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Revision 988 - (view) (download)

1 : bates 988 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 : maechler 976 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 : maechler 956 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 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
22 :    
23 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
24 : maechler 956 default.
25 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
26 :     "pMatrix" now contains "sparseMatrix"
27 : maechler 954
28 : maechler 948 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 : maechler 925 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 : bates 917 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 : maechler 908 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 : maechler 886 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 : bates 876 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 : maechler 871 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 : maechler 868 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 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
119 : maechler 868
120 : maechler 871 * DESCRIPTION (Version): 0.98-5 released to CRAN
121 :    
122 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
123 :     * .....
124 :    
125 : bates 863 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 : maechler 860 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 : bates 854 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 : maechler 860
150 : maechler 848 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 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
158 :    
159 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
160 :    
161 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
162 :     matrix_solve code (which was really, really wrong).
163 :    
164 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
165 : maechler 834
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 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
173 :     for the Harwell-Boeing and the MatrixMarket formats.
174 : maechler 834
175 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
176 :    
177 :     * man/dtrMatrix-class.Rd: add examples
178 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
179 : maechler 834
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 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
194 : bates 820
195 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
196 : maechler 834 * DESCRIPTION (Version): 0.98-1 released to CRAN
197 : bates 820
198 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
199 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
200 :    
201 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
202 :     .Call calls that were producing spurious output.
203 :    
204 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
205 : bates 801
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 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
211 : bates 794
212 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
213 :     unidimensional case.
214 :    
215 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
216 : maechler 791
217 :     * DESCRIPTION (Version): 0.96-1
218 :    
219 :     * moved lmer-class' R and C code moved from lme4 to here
220 :    
221 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
222 : bates 763
223 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
224 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
225 :    
226 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
227 : bates 763
228 :     * src/Makefile.win: Forgot to update this when Makefile changed.
229 :    
230 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
231 : bates 726
232 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
233 :     bug reported by Kurt Hornik and Michael Hahsler.
234 :    
235 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
236 : bates 725
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 : maechler 791
244 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
245 : bates 714
246 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
247 :     colMeans, colSums, rowMeans and rowSums.
248 :    
249 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
250 : bates 692
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 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
263 : bates 692
264 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
265 :    
266 :     * DESCRIPTION: Eliminate import of stats.
267 :    
268 : maechler 791
269 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
270 : bates 692
271 :     * R/AllClass.R : add logical sparse matrix classes
272 :    
273 : maechler 687 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 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
279 : maechler 687
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 : maechler 676 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 : maechler 658 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 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
305 : maechler 658
306 :     * R/pMatrix.R: "pMatrix" class added
307 :     * ....
308 :    
309 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
310 : bates 645
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 : maechler 658 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 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
325 : bates 599
326 :     * src/lmer.c (lmer_fitted): Added.
327 :    
328 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
329 : bates 596
330 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
331 :    
332 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
333 : bates 582
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 : maechler 658
342 : bates 582 * 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 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
352 :    
353 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
354 :    
355 :     * R/dtrMatrix.R: fix t() method
356 :    
357 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
358 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
359 : maechler 578 * 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 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
367 : maechler 578
368 :     * src/dgBCMatrix.c:
369 :     * src/lmer.c: many changes
370 :     * ...
371 :    
372 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
373 :    
374 :     * R/Matrix.R: add more sophisticated show() method.
375 :    
376 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
377 :    
378 :     * */* : almost complete reorganization of classes.
379 :    
380 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
381 : bates 460
382 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
383 :     for the geMatrix class.
384 :    
385 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
386 : bates 460
387 :     * src/Makefile (clean): Remove *.a and *.so
388 :    
389 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
390 :    
391 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
392 : bates 460
393 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
394 : bates 460 had an effect in cases with more than 2 grouping factors.
395 :    
396 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
397 : bates 415
398 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
399 :    
400 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
401 : bates 410
402 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
403 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
404 :    
405 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
406 : bates 392
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 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
413 : bates 388
414 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
415 :     no longer used.
416 :    
417 : bates 388 * 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 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
425 : bates 375
426 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
427 :     scalar grouping factors corrected.
428 :    
429 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
430 : bates 375
431 :     * src/bCrosstab.c: remove diag_update which is no longer used
432 :    
433 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
434 : bates 350
435 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
436 :     .h file can be included.
437 :    
438 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
439 : bates 342
440 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
441 : bates 342 Complete allocation of slots in NEW_OBJECT.
442 :    
443 :     * src/Mutils.h: Moved list of symbols to an include file
444 :    
445 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
446 : bates 342
447 :     * src/geMutils.c (Matrix_init): remove unused function
448 :    
449 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
450 : bates 342
451 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
452 :    
453 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
454 : bates 327
455 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
456 :    
457 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
458 : bates 303
459 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
460 :    
461 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
462 : bates 296
463 :     * src/init.c: Created R_init_Matrix and added registration of C
464 :     routines.
465 :    
466 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
467 : bates 283
468 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
469 :    
470 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
471 : bates 229
472 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
473 :    
474 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
475 :    
476 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
477 :    
478 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
479 :    
480 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
481 :     ssclme_update_mm
482 :    
483 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
484 :    
485 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
486 :     in the order of unconstrained and constrained parameters.
487 :     (ssclme_gradient): Added the gradients (not yet correct for
488 :     multidimensional, unconstrained case).
489 :    
490 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
491 :    
492 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
493 :    
494 :     * src/Makefile.win: Remove unneeded ranlib call
495 :    
496 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
497 :    
498 :     * DESCRIPTION (Version): New release
499 :    
500 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
501 :    
502 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
503 :    
504 :     * src/triplet_to_col.c: Create triplet_to_col as a native
505 : maechler 658 function, not the version from umfpack. There were problems with
506 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
507 :     only one umfpack routine being used so I moved it here.
508 :    
509 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
510 :    
511 :     * src/ssclme.c (ssclme_variances): New function.
512 :    
513 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
514 :    
515 :     * src/ssclme.c (ssclme_fitted): Added function.
516 :    
517 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
518 :    
519 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
520 :     store the dimnames in the XtX and bVar slots
521 :     (ssclme_update_mm): Change the dimensions of the bVar slot
522 :     components and the returned value from ssclme_ranef.
523 :    
524 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
525 :    
526 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
527 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
528 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
529 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
530 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
531 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
532 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
533 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
534 :     Moved the pdMat classes from the lme4 package.
535 :    
536 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
537 :    
538 :     * man/ssclme-class.Rd: Update definition and documentation of the
539 :     ssclme class to include the DIsqrt slot.
540 :    
541 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
542 :     (much faster using dsyrk, a level 3 BLAS routine).
543 :    
544 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
545 :    
546 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
547 :    
548 :     * tests/ssclme.R: Modify the test to account for the permutation
549 :     of the levels of the grouping factors.
550 :    
551 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
552 :    
553 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
554 :     directly into the ssclme class definition.
555 :    
556 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
557 :    
558 :     * DESCRIPTION (Date): New release
559 :    
560 :     * man/ssclme-class.Rd: new file.
561 :    
562 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
563 :     works and it's fast!
564 :    
565 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
566 :    
567 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
568 :    
569 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
570 :    
571 :     * DESCRIPTION (Date): New release
572 :    
573 :     * NAMESPACE: Don't export ssclme.
574 :    
575 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
576 :     school data.
577 :    
578 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
579 :    
580 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
581 :     keep track of the fixed-effects and the response. Counts also
582 :     gets an extra element, which is always one.
583 :    
584 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
585 :    
586 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
587 :    
588 :     * src/cscMatrix.c (csc_transpose): new function
589 :    
590 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
591 :     (csc_components_transpose): new function
592 :    
593 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
594 :    
595 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
596 :     triplets
597 :    
598 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
599 :    
600 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
601 :    
602 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
603 :     and all other .h files in src.
604 :    
605 :     * src/Makefile.win: This and other Makefile.win files contributed
606 :     by Brian Ripley.
607 :    
608 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
609 :    
610 :     * R/syMatrix.R: Added methods for "%*%".
611 :    
612 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
613 :     poMatrix object.
614 :    
615 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
616 :    
617 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
618 :    
619 :     2004-01-25 Douglas Bates <bates@bates2_home>
620 :    
621 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
622 :    
623 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
624 :     of nrow.
625 :    
626 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
627 :    
628 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
629 :     subdirectories.
630 :    
631 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
632 :    
633 :     * src/taucs.h: Accidently referred to global header files
634 :     instead of local files.
635 :    
636 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
637 :    
638 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
639 :     and methods and replaced all classes with S4 classes.
640 :    
641 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
642 :    
643 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
644 :    
645 :     * src/R_LapackPP.cc: Change method of calculating determinants
646 :    
647 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
648 :    
649 :     * DESCRIPTION (Version): removed empty data directory as requested
650 :     by CRAN maintainers. Changed version number and date.
651 :    
652 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
653 :    
654 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
655 :     under Windows.
656 :    
657 :     * Added configure.win and src/Makevars.win as requested by Brian
658 :     Ripley.
659 :    
660 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
661 :    
662 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
663 :     Hornik.
664 :    
665 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
666 :    
667 :     * configure.ac: Replaced configure.in with configure.ac
668 :     contributed by Kurt Hornik.
669 :    
670 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
671 :     version for R-1.5.0
672 :    
673 : maechler 512
674 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
675 :    
676 :     * man/eigen.Rd: Removed the .Alias in the example

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