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Annotation of /pkg/ChangeLog

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1 : maechler 1084 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 : bates 988 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 : maechler 976 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 : maechler 956 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 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
31 :    
32 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
33 : maechler 956 default.
34 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
35 :     "pMatrix" now contains "sparseMatrix"
36 : maechler 954
37 : maechler 948 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 : maechler 925 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 : bates 917 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 : maechler 908 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 : maechler 886 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 : bates 876 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 : maechler 871 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 : maechler 868 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 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
128 : maechler 868
129 : maechler 871 * DESCRIPTION (Version): 0.98-5 released to CRAN
130 :    
131 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
132 :     * .....
133 :    
134 : bates 863 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 : maechler 860 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 : bates 854 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 : maechler 860
159 : maechler 848 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 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
167 :    
168 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
169 :    
170 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
171 :     matrix_solve code (which was really, really wrong).
172 :    
173 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
174 : maechler 834
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 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
182 :     for the Harwell-Boeing and the MatrixMarket formats.
183 : maechler 834
184 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
185 :    
186 :     * man/dtrMatrix-class.Rd: add examples
187 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
188 : maechler 834
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 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
203 : bates 820
204 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
205 : maechler 834 * DESCRIPTION (Version): 0.98-1 released to CRAN
206 : bates 820
207 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
208 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
209 :    
210 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
211 :     .Call calls that were producing spurious output.
212 :    
213 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
214 : bates 801
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 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
220 : bates 794
221 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
222 :     unidimensional case.
223 :    
224 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
225 : maechler 791
226 :     * DESCRIPTION (Version): 0.96-1
227 :    
228 :     * moved lmer-class' R and C code moved from lme4 to here
229 :    
230 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
231 : bates 763
232 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
233 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
234 :    
235 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
236 : bates 763
237 :     * src/Makefile.win: Forgot to update this when Makefile changed.
238 :    
239 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
240 : bates 726
241 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
242 :     bug reported by Kurt Hornik and Michael Hahsler.
243 :    
244 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
245 : bates 725
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 : maechler 791
253 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
254 : bates 714
255 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
256 :     colMeans, colSums, rowMeans and rowSums.
257 :    
258 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
259 : bates 692
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 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
272 : bates 692
273 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
274 :    
275 :     * DESCRIPTION: Eliminate import of stats.
276 :    
277 : maechler 791
278 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
279 : bates 692
280 :     * R/AllClass.R : add logical sparse matrix classes
281 :    
282 : maechler 687 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 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
288 : maechler 687
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 : maechler 676 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 : maechler 658 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 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
314 : maechler 658
315 :     * R/pMatrix.R: "pMatrix" class added
316 :     * ....
317 :    
318 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
319 : bates 645
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 : maechler 658 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 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
334 : bates 599
335 :     * src/lmer.c (lmer_fitted): Added.
336 :    
337 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
338 : bates 596
339 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
340 :    
341 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
342 : bates 582
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 : maechler 658
351 : bates 582 * 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 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
361 :    
362 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
363 :    
364 :     * R/dtrMatrix.R: fix t() method
365 :    
366 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
367 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
368 : maechler 578 * 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 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
376 : maechler 578
377 :     * src/dgBCMatrix.c:
378 :     * src/lmer.c: many changes
379 :     * ...
380 :    
381 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
382 :    
383 :     * R/Matrix.R: add more sophisticated show() method.
384 :    
385 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
386 :    
387 :     * */* : almost complete reorganization of classes.
388 :    
389 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
390 : bates 460
391 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
392 :     for the geMatrix class.
393 :    
394 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
395 : bates 460
396 :     * src/Makefile (clean): Remove *.a and *.so
397 :    
398 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
399 :    
400 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
401 : bates 460
402 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
403 : bates 460 had an effect in cases with more than 2 grouping factors.
404 :    
405 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
406 : bates 415
407 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
408 :    
409 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
410 : bates 410
411 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
412 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
413 :    
414 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
415 : bates 392
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 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
422 : bates 388
423 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
424 :     no longer used.
425 :    
426 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
427 :     with dynamic allocation of scratch arrays.
428 :    
429 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
430 :     for multivariate random effects with multiple grouping factors.
431 :     Fixes part but not all of #15.
432 :    
433 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
434 : bates 375
435 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
436 :     scalar grouping factors corrected.
437 :    
438 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
439 : bates 375
440 :     * src/bCrosstab.c: remove diag_update which is no longer used
441 :    
442 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
443 : bates 350
444 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
445 :     .h file can be included.
446 :    
447 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
448 : bates 342
449 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
450 : bates 342 Complete allocation of slots in NEW_OBJECT.
451 :    
452 :     * src/Mutils.h: Moved list of symbols to an include file
453 :    
454 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
455 : bates 342
456 :     * src/geMutils.c (Matrix_init): remove unused function
457 :    
458 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
459 : bates 342
460 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
461 :    
462 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
463 : bates 327
464 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
465 :    
466 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
467 : bates 303
468 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
469 :    
470 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
471 : bates 296
472 :     * src/init.c: Created R_init_Matrix and added registration of C
473 :     routines.
474 :    
475 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
476 : bates 283
477 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
478 :    
479 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
480 : bates 229
481 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
482 :    
483 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
484 :    
485 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
486 :    
487 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
488 :    
489 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
490 :     ssclme_update_mm
491 :    
492 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
493 :    
494 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
495 :     in the order of unconstrained and constrained parameters.
496 :     (ssclme_gradient): Added the gradients (not yet correct for
497 :     multidimensional, unconstrained case).
498 :    
499 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
500 :    
501 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
502 :    
503 :     * src/Makefile.win: Remove unneeded ranlib call
504 :    
505 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
506 :    
507 :     * DESCRIPTION (Version): New release
508 :    
509 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
510 :    
511 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
512 :    
513 :     * src/triplet_to_col.c: Create triplet_to_col as a native
514 : maechler 658 function, not the version from umfpack. There were problems with
515 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
516 :     only one umfpack routine being used so I moved it here.
517 :    
518 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
519 :    
520 :     * src/ssclme.c (ssclme_variances): New function.
521 :    
522 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
523 :    
524 :     * src/ssclme.c (ssclme_fitted): Added function.
525 :    
526 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
527 :    
528 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
529 :     store the dimnames in the XtX and bVar slots
530 :     (ssclme_update_mm): Change the dimensions of the bVar slot
531 :     components and the returned value from ssclme_ranef.
532 :    
533 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
534 :    
535 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
536 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
537 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
538 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
539 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
540 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
541 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
542 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
543 :     Moved the pdMat classes from the lme4 package.
544 :    
545 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
546 :    
547 :     * man/ssclme-class.Rd: Update definition and documentation of the
548 :     ssclme class to include the DIsqrt slot.
549 :    
550 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
551 :     (much faster using dsyrk, a level 3 BLAS routine).
552 :    
553 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
554 :    
555 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
556 :    
557 :     * tests/ssclme.R: Modify the test to account for the permutation
558 :     of the levels of the grouping factors.
559 :    
560 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
561 :    
562 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
563 :     directly into the ssclme class definition.
564 :    
565 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
566 :    
567 :     * DESCRIPTION (Date): New release
568 :    
569 :     * man/ssclme-class.Rd: new file.
570 :    
571 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
572 :     works and it's fast!
573 :    
574 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
575 :    
576 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
577 :    
578 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
579 :    
580 :     * DESCRIPTION (Date): New release
581 :    
582 :     * NAMESPACE: Don't export ssclme.
583 :    
584 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
585 :     school data.
586 :    
587 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
588 :    
589 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
590 :     keep track of the fixed-effects and the response. Counts also
591 :     gets an extra element, which is always one.
592 :    
593 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
594 :    
595 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
596 :    
597 :     * src/cscMatrix.c (csc_transpose): new function
598 :    
599 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
600 :     (csc_components_transpose): new function
601 :    
602 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
603 :    
604 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
605 :     triplets
606 :    
607 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
608 :    
609 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
610 :    
611 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
612 :     and all other .h files in src.
613 :    
614 :     * src/Makefile.win: This and other Makefile.win files contributed
615 :     by Brian Ripley.
616 :    
617 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
618 :    
619 :     * R/syMatrix.R: Added methods for "%*%".
620 :    
621 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
622 :     poMatrix object.
623 :    
624 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
625 :    
626 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
627 :    
628 :     2004-01-25 Douglas Bates <bates@bates2_home>
629 :    
630 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
631 :    
632 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
633 :     of nrow.
634 :    
635 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
636 :    
637 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
638 :     subdirectories.
639 :    
640 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
641 :    
642 :     * src/taucs.h: Accidently referred to global header files
643 :     instead of local files.
644 :    
645 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
646 :    
647 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
648 :     and methods and replaced all classes with S4 classes.
649 :    
650 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
651 :    
652 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
653 :    
654 :     * src/R_LapackPP.cc: Change method of calculating determinants
655 :    
656 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
657 :    
658 :     * DESCRIPTION (Version): removed empty data directory as requested
659 :     by CRAN maintainers. Changed version number and date.
660 :    
661 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
662 :    
663 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
664 :     under Windows.
665 :    
666 :     * Added configure.win and src/Makevars.win as requested by Brian
667 :     Ripley.
668 :    
669 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
670 :    
671 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
672 :     Hornik.
673 :    
674 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
675 :    
676 :     * configure.ac: Replaced configure.in with configure.ac
677 :     contributed by Kurt Hornik.
678 :    
679 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
680 :     version for R-1.5.0
681 :    
682 : maechler 512
683 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
684 :    
685 :     * man/eigen.Rd: Removed the .Alias in the example

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