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Annotation of /pkg/ChangeLog

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1 : bates 1119 2006-01-07 Douglas Bates <bates@bates4.stat.wisc.edu>
2 :    
3 :     * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
4 :     segfault in cases with multiple non-nested grouping factors.
5 :    
6 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
7 :    
8 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
9 :     (Depends): also on 'utils'
10 :    
11 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
12 :     * R/diagMatrix.R (Diagonal): constructor and methods for
13 :     diagonal matrices
14 :    
15 :     * R/ltTMatrix.R: new "minimal methods"
16 :    
17 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
18 :    
19 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
20 :     all methods (and help files).
21 :    
22 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
23 :    
24 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
25 :     for case (dimn. op no_dimn.)
26 :    
27 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
28 :    
29 :     * DESCRIPTION (Version): 0.99-2 released to CRAN
30 :    
31 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
32 :    
33 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
34 :     by Julian Faraway.
35 :    
36 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
37 :    
38 :     * R/Auxiliaries.R (try_as): new utility
39 :     * R/sparseMatrix.R: use try_as() in coercion to original class
40 :    
41 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
42 :    
43 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
44 :    
45 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
46 :    
47 :     * R/Auxiliaries.R (dimNamesCheck): added
48 :    
49 :     * R/Matrix.R (as.array), (as.vector): new
50 :    
51 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
52 :    
53 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
54 : maechler 956 default.
55 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
56 :     "pMatrix" now contains "sparseMatrix"
57 : maechler 954
58 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
59 :    
60 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
61 :    
62 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
63 :    
64 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
65 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
66 :    
67 :     * R/dspMatrix.R: typo in "t" method
68 :    
69 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
70 :    
71 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
72 :     * R/Tsparse.R: instead of R/gTMatrix.R
73 :     * R/Csparse.R: new
74 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
75 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
76 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
77 :     via cholmod
78 :    
79 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
80 :    
81 :     * R/Auxiliaries.R (non0ind): new function using new C code
82 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
83 :    
84 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
85 :    
86 :     * src/chm_common.h: header file required by all C sources that
87 :     call CHOLMOD functions. It defines a cholmod_common structure
88 :     called 'c' whose address is passed as the last argument to
89 :     (virtually) every CHOLMOD function.
90 :    
91 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
92 :    
93 :     * src/init.c: initialize and finalize the cholmod_common structure.
94 :    
95 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
96 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
97 :    
98 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
99 :    
100 :     * inst/test-tools.R: new file collecting the utility functions used
101 :     in ./tests/*.R
102 :    
103 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
104 :     * R/Matrix.R (cbind2): methods for NULL and missing
105 :    
106 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
107 :    
108 :     * R/AllClass.R: new "index" class for "[" and "[<-":
109 :     First cut at "symmetricMatrix" and "triangularMatrix"
110 :     * R/gTMatrix.R (.ind.prep): new function;
111 :     Logical and character indexing now work too.
112 :     * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
113 :     * tests/indexing.R: new, including *.Rout.save
114 :     * tests/dgTMatrix.R: new
115 :    
116 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
117 :    
118 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
119 :     indicator pos not being updated. Also enforced upper triangular
120 :     for symmetric case. Need to coerce edges component of elements of
121 :     edge list - grr! (Why don't they define their classes cleanly?)
122 :    
123 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
124 :    
125 :     * R/Matrix.R: added first "[<-" methods; not yet functional
126 :     * R/denseMatrix.R: dito
127 :     * man/Subassign-methods.Rd: new help file for these
128 :    
129 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
130 :    
131 :     * DESCRIPTION (Version): 0.98-6
132 :    
133 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
134 :     matrices.
135 :    
136 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
137 :    
138 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
139 :     as( <logical>, "matrix")
140 :    
141 :     * R/pMatrix.R: coercion to "lgTMatrix"
142 :    
143 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
144 :     * man/gTMatrix-class.Rd:
145 :     * General slight re-organization of where "[" methods are defined.
146 :     more to come.
147 :    
148 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
149 : maechler 868
150 : maechler 871 * DESCRIPTION (Version): 0.98-5 released to CRAN
151 :    
152 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
153 :     * .....
154 :    
155 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
156 :    
157 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
158 :     or glmer objects.
159 :    
160 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
161 :    
162 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
163 :    
164 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
165 :    
166 :     * R/HBMM.R: finish re-writing R-only code.
167 :    
168 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
169 :    
170 :     * man/externalFormats.Rd: move documentation for writeHB and
171 :     writeMM here.
172 :    
173 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
174 :     (suggested by Paul Roecker).
175 :    
176 :     * tests/validObj.R (assertError): Comment out test that is failing
177 :     after recent changes in r-devel.
178 :    
179 : maechler 860
180 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
181 :    
182 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
183 :     * man/denseMatrix-class.Rd
184 :     * NAMESPACE: export it, and also export
185 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
186 :    
187 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
188 :    
189 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
190 :    
191 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
192 :     matrix_solve code (which was really, really wrong).
193 :    
194 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
195 : maechler 834
196 :     * DESCRIPTION (Version): 0.98-2
197 :    
198 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
199 :    
200 :     * R/lmer.R (abbrvNms): new
201 :     * R/lmer.R (mcmcsamp): allow transformed parameters
202 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
203 :     for the Harwell-Boeing and the MatrixMarket formats.
204 : maechler 834
205 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
206 :    
207 :     * man/dtrMatrix-class.Rd: add examples
208 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
209 : maechler 834
210 :     * TODO: note the dtpMatrix (docu) bug
211 :    
212 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
213 :     in order to ensure that new as.matrix() is used by old functions,
214 :     e.g., svd(), qr(), eigen(), dist(),..;
215 :     apply(), also matplot() or pairs().
216 :    
217 :    
218 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
219 :    
220 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
221 :     add comments about 'control' / lmerControl() arguments
222 :    
223 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
224 : bates 820
225 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
226 : maechler 834 * DESCRIPTION (Version): 0.98-1 released to CRAN
227 : bates 820
228 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
229 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
230 :    
231 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
232 :     .Call calls that were producing spurious output.
233 :    
234 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
235 : bates 801
236 :     * R/lmer.R (lmer): stored updated variance component estimates in
237 :     mer object for the generalized model. (Bug reported by Renaud
238 :     Lancelot).
239 :    
240 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
241 : bates 794
242 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
243 :     unidimensional case.
244 :    
245 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
246 : maechler 791
247 :     * DESCRIPTION (Version): 0.96-1
248 :    
249 :     * moved lmer-class' R and C code moved from lme4 to here
250 :    
251 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
252 : bates 763
253 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
254 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
255 :    
256 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
257 : bates 763
258 :     * src/Makefile.win: Forgot to update this when Makefile changed.
259 :    
260 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
261 : bates 726
262 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
263 :     bug reported by Kurt Hornik and Michael Hahsler.
264 :    
265 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
266 : bates 725
267 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
268 :     logical sparse matrices. These will also be used in the symbolic
269 :     analysis for lmer objects.
270 :    
271 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
272 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
273 : maechler 791
274 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
275 : bates 714
276 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
277 :     colMeans, colSums, rowMeans and rowSums.
278 :    
279 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
280 : bates 692
281 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
282 :     multiplication operation.
283 :    
284 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
285 :     to dgetrs.
286 :    
287 :     * src/init.c: Fix cut-and-paste error in definition of
288 :     dgeMatrix_matrix_solve
289 :    
290 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
291 :    
292 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
293 : bates 692
294 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
295 :    
296 :     * DESCRIPTION: Eliminate import of stats.
297 :    
298 : maechler 791
299 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
300 : bates 692
301 :     * R/AllClass.R : add logical sparse matrix classes
302 :    
303 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
304 :    
305 :     * R/dgTMatrix.R: add "[" method for triplet matrices
306 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
307 :    
308 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
309 : maechler 687
310 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
311 :    
312 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
313 :     * R/sparseMatrix.R: %*%, crossprod()
314 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
315 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
316 :     * src/lmer.c (lmer_fitted): fix thinko
317 :    
318 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
319 :    
320 :     * R/AllClass.R: add two virtual sparse classes ``on top''
321 :    
322 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
323 :    
324 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
325 :     correspondingly fix examples and tests/ since new()
326 :     doesn't work for virtual classes.
327 :    
328 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
329 :    
330 :     * R/Matrix.R (as.matrix): method and one for unname()
331 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
332 :     also run for R 2.1.0; using as.matrix()
333 :    
334 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
335 : maechler 658
336 :     * R/pMatrix.R: "pMatrix" class added
337 :     * ....
338 :    
339 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
340 : bates 645
341 :     * R/dtpMatrix.R: Add unpack method and an example.
342 :    
343 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
344 :     of general symmetric matrices and associated S4 methods.
345 :    
346 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
347 :     +
348 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
349 :    
350 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
351 :     crossprod() and "%*%" methods added; tests, too.
352 :     * tests/matprod.R: new, for testing these
353 :    
354 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
355 : bates 599
356 :     * src/lmer.c (lmer_fitted): Added.
357 :    
358 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
359 : bates 596
360 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
361 :    
362 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
363 : bates 582
364 :     * src/*.c,po/,inst/po: Internationalization and localization of
365 :     the package.
366 :    
367 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
368 :     R_ldl.c file.
369 :    
370 :     * src/flame.[ch]: Removed these source files.
371 : maechler 658
372 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
373 :    
374 :     * src/LU.[ch],src/init.c: absorb in factorizations
375 :    
376 :     * src/Mutils.h: prepare for internationalization
377 :    
378 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
379 :     this file
380 :    
381 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
382 :    
383 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
384 :    
385 :     * R/dtrMatrix.R: fix t() method
386 :    
387 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
388 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
389 : maechler 578 * tests/group-methods.R : and test them.
390 :    
391 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
392 :     border case
393 :    
394 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
395 :    
396 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
397 : maechler 578
398 :     * src/dgBCMatrix.c:
399 :     * src/lmer.c: many changes
400 :     * ...
401 :    
402 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
403 :    
404 :     * R/Matrix.R: add more sophisticated show() method.
405 :    
406 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
407 :    
408 :     * */* : almost complete reorganization of classes.
409 :    
410 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
411 : bates 460
412 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
413 :     for the geMatrix class.
414 :    
415 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
416 : bates 460
417 :     * src/Makefile (clean): Remove *.a and *.so
418 :    
419 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
420 :    
421 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
422 : bates 460
423 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
424 : bates 460 had an effect in cases with more than 2 grouping factors.
425 :    
426 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
427 : bates 415
428 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
429 :    
430 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
431 : bates 410
432 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
433 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
434 :    
435 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
436 : bates 392
437 :     * R/sscMatrix.R: Add determinant methods
438 :    
439 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
440 :     for tripletMatrix to matrix.
441 :    
442 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
443 : bates 388
444 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
445 :     no longer used.
446 :    
447 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
448 :     with dynamic allocation of scratch arrays.
449 :    
450 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
451 :     for multivariate random effects with multiple grouping factors.
452 :     Fixes part but not all of #15.
453 :    
454 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
455 : bates 375
456 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
457 :     scalar grouping factors corrected.
458 :    
459 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
460 : bates 375
461 :     * src/bCrosstab.c: remove diag_update which is no longer used
462 :    
463 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
464 : bates 350
465 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
466 :     .h file can be included.
467 :    
468 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
469 : bates 342
470 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
471 : bates 342 Complete allocation of slots in NEW_OBJECT.
472 :    
473 :     * src/Mutils.h: Moved list of symbols to an include file
474 :    
475 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
476 : bates 342
477 :     * src/geMutils.c (Matrix_init): remove unused function
478 :    
479 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
480 : bates 342
481 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
482 :    
483 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
484 : bates 327
485 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
486 :    
487 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
488 : bates 303
489 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
490 :    
491 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
492 : bates 296
493 :     * src/init.c: Created R_init_Matrix and added registration of C
494 :     routines.
495 :    
496 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
497 : bates 283
498 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
499 :    
500 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
501 : bates 229
502 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
503 :    
504 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
505 :    
506 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
507 :    
508 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
509 :    
510 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
511 :     ssclme_update_mm
512 :    
513 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
514 :    
515 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
516 :     in the order of unconstrained and constrained parameters.
517 :     (ssclme_gradient): Added the gradients (not yet correct for
518 :     multidimensional, unconstrained case).
519 :    
520 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
521 :    
522 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
523 :    
524 :     * src/Makefile.win: Remove unneeded ranlib call
525 :    
526 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
527 :    
528 :     * DESCRIPTION (Version): New release
529 :    
530 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
531 :    
532 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
533 :    
534 :     * src/triplet_to_col.c: Create triplet_to_col as a native
535 : maechler 658 function, not the version from umfpack. There were problems with
536 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
537 :     only one umfpack routine being used so I moved it here.
538 :    
539 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
540 :    
541 :     * src/ssclme.c (ssclme_variances): New function.
542 :    
543 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
544 :    
545 :     * src/ssclme.c (ssclme_fitted): Added function.
546 :    
547 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
548 :    
549 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
550 :     store the dimnames in the XtX and bVar slots
551 :     (ssclme_update_mm): Change the dimensions of the bVar slot
552 :     components and the returned value from ssclme_ranef.
553 :    
554 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
555 :    
556 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
557 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
558 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
559 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
560 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
561 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
562 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
563 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
564 :     Moved the pdMat classes from the lme4 package.
565 :    
566 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
567 :    
568 :     * man/ssclme-class.Rd: Update definition and documentation of the
569 :     ssclme class to include the DIsqrt slot.
570 :    
571 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
572 :     (much faster using dsyrk, a level 3 BLAS routine).
573 :    
574 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
575 :    
576 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
577 :    
578 :     * tests/ssclme.R: Modify the test to account for the permutation
579 :     of the levels of the grouping factors.
580 :    
581 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
582 :    
583 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
584 :     directly into the ssclme class definition.
585 :    
586 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
587 :    
588 :     * DESCRIPTION (Date): New release
589 :    
590 :     * man/ssclme-class.Rd: new file.
591 :    
592 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
593 :     works and it's fast!
594 :    
595 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
596 :    
597 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
598 :    
599 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
600 :    
601 :     * DESCRIPTION (Date): New release
602 :    
603 :     * NAMESPACE: Don't export ssclme.
604 :    
605 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
606 :     school data.
607 :    
608 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
609 :    
610 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
611 :     keep track of the fixed-effects and the response. Counts also
612 :     gets an extra element, which is always one.
613 :    
614 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
615 :    
616 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
617 :    
618 :     * src/cscMatrix.c (csc_transpose): new function
619 :    
620 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
621 :     (csc_components_transpose): new function
622 :    
623 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
624 :    
625 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
626 :     triplets
627 :    
628 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
629 :    
630 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
631 :    
632 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
633 :     and all other .h files in src.
634 :    
635 :     * src/Makefile.win: This and other Makefile.win files contributed
636 :     by Brian Ripley.
637 :    
638 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
639 :    
640 :     * R/syMatrix.R: Added methods for "%*%".
641 :    
642 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
643 :     poMatrix object.
644 :    
645 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
646 :    
647 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
648 :    
649 :     2004-01-25 Douglas Bates <bates@bates2_home>
650 :    
651 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
652 :    
653 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
654 :     of nrow.
655 :    
656 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
657 :    
658 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
659 :     subdirectories.
660 :    
661 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
662 :    
663 :     * src/taucs.h: Accidently referred to global header files
664 :     instead of local files.
665 :    
666 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
667 :    
668 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
669 :     and methods and replaced all classes with S4 classes.
670 :    
671 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
672 :    
673 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
674 :    
675 :     * src/R_LapackPP.cc: Change method of calculating determinants
676 :    
677 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
678 :    
679 :     * DESCRIPTION (Version): removed empty data directory as requested
680 :     by CRAN maintainers. Changed version number and date.
681 :    
682 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
683 :    
684 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
685 :     under Windows.
686 :    
687 :     * Added configure.win and src/Makevars.win as requested by Brian
688 :     Ripley.
689 :    
690 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
691 :    
692 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
693 :     Hornik.
694 :    
695 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
696 :    
697 :     * configure.ac: Replaced configure.in with configure.ac
698 :     contributed by Kurt Hornik.
699 :    
700 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
701 :     version for R-1.5.0
702 :    
703 : maechler 512
704 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
705 :    
706 :     * man/eigen.Rd: Removed the .Alias in the example

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