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Annotation of /pkg/ChangeLog

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1 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
2 : bates 1119
3 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
4 :    
5 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
6 :     segfault in cases with multiple non-nested grouping factors.
7 :    
8 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
9 :    
10 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
11 :     (Depends): also on 'utils'
12 :    
13 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
14 :     * R/diagMatrix.R (Diagonal): constructor and methods for
15 :     diagonal matrices
16 :    
17 :     * R/ltTMatrix.R: new "minimal methods"
18 :    
19 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
20 :    
21 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
22 :     all methods (and help files).
23 :    
24 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
25 :    
26 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
27 :     for case (dimn. op no_dimn.)
28 :    
29 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
30 :    
31 :     * DESCRIPTION (Version): 0.99-2 released to CRAN
32 :    
33 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
34 :    
35 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
36 :     by Julian Faraway.
37 :    
38 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
39 :    
40 :     * R/Auxiliaries.R (try_as): new utility
41 :     * R/sparseMatrix.R: use try_as() in coercion to original class
42 :    
43 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
44 :    
45 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
46 :    
47 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
48 :    
49 :     * R/Auxiliaries.R (dimNamesCheck): added
50 :    
51 :     * R/Matrix.R (as.array), (as.vector): new
52 :    
53 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
54 :    
55 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
56 : maechler 956 default.
57 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
58 :     "pMatrix" now contains "sparseMatrix"
59 : maechler 954
60 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
61 :    
62 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
63 :    
64 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
65 :    
66 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
67 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
68 :    
69 :     * R/dspMatrix.R: typo in "t" method
70 :    
71 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
72 :    
73 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
74 :     * R/Tsparse.R: instead of R/gTMatrix.R
75 :     * R/Csparse.R: new
76 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
77 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
78 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
79 :     via cholmod
80 :    
81 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
82 :    
83 :     * R/Auxiliaries.R (non0ind): new function using new C code
84 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
85 :    
86 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
87 :    
88 :     * src/chm_common.h: header file required by all C sources that
89 :     call CHOLMOD functions. It defines a cholmod_common structure
90 :     called 'c' whose address is passed as the last argument to
91 :     (virtually) every CHOLMOD function.
92 :    
93 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
94 :    
95 :     * src/init.c: initialize and finalize the cholmod_common structure.
96 :    
97 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
98 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
99 :    
100 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
101 :    
102 :     * inst/test-tools.R: new file collecting the utility functions used
103 :     in ./tests/*.R
104 :    
105 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
106 :     * R/Matrix.R (cbind2): methods for NULL and missing
107 :    
108 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
109 :    
110 :     * R/AllClass.R: new "index" class for "[" and "[<-":
111 :     First cut at "symmetricMatrix" and "triangularMatrix"
112 :     * R/gTMatrix.R (.ind.prep): new function;
113 :     Logical and character indexing now work too.
114 :     * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
115 :     * tests/indexing.R: new, including *.Rout.save
116 :     * tests/dgTMatrix.R: new
117 :    
118 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
119 :    
120 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
121 :     indicator pos not being updated. Also enforced upper triangular
122 :     for symmetric case. Need to coerce edges component of elements of
123 :     edge list - grr! (Why don't they define their classes cleanly?)
124 :    
125 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
126 :    
127 :     * R/Matrix.R: added first "[<-" methods; not yet functional
128 :     * R/denseMatrix.R: dito
129 :     * man/Subassign-methods.Rd: new help file for these
130 :    
131 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
132 :    
133 :     * DESCRIPTION (Version): 0.98-6
134 :    
135 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
136 :     matrices.
137 :    
138 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
139 :    
140 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
141 :     as( <logical>, "matrix")
142 :    
143 :     * R/pMatrix.R: coercion to "lgTMatrix"
144 :    
145 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
146 :     * man/gTMatrix-class.Rd:
147 :     * General slight re-organization of where "[" methods are defined.
148 :     more to come.
149 :    
150 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
151 : maechler 868
152 : maechler 871 * DESCRIPTION (Version): 0.98-5 released to CRAN
153 :    
154 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
155 :     * .....
156 :    
157 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
158 :    
159 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
160 :     or glmer objects.
161 :    
162 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
163 :    
164 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
165 :    
166 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
167 :    
168 :     * R/HBMM.R: finish re-writing R-only code.
169 :    
170 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
171 :    
172 :     * man/externalFormats.Rd: move documentation for writeHB and
173 :     writeMM here.
174 :    
175 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
176 :     (suggested by Paul Roecker).
177 :    
178 :     * tests/validObj.R (assertError): Comment out test that is failing
179 :     after recent changes in r-devel.
180 :    
181 : maechler 860
182 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
183 :    
184 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
185 :     * man/denseMatrix-class.Rd
186 :     * NAMESPACE: export it, and also export
187 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
188 :    
189 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
190 :    
191 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
192 :    
193 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
194 :     matrix_solve code (which was really, really wrong).
195 :    
196 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
197 : maechler 834
198 :     * DESCRIPTION (Version): 0.98-2
199 :    
200 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
201 :    
202 :     * R/lmer.R (abbrvNms): new
203 :     * R/lmer.R (mcmcsamp): allow transformed parameters
204 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
205 :     for the Harwell-Boeing and the MatrixMarket formats.
206 : maechler 834
207 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
208 :    
209 :     * man/dtrMatrix-class.Rd: add examples
210 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
211 : maechler 834
212 :     * TODO: note the dtpMatrix (docu) bug
213 :    
214 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
215 :     in order to ensure that new as.matrix() is used by old functions,
216 :     e.g., svd(), qr(), eigen(), dist(),..;
217 :     apply(), also matplot() or pairs().
218 :    
219 :    
220 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
221 :    
222 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
223 :     add comments about 'control' / lmerControl() arguments
224 :    
225 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
226 : bates 820
227 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
228 : maechler 834 * DESCRIPTION (Version): 0.98-1 released to CRAN
229 : bates 820
230 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
231 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
232 :    
233 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
234 :     .Call calls that were producing spurious output.
235 :    
236 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
237 : bates 801
238 :     * R/lmer.R (lmer): stored updated variance component estimates in
239 :     mer object for the generalized model. (Bug reported by Renaud
240 :     Lancelot).
241 :    
242 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
243 : bates 794
244 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
245 :     unidimensional case.
246 :    
247 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
248 : maechler 791
249 :     * DESCRIPTION (Version): 0.96-1
250 :    
251 :     * moved lmer-class' R and C code moved from lme4 to here
252 :    
253 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
254 : bates 763
255 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
256 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
257 :    
258 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
259 : bates 763
260 :     * src/Makefile.win: Forgot to update this when Makefile changed.
261 :    
262 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
263 : bates 726
264 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
265 :     bug reported by Kurt Hornik and Michael Hahsler.
266 :    
267 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
268 : bates 725
269 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
270 :     logical sparse matrices. These will also be used in the symbolic
271 :     analysis for lmer objects.
272 :    
273 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
274 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
275 : maechler 791
276 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
277 : bates 714
278 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
279 :     colMeans, colSums, rowMeans and rowSums.
280 :    
281 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
282 : bates 692
283 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
284 :     multiplication operation.
285 :    
286 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
287 :     to dgetrs.
288 :    
289 :     * src/init.c: Fix cut-and-paste error in definition of
290 :     dgeMatrix_matrix_solve
291 :    
292 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
293 :    
294 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
295 : bates 692
296 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
297 :    
298 :     * DESCRIPTION: Eliminate import of stats.
299 :    
300 : maechler 791
301 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
302 : bates 692
303 :     * R/AllClass.R : add logical sparse matrix classes
304 :    
305 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
306 :    
307 :     * R/dgTMatrix.R: add "[" method for triplet matrices
308 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
309 :    
310 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
311 : maechler 687
312 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
313 :    
314 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
315 :     * R/sparseMatrix.R: %*%, crossprod()
316 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
317 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
318 :     * src/lmer.c (lmer_fitted): fix thinko
319 :    
320 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
321 :    
322 :     * R/AllClass.R: add two virtual sparse classes ``on top''
323 :    
324 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
325 :    
326 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
327 :     correspondingly fix examples and tests/ since new()
328 :     doesn't work for virtual classes.
329 :    
330 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
331 :    
332 :     * R/Matrix.R (as.matrix): method and one for unname()
333 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
334 :     also run for R 2.1.0; using as.matrix()
335 :    
336 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
337 : maechler 658
338 :     * R/pMatrix.R: "pMatrix" class added
339 :     * ....
340 :    
341 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
342 : bates 645
343 :     * R/dtpMatrix.R: Add unpack method and an example.
344 :    
345 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
346 :     of general symmetric matrices and associated S4 methods.
347 :    
348 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
349 :     +
350 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
351 :    
352 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
353 :     crossprod() and "%*%" methods added; tests, too.
354 :     * tests/matprod.R: new, for testing these
355 :    
356 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
357 : bates 599
358 :     * src/lmer.c (lmer_fitted): Added.
359 :    
360 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
361 : bates 596
362 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
363 :    
364 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
365 : bates 582
366 :     * src/*.c,po/,inst/po: Internationalization and localization of
367 :     the package.
368 :    
369 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
370 :     R_ldl.c file.
371 :    
372 :     * src/flame.[ch]: Removed these source files.
373 : maechler 658
374 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
375 :    
376 :     * src/LU.[ch],src/init.c: absorb in factorizations
377 :    
378 :     * src/Mutils.h: prepare for internationalization
379 :    
380 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
381 :     this file
382 :    
383 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
384 :    
385 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
386 :    
387 :     * R/dtrMatrix.R: fix t() method
388 :    
389 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
390 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
391 : maechler 578 * tests/group-methods.R : and test them.
392 :    
393 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
394 :     border case
395 :    
396 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
397 :    
398 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
399 : maechler 578
400 :     * src/dgBCMatrix.c:
401 :     * src/lmer.c: many changes
402 :     * ...
403 :    
404 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
405 :    
406 :     * R/Matrix.R: add more sophisticated show() method.
407 :    
408 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
409 :    
410 :     * */* : almost complete reorganization of classes.
411 :    
412 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
413 : bates 460
414 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
415 :     for the geMatrix class.
416 :    
417 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
418 : bates 460
419 :     * src/Makefile (clean): Remove *.a and *.so
420 :    
421 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
422 :    
423 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
424 : bates 460
425 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
426 : bates 460 had an effect in cases with more than 2 grouping factors.
427 :    
428 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
429 : bates 415
430 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
431 :    
432 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
433 : bates 410
434 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
435 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
436 :    
437 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
438 : bates 392
439 :     * R/sscMatrix.R: Add determinant methods
440 :    
441 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
442 :     for tripletMatrix to matrix.
443 :    
444 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
445 : bates 388
446 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
447 :     no longer used.
448 :    
449 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
450 :     with dynamic allocation of scratch arrays.
451 :    
452 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
453 :     for multivariate random effects with multiple grouping factors.
454 :     Fixes part but not all of #15.
455 :    
456 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
457 : bates 375
458 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
459 :     scalar grouping factors corrected.
460 :    
461 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
462 : bates 375
463 :     * src/bCrosstab.c: remove diag_update which is no longer used
464 :    
465 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
466 : bates 350
467 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
468 :     .h file can be included.
469 :    
470 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
471 : bates 342
472 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
473 : bates 342 Complete allocation of slots in NEW_OBJECT.
474 :    
475 :     * src/Mutils.h: Moved list of symbols to an include file
476 :    
477 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
478 : bates 342
479 :     * src/geMutils.c (Matrix_init): remove unused function
480 :    
481 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
482 : bates 342
483 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
484 :    
485 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
486 : bates 327
487 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
488 :    
489 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
490 : bates 303
491 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
492 :    
493 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
494 : bates 296
495 :     * src/init.c: Created R_init_Matrix and added registration of C
496 :     routines.
497 :    
498 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
499 : bates 283
500 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
501 :    
502 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
503 : bates 229
504 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
505 :    
506 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
507 :    
508 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
509 :    
510 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
511 :    
512 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
513 :     ssclme_update_mm
514 :    
515 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
516 :    
517 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
518 :     in the order of unconstrained and constrained parameters.
519 :     (ssclme_gradient): Added the gradients (not yet correct for
520 :     multidimensional, unconstrained case).
521 :    
522 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
523 :    
524 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
525 :    
526 :     * src/Makefile.win: Remove unneeded ranlib call
527 :    
528 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
529 :    
530 :     * DESCRIPTION (Version): New release
531 :    
532 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
533 :    
534 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
535 :    
536 :     * src/triplet_to_col.c: Create triplet_to_col as a native
537 : maechler 658 function, not the version from umfpack. There were problems with
538 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
539 :     only one umfpack routine being used so I moved it here.
540 :    
541 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
542 :    
543 :     * src/ssclme.c (ssclme_variances): New function.
544 :    
545 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
546 :    
547 :     * src/ssclme.c (ssclme_fitted): Added function.
548 :    
549 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
550 :    
551 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
552 :     store the dimnames in the XtX and bVar slots
553 :     (ssclme_update_mm): Change the dimensions of the bVar slot
554 :     components and the returned value from ssclme_ranef.
555 :    
556 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
557 :    
558 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
559 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
560 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
561 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
562 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
563 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
564 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
565 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
566 :     Moved the pdMat classes from the lme4 package.
567 :    
568 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
569 :    
570 :     * man/ssclme-class.Rd: Update definition and documentation of the
571 :     ssclme class to include the DIsqrt slot.
572 :    
573 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
574 :     (much faster using dsyrk, a level 3 BLAS routine).
575 :    
576 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
577 :    
578 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
579 :    
580 :     * tests/ssclme.R: Modify the test to account for the permutation
581 :     of the levels of the grouping factors.
582 :    
583 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
584 :    
585 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
586 :     directly into the ssclme class definition.
587 :    
588 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
589 :    
590 :     * DESCRIPTION (Date): New release
591 :    
592 :     * man/ssclme-class.Rd: new file.
593 :    
594 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
595 :     works and it's fast!
596 :    
597 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
598 :    
599 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
600 :    
601 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
602 :    
603 :     * DESCRIPTION (Date): New release
604 :    
605 :     * NAMESPACE: Don't export ssclme.
606 :    
607 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
608 :     school data.
609 :    
610 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
611 :    
612 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
613 :     keep track of the fixed-effects and the response. Counts also
614 :     gets an extra element, which is always one.
615 :    
616 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
617 :    
618 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
619 :    
620 :     * src/cscMatrix.c (csc_transpose): new function
621 :    
622 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
623 :     (csc_components_transpose): new function
624 :    
625 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
626 :    
627 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
628 :     triplets
629 :    
630 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
631 :    
632 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
633 :    
634 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
635 :     and all other .h files in src.
636 :    
637 :     * src/Makefile.win: This and other Makefile.win files contributed
638 :     by Brian Ripley.
639 :    
640 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
641 :    
642 :     * R/syMatrix.R: Added methods for "%*%".
643 :    
644 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
645 :     poMatrix object.
646 :    
647 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
648 :    
649 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
650 :    
651 :     2004-01-25 Douglas Bates <bates@bates2_home>
652 :    
653 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
654 :    
655 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
656 :     of nrow.
657 :    
658 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
659 :    
660 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
661 :     subdirectories.
662 :    
663 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
664 :    
665 :     * src/taucs.h: Accidently referred to global header files
666 :     instead of local files.
667 :    
668 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
669 :    
670 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
671 :     and methods and replaced all classes with S4 classes.
672 :    
673 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
674 :    
675 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
676 :    
677 :     * src/R_LapackPP.cc: Change method of calculating determinants
678 :    
679 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
680 :    
681 :     * DESCRIPTION (Version): removed empty data directory as requested
682 :     by CRAN maintainers. Changed version number and date.
683 :    
684 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
685 :    
686 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
687 :     under Windows.
688 :    
689 :     * Added configure.win and src/Makevars.win as requested by Brian
690 :     Ripley.
691 :    
692 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
693 :    
694 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
695 :     Hornik.
696 :    
697 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
698 :    
699 :     * configure.ac: Replaced configure.in with configure.ac
700 :     contributed by Kurt Hornik.
701 :    
702 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
703 :     version for R-1.5.0
704 :    
705 : maechler 512
706 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
707 :    
708 :     * man/eigen.Rd: Removed the .Alias in the example

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