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Annotation of /pkg/ChangeLog

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

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