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Annotation of /pkg/ChangeLog

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

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