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Annotation of /pkg/ChangeLog

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

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