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Annotation of /pkg/ChangeLog

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

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