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Annotation of /pkg/ChangeLog

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

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