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Annotation of /pkg/ChangeLog

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1 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
4 :     many different kinds of matrices.
5 :     * R/*.R: quite a few new methods were needed for R CMD check with
6 :     new Matrix(). Very good for users playing around.
7 :    
8 :    
9 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
10 :    
11 :     * src/dgeMatrix.c (dMatrix_validate): new
12 :     * src/Mutils.c (dense_nonpacked_validate): new
13 :    
14 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
15 :    
16 :    
17 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
18 :    
19 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
20 :    
21 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
22 : bates 1119
23 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
24 :    
25 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
26 :     segfault in cases with multiple non-nested grouping factors.
27 :    
28 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
29 :    
30 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
31 :     (Depends): also on 'utils'
32 :    
33 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
34 :     * R/diagMatrix.R (Diagonal): constructor and methods for
35 :     diagonal matrices
36 :    
37 :     * R/ltTMatrix.R: new "minimal methods"
38 :    
39 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
40 :    
41 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
42 :     all methods (and help files).
43 :    
44 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
45 :    
46 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
47 :     for case (dimn. op no_dimn.)
48 :    
49 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
50 :    
51 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
52 : maechler 1084
53 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
54 :    
55 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
56 :     by Julian Faraway.
57 :    
58 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
59 :    
60 :     * R/Auxiliaries.R (try_as): new utility
61 :     * R/sparseMatrix.R: use try_as() in coercion to original class
62 :    
63 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
64 :    
65 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
66 :    
67 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
68 :    
69 :     * R/Auxiliaries.R (dimNamesCheck): added
70 :    
71 :     * R/Matrix.R (as.array), (as.vector): new
72 :    
73 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
74 :    
75 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
76 : maechler 956 default.
77 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
78 :     "pMatrix" now contains "sparseMatrix"
79 : maechler 954
80 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
81 :    
82 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
83 :    
84 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
85 :    
86 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
87 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
88 :    
89 :     * R/dspMatrix.R: typo in "t" method
90 :    
91 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
92 :    
93 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
94 :     * R/Tsparse.R: instead of R/gTMatrix.R
95 :     * R/Csparse.R: new
96 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
97 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
98 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
99 :     via cholmod
100 :    
101 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
102 :    
103 :     * R/Auxiliaries.R (non0ind): new function using new C code
104 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
105 :    
106 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
107 :    
108 :     * src/chm_common.h: header file required by all C sources that
109 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
110 : bates 917 called 'c' whose address is passed as the last argument to
111 :     (virtually) every CHOLMOD function.
112 :    
113 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
114 :    
115 :     * src/init.c: initialize and finalize the cholmod_common structure.
116 :    
117 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
118 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
119 :    
120 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
121 :    
122 :     * inst/test-tools.R: new file collecting the utility functions used
123 :     in ./tests/*.R
124 :    
125 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
126 :     * R/Matrix.R (cbind2): methods for NULL and missing
127 :    
128 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
129 :    
130 :     * R/AllClass.R: new "index" class for "[" and "[<-":
131 :     First cut at "symmetricMatrix" and "triangularMatrix"
132 :     * R/gTMatrix.R (.ind.prep): new function;
133 : maechler 1174 Logical and character indexing now work too.
134 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
135 :     * tests/indexing.R: new, including *.Rout.save
136 :     * tests/dgTMatrix.R: new
137 :    
138 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
139 :    
140 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
141 :     indicator pos not being updated. Also enforced upper triangular
142 :     for symmetric case. Need to coerce edges component of elements of
143 :     edge list - grr! (Why don't they define their classes cleanly?)
144 :    
145 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
146 :    
147 :     * R/Matrix.R: added first "[<-" methods; not yet functional
148 :     * R/denseMatrix.R: dito
149 :     * man/Subassign-methods.Rd: new help file for these
150 :    
151 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
152 :    
153 :     * DESCRIPTION (Version): 0.98-6
154 :    
155 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
156 :     matrices.
157 :    
158 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
159 :    
160 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
161 :     as( <logical>, "matrix")
162 :    
163 :     * R/pMatrix.R: coercion to "lgTMatrix"
164 :    
165 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
166 :     * man/gTMatrix-class.Rd:
167 :     * General slight re-organization of where "[" methods are defined.
168 :     more to come.
169 :    
170 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
171 : maechler 868
172 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
173 : maechler 871
174 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
175 :     * .....
176 :    
177 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
178 :    
179 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
180 :     or glmer objects.
181 :    
182 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
183 :    
184 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
185 :    
186 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
187 :    
188 :     * R/HBMM.R: finish re-writing R-only code.
189 :    
190 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
191 :    
192 :     * man/externalFormats.Rd: move documentation for writeHB and
193 :     writeMM here.
194 :    
195 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
196 :     (suggested by Paul Roecker).
197 :    
198 :     * tests/validObj.R (assertError): Comment out test that is failing
199 :     after recent changes in r-devel.
200 :    
201 : maechler 860
202 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
203 :    
204 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
205 :     * man/denseMatrix-class.Rd
206 :     * NAMESPACE: export it, and also export
207 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
208 :    
209 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
210 :    
211 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
212 :    
213 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
214 :     matrix_solve code (which was really, really wrong).
215 :    
216 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
217 : maechler 834
218 :     * DESCRIPTION (Version): 0.98-2
219 :    
220 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
221 :    
222 :     * R/lmer.R (abbrvNms): new
223 :     * R/lmer.R (mcmcsamp): allow transformed parameters
224 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
225 :     for the Harwell-Boeing and the MatrixMarket formats.
226 : maechler 834
227 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
228 :    
229 :     * man/dtrMatrix-class.Rd: add examples
230 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
231 : maechler 834
232 :     * TODO: note the dtpMatrix (docu) bug
233 :    
234 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
235 :     in order to ensure that new as.matrix() is used by old functions,
236 :     e.g., svd(), qr(), eigen(), dist(),..;
237 :     apply(), also matplot() or pairs().
238 :    
239 :    
240 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
241 :    
242 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
243 :     add comments about 'control' / lmerControl() arguments
244 :    
245 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
246 : bates 820
247 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
248 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
249 : bates 820
250 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
251 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
252 :    
253 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
254 :     .Call calls that were producing spurious output.
255 :    
256 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
257 : bates 801
258 :     * R/lmer.R (lmer): stored updated variance component estimates in
259 :     mer object for the generalized model. (Bug reported by Renaud
260 :     Lancelot).
261 :    
262 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
263 : bates 794
264 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
265 :     unidimensional case.
266 :    
267 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
268 : maechler 791
269 :     * DESCRIPTION (Version): 0.96-1
270 :    
271 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
272 : maechler 791
273 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
274 : bates 763
275 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
276 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
277 :    
278 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
279 : bates 763
280 :     * src/Makefile.win: Forgot to update this when Makefile changed.
281 :    
282 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
283 : bates 726
284 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
285 :     bug reported by Kurt Hornik and Michael Hahsler.
286 :    
287 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
288 : bates 725
289 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
290 :     logical sparse matrices. These will also be used in the symbolic
291 :     analysis for lmer objects.
292 :    
293 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
294 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
295 : maechler 791
296 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
297 : bates 714
298 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
299 :     colMeans, colSums, rowMeans and rowSums.
300 :    
301 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
302 : bates 692
303 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
304 :     multiplication operation.
305 :    
306 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
307 :     to dgetrs.
308 :    
309 :     * src/init.c: Fix cut-and-paste error in definition of
310 :     dgeMatrix_matrix_solve
311 :    
312 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
313 :    
314 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
315 : bates 692
316 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
317 :    
318 :     * DESCRIPTION: Eliminate import of stats.
319 :    
320 : maechler 791
321 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
322 : bates 692
323 :     * R/AllClass.R : add logical sparse matrix classes
324 :    
325 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
326 :    
327 :     * R/dgTMatrix.R: add "[" method for triplet matrices
328 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
329 :    
330 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
331 : maechler 687
332 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
333 :    
334 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
335 :     * R/sparseMatrix.R: %*%, crossprod()
336 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
337 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
338 :     * src/lmer.c (lmer_fitted): fix thinko
339 :    
340 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
341 :    
342 :     * R/AllClass.R: add two virtual sparse classes ``on top''
343 :    
344 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
345 :    
346 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
347 :     correspondingly fix examples and tests/ since new()
348 :     doesn't work for virtual classes.
349 :    
350 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
351 :    
352 :     * R/Matrix.R (as.matrix): method and one for unname()
353 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
354 :     also run for R 2.1.0; using as.matrix()
355 :    
356 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
357 : maechler 658
358 :     * R/pMatrix.R: "pMatrix" class added
359 :     * ....
360 :    
361 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
362 : bates 645
363 :     * R/dtpMatrix.R: Add unpack method and an example.
364 :    
365 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
366 :     of general symmetric matrices and associated S4 methods.
367 :    
368 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
369 :     +
370 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
371 :    
372 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
373 :     crossprod() and "%*%" methods added; tests, too.
374 :     * tests/matprod.R: new, for testing these
375 :    
376 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
377 : bates 599
378 :     * src/lmer.c (lmer_fitted): Added.
379 :    
380 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
381 : bates 596
382 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
383 :    
384 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
385 : bates 582
386 :     * src/*.c,po/,inst/po: Internationalization and localization of
387 :     the package.
388 :    
389 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
390 :     R_ldl.c file.
391 :    
392 :     * src/flame.[ch]: Removed these source files.
393 : maechler 658
394 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
395 :    
396 :     * src/LU.[ch],src/init.c: absorb in factorizations
397 :    
398 :     * src/Mutils.h: prepare for internationalization
399 :    
400 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
401 :     this file
402 :    
403 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
404 :    
405 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
406 :    
407 :     * R/dtrMatrix.R: fix t() method
408 :    
409 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
410 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
411 : maechler 578 * tests/group-methods.R : and test them.
412 :    
413 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
414 :     border case
415 :    
416 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
417 :    
418 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
419 : maechler 578
420 :     * src/dgBCMatrix.c:
421 :     * src/lmer.c: many changes
422 :     * ...
423 :    
424 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
425 :    
426 :     * R/Matrix.R: add more sophisticated show() method.
427 :    
428 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
429 :    
430 :     * */* : almost complete reorganization of classes.
431 :    
432 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
433 : bates 460
434 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
435 :     for the geMatrix class.
436 :    
437 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
438 : bates 460
439 :     * src/Makefile (clean): Remove *.a and *.so
440 :    
441 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
442 :    
443 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
444 : bates 460
445 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
446 : bates 460 had an effect in cases with more than 2 grouping factors.
447 :    
448 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
449 : bates 415
450 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
451 :    
452 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
453 : bates 410
454 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
455 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
456 :    
457 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
458 : bates 392
459 :     * R/sscMatrix.R: Add determinant methods
460 :    
461 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
462 :     for tripletMatrix to matrix.
463 :    
464 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
465 : bates 388
466 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
467 :     no longer used.
468 :    
469 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
470 :     with dynamic allocation of scratch arrays.
471 :    
472 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
473 :     for multivariate random effects with multiple grouping factors.
474 :     Fixes part but not all of #15.
475 :    
476 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
477 : bates 375
478 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
479 :     scalar grouping factors corrected.
480 :    
481 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
482 : bates 375
483 :     * src/bCrosstab.c: remove diag_update which is no longer used
484 :    
485 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
486 : bates 350
487 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
488 :     .h file can be included.
489 :    
490 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
491 : bates 342
492 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
493 : bates 342 Complete allocation of slots in NEW_OBJECT.
494 :    
495 :     * src/Mutils.h: Moved list of symbols to an include file
496 :    
497 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
498 : bates 342
499 :     * src/geMutils.c (Matrix_init): remove unused function
500 :    
501 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
502 : bates 342
503 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
504 :    
505 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
506 : bates 327
507 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
508 :    
509 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
510 : bates 303
511 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
512 :    
513 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
514 : bates 296
515 :     * src/init.c: Created R_init_Matrix and added registration of C
516 :     routines.
517 :    
518 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
519 : bates 283
520 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
521 :    
522 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
523 : bates 229
524 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
525 :    
526 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
527 :    
528 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
529 :    
530 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
531 :    
532 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
533 :     ssclme_update_mm
534 :    
535 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
536 :    
537 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
538 :     in the order of unconstrained and constrained parameters.
539 :     (ssclme_gradient): Added the gradients (not yet correct for
540 :     multidimensional, unconstrained case).
541 :    
542 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
543 :    
544 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
545 :    
546 :     * src/Makefile.win: Remove unneeded ranlib call
547 :    
548 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
549 :    
550 :     * DESCRIPTION (Version): New release
551 :    
552 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
553 :    
554 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
555 :    
556 :     * src/triplet_to_col.c: Create triplet_to_col as a native
557 : maechler 658 function, not the version from umfpack. There were problems with
558 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
559 :     only one umfpack routine being used so I moved it here.
560 :    
561 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
562 :    
563 :     * src/ssclme.c (ssclme_variances): New function.
564 :    
565 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
566 :    
567 :     * src/ssclme.c (ssclme_fitted): Added function.
568 :    
569 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
570 :    
571 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
572 :     store the dimnames in the XtX and bVar slots
573 :     (ssclme_update_mm): Change the dimensions of the bVar slot
574 :     components and the returned value from ssclme_ranef.
575 :    
576 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
577 :    
578 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
579 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
580 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
581 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
582 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
583 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
584 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
585 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
586 :     Moved the pdMat classes from the lme4 package.
587 :    
588 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
589 :    
590 :     * man/ssclme-class.Rd: Update definition and documentation of the
591 :     ssclme class to include the DIsqrt slot.
592 :    
593 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
594 :     (much faster using dsyrk, a level 3 BLAS routine).
595 :    
596 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
597 :    
598 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
599 :    
600 :     * tests/ssclme.R: Modify the test to account for the permutation
601 :     of the levels of the grouping factors.
602 :    
603 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
604 :    
605 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
606 :     directly into the ssclme class definition.
607 :    
608 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
609 :    
610 :     * DESCRIPTION (Date): New release
611 :    
612 :     * man/ssclme-class.Rd: new file.
613 :    
614 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
615 :     works and it's fast!
616 :    
617 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
618 :    
619 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
620 :    
621 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
622 :    
623 :     * DESCRIPTION (Date): New release
624 :    
625 :     * NAMESPACE: Don't export ssclme.
626 :    
627 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
628 :     school data.
629 :    
630 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
631 :    
632 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
633 :     keep track of the fixed-effects and the response. Counts also
634 :     gets an extra element, which is always one.
635 :    
636 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
637 :    
638 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
639 :    
640 :     * src/cscMatrix.c (csc_transpose): new function
641 :    
642 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
643 :     (csc_components_transpose): new function
644 :    
645 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
646 :    
647 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
648 :     triplets
649 :    
650 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
651 :    
652 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
653 :    
654 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
655 :     and all other .h files in src.
656 :    
657 :     * src/Makefile.win: This and other Makefile.win files contributed
658 :     by Brian Ripley.
659 :    
660 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
661 :    
662 :     * R/syMatrix.R: Added methods for "%*%".
663 :    
664 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
665 :     poMatrix object.
666 :    
667 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
668 :    
669 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
670 :    
671 :     2004-01-25 Douglas Bates <bates@bates2_home>
672 :    
673 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
674 :    
675 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
676 :     of nrow.
677 :    
678 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
679 :    
680 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
681 :     subdirectories.
682 :    
683 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
684 :    
685 :     * src/taucs.h: Accidently referred to global header files
686 :     instead of local files.
687 :    
688 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
689 :    
690 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
691 :     and methods and replaced all classes with S4 classes.
692 :    
693 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
694 :    
695 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
696 :    
697 :     * src/R_LapackPP.cc: Change method of calculating determinants
698 :    
699 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
700 :    
701 :     * DESCRIPTION (Version): removed empty data directory as requested
702 :     by CRAN maintainers. Changed version number and date.
703 :    
704 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
705 :    
706 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
707 :     under Windows.
708 :    
709 :     * Added configure.win and src/Makevars.win as requested by Brian
710 :     Ripley.
711 :    
712 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
713 :    
714 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
715 :     Hornik.
716 :    
717 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
718 :    
719 :     * configure.ac: Replaced configure.in with configure.ac
720 :     contributed by Kurt Hornik.
721 :    
722 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
723 :     version for R-1.5.0
724 :    
725 : maechler 512
726 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
727 :    
728 :     * man/eigen.Rd: Removed the .Alias in the example

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