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Annotation of /pkg/ChangeLog

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1 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
4 :     testing; now again of all actual classes.
5 :    
6 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
7 :     use macros and define make_d_matrix_* and make_i_matrix_*
8 :     where _i_ is for the ldense routines:
9 :    
10 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
11 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
12 :    
13 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
14 :    
15 :    
16 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
17 :    
18 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
19 :     many different kinds of matrices.
20 :     * R/*.R: quite a few new methods were needed for R CMD check with
21 :     new Matrix(). Very good for users playing around.
22 :    
23 :    
24 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
25 :    
26 :     * src/dgeMatrix.c (dMatrix_validate): new
27 :     * src/Mutils.c (dense_nonpacked_validate): new
28 :    
29 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
30 :    
31 :    
32 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
33 :    
34 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
35 :    
36 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
37 : bates 1119
38 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
39 :    
40 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
41 :     segfault in cases with multiple non-nested grouping factors.
42 :    
43 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
44 :    
45 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
46 :     (Depends): also on 'utils'
47 :    
48 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
49 :     * R/diagMatrix.R (Diagonal): constructor and methods for
50 :     diagonal matrices
51 :    
52 :     * R/ltTMatrix.R: new "minimal methods"
53 :    
54 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
55 :    
56 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
57 :     all methods (and help files).
58 :    
59 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
60 :    
61 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
62 :     for case (dimn. op no_dimn.)
63 :    
64 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
65 :    
66 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
67 : maechler 1084
68 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
69 :    
70 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
71 :     by Julian Faraway.
72 :    
73 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
74 :    
75 :     * R/Auxiliaries.R (try_as): new utility
76 :     * R/sparseMatrix.R: use try_as() in coercion to original class
77 :    
78 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
79 :    
80 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
81 :    
82 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
83 :    
84 :     * R/Auxiliaries.R (dimNamesCheck): added
85 :    
86 :     * R/Matrix.R (as.array), (as.vector): new
87 :    
88 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
89 :    
90 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
91 : maechler 956 default.
92 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
93 :     "pMatrix" now contains "sparseMatrix"
94 : maechler 954
95 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
96 :    
97 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
98 :    
99 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
100 :    
101 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
102 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
103 :    
104 :     * R/dspMatrix.R: typo in "t" method
105 :    
106 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
107 :    
108 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
109 :     * R/Tsparse.R: instead of R/gTMatrix.R
110 :     * R/Csparse.R: new
111 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
112 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
113 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
114 :     via cholmod
115 :    
116 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
117 :    
118 :     * R/Auxiliaries.R (non0ind): new function using new C code
119 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
120 :    
121 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
122 :    
123 :     * src/chm_common.h: header file required by all C sources that
124 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
125 : bates 917 called 'c' whose address is passed as the last argument to
126 :     (virtually) every CHOLMOD function.
127 :    
128 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
129 :    
130 :     * src/init.c: initialize and finalize the cholmod_common structure.
131 :    
132 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
133 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
134 :    
135 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
136 :    
137 :     * inst/test-tools.R: new file collecting the utility functions used
138 :     in ./tests/*.R
139 :    
140 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
141 :     * R/Matrix.R (cbind2): methods for NULL and missing
142 :    
143 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
144 :    
145 :     * R/AllClass.R: new "index" class for "[" and "[<-":
146 :     First cut at "symmetricMatrix" and "triangularMatrix"
147 :     * R/gTMatrix.R (.ind.prep): new function;
148 : maechler 1174 Logical and character indexing now work too.
149 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
150 :     * tests/indexing.R: new, including *.Rout.save
151 :     * tests/dgTMatrix.R: new
152 :    
153 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
154 :    
155 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
156 :     indicator pos not being updated. Also enforced upper triangular
157 :     for symmetric case. Need to coerce edges component of elements of
158 :     edge list - grr! (Why don't they define their classes cleanly?)
159 :    
160 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
161 :    
162 :     * R/Matrix.R: added first "[<-" methods; not yet functional
163 :     * R/denseMatrix.R: dito
164 :     * man/Subassign-methods.Rd: new help file for these
165 :    
166 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
167 :    
168 :     * DESCRIPTION (Version): 0.98-6
169 :    
170 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
171 :     matrices.
172 :    
173 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
174 :    
175 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
176 :     as( <logical>, "matrix")
177 :    
178 :     * R/pMatrix.R: coercion to "lgTMatrix"
179 :    
180 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
181 :     * man/gTMatrix-class.Rd:
182 :     * General slight re-organization of where "[" methods are defined.
183 :     more to come.
184 :    
185 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
186 : maechler 868
187 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
188 : maechler 871
189 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
190 :     * .....
191 :    
192 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
193 :    
194 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
195 :     or glmer objects.
196 :    
197 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
198 :    
199 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
200 :    
201 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
202 :    
203 :     * R/HBMM.R: finish re-writing R-only code.
204 :    
205 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
206 :    
207 :     * man/externalFormats.Rd: move documentation for writeHB and
208 :     writeMM here.
209 :    
210 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
211 :     (suggested by Paul Roecker).
212 :    
213 :     * tests/validObj.R (assertError): Comment out test that is failing
214 :     after recent changes in r-devel.
215 :    
216 : maechler 860
217 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
218 :    
219 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
220 :     * man/denseMatrix-class.Rd
221 :     * NAMESPACE: export it, and also export
222 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
223 :    
224 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
225 :    
226 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
227 :    
228 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
229 :     matrix_solve code (which was really, really wrong).
230 :    
231 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
232 : maechler 834
233 :     * DESCRIPTION (Version): 0.98-2
234 :    
235 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
236 :    
237 :     * R/lmer.R (abbrvNms): new
238 :     * R/lmer.R (mcmcsamp): allow transformed parameters
239 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
240 :     for the Harwell-Boeing and the MatrixMarket formats.
241 : maechler 834
242 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
243 :    
244 :     * man/dtrMatrix-class.Rd: add examples
245 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
246 : maechler 834
247 :     * TODO: note the dtpMatrix (docu) bug
248 :    
249 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
250 :     in order to ensure that new as.matrix() is used by old functions,
251 :     e.g., svd(), qr(), eigen(), dist(),..;
252 :     apply(), also matplot() or pairs().
253 :    
254 :    
255 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
256 :    
257 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
258 :     add comments about 'control' / lmerControl() arguments
259 :    
260 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
261 : bates 820
262 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
263 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
264 : bates 820
265 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
266 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
267 :    
268 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
269 :     .Call calls that were producing spurious output.
270 :    
271 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
272 : bates 801
273 :     * R/lmer.R (lmer): stored updated variance component estimates in
274 :     mer object for the generalized model. (Bug reported by Renaud
275 :     Lancelot).
276 :    
277 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
278 : bates 794
279 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
280 :     unidimensional case.
281 :    
282 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
283 : maechler 791
284 :     * DESCRIPTION (Version): 0.96-1
285 :    
286 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
287 : maechler 791
288 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
289 : bates 763
290 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
291 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
292 :    
293 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
294 : bates 763
295 :     * src/Makefile.win: Forgot to update this when Makefile changed.
296 :    
297 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
298 : bates 726
299 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
300 :     bug reported by Kurt Hornik and Michael Hahsler.
301 :    
302 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
303 : bates 725
304 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
305 :     logical sparse matrices. These will also be used in the symbolic
306 :     analysis for lmer objects.
307 :    
308 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
309 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
310 : maechler 791
311 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
312 : bates 714
313 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
314 :     colMeans, colSums, rowMeans and rowSums.
315 :    
316 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
317 : bates 692
318 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
319 :     multiplication operation.
320 :    
321 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
322 :     to dgetrs.
323 :    
324 :     * src/init.c: Fix cut-and-paste error in definition of
325 :     dgeMatrix_matrix_solve
326 :    
327 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
328 :    
329 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
330 : bates 692
331 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
332 :    
333 :     * DESCRIPTION: Eliminate import of stats.
334 :    
335 : maechler 791
336 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
337 : bates 692
338 :     * R/AllClass.R : add logical sparse matrix classes
339 :    
340 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
341 :    
342 :     * R/dgTMatrix.R: add "[" method for triplet matrices
343 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
344 :    
345 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
346 : maechler 687
347 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
348 :    
349 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
350 :     * R/sparseMatrix.R: %*%, crossprod()
351 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
352 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
353 :     * src/lmer.c (lmer_fitted): fix thinko
354 :    
355 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
356 :    
357 :     * R/AllClass.R: add two virtual sparse classes ``on top''
358 :    
359 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
360 :    
361 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
362 :     correspondingly fix examples and tests/ since new()
363 :     doesn't work for virtual classes.
364 :    
365 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
366 :    
367 :     * R/Matrix.R (as.matrix): method and one for unname()
368 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
369 :     also run for R 2.1.0; using as.matrix()
370 :    
371 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
372 : maechler 658
373 :     * R/pMatrix.R: "pMatrix" class added
374 :     * ....
375 :    
376 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
377 : bates 645
378 :     * R/dtpMatrix.R: Add unpack method and an example.
379 :    
380 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
381 :     of general symmetric matrices and associated S4 methods.
382 :    
383 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
384 :     +
385 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
386 :    
387 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
388 :     crossprod() and "%*%" methods added; tests, too.
389 :     * tests/matprod.R: new, for testing these
390 :    
391 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
392 : bates 599
393 :     * src/lmer.c (lmer_fitted): Added.
394 :    
395 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
396 : bates 596
397 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
398 :    
399 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
400 : bates 582
401 :     * src/*.c,po/,inst/po: Internationalization and localization of
402 :     the package.
403 :    
404 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
405 :     R_ldl.c file.
406 :    
407 :     * src/flame.[ch]: Removed these source files.
408 : maechler 658
409 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
410 :    
411 :     * src/LU.[ch],src/init.c: absorb in factorizations
412 :    
413 :     * src/Mutils.h: prepare for internationalization
414 :    
415 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
416 :     this file
417 :    
418 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
419 :    
420 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
421 :    
422 :     * R/dtrMatrix.R: fix t() method
423 :    
424 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
425 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
426 : maechler 578 * tests/group-methods.R : and test them.
427 :    
428 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
429 :     border case
430 :    
431 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
432 :    
433 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
434 : maechler 578
435 :     * src/dgBCMatrix.c:
436 :     * src/lmer.c: many changes
437 :     * ...
438 :    
439 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
440 :    
441 :     * R/Matrix.R: add more sophisticated show() method.
442 :    
443 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
444 :    
445 :     * */* : almost complete reorganization of classes.
446 :    
447 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
448 : bates 460
449 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
450 :     for the geMatrix class.
451 :    
452 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
453 : bates 460
454 :     * src/Makefile (clean): Remove *.a and *.so
455 :    
456 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
457 :    
458 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
459 : bates 460
460 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
461 : bates 460 had an effect in cases with more than 2 grouping factors.
462 :    
463 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
464 : bates 415
465 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
466 :    
467 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
468 : bates 410
469 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
470 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
471 :    
472 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
473 : bates 392
474 :     * R/sscMatrix.R: Add determinant methods
475 :    
476 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
477 :     for tripletMatrix to matrix.
478 :    
479 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
480 : bates 388
481 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
482 :     no longer used.
483 :    
484 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
485 :     with dynamic allocation of scratch arrays.
486 :    
487 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
488 :     for multivariate random effects with multiple grouping factors.
489 :     Fixes part but not all of #15.
490 :    
491 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
492 : bates 375
493 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
494 :     scalar grouping factors corrected.
495 :    
496 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
497 : bates 375
498 :     * src/bCrosstab.c: remove diag_update which is no longer used
499 :    
500 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
501 : bates 350
502 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
503 :     .h file can be included.
504 :    
505 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
506 : bates 342
507 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
508 : bates 342 Complete allocation of slots in NEW_OBJECT.
509 :    
510 :     * src/Mutils.h: Moved list of symbols to an include file
511 :    
512 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
513 : bates 342
514 :     * src/geMutils.c (Matrix_init): remove unused function
515 :    
516 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
517 : bates 342
518 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
519 :    
520 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
521 : bates 327
522 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
523 :    
524 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
525 : bates 303
526 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
527 :    
528 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
529 : bates 296
530 :     * src/init.c: Created R_init_Matrix and added registration of C
531 :     routines.
532 :    
533 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
534 : bates 283
535 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
536 :    
537 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
538 : bates 229
539 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
540 :    
541 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
542 :    
543 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
544 :    
545 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
546 :    
547 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
548 :     ssclme_update_mm
549 :    
550 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
551 :    
552 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
553 :     in the order of unconstrained and constrained parameters.
554 :     (ssclme_gradient): Added the gradients (not yet correct for
555 :     multidimensional, unconstrained case).
556 :    
557 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
558 :    
559 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
560 :    
561 :     * src/Makefile.win: Remove unneeded ranlib call
562 :    
563 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
564 :    
565 :     * DESCRIPTION (Version): New release
566 :    
567 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
568 :    
569 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
570 :    
571 :     * src/triplet_to_col.c: Create triplet_to_col as a native
572 : maechler 658 function, not the version from umfpack. There were problems with
573 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
574 :     only one umfpack routine being used so I moved it here.
575 :    
576 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
577 :    
578 :     * src/ssclme.c (ssclme_variances): New function.
579 :    
580 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
581 :    
582 :     * src/ssclme.c (ssclme_fitted): Added function.
583 :    
584 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
585 :    
586 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
587 :     store the dimnames in the XtX and bVar slots
588 :     (ssclme_update_mm): Change the dimensions of the bVar slot
589 :     components and the returned value from ssclme_ranef.
590 :    
591 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
592 :    
593 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
594 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
595 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
596 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
597 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
598 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
599 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
600 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
601 :     Moved the pdMat classes from the lme4 package.
602 :    
603 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
604 :    
605 :     * man/ssclme-class.Rd: Update definition and documentation of the
606 :     ssclme class to include the DIsqrt slot.
607 :    
608 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
609 :     (much faster using dsyrk, a level 3 BLAS routine).
610 :    
611 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
612 :    
613 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
614 :    
615 :     * tests/ssclme.R: Modify the test to account for the permutation
616 :     of the levels of the grouping factors.
617 :    
618 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
619 :    
620 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
621 :     directly into the ssclme class definition.
622 :    
623 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
624 :    
625 :     * DESCRIPTION (Date): New release
626 :    
627 :     * man/ssclme-class.Rd: new file.
628 :    
629 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
630 :     works and it's fast!
631 :    
632 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
633 :    
634 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
635 :    
636 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
637 :    
638 :     * DESCRIPTION (Date): New release
639 :    
640 :     * NAMESPACE: Don't export ssclme.
641 :    
642 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
643 :     school data.
644 :    
645 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
646 :    
647 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
648 :     keep track of the fixed-effects and the response. Counts also
649 :     gets an extra element, which is always one.
650 :    
651 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
652 :    
653 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
654 :    
655 :     * src/cscMatrix.c (csc_transpose): new function
656 :    
657 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
658 :     (csc_components_transpose): new function
659 :    
660 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
661 :    
662 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
663 :     triplets
664 :    
665 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
666 :    
667 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
668 :    
669 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
670 :     and all other .h files in src.
671 :    
672 :     * src/Makefile.win: This and other Makefile.win files contributed
673 :     by Brian Ripley.
674 :    
675 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
676 :    
677 :     * R/syMatrix.R: Added methods for "%*%".
678 :    
679 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
680 :     poMatrix object.
681 :    
682 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
683 :    
684 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
685 :    
686 :     2004-01-25 Douglas Bates <bates@bates2_home>
687 :    
688 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
689 :    
690 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
691 :     of nrow.
692 :    
693 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
694 :    
695 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
696 :     subdirectories.
697 :    
698 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
699 :    
700 :     * src/taucs.h: Accidently referred to global header files
701 :     instead of local files.
702 :    
703 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
704 :    
705 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
706 :     and methods and replaced all classes with S4 classes.
707 :    
708 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
709 :    
710 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
711 :    
712 :     * src/R_LapackPP.cc: Change method of calculating determinants
713 :    
714 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
715 :    
716 :     * DESCRIPTION (Version): removed empty data directory as requested
717 :     by CRAN maintainers. Changed version number and date.
718 :    
719 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
720 :    
721 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
722 :     under Windows.
723 :    
724 :     * Added configure.win and src/Makevars.win as requested by Brian
725 :     Ripley.
726 :    
727 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
728 :    
729 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
730 :     Hornik.
731 :    
732 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
733 :    
734 :     * configure.ac: Replaced configure.in with configure.ac
735 :     contributed by Kurt Hornik.
736 :    
737 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
738 :     version for R-1.5.0
739 :    
740 : maechler 512
741 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
742 :    
743 :     * man/eigen.Rd: Removed the .Alias in the example

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