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Annotation of /pkg/ChangeLog

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1 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
4 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
5 :     * R/lmer.R (show): now works with summary()
6 :    
7 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
8 :    
9 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
10 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
11 :     support the above
12 :    
13 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
14 :    
15 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
16 :     Use glmFit$prior.weights for weights in a glmm.
17 :     Allow an option usePQL = FALSE to skip the PQL steps for the
18 :     Laplace method (and, in time, the AGQ method).
19 :    
20 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
21 :     into a separate function internal_mer_Xfactor to be able to call
22 :     it from internal_bhat.
23 :    
24 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
25 :    
26 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
27 :     testing; now again of all actual classes.
28 :    
29 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
30 :     use macros and define make_d_matrix_* and make_i_matrix_*
31 :     where _i_ is for the ldense routines:
32 :    
33 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
34 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
35 :    
36 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
37 :    
38 :    
39 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
40 :    
41 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
42 :     many different kinds of matrices.
43 :     * R/*.R: quite a few new methods were needed for R CMD check with
44 :     new Matrix(). Very good for users playing around.
45 :    
46 :    
47 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
48 :    
49 :     * src/dgeMatrix.c (dMatrix_validate): new
50 :     * src/Mutils.c (dense_nonpacked_validate): new
51 :    
52 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
53 :    
54 :    
55 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
56 :    
57 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
58 :    
59 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
60 : bates 1119
61 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
62 :    
63 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
64 :     segfault in cases with multiple non-nested grouping factors.
65 :    
66 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
67 :    
68 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
69 :     (Depends): also on 'utils'
70 :    
71 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
72 :     * R/diagMatrix.R (Diagonal): constructor and methods for
73 :     diagonal matrices
74 :    
75 :     * R/ltTMatrix.R: new "minimal methods"
76 :    
77 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
78 :    
79 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
80 :     all methods (and help files).
81 :    
82 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
83 :    
84 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
85 :     for case (dimn. op no_dimn.)
86 :    
87 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
88 :    
89 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
90 : maechler 1084
91 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
92 :    
93 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
94 :     by Julian Faraway.
95 :    
96 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
97 :    
98 :     * R/Auxiliaries.R (try_as): new utility
99 :     * R/sparseMatrix.R: use try_as() in coercion to original class
100 :    
101 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
102 :    
103 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
104 :    
105 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
106 :    
107 :     * R/Auxiliaries.R (dimNamesCheck): added
108 :    
109 :     * R/Matrix.R (as.array), (as.vector): new
110 :    
111 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
112 :    
113 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
114 : maechler 956 default.
115 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
116 :     "pMatrix" now contains "sparseMatrix"
117 : maechler 954
118 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
119 :    
120 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
121 :    
122 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
123 :    
124 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
125 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
126 :    
127 :     * R/dspMatrix.R: typo in "t" method
128 :    
129 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
130 :    
131 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
132 :     * R/Tsparse.R: instead of R/gTMatrix.R
133 :     * R/Csparse.R: new
134 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
135 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
136 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
137 :     via cholmod
138 :    
139 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
140 :    
141 :     * R/Auxiliaries.R (non0ind): new function using new C code
142 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
143 :    
144 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
145 :    
146 :     * src/chm_common.h: header file required by all C sources that
147 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
148 : bates 917 called 'c' whose address is passed as the last argument to
149 :     (virtually) every CHOLMOD function.
150 :    
151 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
152 :    
153 :     * src/init.c: initialize and finalize the cholmod_common structure.
154 :    
155 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
156 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
157 :    
158 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
159 :    
160 :     * inst/test-tools.R: new file collecting the utility functions used
161 :     in ./tests/*.R
162 :    
163 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
164 :     * R/Matrix.R (cbind2): methods for NULL and missing
165 :    
166 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
167 :    
168 :     * R/AllClass.R: new "index" class for "[" and "[<-":
169 :     First cut at "symmetricMatrix" and "triangularMatrix"
170 :     * R/gTMatrix.R (.ind.prep): new function;
171 : maechler 1174 Logical and character indexing now work too.
172 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
173 :     * tests/indexing.R: new, including *.Rout.save
174 :     * tests/dgTMatrix.R: new
175 :    
176 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
177 :    
178 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
179 :     indicator pos not being updated. Also enforced upper triangular
180 :     for symmetric case. Need to coerce edges component of elements of
181 :     edge list - grr! (Why don't they define their classes cleanly?)
182 :    
183 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
184 :    
185 :     * R/Matrix.R: added first "[<-" methods; not yet functional
186 :     * R/denseMatrix.R: dito
187 :     * man/Subassign-methods.Rd: new help file for these
188 :    
189 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
190 :    
191 :     * DESCRIPTION (Version): 0.98-6
192 :    
193 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
194 :     matrices.
195 :    
196 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
197 :    
198 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
199 :     as( <logical>, "matrix")
200 :    
201 :     * R/pMatrix.R: coercion to "lgTMatrix"
202 :    
203 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
204 :     * man/gTMatrix-class.Rd:
205 :     * General slight re-organization of where "[" methods are defined.
206 :     more to come.
207 :    
208 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
209 : maechler 868
210 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
211 : maechler 871
212 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
213 :     * .....
214 :    
215 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
216 :    
217 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
218 :     or glmer objects.
219 :    
220 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
221 :    
222 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
223 :    
224 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
225 :    
226 :     * R/HBMM.R: finish re-writing R-only code.
227 :    
228 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
229 :    
230 :     * man/externalFormats.Rd: move documentation for writeHB and
231 :     writeMM here.
232 :    
233 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
234 :     (suggested by Paul Roecker).
235 :    
236 :     * tests/validObj.R (assertError): Comment out test that is failing
237 :     after recent changes in r-devel.
238 :    
239 : maechler 860
240 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
241 :    
242 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
243 :     * man/denseMatrix-class.Rd
244 :     * NAMESPACE: export it, and also export
245 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
246 :    
247 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
248 :    
249 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
250 :    
251 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
252 :     matrix_solve code (which was really, really wrong).
253 :    
254 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
255 : maechler 834
256 :     * DESCRIPTION (Version): 0.98-2
257 :    
258 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
259 :    
260 :     * R/lmer.R (abbrvNms): new
261 :     * R/lmer.R (mcmcsamp): allow transformed parameters
262 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
263 :     for the Harwell-Boeing and the MatrixMarket formats.
264 : maechler 834
265 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
266 :    
267 :     * man/dtrMatrix-class.Rd: add examples
268 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
269 : maechler 834
270 :     * TODO: note the dtpMatrix (docu) bug
271 :    
272 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
273 :     in order to ensure that new as.matrix() is used by old functions,
274 :     e.g., svd(), qr(), eigen(), dist(),..;
275 :     apply(), also matplot() or pairs().
276 :    
277 :    
278 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
279 :    
280 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
281 :     add comments about 'control' / lmerControl() arguments
282 :    
283 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
284 : bates 820
285 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
286 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
287 : bates 820
288 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
289 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
290 :    
291 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
292 :     .Call calls that were producing spurious output.
293 :    
294 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
295 : bates 801
296 :     * R/lmer.R (lmer): stored updated variance component estimates in
297 :     mer object for the generalized model. (Bug reported by Renaud
298 :     Lancelot).
299 :    
300 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
301 : bates 794
302 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
303 :     unidimensional case.
304 :    
305 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
306 : maechler 791
307 :     * DESCRIPTION (Version): 0.96-1
308 :    
309 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
310 : maechler 791
311 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
312 : bates 763
313 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
314 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
315 :    
316 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
317 : bates 763
318 :     * src/Makefile.win: Forgot to update this when Makefile changed.
319 :    
320 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
321 : bates 726
322 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
323 :     bug reported by Kurt Hornik and Michael Hahsler.
324 :    
325 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
326 : bates 725
327 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
328 :     logical sparse matrices. These will also be used in the symbolic
329 :     analysis for lmer objects.
330 :    
331 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
332 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
333 : maechler 791
334 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
335 : bates 714
336 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
337 :     colMeans, colSums, rowMeans and rowSums.
338 :    
339 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
340 : bates 692
341 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
342 :     multiplication operation.
343 :    
344 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
345 :     to dgetrs.
346 :    
347 :     * src/init.c: Fix cut-and-paste error in definition of
348 :     dgeMatrix_matrix_solve
349 :    
350 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
351 :    
352 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
353 : bates 692
354 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
355 :    
356 :     * DESCRIPTION: Eliminate import of stats.
357 :    
358 : maechler 791
359 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
360 : bates 692
361 :     * R/AllClass.R : add logical sparse matrix classes
362 :    
363 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
364 :    
365 :     * R/dgTMatrix.R: add "[" method for triplet matrices
366 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
367 :    
368 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
369 : maechler 687
370 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
371 :    
372 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
373 :     * R/sparseMatrix.R: %*%, crossprod()
374 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
375 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
376 :     * src/lmer.c (lmer_fitted): fix thinko
377 :    
378 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
379 :    
380 :     * R/AllClass.R: add two virtual sparse classes ``on top''
381 :    
382 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
383 :    
384 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
385 :     correspondingly fix examples and tests/ since new()
386 :     doesn't work for virtual classes.
387 :    
388 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
389 :    
390 :     * R/Matrix.R (as.matrix): method and one for unname()
391 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
392 :     also run for R 2.1.0; using as.matrix()
393 :    
394 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
395 : maechler 658
396 :     * R/pMatrix.R: "pMatrix" class added
397 :     * ....
398 :    
399 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
400 : bates 645
401 :     * R/dtpMatrix.R: Add unpack method and an example.
402 :    
403 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
404 :     of general symmetric matrices and associated S4 methods.
405 :    
406 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
407 :     +
408 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
409 :    
410 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
411 :     crossprod() and "%*%" methods added; tests, too.
412 :     * tests/matprod.R: new, for testing these
413 :    
414 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
415 : bates 599
416 :     * src/lmer.c (lmer_fitted): Added.
417 :    
418 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
419 : bates 596
420 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
421 :    
422 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
423 : bates 582
424 :     * src/*.c,po/,inst/po: Internationalization and localization of
425 :     the package.
426 :    
427 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
428 :     R_ldl.c file.
429 :    
430 :     * src/flame.[ch]: Removed these source files.
431 : maechler 658
432 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
433 :    
434 :     * src/LU.[ch],src/init.c: absorb in factorizations
435 :    
436 :     * src/Mutils.h: prepare for internationalization
437 :    
438 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
439 :     this file
440 :    
441 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
442 :    
443 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
444 :    
445 :     * R/dtrMatrix.R: fix t() method
446 :    
447 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
448 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
449 : maechler 578 * tests/group-methods.R : and test them.
450 :    
451 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
452 :     border case
453 :    
454 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
455 :    
456 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
457 : maechler 578
458 :     * src/dgBCMatrix.c:
459 :     * src/lmer.c: many changes
460 :     * ...
461 :    
462 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
463 :    
464 :     * R/Matrix.R: add more sophisticated show() method.
465 :    
466 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
467 :    
468 :     * */* : almost complete reorganization of classes.
469 :    
470 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
471 : bates 460
472 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
473 :     for the geMatrix class.
474 :    
475 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
476 : bates 460
477 :     * src/Makefile (clean): Remove *.a and *.so
478 :    
479 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
480 :    
481 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
482 : bates 460
483 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
484 : bates 460 had an effect in cases with more than 2 grouping factors.
485 :    
486 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
487 : bates 415
488 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
489 :    
490 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
491 : bates 410
492 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
493 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
494 :    
495 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
496 : bates 392
497 :     * R/sscMatrix.R: Add determinant methods
498 :    
499 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
500 :     for tripletMatrix to matrix.
501 :    
502 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
503 : bates 388
504 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
505 :     no longer used.
506 :    
507 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
508 :     with dynamic allocation of scratch arrays.
509 :    
510 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
511 :     for multivariate random effects with multiple grouping factors.
512 :     Fixes part but not all of #15.
513 :    
514 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
515 : bates 375
516 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
517 :     scalar grouping factors corrected.
518 :    
519 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
520 : bates 375
521 :     * src/bCrosstab.c: remove diag_update which is no longer used
522 :    
523 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
524 : bates 350
525 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
526 :     .h file can be included.
527 :    
528 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
529 : bates 342
530 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
531 : bates 342 Complete allocation of slots in NEW_OBJECT.
532 :    
533 :     * src/Mutils.h: Moved list of symbols to an include file
534 :    
535 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
536 : bates 342
537 :     * src/geMutils.c (Matrix_init): remove unused function
538 :    
539 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
540 : bates 342
541 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
542 :    
543 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
544 : bates 327
545 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
546 :    
547 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
548 : bates 303
549 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
550 :    
551 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
552 : bates 296
553 :     * src/init.c: Created R_init_Matrix and added registration of C
554 :     routines.
555 :    
556 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
557 : bates 283
558 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
559 :    
560 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
561 : bates 229
562 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
563 :    
564 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
565 :    
566 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
567 :    
568 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
569 :    
570 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
571 :     ssclme_update_mm
572 :    
573 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
574 :    
575 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
576 :     in the order of unconstrained and constrained parameters.
577 :     (ssclme_gradient): Added the gradients (not yet correct for
578 :     multidimensional, unconstrained case).
579 :    
580 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
581 :    
582 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
583 :    
584 :     * src/Makefile.win: Remove unneeded ranlib call
585 :    
586 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
587 :    
588 :     * DESCRIPTION (Version): New release
589 :    
590 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
591 :    
592 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
593 :    
594 :     * src/triplet_to_col.c: Create triplet_to_col as a native
595 : maechler 658 function, not the version from umfpack. There were problems with
596 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
597 :     only one umfpack routine being used so I moved it here.
598 :    
599 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
600 :    
601 :     * src/ssclme.c (ssclme_variances): New function.
602 :    
603 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
604 :    
605 :     * src/ssclme.c (ssclme_fitted): Added function.
606 :    
607 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
608 :    
609 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
610 :     store the dimnames in the XtX and bVar slots
611 :     (ssclme_update_mm): Change the dimensions of the bVar slot
612 :     components and the returned value from ssclme_ranef.
613 :    
614 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
615 :    
616 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
617 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
618 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
619 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
620 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
621 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
622 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
623 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
624 :     Moved the pdMat classes from the lme4 package.
625 :    
626 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
627 :    
628 :     * man/ssclme-class.Rd: Update definition and documentation of the
629 :     ssclme class to include the DIsqrt slot.
630 :    
631 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
632 :     (much faster using dsyrk, a level 3 BLAS routine).
633 :    
634 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
635 :    
636 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
637 :    
638 :     * tests/ssclme.R: Modify the test to account for the permutation
639 :     of the levels of the grouping factors.
640 :    
641 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
642 :    
643 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
644 :     directly into the ssclme class definition.
645 :    
646 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
647 :    
648 :     * DESCRIPTION (Date): New release
649 :    
650 :     * man/ssclme-class.Rd: new file.
651 :    
652 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
653 :     works and it's fast!
654 :    
655 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
656 :    
657 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
658 :    
659 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
660 :    
661 :     * DESCRIPTION (Date): New release
662 :    
663 :     * NAMESPACE: Don't export ssclme.
664 :    
665 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
666 :     school data.
667 :    
668 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
669 :    
670 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
671 :     keep track of the fixed-effects and the response. Counts also
672 :     gets an extra element, which is always one.
673 :    
674 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
675 :    
676 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
677 :    
678 :     * src/cscMatrix.c (csc_transpose): new function
679 :    
680 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
681 :     (csc_components_transpose): new function
682 :    
683 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
684 :    
685 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
686 :     triplets
687 :    
688 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
689 :    
690 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
691 :    
692 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
693 :     and all other .h files in src.
694 :    
695 :     * src/Makefile.win: This and other Makefile.win files contributed
696 :     by Brian Ripley.
697 :    
698 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
699 :    
700 :     * R/syMatrix.R: Added methods for "%*%".
701 :    
702 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
703 :     poMatrix object.
704 :    
705 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
706 :    
707 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
708 :    
709 :     2004-01-25 Douglas Bates <bates@bates2_home>
710 :    
711 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
712 :    
713 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
714 :     of nrow.
715 :    
716 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
717 :    
718 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
719 :     subdirectories.
720 :    
721 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
722 :    
723 :     * src/taucs.h: Accidently referred to global header files
724 :     instead of local files.
725 :    
726 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
727 :    
728 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
729 :     and methods and replaced all classes with S4 classes.
730 :    
731 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
732 :    
733 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
734 :    
735 :     * src/R_LapackPP.cc: Change method of calculating determinants
736 :    
737 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
738 :    
739 :     * DESCRIPTION (Version): removed empty data directory as requested
740 :     by CRAN maintainers. Changed version number and date.
741 :    
742 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
743 :    
744 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
745 :     under Windows.
746 :    
747 :     * Added configure.win and src/Makevars.win as requested by Brian
748 :     Ripley.
749 :    
750 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
751 :    
752 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
753 :     Hornik.
754 :    
755 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
756 :    
757 :     * configure.ac: Replaced configure.in with configure.ac
758 :     contributed by Kurt Hornik.
759 :    
760 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
761 :     version for R-1.5.0
762 :    
763 : maechler 512
764 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
765 :    
766 :     * man/eigen.Rd: Removed the .Alias in the example

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