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Annotation of /pkg/ChangeLog

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1 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
2 :    
3 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
4 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
5 :    
6 :     * DESCRIPTION (Date): New release
7 :    
8 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
9 :    
10 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
11 :    
12 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
13 :     * man/KNex.Rd: and other help files
14 :     * tests/*.R: several ones needed adaption
15 :     * inst/doc/Comparisons.Rnw: dito
16 :    
17 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
18 :    
19 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
20 :    
21 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
22 :    
23 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
24 :    
25 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
26 :    
27 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
28 :    
29 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
30 :    
31 :     * R/dMatrix.R: enable things like M [ M < 10 ]
32 :     * R/dgeMatrix.R: implement it
33 :    
34 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
35 :    
36 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
37 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
38 :     * R/lmer.R (show): now works with summary()
39 :    
40 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
41 :    
42 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
43 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
44 :     support the above
45 :    
46 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
47 :    
48 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
49 :     Use glmFit$prior.weights for weights in a glmm.
50 :     Allow an option usePQL = FALSE to skip the PQL steps for the
51 :     Laplace method (and, in time, the AGQ method).
52 :    
53 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
54 :     into a separate function internal_mer_Xfactor to be able to call
55 :     it from internal_bhat.
56 :    
57 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
58 :    
59 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
60 :     testing; now again of all actual classes.
61 :    
62 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
63 :     use macros and define make_d_matrix_* and make_i_matrix_*
64 :     where _i_ is for the ldense routines:
65 :    
66 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
67 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
68 :    
69 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
70 :    
71 :    
72 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
73 :    
74 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
75 :     many different kinds of matrices.
76 :     * R/*.R: quite a few new methods were needed for R CMD check with
77 :     new Matrix(). Very good for users playing around.
78 :    
79 :    
80 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
81 :    
82 :     * src/dgeMatrix.c (dMatrix_validate): new
83 :     * src/Mutils.c (dense_nonpacked_validate): new
84 :    
85 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
86 :    
87 :    
88 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
89 :    
90 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
91 :    
92 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
93 : bates 1119
94 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
95 :    
96 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
97 :     segfault in cases with multiple non-nested grouping factors.
98 :    
99 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
100 :    
101 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
102 :     (Depends): also on 'utils'
103 :    
104 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
105 :     * R/diagMatrix.R (Diagonal): constructor and methods for
106 :     diagonal matrices
107 :    
108 :     * R/ltTMatrix.R: new "minimal methods"
109 :    
110 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
111 :    
112 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
113 :     all methods (and help files).
114 :    
115 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
116 :    
117 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
118 :     for case (dimn. op no_dimn.)
119 :    
120 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
121 :    
122 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
123 : maechler 1084
124 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
125 :    
126 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
127 :     by Julian Faraway.
128 :    
129 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
130 :    
131 :     * R/Auxiliaries.R (try_as): new utility
132 :     * R/sparseMatrix.R: use try_as() in coercion to original class
133 :    
134 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
135 :    
136 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
137 :    
138 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
139 :    
140 :     * R/Auxiliaries.R (dimNamesCheck): added
141 :    
142 :     * R/Matrix.R (as.array), (as.vector): new
143 :    
144 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
145 :    
146 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
147 : maechler 956 default.
148 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
149 :     "pMatrix" now contains "sparseMatrix"
150 : maechler 954
151 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
152 :    
153 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
154 :    
155 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
156 :    
157 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
158 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
159 :    
160 :     * R/dspMatrix.R: typo in "t" method
161 :    
162 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
163 :    
164 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
165 :     * R/Tsparse.R: instead of R/gTMatrix.R
166 :     * R/Csparse.R: new
167 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
168 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
169 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
170 :     via cholmod
171 :    
172 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
173 :    
174 :     * R/Auxiliaries.R (non0ind): new function using new C code
175 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
176 :    
177 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
178 :    
179 :     * src/chm_common.h: header file required by all C sources that
180 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
181 : bates 917 called 'c' whose address is passed as the last argument to
182 :     (virtually) every CHOLMOD function.
183 :    
184 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
185 :    
186 :     * src/init.c: initialize and finalize the cholmod_common structure.
187 :    
188 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
189 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
190 :    
191 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
192 :    
193 :     * inst/test-tools.R: new file collecting the utility functions used
194 :     in ./tests/*.R
195 :    
196 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
197 :     * R/Matrix.R (cbind2): methods for NULL and missing
198 :    
199 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
200 :    
201 :     * R/AllClass.R: new "index" class for "[" and "[<-":
202 :     First cut at "symmetricMatrix" and "triangularMatrix"
203 :     * R/gTMatrix.R (.ind.prep): new function;
204 : maechler 1174 Logical and character indexing now work too.
205 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
206 :     * tests/indexing.R: new, including *.Rout.save
207 :     * tests/dgTMatrix.R: new
208 :    
209 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
210 :    
211 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
212 :     indicator pos not being updated. Also enforced upper triangular
213 :     for symmetric case. Need to coerce edges component of elements of
214 :     edge list - grr! (Why don't they define their classes cleanly?)
215 :    
216 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
217 :    
218 :     * R/Matrix.R: added first "[<-" methods; not yet functional
219 :     * R/denseMatrix.R: dito
220 :     * man/Subassign-methods.Rd: new help file for these
221 :    
222 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
223 :    
224 :     * DESCRIPTION (Version): 0.98-6
225 :    
226 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
227 :     matrices.
228 :    
229 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
230 :    
231 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
232 :     as( <logical>, "matrix")
233 :    
234 :     * R/pMatrix.R: coercion to "lgTMatrix"
235 :    
236 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
237 :     * man/gTMatrix-class.Rd:
238 :     * General slight re-organization of where "[" methods are defined.
239 :     more to come.
240 :    
241 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
242 : maechler 868
243 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
244 : maechler 871
245 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
246 :     * .....
247 :    
248 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
249 :    
250 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
251 :     or glmer objects.
252 :    
253 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
254 :    
255 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
256 :    
257 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
258 :    
259 :     * R/HBMM.R: finish re-writing R-only code.
260 :    
261 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
262 :    
263 :     * man/externalFormats.Rd: move documentation for writeHB and
264 :     writeMM here.
265 :    
266 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
267 :     (suggested by Paul Roecker).
268 :    
269 :     * tests/validObj.R (assertError): Comment out test that is failing
270 :     after recent changes in r-devel.
271 :    
272 : maechler 860
273 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
274 :    
275 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
276 :     * man/denseMatrix-class.Rd
277 :     * NAMESPACE: export it, and also export
278 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
279 :    
280 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
281 :    
282 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
283 :    
284 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
285 :     matrix_solve code (which was really, really wrong).
286 :    
287 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
288 : maechler 834
289 :     * DESCRIPTION (Version): 0.98-2
290 :    
291 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
292 :    
293 :     * R/lmer.R (abbrvNms): new
294 :     * R/lmer.R (mcmcsamp): allow transformed parameters
295 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
296 :     for the Harwell-Boeing and the MatrixMarket formats.
297 : maechler 834
298 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
299 :    
300 :     * man/dtrMatrix-class.Rd: add examples
301 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
302 : maechler 834
303 :     * TODO: note the dtpMatrix (docu) bug
304 :    
305 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
306 :     in order to ensure that new as.matrix() is used by old functions,
307 :     e.g., svd(), qr(), eigen(), dist(),..;
308 :     apply(), also matplot() or pairs().
309 :    
310 :    
311 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
312 :    
313 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
314 :     add comments about 'control' / lmerControl() arguments
315 :    
316 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
317 : bates 820
318 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
319 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
320 : bates 820
321 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
322 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
323 :    
324 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
325 :     .Call calls that were producing spurious output.
326 :    
327 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
328 : bates 801
329 :     * R/lmer.R (lmer): stored updated variance component estimates in
330 :     mer object for the generalized model. (Bug reported by Renaud
331 :     Lancelot).
332 :    
333 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
334 : bates 794
335 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
336 :     unidimensional case.
337 :    
338 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
339 : maechler 791
340 :     * DESCRIPTION (Version): 0.96-1
341 :    
342 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
343 : maechler 791
344 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
345 : bates 763
346 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
347 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
348 :    
349 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
350 : bates 763
351 :     * src/Makefile.win: Forgot to update this when Makefile changed.
352 :    
353 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
354 : bates 726
355 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
356 :     bug reported by Kurt Hornik and Michael Hahsler.
357 :    
358 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
359 : bates 725
360 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
361 :     logical sparse matrices. These will also be used in the symbolic
362 :     analysis for lmer objects.
363 :    
364 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
365 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
366 : maechler 791
367 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
368 : bates 714
369 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
370 :     colMeans, colSums, rowMeans and rowSums.
371 :    
372 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
373 : bates 692
374 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
375 :     multiplication operation.
376 :    
377 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
378 :     to dgetrs.
379 :    
380 :     * src/init.c: Fix cut-and-paste error in definition of
381 :     dgeMatrix_matrix_solve
382 :    
383 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
384 :    
385 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
386 : bates 692
387 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
388 :    
389 :     * DESCRIPTION: Eliminate import of stats.
390 :    
391 : maechler 791
392 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
393 : bates 692
394 :     * R/AllClass.R : add logical sparse matrix classes
395 :    
396 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
397 :    
398 :     * R/dgTMatrix.R: add "[" method for triplet matrices
399 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
400 :    
401 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
402 : maechler 687
403 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
404 :    
405 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
406 :     * R/sparseMatrix.R: %*%, crossprod()
407 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
408 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
409 :     * src/lmer.c (lmer_fitted): fix thinko
410 :    
411 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
412 :    
413 :     * R/AllClass.R: add two virtual sparse classes ``on top''
414 :    
415 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
416 :    
417 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
418 :     correspondingly fix examples and tests/ since new()
419 :     doesn't work for virtual classes.
420 :    
421 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
422 :    
423 :     * R/Matrix.R (as.matrix): method and one for unname()
424 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
425 :     also run for R 2.1.0; using as.matrix()
426 :    
427 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
428 : maechler 658
429 :     * R/pMatrix.R: "pMatrix" class added
430 :     * ....
431 :    
432 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
433 : bates 645
434 :     * R/dtpMatrix.R: Add unpack method and an example.
435 :    
436 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
437 :     of general symmetric matrices and associated S4 methods.
438 :    
439 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
440 :     +
441 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
442 :    
443 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
444 :     crossprod() and "%*%" methods added; tests, too.
445 :     * tests/matprod.R: new, for testing these
446 :    
447 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
448 : bates 599
449 :     * src/lmer.c (lmer_fitted): Added.
450 :    
451 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
452 : bates 596
453 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
454 :    
455 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
456 : bates 582
457 :     * src/*.c,po/,inst/po: Internationalization and localization of
458 :     the package.
459 :    
460 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
461 :     R_ldl.c file.
462 :    
463 :     * src/flame.[ch]: Removed these source files.
464 : maechler 658
465 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
466 :    
467 :     * src/LU.[ch],src/init.c: absorb in factorizations
468 :    
469 :     * src/Mutils.h: prepare for internationalization
470 :    
471 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
472 :     this file
473 :    
474 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
475 :    
476 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
477 :    
478 :     * R/dtrMatrix.R: fix t() method
479 :    
480 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
481 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
482 : maechler 578 * tests/group-methods.R : and test them.
483 :    
484 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
485 :     border case
486 :    
487 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
488 :    
489 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
490 : maechler 578
491 :     * src/dgBCMatrix.c:
492 :     * src/lmer.c: many changes
493 :     * ...
494 :    
495 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
496 :    
497 :     * R/Matrix.R: add more sophisticated show() method.
498 :    
499 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
500 :    
501 :     * */* : almost complete reorganization of classes.
502 :    
503 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
504 : bates 460
505 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
506 :     for the geMatrix class.
507 :    
508 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
509 : bates 460
510 :     * src/Makefile (clean): Remove *.a and *.so
511 :    
512 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
513 :    
514 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
515 : bates 460
516 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
517 : bates 460 had an effect in cases with more than 2 grouping factors.
518 :    
519 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
520 : bates 415
521 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
522 :    
523 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
524 : bates 410
525 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
526 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
527 :    
528 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
529 : bates 392
530 :     * R/sscMatrix.R: Add determinant methods
531 :    
532 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
533 :     for tripletMatrix to matrix.
534 :    
535 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
536 : bates 388
537 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
538 :     no longer used.
539 :    
540 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
541 :     with dynamic allocation of scratch arrays.
542 :    
543 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
544 :     for multivariate random effects with multiple grouping factors.
545 :     Fixes part but not all of #15.
546 :    
547 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
548 : bates 375
549 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
550 :     scalar grouping factors corrected.
551 :    
552 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
553 : bates 375
554 :     * src/bCrosstab.c: remove diag_update which is no longer used
555 :    
556 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
557 : bates 350
558 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
559 :     .h file can be included.
560 :    
561 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
562 : bates 342
563 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
564 : bates 342 Complete allocation of slots in NEW_OBJECT.
565 :    
566 :     * src/Mutils.h: Moved list of symbols to an include file
567 :    
568 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
569 : bates 342
570 :     * src/geMutils.c (Matrix_init): remove unused function
571 :    
572 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
573 : bates 342
574 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
575 :    
576 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
577 : bates 327
578 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
579 :    
580 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
581 : bates 303
582 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
583 :    
584 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
585 : bates 296
586 :     * src/init.c: Created R_init_Matrix and added registration of C
587 :     routines.
588 :    
589 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
590 : bates 283
591 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
592 :    
593 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
594 : bates 229
595 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
596 :    
597 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
598 :    
599 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
600 :    
601 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
602 :    
603 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
604 :     ssclme_update_mm
605 :    
606 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
607 :    
608 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
609 :     in the order of unconstrained and constrained parameters.
610 :     (ssclme_gradient): Added the gradients (not yet correct for
611 :     multidimensional, unconstrained case).
612 :    
613 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
614 :    
615 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
616 :    
617 :     * src/Makefile.win: Remove unneeded ranlib call
618 :    
619 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
620 :    
621 :     * DESCRIPTION (Version): New release
622 :    
623 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
624 :    
625 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
626 :    
627 :     * src/triplet_to_col.c: Create triplet_to_col as a native
628 : maechler 658 function, not the version from umfpack. There were problems with
629 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
630 :     only one umfpack routine being used so I moved it here.
631 :    
632 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
633 :    
634 :     * src/ssclme.c (ssclme_variances): New function.
635 :    
636 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
637 :    
638 :     * src/ssclme.c (ssclme_fitted): Added function.
639 :    
640 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
641 :    
642 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
643 :     store the dimnames in the XtX and bVar slots
644 :     (ssclme_update_mm): Change the dimensions of the bVar slot
645 :     components and the returned value from ssclme_ranef.
646 :    
647 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
648 :    
649 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
650 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
651 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
652 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
653 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
654 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
655 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
656 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
657 :     Moved the pdMat classes from the lme4 package.
658 :    
659 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
660 :    
661 :     * man/ssclme-class.Rd: Update definition and documentation of the
662 :     ssclme class to include the DIsqrt slot.
663 :    
664 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
665 :     (much faster using dsyrk, a level 3 BLAS routine).
666 :    
667 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
668 :    
669 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
670 :    
671 :     * tests/ssclme.R: Modify the test to account for the permutation
672 :     of the levels of the grouping factors.
673 :    
674 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
675 :    
676 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
677 :     directly into the ssclme class definition.
678 :    
679 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
680 :    
681 :     * DESCRIPTION (Date): New release
682 :    
683 :     * man/ssclme-class.Rd: new file.
684 :    
685 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
686 :     works and it's fast!
687 :    
688 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
689 :    
690 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
691 :    
692 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
693 :    
694 :     * DESCRIPTION (Date): New release
695 :    
696 :     * NAMESPACE: Don't export ssclme.
697 :    
698 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
699 :     school data.
700 :    
701 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
702 :    
703 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
704 :     keep track of the fixed-effects and the response. Counts also
705 :     gets an extra element, which is always one.
706 :    
707 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
708 :    
709 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
710 :    
711 :     * src/cscMatrix.c (csc_transpose): new function
712 :    
713 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
714 :     (csc_components_transpose): new function
715 :    
716 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
717 :    
718 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
719 :     triplets
720 :    
721 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
722 :    
723 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
724 :    
725 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
726 :     and all other .h files in src.
727 :    
728 :     * src/Makefile.win: This and other Makefile.win files contributed
729 :     by Brian Ripley.
730 :    
731 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
732 :    
733 :     * R/syMatrix.R: Added methods for "%*%".
734 :    
735 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
736 :     poMatrix object.
737 :    
738 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
739 :    
740 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
741 :    
742 :     2004-01-25 Douglas Bates <bates@bates2_home>
743 :    
744 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
745 :    
746 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
747 :     of nrow.
748 :    
749 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
750 :    
751 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
752 :     subdirectories.
753 :    
754 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
755 :    
756 :     * src/taucs.h: Accidently referred to global header files
757 :     instead of local files.
758 :    
759 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
760 :    
761 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
762 :     and methods and replaced all classes with S4 classes.
763 :    
764 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
765 :    
766 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
767 :    
768 :     * src/R_LapackPP.cc: Change method of calculating determinants
769 :    
770 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
771 :    
772 :     * DESCRIPTION (Version): removed empty data directory as requested
773 :     by CRAN maintainers. Changed version number and date.
774 :    
775 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
776 :    
777 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
778 :     under Windows.
779 :    
780 :     * Added configure.win and src/Makevars.win as requested by Brian
781 :     Ripley.
782 :    
783 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
784 :    
785 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
786 :     Hornik.
787 :    
788 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
789 :    
790 :     * configure.ac: Replaced configure.in with configure.ac
791 :     contributed by Kurt Hornik.
792 :    
793 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
794 :     version for R-1.5.0
795 :    
796 : maechler 512
797 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
798 :    
799 :     * man/eigen.Rd: Removed the .Alias in the example

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