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Annotation of /pkg/ChangeLog

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Revision 1247 - (view) (download)

1 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
2 :    
3 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
4 :     and methods for it.
5 :    
6 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
7 :    
8 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
9 :     arguments, such that M %*% 1:6 now works
10 :     * Tests/matprod.R: test the above
11 :    
12 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
13 : bates 1243
14 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
15 :     the ranef.lmer class.
16 :    
17 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
18 :     methods to extract the posterior variances from the bVar slot.
19 :    
20 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
21 :    
22 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
23 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
24 :    
25 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
26 :     * tests/simple: (extended)
27 :    
28 :     * R/sparseMatrix.R (isTriangular): now using much improved
29 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
30 :    
31 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
32 :    
33 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
34 :     (problem report from Franklin Parlamis). This should be done
35 : maechler 1238 generally.
36 : bates 1236
37 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
38 :    
39 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
40 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
41 :     update the plot methods.
42 :    
43 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
44 :    
45 :     * R/lmer.R (resid and ranef methods): Added methods for the
46 :     "residuals" and "resid" generic but only for linear mixed model
47 :     fits. Changed the ranef method to return a list of data frames so
48 :     that the plot methods now work.
49 :    
50 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
51 :    
52 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
53 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
54 :    
55 :     * DESCRIPTION (Date): New release
56 :    
57 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
58 :    
59 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
60 :    
61 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
62 :     * man/KNex.Rd: and other help files
63 :     * tests/*.R: several ones needed adaption
64 :     * inst/doc/Comparisons.Rnw: dito
65 :    
66 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
67 :    
68 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
69 :    
70 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
71 :    
72 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
73 :    
74 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
75 :    
76 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
77 :    
78 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
79 :    
80 :     * R/dMatrix.R: enable things like M [ M < 10 ]
81 :     * R/dgeMatrix.R: implement it
82 :    
83 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
84 :    
85 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
86 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
87 :     * R/lmer.R (show): now works with summary()
88 :    
89 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
90 :    
91 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
92 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
93 :     support the above
94 :    
95 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
96 :    
97 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
98 :     Use glmFit$prior.weights for weights in a glmm.
99 :     Allow an option usePQL = FALSE to skip the PQL steps for the
100 :     Laplace method (and, in time, the AGQ method).
101 :    
102 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
103 :     into a separate function internal_mer_Xfactor to be able to call
104 :     it from internal_bhat.
105 :    
106 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
107 :    
108 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
109 :     testing; now again of all actual classes.
110 :    
111 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
112 :     use macros and define make_d_matrix_* and make_i_matrix_*
113 :     where _i_ is for the ldense routines:
114 :    
115 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
116 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
117 :    
118 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
119 :    
120 :    
121 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
122 :    
123 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
124 :     many different kinds of matrices.
125 :     * R/*.R: quite a few new methods were needed for R CMD check with
126 :     new Matrix(). Very good for users playing around.
127 :    
128 :    
129 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
130 :    
131 :     * src/dgeMatrix.c (dMatrix_validate): new
132 :     * src/Mutils.c (dense_nonpacked_validate): new
133 :    
134 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
135 :    
136 :    
137 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
138 :    
139 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
140 :    
141 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
142 : bates 1119
143 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
144 :    
145 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
146 :     segfault in cases with multiple non-nested grouping factors.
147 :    
148 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
149 :    
150 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
151 :     (Depends): also on 'utils'
152 :    
153 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
154 :     * R/diagMatrix.R (Diagonal): constructor and methods for
155 :     diagonal matrices
156 :    
157 :     * R/ltTMatrix.R: new "minimal methods"
158 :    
159 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
160 :    
161 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
162 :     all methods (and help files).
163 :    
164 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
165 :    
166 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
167 :     for case (dimn. op no_dimn.)
168 :    
169 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
170 :    
171 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
172 : maechler 1084
173 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
174 :    
175 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
176 :     by Julian Faraway.
177 :    
178 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
179 :    
180 :     * R/Auxiliaries.R (try_as): new utility
181 :     * R/sparseMatrix.R: use try_as() in coercion to original class
182 :    
183 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
184 :    
185 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
186 :    
187 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
188 :    
189 :     * R/Auxiliaries.R (dimNamesCheck): added
190 :    
191 :     * R/Matrix.R (as.array), (as.vector): new
192 :    
193 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
194 :    
195 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
196 : maechler 956 default.
197 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
198 :     "pMatrix" now contains "sparseMatrix"
199 : maechler 954
200 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
201 :    
202 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
203 :    
204 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
205 :    
206 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
207 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
208 :    
209 :     * R/dspMatrix.R: typo in "t" method
210 :    
211 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
212 :    
213 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
214 :     * R/Tsparse.R: instead of R/gTMatrix.R
215 :     * R/Csparse.R: new
216 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
217 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
218 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
219 :     via cholmod
220 :    
221 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
222 :    
223 :     * R/Auxiliaries.R (non0ind): new function using new C code
224 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
225 :    
226 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
227 :    
228 :     * src/chm_common.h: header file required by all C sources that
229 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
230 : bates 917 called 'c' whose address is passed as the last argument to
231 :     (virtually) every CHOLMOD function.
232 :    
233 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
234 :    
235 :     * src/init.c: initialize and finalize the cholmod_common structure.
236 :    
237 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
238 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
239 :    
240 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
241 :    
242 :     * inst/test-tools.R: new file collecting the utility functions used
243 :     in ./tests/*.R
244 :    
245 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
246 :     * R/Matrix.R (cbind2): methods for NULL and missing
247 :    
248 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
249 :    
250 :     * R/AllClass.R: new "index" class for "[" and "[<-":
251 :     First cut at "symmetricMatrix" and "triangularMatrix"
252 :     * R/gTMatrix.R (.ind.prep): new function;
253 : maechler 1174 Logical and character indexing now work too.
254 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
255 :     * tests/indexing.R: new, including *.Rout.save
256 :     * tests/dgTMatrix.R: new
257 :    
258 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
259 :    
260 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
261 :     indicator pos not being updated. Also enforced upper triangular
262 :     for symmetric case. Need to coerce edges component of elements of
263 :     edge list - grr! (Why don't they define their classes cleanly?)
264 :    
265 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
266 :    
267 :     * R/Matrix.R: added first "[<-" methods; not yet functional
268 :     * R/denseMatrix.R: dito
269 :     * man/Subassign-methods.Rd: new help file for these
270 :    
271 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
272 :    
273 :     * DESCRIPTION (Version): 0.98-6
274 :    
275 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
276 :     matrices.
277 :    
278 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
279 :    
280 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
281 :     as( <logical>, "matrix")
282 :    
283 :     * R/pMatrix.R: coercion to "lgTMatrix"
284 :    
285 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
286 :     * man/gTMatrix-class.Rd:
287 :     * General slight re-organization of where "[" methods are defined.
288 :     more to come.
289 :    
290 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
291 : maechler 868
292 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
293 : maechler 871
294 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
295 :     * .....
296 :    
297 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
298 :    
299 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
300 :     or glmer objects.
301 :    
302 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
303 :    
304 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
305 :    
306 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
307 :    
308 :     * R/HBMM.R: finish re-writing R-only code.
309 :    
310 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
311 :    
312 :     * man/externalFormats.Rd: move documentation for writeHB and
313 :     writeMM here.
314 :    
315 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
316 :     (suggested by Paul Roecker).
317 :    
318 :     * tests/validObj.R (assertError): Comment out test that is failing
319 :     after recent changes in r-devel.
320 :    
321 : maechler 860
322 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
323 :    
324 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
325 :     * man/denseMatrix-class.Rd
326 :     * NAMESPACE: export it, and also export
327 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
328 :    
329 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
330 :    
331 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
332 :    
333 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
334 :     matrix_solve code (which was really, really wrong).
335 :    
336 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
337 : maechler 834
338 :     * DESCRIPTION (Version): 0.98-2
339 :    
340 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
341 :    
342 :     * R/lmer.R (abbrvNms): new
343 :     * R/lmer.R (mcmcsamp): allow transformed parameters
344 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
345 :     for the Harwell-Boeing and the MatrixMarket formats.
346 : maechler 834
347 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
348 :    
349 :     * man/dtrMatrix-class.Rd: add examples
350 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
351 : maechler 834
352 :     * TODO: note the dtpMatrix (docu) bug
353 :    
354 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
355 :     in order to ensure that new as.matrix() is used by old functions,
356 :     e.g., svd(), qr(), eigen(), dist(),..;
357 :     apply(), also matplot() or pairs().
358 :    
359 :    
360 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
361 :    
362 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
363 :     add comments about 'control' / lmerControl() arguments
364 :    
365 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
366 : bates 820
367 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
368 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
369 : bates 820
370 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
371 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
372 :    
373 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
374 :     .Call calls that were producing spurious output.
375 :    
376 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
377 : bates 801
378 :     * R/lmer.R (lmer): stored updated variance component estimates in
379 :     mer object for the generalized model. (Bug reported by Renaud
380 :     Lancelot).
381 :    
382 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
383 : bates 794
384 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
385 :     unidimensional case.
386 :    
387 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
388 : maechler 791
389 :     * DESCRIPTION (Version): 0.96-1
390 :    
391 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
392 : maechler 791
393 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
394 : bates 763
395 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
396 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
397 :    
398 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
399 : bates 763
400 :     * src/Makefile.win: Forgot to update this when Makefile changed.
401 :    
402 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
403 : bates 726
404 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
405 :     bug reported by Kurt Hornik and Michael Hahsler.
406 :    
407 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
408 : bates 725
409 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
410 :     logical sparse matrices. These will also be used in the symbolic
411 :     analysis for lmer objects.
412 :    
413 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
414 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
415 : maechler 791
416 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
417 : bates 714
418 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
419 :     colMeans, colSums, rowMeans and rowSums.
420 :    
421 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
422 : bates 692
423 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
424 :     multiplication operation.
425 :    
426 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
427 :     to dgetrs.
428 :    
429 :     * src/init.c: Fix cut-and-paste error in definition of
430 :     dgeMatrix_matrix_solve
431 :    
432 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
433 :    
434 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
435 : bates 692
436 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
437 :    
438 :     * DESCRIPTION: Eliminate import of stats.
439 :    
440 : maechler 791
441 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
442 : bates 692
443 :     * R/AllClass.R : add logical sparse matrix classes
444 :    
445 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
446 :    
447 :     * R/dgTMatrix.R: add "[" method for triplet matrices
448 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
449 :    
450 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
451 : maechler 687
452 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
453 :    
454 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
455 :     * R/sparseMatrix.R: %*%, crossprod()
456 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
457 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
458 :     * src/lmer.c (lmer_fitted): fix thinko
459 :    
460 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
461 :    
462 :     * R/AllClass.R: add two virtual sparse classes ``on top''
463 :    
464 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
465 :    
466 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
467 :     correspondingly fix examples and tests/ since new()
468 :     doesn't work for virtual classes.
469 :    
470 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
471 :    
472 :     * R/Matrix.R (as.matrix): method and one for unname()
473 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
474 :     also run for R 2.1.0; using as.matrix()
475 :    
476 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
477 : maechler 658
478 :     * R/pMatrix.R: "pMatrix" class added
479 :     * ....
480 :    
481 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
482 : bates 645
483 :     * R/dtpMatrix.R: Add unpack method and an example.
484 :    
485 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
486 :     of general symmetric matrices and associated S4 methods.
487 :    
488 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
489 :     +
490 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
491 :    
492 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
493 :     crossprod() and "%*%" methods added; tests, too.
494 :     * tests/matprod.R: new, for testing these
495 :    
496 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
497 : bates 599
498 :     * src/lmer.c (lmer_fitted): Added.
499 :    
500 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
501 : bates 596
502 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
503 :    
504 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
505 : bates 582
506 :     * src/*.c,po/,inst/po: Internationalization and localization of
507 :     the package.
508 :    
509 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
510 :     R_ldl.c file.
511 :    
512 :     * src/flame.[ch]: Removed these source files.
513 : maechler 658
514 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
515 :    
516 :     * src/LU.[ch],src/init.c: absorb in factorizations
517 :    
518 :     * src/Mutils.h: prepare for internationalization
519 :    
520 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
521 :     this file
522 :    
523 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
524 :    
525 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
526 :    
527 :     * R/dtrMatrix.R: fix t() method
528 :    
529 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
530 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
531 : maechler 578 * tests/group-methods.R : and test them.
532 :    
533 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
534 :     border case
535 :    
536 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
537 :    
538 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
539 : maechler 578
540 :     * src/dgBCMatrix.c:
541 :     * src/lmer.c: many changes
542 :     * ...
543 :    
544 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
545 :    
546 :     * R/Matrix.R: add more sophisticated show() method.
547 :    
548 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
549 :    
550 :     * */* : almost complete reorganization of classes.
551 :    
552 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
553 : bates 460
554 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
555 :     for the geMatrix class.
556 :    
557 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
558 : bates 460
559 :     * src/Makefile (clean): Remove *.a and *.so
560 :    
561 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
562 :    
563 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
564 : bates 460
565 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
566 : bates 460 had an effect in cases with more than 2 grouping factors.
567 :    
568 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
569 : bates 415
570 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
571 :    
572 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
573 : bates 410
574 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
575 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
576 :    
577 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
578 : bates 392
579 :     * R/sscMatrix.R: Add determinant methods
580 :    
581 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
582 :     for tripletMatrix to matrix.
583 :    
584 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
585 : bates 388
586 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
587 :     no longer used.
588 :    
589 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
590 :     with dynamic allocation of scratch arrays.
591 :    
592 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
593 :     for multivariate random effects with multiple grouping factors.
594 :     Fixes part but not all of #15.
595 :    
596 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
597 : bates 375
598 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
599 :     scalar grouping factors corrected.
600 :    
601 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
602 : bates 375
603 :     * src/bCrosstab.c: remove diag_update which is no longer used
604 :    
605 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
606 : bates 350
607 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
608 :     .h file can be included.
609 :    
610 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
611 : bates 342
612 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
613 : bates 342 Complete allocation of slots in NEW_OBJECT.
614 :    
615 :     * src/Mutils.h: Moved list of symbols to an include file
616 :    
617 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
618 : bates 342
619 :     * src/geMutils.c (Matrix_init): remove unused function
620 :    
621 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
622 : bates 342
623 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
624 :    
625 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
626 : bates 327
627 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
628 :    
629 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
630 : bates 303
631 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
632 :    
633 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
634 : bates 296
635 :     * src/init.c: Created R_init_Matrix and added registration of C
636 :     routines.
637 :    
638 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
639 : bates 283
640 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
641 :    
642 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
643 : bates 229
644 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
645 :    
646 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
647 :    
648 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
649 :    
650 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
651 :    
652 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
653 :     ssclme_update_mm
654 :    
655 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
656 :    
657 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
658 :     in the order of unconstrained and constrained parameters.
659 :     (ssclme_gradient): Added the gradients (not yet correct for
660 :     multidimensional, unconstrained case).
661 :    
662 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
663 :    
664 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
665 :    
666 :     * src/Makefile.win: Remove unneeded ranlib call
667 :    
668 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
669 :    
670 :     * DESCRIPTION (Version): New release
671 :    
672 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
673 :    
674 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
675 :    
676 :     * src/triplet_to_col.c: Create triplet_to_col as a native
677 : maechler 658 function, not the version from umfpack. There were problems with
678 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
679 :     only one umfpack routine being used so I moved it here.
680 :    
681 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
682 :    
683 :     * src/ssclme.c (ssclme_variances): New function.
684 :    
685 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
686 :    
687 :     * src/ssclme.c (ssclme_fitted): Added function.
688 :    
689 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
690 :    
691 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
692 :     store the dimnames in the XtX and bVar slots
693 :     (ssclme_update_mm): Change the dimensions of the bVar slot
694 :     components and the returned value from ssclme_ranef.
695 :    
696 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
697 :    
698 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
699 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
700 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
701 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
702 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
703 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
704 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
705 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
706 :     Moved the pdMat classes from the lme4 package.
707 :    
708 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
709 :    
710 :     * man/ssclme-class.Rd: Update definition and documentation of the
711 :     ssclme class to include the DIsqrt slot.
712 :    
713 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
714 :     (much faster using dsyrk, a level 3 BLAS routine).
715 :    
716 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
717 :    
718 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
719 :    
720 :     * tests/ssclme.R: Modify the test to account for the permutation
721 :     of the levels of the grouping factors.
722 :    
723 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
724 :    
725 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
726 :     directly into the ssclme class definition.
727 :    
728 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
729 :    
730 :     * DESCRIPTION (Date): New release
731 :    
732 :     * man/ssclme-class.Rd: new file.
733 :    
734 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
735 :     works and it's fast!
736 :    
737 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
738 :    
739 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
740 :    
741 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
742 :    
743 :     * DESCRIPTION (Date): New release
744 :    
745 :     * NAMESPACE: Don't export ssclme.
746 :    
747 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
748 :     school data.
749 :    
750 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
751 :    
752 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
753 :     keep track of the fixed-effects and the response. Counts also
754 :     gets an extra element, which is always one.
755 :    
756 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
757 :    
758 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
759 :    
760 :     * src/cscMatrix.c (csc_transpose): new function
761 :    
762 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
763 :     (csc_components_transpose): new function
764 :    
765 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
766 :    
767 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
768 :     triplets
769 :    
770 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
771 :    
772 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
773 :    
774 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
775 :     and all other .h files in src.
776 :    
777 :     * src/Makefile.win: This and other Makefile.win files contributed
778 :     by Brian Ripley.
779 :    
780 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
781 :    
782 :     * R/syMatrix.R: Added methods for "%*%".
783 :    
784 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
785 :     poMatrix object.
786 :    
787 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
788 :    
789 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
790 :    
791 :     2004-01-25 Douglas Bates <bates@bates2_home>
792 :    
793 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
794 :    
795 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
796 :     of nrow.
797 :    
798 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
799 :    
800 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
801 :     subdirectories.
802 :    
803 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
804 :    
805 :     * src/taucs.h: Accidently referred to global header files
806 :     instead of local files.
807 :    
808 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
809 :    
810 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
811 :     and methods and replaced all classes with S4 classes.
812 :    
813 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
814 :    
815 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
816 :    
817 :     * src/R_LapackPP.cc: Change method of calculating determinants
818 :    
819 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
820 :    
821 :     * DESCRIPTION (Version): removed empty data directory as requested
822 :     by CRAN maintainers. Changed version number and date.
823 :    
824 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
825 :    
826 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
827 :     under Windows.
828 :    
829 :     * Added configure.win and src/Makevars.win as requested by Brian
830 :     Ripley.
831 :    
832 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
833 :    
834 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
835 :     Hornik.
836 :    
837 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
838 :    
839 :     * configure.ac: Replaced configure.in with configure.ac
840 :     contributed by Kurt Hornik.
841 :    
842 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
843 :     version for R-1.5.0
844 :    
845 : maechler 512
846 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
847 :    
848 :     * man/eigen.Rd: Removed the .Alias in the example

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