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Annotation of /pkg/ChangeLog

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

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