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Annotation of /pkg/ChangeLog

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

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