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Annotation of /pkg/ChangeLog

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

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