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Annotation of /pkg/ChangeLog

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

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