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Annotation of /pkg/ChangeLog

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

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